Angular photogrammetric analysis of the soft-tissue facial profile of Indian adults.

PubMed

Pandian, K Saravana; Krishnan, Sindhuja; Kumar, S Aravind

2018-01-01

Soft-tissue analysis has become an important component of orthodontic diagnosis and treatment planning. Photographic evaluation of an orthodontic patient is a very close representation of the appearance of the person. The previously established norms for soft-tissue analysis will vary for different ethnic groups. Thus, there is a need to develop soft-tissue facial profile norms pertaining to Indian ethnic groups. The aim of this study is to establish the angular photogrammetric standards of soft-tissue facial profile for Indian males and females and also to compare sexual dimorphism present between them. The lateral profile photographs of 300 random participants (150 males and 150 females) between ages 18 and 25 years were taken and analyzed using FACAD tracing software. Inclusion criteria were angles Class I molar occlusion with acceptable crowding and proclination, normal growth and development with well-aligned dental arches, and full complements of permanent teeth irrespective of third molar status. This study was conducted in Indian population, and samples were taken from various cities across India. Descriptive statistical analysis was carried out, and sexual dimorphism was evaluated by Student's t-test between males and females. The results of the present study showed statistically significant (P < 0.05) gender difference in 5 parameters out of 12 parameters in Indian population. In the present study, soft-tissue facial measurements were established by means of photogrammetric analysis to facilitate orthodontists to carry out more quantitative evaluation and make disciplined decisions. The mean values obtained can be used for comparison with records of participants with the same characteristics by following this photogrammetric technique.

3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

PubMed Central

Cho, Nam-Hoon; Choi, Heung-Kook

2014-01-01

One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system. PMID:25371701

Fluorescent biopsy of biological tissues in differentiation of benign and malignant tumors of prostate

NASA Astrophysics Data System (ADS)

Trifoniuk, L. I.; Ushenko, Yu. A.; Sidor, M. I.; Minzer, O. P.; Gritsyuk, M. V.; Novakovskaya, O. Y.

2014-08-01

The work consists of investigation results of diagnostic efficiency of a new azimuthally stable Mueller-matrix method of analysis of laser autofluorescence coordinate distributions of biological tissues histological sections. A new model of generalized optical anisotropy of biological tissues protein networks is proposed in order to define the processes of laser autofluorescence. The influence of complex mechanisms of both phase anisotropy (linear birefringence and optical activity) and linear (circular) dichroism is taken into account. The interconnections between the azimuthally stable Mueller-matrix elements characterizing laser autofluorescence and different mechanisms of optical anisotropy are determined. The statistic analysis of coordinate distributions of such Mueller-matrix rotation invariants is proposed. Thereupon the quantitative criteria (statistic moments of the 1st to the 4th order) of differentiation of histological sections of uterus wall tumor - group 1 (dysplasia) and group 2 (adenocarcinoma) are estimated.

Kinetic Analysis of Dynamic Positron Emission Tomography Data using Open-Source Image Processing and Statistical Inference Tools.

PubMed

Hawe, David; Hernández Fernández, Francisco R; O'Suilleabháin, Liam; Huang, Jian; Wolsztynski, Eric; O'Sullivan, Finbarr

2012-05-01

In dynamic mode, positron emission tomography (PET) can be used to track the evolution of injected radio-labelled molecules in living tissue. This is a powerful diagnostic imaging technique that provides a unique opportunity to probe the status of healthy and pathological tissue by examining how it processes substrates. The spatial aspect of PET is well established in the computational statistics literature. This article focuses on its temporal aspect. The interpretation of PET time-course data is complicated because the measured signal is a combination of vascular delivery and tissue retention effects. If the arterial time-course is known, the tissue time-course can typically be expressed in terms of a linear convolution between the arterial time-course and the tissue residue. In statistical terms, the residue function is essentially a survival function - a familiar life-time data construct. Kinetic analysis of PET data is concerned with estimation of the residue and associated functionals such as flow, flux, volume of distribution and transit time summaries. This review emphasises a nonparametric approach to the estimation of the residue based on a piecewise linear form. Rapid implementation of this by quadratic programming is described. The approach provides a reference for statistical assessment of widely used one- and two-compartmental model forms. We illustrate the method with data from two of the most well-established PET radiotracers, (15)O-H(2)O and (18)F-fluorodeoxyglucose, used for assessment of blood perfusion and glucose metabolism respectively. The presentation illustrates the use of two open-source tools, AMIDE and R, for PET scan manipulation and model inference.

Fisher statistics for analysis of diffusion tensor directional information.

PubMed

Hutchinson, Elizabeth B; Rutecki, Paul A; Alexander, Andrew L; Sutula, Thomas P

2012-04-30

A statistical approach is presented for the quantitative analysis of diffusion tensor imaging (DTI) directional information using Fisher statistics, which were originally developed for the analysis of vectors in the field of paleomagnetism. In this framework, descriptive and inferential statistics have been formulated based on the Fisher probability density function, a spherical analogue of the normal distribution. The Fisher approach was evaluated for investigation of rat brain DTI maps to characterize tissue orientation in the corpus callosum, fornix, and hilus of the dorsal hippocampal dentate gyrus, and to compare directional properties in these regions following status epilepticus (SE) or traumatic brain injury (TBI) with values in healthy brains. Direction vectors were determined for each region of interest (ROI) for each brain sample and Fisher statistics were applied to calculate the mean direction vector and variance parameters in the corpus callosum, fornix, and dentate gyrus of normal rats and rats that experienced TBI or SE. Hypothesis testing was performed by calculation of Watson's F-statistic and associated p-value giving the likelihood that grouped observations were from the same directional distribution. In the fornix and midline corpus callosum, no directional differences were detected between groups, however in the hilus, significant (p<0.0005) differences were found that robustly confirmed observations that were suggested by visual inspection of directionally encoded color DTI maps. The Fisher approach is a potentially useful analysis tool that may extend the current capabilities of DTI investigation by providing a means of statistical comparison of tissue structural orientation. Copyright © 2012 Elsevier B.V. All rights reserved.

Nonparametric Residue Analysis of Dynamic PET Data With Application to Cerebral FDG Studies in Normals.

PubMed

O'Sullivan, Finbarr; Muzi, Mark; Spence, Alexander M; Mankoff, David M; O'Sullivan, Janet N; Fitzgerald, Niall; Newman, George C; Krohn, Kenneth A

2009-06-01

Kinetic analysis is used to extract metabolic information from dynamic positron emission tomography (PET) uptake data. The theory of indicator dilutions, developed in the seminal work of Meier and Zierler (1954), provides a probabilistic framework for representation of PET tracer uptake data in terms of a convolution between an arterial input function and a tissue residue. The residue is a scaled survival function associated with tracer residence in the tissue. Nonparametric inference for the residue, a deconvolution problem, provides a novel approach to kinetic analysis-critically one that is not reliant on specific compartmental modeling assumptions. A practical computational technique based on regularized cubic B-spline approximation of the residence time distribution is proposed. Nonparametric residue analysis allows formal statistical evaluation of specific parametric models to be considered. This analysis needs to properly account for the increased flexibility of the nonparametric estimator. The methodology is illustrated using data from a series of cerebral studies with PET and fluorodeoxyglucose (FDG) in normal subjects. Comparisons are made between key functionals of the residue, tracer flux, flow, etc., resulting from a parametric (the standard two-compartment of Phelps et al. 1979) and a nonparametric analysis. Strong statistical evidence against the compartment model is found. Primarily these differences relate to the representation of the early temporal structure of the tracer residence-largely a function of the vascular supply network. There are convincing physiological arguments against the representations implied by the compartmental approach but this is the first time that a rigorous statistical confirmation using PET data has been reported. The compartmental analysis produces suspect values for flow but, notably, the impact on the metabolic flux, though statistically significant, is limited to deviations on the order of 3%-4%. The general advantage of the nonparametric residue analysis is the ability to provide a valid kinetic quantitation in the context of studies where there may be heterogeneity or other uncertainty about the accuracy of a compartmental model approximation of the tissue residue.

VOXEL-LEVEL MAPPING OF TRACER KINETICS IN PET STUDIES: A STATISTICAL APPROACH EMPHASIZING TISSUE LIFE TABLES.

PubMed

O'Sullivan, Finbarr; Muzi, Mark; Mankoff, David A; Eary, Janet F; Spence, Alexander M; Krohn, Kenneth A

2014-06-01

Most radiotracers used in dynamic positron emission tomography (PET) scanning act in a linear time-invariant fashion so that the measured time-course data are a convolution between the time course of the tracer in the arterial supply and the local tissue impulse response, known as the tissue residue function. In statistical terms the residue is a life table for the transit time of injected radiotracer atoms. The residue provides a description of the tracer kinetic information measurable by a dynamic PET scan. Decomposition of the residue function allows separation of rapid vascular kinetics from slower blood-tissue exchanges and tissue retention. For voxel-level analysis, we propose that residues be modeled by mixtures of nonparametrically derived basis residues obtained by segmentation of the full data volume. Spatial and temporal aspects of diagnostics associated with voxel-level model fitting are emphasized. Illustrative examples, some involving cancer imaging studies, are presented. Data from cerebral PET scanning with 18 F fluoro-deoxyglucose (FDG) and 15 O water (H2O) in normal subjects is used to evaluate the approach. Cross-validation is used to make regional comparisons between residues estimated using adaptive mixture models with more conventional compartmental modeling techniques. Simulations studies are used to theoretically examine mean square error performance and to explore the benefit of voxel-level analysis when the primary interest is a statistical summary of regional kinetics. The work highlights the contribution that multivariate analysis tools and life-table concepts can make in the recovery of local metabolic information from dynamic PET studies, particularly ones in which the assumptions of compartmental-like models, with residues that are sums of exponentials, might not be certain.

Biomaterial Characterization of Off-the-Shelf Decellularized Porcine Pericardial Tissue for use in Prosthetic Valvular Applications.

PubMed

Choe, Joshua A; Jana, Soumen; Tefft, Brandon J; Hennessy, Ryan S; Go, Jason; Morse, David; Lerman, Amir; Young, Melissa D

2018-05-10

Fixed pericardial tissue is commonly used for commercially available xenograft valve implants, and has proven durability, but lacks the capability to remodel and grow. Decellularized porcine pericardial tissue has the promise to outperform fixed tissue and remodel, but the decellularization process has been shown to damage the collagen structure and reduce mechanical integrity of the tissue. Therefore, a comparison of uniaxial tensile properties was performed on decellularized, decellularized-sterilized, fixed, and native porcine pericardial tissue, versus native valve leaflet cusps. The results of non-parametric analysis showed statistically significant differences (p<0.05) between the stiffness of 1) decellularized vs. native pericardium, and native cusps as well as fixed tissue respectively; however decellularized tissue showed large increases in elastic properties. Porosity testing of the tissues showed no statistical difference between decellularized or decell-sterilized tissue compared to native cusps (p>0.05). SEM confirmed that valvular endothelial and interstitial cells colonized the decellularized pericardial surface when seeded and grown for 30 days in static culture. Collagen assays and TEM analysis showed limited reductions in collagen with processing; yet, GAG assays showed great reductions in the processed pericardium relative to native cusps. Decellularized pericardium had comparatively lower mechanical properties amongst the groups studied; yet, the stiffness was comparatively similar to the native cusps and demonstrated a lack of cytotoxicity. Suture retention, accelerated wear, and hydrodynamic testing of prototype decellularized and decell-sterilized valves showed positive functionality. Sterilized tissue could mimic valvular mechanical environment in vitro, therefore making it a viable potential candidate for off-the-shelf tissue engineered valvular applications. KEYTERMS Decellularization, Sterilization, Pericardial Tissue, Heart Valves, Tissue Engineering, Biomechanics. This article is protected by copyright. All rights reserved.

Characterizing microstructural features of biomedical samples by statistical analysis of Mueller matrix images

NASA Astrophysics Data System (ADS)

He, Honghui; Dong, Yang; Zhou, Jialing; Ma, Hui

2017-03-01

As one of the salient features of light, polarization contains abundant structural and optical information of media. Recently, as a comprehensive description of polarization property, the Mueller matrix polarimetry has been applied to various biomedical studies such as cancerous tissues detections. In previous works, it has been found that the structural information encoded in the 2D Mueller matrix images can be presented by other transformed parameters with more explicit relationship to certain microstructural features. In this paper, we present a statistical analyzing method to transform the 2D Mueller matrix images into frequency distribution histograms (FDHs) and their central moments to reveal the dominant structural features of samples quantitatively. The experimental results of porcine heart, intestine, stomach, and liver tissues demonstrate that the transformation parameters and central moments based on the statistical analysis of Mueller matrix elements have simple relationships to the dominant microstructural properties of biomedical samples, including the density and orientation of fibrous structures, the depolarization power, diattenuation and absorption abilities. It is shown in this paper that the statistical analysis of 2D images of Mueller matrix elements may provide quantitative or semi-quantitative criteria for biomedical diagnosis.

Assessment of Caudal Fin Clips as a Non-lethal Technique for Predicting Muscle Tissue Mercury Concentrations in Largeouth Bass

EPA Science Inventory

The statistical relationship between total mercury (Hg) concentration in clips from the caudal fin and muscle tissue of largemouth bass (Micropterus salmoides) from 26 freshwater sites in Rhode Island, USA was developed and evaluated to determine the utility of fin clip analysis ...

Wavelet analysis of polarization azimuths maps for laser images of myocardial tissue for the purpose of diagnosing acute coronary insufficiency

NASA Astrophysics Data System (ADS)

Wanchuliak, O. Ya.; Peresunko, A. P.; Bakko, Bouzan Adel; Kushnerick, L. Ya.

2011-09-01

This paper presents the foundations of a large scale - localized wavelet - polarization analysis - inhomogeneous laser images of histological sections of myocardial tissue. Opportunities were identified defining relations between the structures of wavelet coefficients and causes of death. The optical model of polycrystalline networks of myocardium protein fibrils is presented. The technique of determining the coordinate distribution of polarization azimuth of the points of laser images of myocardium histological sections is suggested. The results of investigating the interrelation between the values of statistical (statistical moments of the 1st-4th order) parameters are presented which characterize distributions of wavelet - coefficients polarization maps of myocardium layers and death reasons.

Optical properties of mice skin for optical therapy relevant wavelengths: influence of gender and pigmentation

NASA Astrophysics Data System (ADS)

Sabino, C. P.; Deana, A. M.; Silva, D. F. T.; França, C. M.; Yoshimura, T. M.; Ribeiro, M. S.

2015-03-01

Red and near-infrared light have been widely employed in optical therapies. Skin is the most common optical barrier in non-invasive techniques and in many cases it is the target tissue itself. Consequently, to optimize the outcomes brought by lightbased therapies, the optical properties of skin tissue must be very well elucidated. In the present study, we evaluated the dorsal skin optical properties of albino (BALB/c) and pigmented (C57BL/6) mice using the Kubelka-Munk photon transport model. We evaluated samples from male and female young mice of both strains. Analysis was performed for wavelengths at 630, 660, 780, 810 and 905 nm due to their prevalent use in optical therapies, such as low-level light (or laser) and photodynamic therapies. Spectrophotometric measurements of diffuse transmittance and reflectance were performed using a single integrating sphere coupled to a proper spectrophotometer. Statistic analysis was made by two-way ANOVA, with Tukey as post-test and Levenne and Shapiro-Wilks as pre-tests. Statistical significance was considered when p<0.05. Our results show only a slight transmittance increment (<10 %) as wavelengths are increased from 630 to 905 nm, and no statistical significance was observed. Albino male mice present reduced transmittance levels for all wavelengths. The organization and abundance of skin composing tissues significantly influence its scattering optical properties although absorption remains constant. We conclude that factors such as subcutaneous adiposity and connective tissue structure can have statistically significant influence on mice skin optical properties and these factors have relevant variations among different gender and strains.

Objective Diagnosis of Cervical Cancer by Tissue Protein Profile Analysis

NASA Astrophysics Data System (ADS)

Patil, Ajeetkumar; Bhat, Sujatha; Rai, Lavanya; Kartha, V. B.; Chidangil, Santhosh

2011-07-01

Protein profiles of homogenized normal cervical tissue samples from hysterectomy subjects and cancerous cervical tissues from biopsy samples collected from patients with different stages of cervical cancer were recorded using High Performance Liquid Chromatography coupled with Laser Induced Fluorescence (HPLC-LIF). The Protein profiles were subjected to Principle Component Analysis to derive statistically significant parameters. Diagnosis of sample types were carried out by matching three parameters—scores of factors, squared residuals, and Mahalanobis Distance. ROC and Youden's Index curves for calibration standards were used for objective estimation of the optimum threshold for decision making and performance.

Computation and application of tissue-specific gene set weights.

PubMed

Frost, H Robert

2018-04-06

Gene set testing, or pathway analysis, has become a critical tool for the analysis of highdimensional genomic data. Although the function and activity of many genes and higher-level processes is tissue-specific, gene set testing is typically performed in a tissue agnostic fashion, which impacts statistical power and the interpretation and replication of results. To address this challenge, we have developed a bioinformatics approach to compute tissuespecific weights for individual gene sets using information on tissue-specific gene activity from the Human Protein Atlas (HPA). We used this approach to create a public repository of tissue-specific gene set weights for 37 different human tissue types from the HPA and all collections in the Molecular Signatures Database (MSigDB). To demonstrate the validity and utility of these weights, we explored three different applications: the functional characterization of human tissues, multi-tissue analysis for systemic diseases and tissue-specific gene set testing. All data used in the reported analyses is publicly available. An R implementation of the method and tissue-specific weights for MSigDB gene set collections can be downloaded at http://www.dartmouth.edu/∼hrfrost/TissueSpecificGeneSets. rob.frost@dartmouth.edu.

Ensembles of radial basis function networks for spectroscopic detection of cervical precancer

NASA Technical Reports Server (NTRS)

Tumer, K.; Ramanujam, N.; Ghosh, J.; Richards-Kortum, R.

1998-01-01

The mortality related to cervical cancer can be substantially reduced through early detection and treatment. However, current detection techniques, such as Pap smear and colposcopy, fail to achieve a concurrently high sensitivity and specificity. In vivo fluorescence spectroscopy is a technique which quickly, noninvasively and quantitatively probes the biochemical and morphological changes that occur in precancerous tissue. A multivariate statistical algorithm was used to extract clinically useful information from tissue spectra acquired from 361 cervical sites from 95 patients at 337-, 380-, and 460-nm excitation wavelengths. The multivariate statistical analysis was also employed to reduce the number of fluorescence excitation-emission wavelength pairs required to discriminate healthy tissue samples from precancerous tissue samples. The use of connectionist methods such as multilayered perceptrons, radial basis function (RBF) networks, and ensembles of such networks was investigated. RBF ensemble algorithms based on fluorescence spectra potentially provide automated and near real-time implementation of precancer detection in the hands of nonexperts. The results are more reliable, direct, and accurate than those achieved by either human experts or multivariate statistical algorithms.

3D Mueller-matrix mapping of biological optically anisotropic networks

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Ushenko, V. O.; Bodnar, G. B.; Zhytaryuk, V. G.; Prydiy, O. G.; Koval, G.; Lukashevich, I.; Vanchuliak, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of azimuthally-invariant Mueller-matrix description of optical anisotropy of biological tissues. It was provided experimentally measured coordinate distributions of Mueller-matrix invariants (MMI) of linear and circular birefringences of skeletal muscle tissue. It was defined the values of statistic moments, which characterize the distributions of amplitudes of wavelet coefficients of MMI at different scales of scanning. The second part presents the data of statistic analysis of the distributions of amplitude of wavelet coefficients of the distributions of linear birefringence of myocardium tissue died after the infarction and ischemic heart disease. It was defined the objective criteria of differentiation of the cause of death.

Multiscale polarization diagnostics of birefringent networks in problems of necrotic changes diagnostics

NASA Astrophysics Data System (ADS)

Sakhnovskiy, M. Yu.; Ushenko, Yu. O.; Ushenko, V. O.; Besaha, R. N.; Pavlyukovich, N.; Pavlyukovich, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of azimuthally-invariant Mueller-matrix description of optical anisotropy of biological tissues. It was provided experimentally measured coordinate distributions of Mueller-matrix invariants (MMI) of linear and circular birefringences of skeletal muscle tissue. It was defined the values of statistic moments, which characterize the distributions of amplitudes of wavelet coefficients of MMI at different scales of scanning. The second part presents the data of statistic analysis of the distributions of amplitude of wavelet coefficients of the distributions of linear birefringence of myocardium tissue died after the infarction and ischemic heart disease. It was defined the objective criteria of differentiation of the cause of death.

The Effect of Tissue Entrapment on Screw Loosening at the Implant/Abutment Interface of External- and Internal-Connection Implants: An In Vitro Study.

PubMed

Zeno, Helios A; Buitrago, Renan L; Sternberger, Sidney S; Patt, Marisa E; Tovar, Nick; Coelho, Paulo; Kurtz, Kenneth S; Tuminelli, Frank J

2016-04-01

To compare the removal of torque values of machined implant abutment connections (internal and external) with and without soft tissue entrapment using an in vitro model. Thirty external- and 30 internal-connection implants were embedded in urethane dimethacrylate. Porcine tissue was prepared and measured to thicknesses of 0.5 and 1.0 mm. Six groups (n = 10) were studied: External- and internal-connection implants with no tissue (control), 0.5, and 1.0 mm of tissue were entrapped at the implant/abutment interface. Abutments were inserted to 20 Ncm for all six groups. Insertion torque values were recorded using a digital torque gauge. All groups were then immersed in 1 M NaOH for 48 hours to dissolve tissue. Subsequent reverse torque measurements were recorded. Mean and standard deviation were determined for each group, and one-way ANOVA and Bonferroni test were used for statistical analysis. All 60 specimens achieved a 20-Ncm insertion torque, despite tissue entrapment. Reverse torque measurements for external connection displayed a statistically significant difference (p < 0.05) between all groups with mean reverse torque values for the control (13.71 ± 1.4 Ncm), 0.5 mm (7.83 ± 2.4 Ncm), and 1.0 mm tissue entrapment (2.29 ± 1.4 Ncm) groups. Some statistically significant differences (p < 0.05) were found between internal-connection groups. In all specimens, tissue did not completely dissolve after 48 hours. External-connection implants were significantly affected by tissue entrapment; the thicker the tissue, the lower the reverse torque values noted. Internal-connection implants were less affected by tissue entrapment. © 2015 by the American College of Prosthodontists.

Alveolar ridge augmentation by connective tissue grafting using a pouch method and modified connective tissue technique: A prospective study.

PubMed

Agarwal, Ashish; Gupta, Narinder Dev

2015-01-01

Localized alveolar ridge defect may create physiological and pathological problems. Developments in surgical techniques have made it simpler to change the configuration of a ridge to create a more aesthetic and more easily cleansable shape. The purpose of this study was to compare the efficacy of alveolar ridge augmentation using a subepithelial connective tissue graft in pouch and modified connective tissue graft technique. In this randomized, double blind, parallel and prospective study, 40 non-smoker individuals with 40 class III alveolar ridge defects in maxillary anterior were randomly divided in two groups. Group I received modified connective tissue graft, while group II were treated with subepithelial connective tissue graft in pouch technique. The defect size was measured in its horizontal and vertical dimension by utilizing a periodontal probe in a stone cast at base line, after 3 months, and 6 months post surgically. Analysis of variance and Bonferroni post-hoc test were used for statistical analysis. A two-tailed P < 0.05 was considered to be statistically significant. Mean values in horizontal width after 6 months were 4.70 ± 0.87 mm, and 4.05 ± 0.89 mm for group I and II, respectively. Regarding vertical heights, obtained mean values were 4.75 ± 0.97 mm and 3.70 ± 0.92 mm for group I and group II, respectively. Within the limitations of this study, connective tissue graft proposed significantly more improvement as compare to connective tissue graft in pouch.

Clinical evaluation of subepithelial connective tissue graft and guided tissue regeneration for treatment of Miller’s class 1 gingival recession (comparative, split mouth, six months study)

PubMed Central

Bhavsar, Neeta-V.; Dulani, Kirti; Trivedi, Rahul

2014-01-01

Objectives: The present study aims to clinically compare and evaluate subepithelial connective tissue graft and the GTR based root coverage in treatment of Miller’s Class I gingival recession. Study Design: 30 patients with at least one pair of Miller’s Class I gingival recession were treated either with Subepithelial connective tissue graft (Group A) or Guided tissue regeneration (Group B). Clinical parameters monitored included recession RD, width of keratinized gingiva (KG), probing depth (PD), clinical attachment level (CAL), attached gingiva (AG), residual probing depth (RPD) and % of Root coverage(%RC). Measurements were taken at baseline, three months and six months. A standard surgical procedure was used for both Group A and Group B. Data were recorded and statistical analysis was done for both intergroup and intragroup. Results: At end of six months % RC obtained were 84.47% (Group A) and 81.67% (Group B). Both treatments resulted in statistically significant improvement in clinical parameters. When compared, no statistically significant difference was found between both groups except in RPD, where it was significantly greater in Group A. Conclusions: GTR technique has advantages over subepithelial connective tissue graft for shallow Miller’s Class I defects and this procedure can be used to avoid patient discomfort and reduce treatment time. Key words:Collagen membrane, comparative split mouth study, gingival recession, subepithelial connective tissue graft, guided tissue regeneration (GTR). PMID:25136420

Histological analysis of effects of 24% EDTA gel for nonsurgical treatment of periodontal tissues.

PubMed

de Vasconcellos, Luana Marotta Reis; Ricardo, Lucilene Hernandes; Balducci, Ivan; de Vasconcellos, Luis Gustavo Oliveira; Carvalho, Yasmin Rodarte

2006-12-01

The aim of this study was to investigate, by means of histological and histomorphometric analysis, the effects of 24% ethylenediaminetetraacetic acid (EDTA) gel in periodontal tissue when used in combination with conventional periodontal treatment. Periodontitis was induced in the 2nd upper left permanent molars of 45 male Wistar rats by means of ligature. After 5 weeks, this was removed and debridement was performed. The animals were then randomly divided into 3 groups; group 1: mechanical treatment, group 2: mechanical treatment and EDTA gel application for 2 min, and group 3: mechanical treatment and placebo gel application for 2 min. After the treatment, rinsing was done with 0.9% saline solution for 1 min in all cases, followed by root notching in the deepest part of the pocket. After 4, 10, and 28 days the animals were sacrificed. The averages obtained were evaluated by means of test two-way analysis of variance (ANOVA) and Tukey statistical tests (P < 0.05). The results showed that with respect to the type of treatment employed, there were no statistically significant differences in the vitality of the periodontal tissue. It was concluded that 24% EDTA gel did not interfere with periodontal tissue repair when used in combination with conventional periodontal treatment.

Causal network analysis of head and neck keloid tissue identifies potential master regulators.

PubMed

Garcia-Rodriguez, Laura; Jones, Lamont; Chen, Kang Mei; Datta, Indrani; Divine, George; Worsham, Maria J

2016-10-01

To generate novel insights and hypotheses in keloid development from potential master regulators. Prospective cohort. Six fresh keloid and six normal skin samples from 12 anonymous donors were used in a prospective cohort study. Genome-wide profiling was done previously on the cohort using the Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA). The 190 statistically significant CpG islands between keloid and normal tissue mapped to 152 genes (P < .05). The top 10 statistically significant genes (VAMP5, ACTR3C, GALNT3, KCNAB2, LRRC61, SCML4, SYNGR1, TNS1, PLEKHG5, PPP1R13-α, false discovery rate <.015) were uploaded into the Ingenuity Pathway Analysis software's Causal Network Analysis (QIAGEN, Redwood City, CA). To reflect expected gene expression direction in the context of methylation changes, the inverse of the methylation ratio from keloid versus normal tissue was used for the analysis. Causal Network Analysis identified disease-specific master regulator molecules based on downstream differentially expressed keloid-specific genes and expected directionality of expression (hypermethylated vs. hypomethylated). Causal Network Analysis software identified four hierarchical networks that included four master regulators (pyroxamide, tributyrin, PRKG2, and PENK) and 19 intermediate regulators. Causal Network Analysis of differentiated methylated gene data of keloid versus normal skin demonstrated four causal networks with four master regulators. These hierarchical networks suggest potential driver roles for their downstream keloid gene targets in the pathogenesis of the keloid phenotype, likely triggered due to perturbation/injury to normal tissue. NA Laryngoscope, 126:E319-E324, 2016. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

Tissue classification using depth-dependent ultrasound time series analysis: in-vitro animal study

NASA Astrophysics Data System (ADS)

Imani, Farhad; Daoud, Mohammad; Moradi, Mehdi; Abolmaesumi, Purang; Mousavi, Parvin

2011-03-01

Time series analysis of ultrasound radio-frequency (RF) signals has been shown to be an effective tissue classification method. Previous studies of this method for tissue differentiation at high and clinical-frequencies have been reported. In this paper, analysis of RF time series is extended to improve tissue classification at the clinical frequencies by including novel features extracted from the time series spectrum. The primary feature examined is the Mean Central Frequency (MCF) computed for regions of interest (ROIs) in the tissue extending along the axial axis of the transducer. In addition, the intercept and slope of a line fitted to the MCF-values of the RF time series as a function of depth have been included. To evaluate the accuracy of the new features, an in vitro animal study is performed using three tissue types: bovine muscle, bovine liver, and chicken breast, where perfect two-way classification is achieved. The results show statistically significant improvements over the classification accuracies with previously reported features.

A study of cephalometric soft tissue profile among adolescents from the three West African countries of Nigeria, Ghana and Senegal.

PubMed

Fadeju, A D; Otuyemi, O D; Ngom, P I; Newman-Nartey, M

2013-03-01

Since the introduction of cephalometry, numerous studies have established normal values for Caucasian populations. In Africa, most investigations have established norms and ethnic variations associated with the skeletal pattern. To date, there has been no study comparing soft tissue patterns among adolescents in the West African sub-region. The objective of this investigation was to determine and compare soft tissue patterns among 12- to 16-year-old Nigerian, Ghanaian and Senegalese adolescents, establish any gender dimorphism and compare them with published Caucasian norms. Lateral cephalometric radiographs of adolescents with a normal incisor relationship aged between 12 and 16 years from Nigeria, Ghana, and Senegal were taken under standardized conditions and traced to determine soft tissue patterns. Data obtained were subjected to statistical analysis. The total sample consisted of 165 females and 135 males with a mean age of 13·96 (1·58) years. A number of soft tissue parameters showed significant differences (P<0·05). These included comparison between males and females, and Nigerian, Ghanaian and Senegalese, including lip separation, upper lip length, upper lip exposure, Li-esthetic line, lower lip-NP, nasal tip angle, N-Pr-Pg, Pg-Ls, B-N pogonion and pogonion-mandibular angle. Differences also existed between these West African soft tissue values and published Caucasian norms, including nasolabial angle, mentolabial angle, nasal depth, nose tip, total soft tissue facial convexity and nasal depth angle. The comparative analysis of soft tissue patterns among 12- to 16-year-old adolescents from Nigeria, Ghana and Senegal demonstrated statistically significant differences in soft tissue value between these West African adolescents and published Caucasian soft tissue norms. This study provides useful data in relation to soft tissue parameters for subjects originating from the West African sub-region.

[Study of susceptibility weighted imaging on MR and pathologic findings to distinguish benign or malignant soft tissue tumor].

PubMed

Liu, J; Chen, Y; Bao, X M; Ling, X L; Ding, J P; Zhang, Z K

2017-05-23

Objective: To explore the diagnostic performance of susceptibility weighted imaging (SWI)in distinguishing benign or malignant soft tissue tumor, and to study pathological observation. Methods: Sixty-eight patients with soft tissue tumor, who received no previous treatment or invasive examination, received routine preoperative MRI examination and SWI scanning. The graduation and distribution of intratumoral susceptibility signal intensity(ITSS) and proportion of tumor volume were observed.The pathological results were also included for comparative analysis. Results: Fourty of 68 patients were benign and 28 were malignant. 72.5% (29/40) patients with benign soft tissue tumors were ITSS grade 1 and ITSS grade 3 (hemangioma). 89.3%(25/28) patients with malignant soft tissue tumors were ITSS grade 2 and ITSS grade 3. The difference was statistically significant ( P <0.01). The distribution of ITSS in patients with benign soft tissue tumors was dominated by peripheral distribution and diffuse distribution (hemangioma), accounting for 90.0% (36/40). The distribution of ITSS in patients with malignant soft tissue tumors mainly distributed in the central region, accounting for 78.6% (22 /28). The difference was statistically significant ( P <0.01). The proportion of tumor volume occupied by ITSS in benign soft tissue tumors was <1/3 and> 2/3 (hemangioma), accounting for 90.0% (36/40). The volume of malignant soft tissue tumors were predominantly <1/3 , accounting for 82.1% (23/28). The difference was statistically significant ( P <0.01). Conclusion: SWI is sensitive in displaying the vein and blood metabolites in soft tissue lesions, which is helpful for the differential diagnosis of benign and malignant tumors in soft tissue.

Cancer testis antigen OY-TES-1: analysis of protein expression in ovarian cancer with tissue microarrays.

PubMed

Fan, R; Huang, W; Luo, B; Zhang, Q M; Xiao, S W; Xie, X X

2015-01-01

Revised manuscript accepted for publication March 5, Objectives: The purpose of this study was to determine the potential of cancer testis antigen OY-TES-1 as a vaccine for ovarian cancer (OC). A tissue microarray (TMA) containing 107 samples from OC tissues and 48 samples from OC adjacent tissues was analyzed by immunohistochemistry with the OY-TES-1 polyclonal antibody. The correlation between OY-TES-1 and clinic pathological traits of OC was statistically analyzed. The expression of OY-TES-1 protein was found in 81% (87/107) of OC tissues and 56% (27/48) of OC adjacent tissues. The immunostaining intensity of OY-TES-1 in OC tissues was significantly higher than that in OC adjacent tissues tested (p = 0.040). OC adjacent tissues only demonstrated lower immunostaining intensity, whereas some of OC tissues presented higher immunostaining intensity and majority showed the heterogeneity of protein distribution. There was no statistically significant correlation found between OY-TES-1 expression and any other clinicopathological traits such as age, FIGO stage, pathological grade, and histological type. OY-TES-1 was expressed in OC tissues with a high proportion, and some of OC tissues presented OY-TES-1 expression in high level vs OC adjacent tissues. OY-TES-1 could be an attractive target for immunotherapy for OC in the future.

Doppler and speckle methods for diagnostics in dentistry

NASA Astrophysics Data System (ADS)

Ulyanov, Sergey S.; Lepilin, Alexander V.; Lebedeva, Nina G.; Sedykh, Alexey V.; Kharish, Natalia A.; Osipova, Yulia; Karpovich, Alexander

2002-02-01

The results of statistical analysis of Doppler spectra of scattered intensity, obtained from tissues of oral cavity membrane of healthy volunteers, are presented. The dependence of the spectral moments of Doppler signal on cutoff frequency is investigated. Some results of statistical analysis of Doppler spectra, obtained from tooth pulp of patients, are presented. New approach for monitoring of blood microcirculation in orthodontics is suggested. Influence of own noise of measuring system on formation of speckle-interferometric signal is studied.

The value of "liver windows" settings in the detection of small renal cell carcinomas on unenhanced computed tomography.

PubMed

Sahi, Kamal; Jackson, Stuart; Wiebe, Edward; Armstrong, Gavin; Winters, Sean; Moore, Ronald; Low, Gavin

2014-02-01

To assess if "liver window" settings improve the conspicuity of small renal cell carcinomas (RCC). Patients were analysed from our institution's pathology-confirmed RCC database that included the following: (1) stage T1a RCCs, (2) an unenhanced computed tomography (CT) abdomen performed ≤ 6 months before histologic diagnosis, and (3) age ≥ 17 years. Patients with multiple tumours, prior nephrectomy, von Hippel-Lindau disease, and polycystic kidney disease were excluded. The unenhanced CT was analysed, and the tumour locations were confirmed by using corresponding contrast-enhanced CT or magnetic resonance imaging studies. Representative single-slice axial, coronal, and sagittal unenhanced CT images were acquired in "soft tissue windows" (width, 400 Hounsfield unit (HU); level, 40 HU) and liver windows (width, 150 HU; level, 88 HU). In addition, single-slice axial, coronal, and sagittal unenhanced CT images of nontumourous renal tissue (obtained from the same cases) were acquired in soft tissue windows and liver windows. These data sets were randomized, unpaired, and were presented independently to 3 blinded radiologists for analysis. The presence or absence of suspicious findings for tumour was scored on a 5-point confidence scale. Eighty-three of 415 patients met the study criteria. Receiver operating characteristics (ROC) analysis, t test analysis, and kappa analysis were used. ROC analysis showed statistically superior diagnostic performance for liver windows compared with soft tissue windows (area under the curve of 0.923 vs 0.879; P = .0002). Kappa statistics showed "good" vs "moderate" agreement between readers for liver windows compared with soft tissue windows. Use of liver windows settings improves the detection of small RCCs on the unenhanced CT. Copyright © 2014 Canadian Association of Radiologists. Published by Elsevier Inc. All rights reserved.

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.

PubMed

Wong, Aaron K; Krishnan, Arjun; Troyanskaya, Olga G

2018-05-25

GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional maps of human tissues. The precise actions of genes are frequently dependent on their tissue context, yet direct assay of tissue-specific protein function and interactions remains infeasible in many normal human tissues and cell-types. With GIANT2, researchers can explore predicted tissue-specific functional roles of genes and reveal changes in those roles across tissues, all through interactive multi-network visualizations and analyses. Additionally, the NetWAS approach available through the server uses tissue-specific/cell-type networks predicted by GIANT2 to re-prioritize statistical associations from GWAS studies and identify disease-associated genes. GIANT2 predicts tissue-specific interactions by integrating diverse functional genomics data from now over 61 400 experiments for 283 diverse tissues and cell-types. GIANT2 does not require any registration or installation and is freely available for use at http://giant-v2.princeton.edu.

Discrimination of soft tissues using laser-induced breakdown spectroscopy in combination with k nearest neighbors (kNN) and support vector machine (SVM) classifiers

NASA Astrophysics Data System (ADS)

Li, Xiaohui; Yang, Sibo; Fan, Rongwei; Yu, Xin; Chen, Deying

2018-06-01

In this paper, discrimination of soft tissues using laser-induced breakdown spectroscopy (LIBS) in combination with multivariate statistical methods is presented. Fresh pork fat, skin, ham, loin and tenderloin muscle tissues are manually cut into slices and ablated using a 1064 nm pulsed Nd:YAG laser. Discrimination analyses between fat, skin and muscle tissues, and further between highly similar ham, loin and tenderloin muscle tissues, are performed based on the LIBS spectra in combination with multivariate statistical methods, including principal component analysis (PCA), k nearest neighbors (kNN) classification, and support vector machine (SVM) classification. Performances of the discrimination models, including accuracy, sensitivity and specificity, are evaluated using 10-fold cross validation. The classification models are optimized to achieve best discrimination performances. The fat, skin and muscle tissues can be definitely discriminated using both kNN and SVM classifiers, with accuracy of over 99.83%, sensitivity of over 0.995 and specificity of over 0.998. The highly similar ham, loin and tenderloin muscle tissues can also be discriminated with acceptable performances. The best performances are achieved with SVM classifier using Gaussian kernel function, with accuracy of 76.84%, sensitivity of over 0.742 and specificity of over 0.869. The results show that the LIBS technique assisted with multivariate statistical methods could be a powerful tool for online discrimination of soft tissues, even for tissues of high similarity, such as muscles from different parts of the animal body. This technique could be used for discrimination of tissues suffering minor clinical changes, thus may advance the diagnosis of early lesions and abnormalities.

The implementation of CMOS sensors within a real time digital mammography intelligent imaging system: The I-ImaS System

NASA Astrophysics Data System (ADS)

Esbrand, C.; Royle, G.; Griffiths, J.; Speller, R.

2009-07-01

The integration of technology with healthcare has undoubtedly propelled the medical imaging sector well into the twenty first century. The concept of digital imaging introduced during the 1970s has since paved the way for established imaging techniques where digital mammography, phase contrast imaging and CT imaging are just a few examples. This paper presents a prototype intelligent digital mammography system designed and developed by a European consortium. The final system, the I-ImaS system, utilises CMOS monolithic active pixel sensor (MAPS) technology promoting on-chip data processing, enabling the acts of data processing and image acquisition to be achieved simultaneously; consequently, statistical analysis of tissue is achievable in real-time for the purpose of x-ray beam modulation via a feedback mechanism during the image acquisition procedure. The imager implements a dual array of twenty 520 pixel × 40 pixel CMOS MAPS sensing devices with a 32μm pixel size, each individually coupled to a 100μm thick thallium doped structured CsI scintillator. This paper presents the first intelligent images of real breast tissue obtained from the prototype system of real excised breast tissue where the x-ray exposure was modulated via the statistical information extracted from the breast tissue itself. Conventional images were experimentally acquired where the statistical analysis of the data was done off-line, resulting in the production of simulated real-time intelligently optimised images. The results obtained indicate real-time image optimisation using the statistical information extracted from the breast as a means of a feedback mechanisms is beneficial and foreseeable in the near future.

Probability density function formalism for optical coherence tomography signal analysis: a controlled phantom study.

PubMed

Weatherbee, Andrew; Sugita, Mitsuro; Bizheva, Kostadinka; Popov, Ivan; Vitkin, Alex

2016-06-15

The distribution of backscattered intensities as described by the probability density function (PDF) of tissue-scattered light contains information that may be useful for tissue assessment and diagnosis, including characterization of its pathology. In this Letter, we examine the PDF description of the light scattering statistics in a well characterized tissue-like particulate medium using optical coherence tomography (OCT). It is shown that for low scatterer density, the governing statistics depart considerably from a Gaussian description and follow the K distribution for both OCT amplitude and intensity. The PDF formalism is shown to be independent of the scatterer flow conditions; this is expected from theory, and suggests robustness and motion independence of the OCT amplitude (and OCT intensity) PDF metrics in the context of potential biomedical applications.

Alveolar ridge augmentation by connective tissue grafting using a pouch method and modified connective tissue technique: A prospective study

PubMed Central

Agarwal, Ashish; Gupta, Narinder Dev

2015-01-01

Background: Localized alveolar ridge defect may create physiological and pathological problems. Developments in surgical techniques have made it simpler to change the configuration of a ridge to create a more aesthetic and more easily cleansable shape. The purpose of this study was to compare the efficacy of alveolar ridge augmentation using a subepithelial connective tissue graft in pouch and modified connective tissue graft technique. Materials and Methods: In this randomized, double blind, parallel and prospective study, 40 non-smoker individuals with 40 class III alveolar ridge defects in maxillary anterior were randomly divided in two groups. Group I received modified connective tissue graft, while group II were treated with subepithelial connective tissue graft in pouch technique. The defect size was measured in its horizontal and vertical dimension by utilizing a periodontal probe in a stone cast at base line, after 3 months, and 6 months post surgically. Analysis of variance and Bonferroni post-hoc test were used for statistical analysis. A two-tailed P < 0.05 was considered to be statistically significant. Results: Mean values in horizontal width after 6 months were 4.70 ± 0.87 mm, and 4.05 ± 0.89 mm for group I and II, respectively. Regarding vertical heights, obtained mean values were 4.75 ± 0.97 mm and 3.70 ± 0.92 mm for group I and group II, respectively. Conclusion: Within the limitations of this study, connective tissue graft proposed significantly more improvement as compare to connective tissue graft in pouch. PMID:26759591

Analysis of Two Methods to Evaluate Antioxidants

ERIC Educational Resources Information Center

Tomasina, Florencia; Carabio, Claudio; Celano, Laura; Thomson, Leonor

2012-01-01

This exercise is intended to introduce undergraduate biochemistry students to the analysis of antioxidants as a biotechnological tool. In addition, some statistical resources will also be used and discussed. Antioxidants play an important metabolic role, preventing oxidative stress-mediated cell and tissue injury. Knowing the antioxidant content…

Intraoperative optical biopsy for brain tumors using spectro-lifetime properties of intrinsic fluorophores

NASA Astrophysics Data System (ADS)

Vasefi, Fartash; Kittle, David S.; Nie, Zhaojun; Falcone, Christina; Patil, Chirag G.; Chu, Ray M.; Mamelak, Adam N.; Black, Keith L.; Butte, Pramod V.

2016-04-01

We have developed and tested a system for real-time intra-operative optical identification and classification of brain tissues using time-resolved fluorescence spectroscopy (TRFS). A supervised learning algorithm using linear discriminant analysis (LDA) employing selected intrinsic fluorescence decay temporal points in 6 spectral bands was employed to maximize statistical significance difference between training groups. The linear discriminant analysis on in vivo human tissues obtained by TRFS measurements (N = 35) were validated by histopathologic analysis and neuronavigation correlation to pre-operative MRI images. These results demonstrate that TRFS can differentiate between normal cortex, white matter and glioma.

Stokes-correlometry of polarization-inhomogeneous objects

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Dubolazov, A.; Bodnar, G. B.; Bachynskiy, V. T.; Vanchulyak, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of Stokes-correlometry description of optical anisotropy of biological tissues. It was provided experimentally measured coordinate distributions of modulus (MSV) and phase (PhSV) of complex Stokes vector of skeletal muscle tissue. It was defined the values and ranges of changes of statistic moments of the 1st-4th orders, which characterize the distributions of values of MSV and PhSV. The second part presents the data of statistic analysis of the distributions of modulus MSV and PhSV. It was defined the objective criteria of differentiation of samples with urinary incontinence.

Efficacy of Exclusive Lingual Nerve Block versus Conventional Inferior Alveolar Nerve Block in Achieving Lingual Soft-tissue Anesthesia.

PubMed

Balasubramanian, Sasikala; Paneerselvam, Elavenil; Guruprasad, T; Pathumai, M; Abraham, Simin; Krishnakumar Raja, V B

2017-01-01

The aim of this randomized clinical trial was to assess the efficacy of exclusive lingual nerve block (LNB) in achieving selective lingual soft-tissue anesthesia in comparison with conventional inferior alveolar nerve block (IANB). A total of 200 patients indicated for the extraction of lower premolars were recruited for the study. The samples were allocated by randomization into control and study groups. Lingual soft-tissue anesthesia was achieved by IANB and exclusive LNB in the control and study group, respectively. The primary outcome variable studied was anesthesia of ipsilateral lingual mucoperiosteum, floor of mouth and tongue. The secondary variables assessed were (1) taste sensation immediately following administration of local anesthesia and (2) mouth opening and lingual nerve paresthesia on the first postoperative day. Data analysis for descriptive and inferential statistics was performed using SPSS (IBM SPSS Statistics for Windows, Version 22.0, Armonk, NY: IBM Corp. Released 2013) and a P < 0.05 was considered statistically significant. In comparison with the control group, the study group (LNB) showed statistically significant anesthesia of the lingual gingiva of incisors, molars, anterior floor of the mouth, and anterior tongue. Exclusive LNB is superior to IAN nerve block in achieving selective anesthesia of lingual soft tissues. It is technically simple and associated with minimal complications as compared to IAN block.

Efficacy of Exclusive Lingual Nerve Block versus Conventional Inferior Alveolar Nerve Block in Achieving Lingual Soft-tissue Anesthesia

PubMed Central

Balasubramanian, Sasikala; Paneerselvam, Elavenil; Guruprasad, T; Pathumai, M; Abraham, Simin; Krishnakumar Raja, V. B.

2017-01-01

Objective: The aim of this randomized clinical trial was to assess the efficacy of exclusive lingual nerve block (LNB) in achieving selective lingual soft-tissue anesthesia in comparison with conventional inferior alveolar nerve block (IANB). Materials and Methods: A total of 200 patients indicated for the extraction of lower premolars were recruited for the study. The samples were allocated by randomization into control and study groups. Lingual soft-tissue anesthesia was achieved by IANB and exclusive LNB in the control and study group, respectively. The primary outcome variable studied was anesthesia of ipsilateral lingual mucoperiosteum, floor of mouth and tongue. The secondary variables assessed were (1) taste sensation immediately following administration of local anesthesia and (2) mouth opening and lingual nerve paresthesia on the first postoperative day. Results: Data analysis for descriptive and inferential statistics was performed using SPSS (IBM SPSS Statistics for Windows, Version 22.0, Armonk, NY: IBM Corp. Released 2013) and a P < 0.05 was considered statistically significant. In comparison with the control group, the study group (LNB) showed statistically significant anesthesia of the lingual gingiva of incisors, molars, anterior floor of the mouth, and anterior tongue. Conclusion: Exclusive LNB is superior to IAN nerve block in achieving selective anesthesia of lingual soft tissues. It is technically simple and associated with minimal complications as compared to IAN block. PMID:29264294

Statistical analysis and machine learning algorithms for optical biopsy

NASA Astrophysics Data System (ADS)

Wu, Binlin; Liu, Cheng-hui; Boydston-White, Susie; Beckman, Hugh; Sriramoju, Vidyasagar; Sordillo, Laura; Zhang, Chunyuan; Zhang, Lin; Shi, Lingyan; Smith, Jason; Bailin, Jacob; Alfano, Robert R.

2018-02-01

Analyzing spectral or imaging data collected with various optical biopsy methods is often times difficult due to the complexity of the biological basis. Robust methods that can utilize the spectral or imaging data and detect the characteristic spectral or spatial signatures for different types of tissue is challenging but highly desired. In this study, we used various machine learning algorithms to analyze a spectral dataset acquired from human skin normal and cancerous tissue samples using resonance Raman spectroscopy with 532nm excitation. The algorithms including principal component analysis, nonnegative matrix factorization, and autoencoder artificial neural network are used to reduce dimension of the dataset and detect features. A support vector machine with a linear kernel is used to classify the normal tissue and cancerous tissue samples. The efficacies of the methods are compared.

Nonlinear histogram binning for quantitative analysis of lung tissue fibrosis in high-resolution CT data

NASA Astrophysics Data System (ADS)

Zavaletta, Vanessa A.; Bartholmai, Brian J.; Robb, Richard A.

2007-03-01

Diffuse lung diseases, such as idiopathic pulmonary fibrosis (IPF), can be characterized and quantified by analysis of volumetric high resolution CT scans of the lungs. These data sets typically have dimensions of 512 x 512 x 400. It is too subjective and labor intensive for a radiologist to analyze each slice and quantify regional abnormalities manually. Thus, computer aided techniques are necessary, particularly texture analysis techniques which classify various lung tissue types. Second and higher order statistics which relate the spatial variation of the intensity values are good discriminatory features for various textures. The intensity values in lung CT scans range between [-1024, 1024]. Calculation of second order statistics on this range is too computationally intensive so the data is typically binned between 16 or 32 gray levels. There are more effective ways of binning the gray level range to improve classification. An optimal and very efficient way to nonlinearly bin the histogram is to use a dynamic programming algorithm. The objective of this paper is to show that nonlinear binning using dynamic programming is computationally efficient and improves the discriminatory power of the second and higher order statistics for more accurate quantification of diffuse lung disease.

Cellular Consequences of Telomere Shortening in Histologically Normal Breast Tissues

DTIC Science & Technology

2013-09-01

using the open source, JAVA -based image analysis software package ImageJ (http://rsb.info.nih.gov/ij/) and a custom designed plugin (“Telometer...Tabulated data were stored in a MySQL (http://www.mysql.com) database and viewed through Microsoft Access (Microsoft Corp.). Statistical Analysis For

The effect of zirconia or titanium as abutment material on soft peri-implant tissues: a systematic review and meta-analysis.

PubMed

Linkevicius, Tomas; Vaitelis, Julius

2015-09-01

The objective of this review was to analyze research with regard to the effect of zirconia or titanium as abutment material on soft peri-implant tissues. Clinical studies were selected via electronic and hand searches in English language journals until December 1, 2014. Only randomized clinical trials (RCTs) and prospective controlled clinical trials (CCTs) showing direct comparison between zirconia (Zr) and titanium (Ti) abutments in the same patient were considered. The outcome measures were (1) soft tissue color, (2) soft tissue recession, (3) peri-implant probing, (4) bleeding on probing, (5) esthetic indexes, (6) patient-reported outcome, (7) marginal bone level, and (8) biological complications. Nine relevant studies (11 papers) were identified: 4 RCTs and 5 CCTs. Due to heterogeneity in the study design, statistical methods, and reported results, a meta-analysis of the data was feasible only for soft tissue color. The outcome was found to be significantly superior for Zr abutments. For the other outcome measures, a qualitative analysis of the selected articles was performed. The studies did not show any statistically significant differences between Zr and Ti abutments on soft tissue recession, probing depths, bleeding on probing, marginal bone level, and patient-reported outcome. One study reported significantly higher pink esthetic score (PES) scores at Zr implants with Zr abutments, compared to metal implants and Ti abutments. Overall, the research does not support any obvious advantage of Ti or Zr abutments over each other. However, there is a significant tendency in Zr abutments evoking better color response of peri-implant mucosa and superior esthetic outcome measured by PES score. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

NASA Astrophysics Data System (ADS)

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

2012-01-01

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

Azimuth-invariant mueller-matrix differentiation of the optical anisotropy of biological tissues

NASA Astrophysics Data System (ADS)

Ushenko, V. A.; Sidor, M. I.; Marchuk, Yu. F.; Pashkovskaya, N. V.; Andreichuk, D. R.

2014-07-01

A Mueller-matrix model is proposed for analysis of the optical anisotropy of protein networks of optically thin nondepolarizing layers of biological tissues with allowance for birefringence and dichroism. The model is used to construct algorithms for reconstruction of coordinate distributions of phase shifts and coefficient of linear dichroism. Objective criteria for differentiation of benign and malignant tissues of female genitals are formulated in the framework of the statistical analysis of such distributions. Approaches of evidence-based medicine are used to determine the working characteristics (sensitivity, specificity, and accuracy) of the Mueller-matrix method for the reconstruction of the parameters of optical anisotropy and show its efficiency in the differentiation of benign and malignant tumors.

A mixed-effects model approach for the statistical analysis of vocal fold viscoelastic shear properties.

PubMed

Xu, Chet C; Chan, Roger W; Sun, Han; Zhan, Xiaowei

2017-11-01

A mixed-effects model approach was introduced in this study for the statistical analysis of rheological data of vocal fold tissues, in order to account for the data correlation caused by multiple measurements of each tissue sample across the test frequency range. Such data correlation had often been overlooked in previous studies in the past decades. The viscoelastic shear properties of the vocal fold lamina propria of two commonly used laryngeal research animal species (i.e. rabbit, porcine) were measured by a linear, controlled-strain simple-shear rheometer. Along with published canine and human rheological data, the vocal fold viscoelastic shear moduli of these animal species were compared to those of human over a frequency range of 1-250Hz using the mixed-effects models. Our results indicated that tissues of the rabbit, canine and porcine vocal fold lamina propria were significantly stiffer and more viscous than those of human. Mixed-effects models were shown to be able to more accurately analyze rheological data generated from repeated measurements. Copyright © 2017 Elsevier Ltd. All rights reserved.

Micro-polarimetry for pre-clinical diagnostics of pathological changes in human tissues

NASA Astrophysics Data System (ADS)

Golnik, Andrzej; Golnik, Natalia; Pałko, Tadeusz; Sołtysiński, Tomasz

2008-05-01

The paper presents a practical study of several methods of image analysis applied to polarimetric images of regular and malignant human tissues. The images of physiological and pathologically changed tissues from body and cervix of uterus, intestine, kidneys and breast were recorded in transmitted light of different polarization state. The set up of the conventional optical microscope with CCD camera and rotating polarizer's were used for analysis of the polarization state of the light transmitted through the tissue slice for each pixel of the camera image. The set of images corresponding to the different coefficients of the Stockes vectors, a 3×3 subset of the Mueller matrix as well as the maps of the magnitude and in-plane direction of the birefringent components in the sample were calculated. Then, the statistical analysis and the Fourier transform as well as the autocorrelation methods were used to analyze spatial distribution of birefringent elements in the tissue samples. For better recognition of tissue state we proposed a novel method that takes advantage of multiscale image data decomposition The results were used for selection of the optical characteristics with significantly different values for regular and malignant tissues.

Comparative study of Hsp27, GSK3β, Wnt1 and PRDX3 in Hirschsprung's disease.

PubMed

Gao, Hong; Liu, Xiaomei; Chen, Dong; Lv, Liangying; Wu, Mei; Mi, Jie; Wang, Weilin

2014-06-01

Hirschsprung's disease (HSCR) is a developmental disorder of the enteric nervous system characterized by aganglionosis in distal gut. In this study, we used two-dimensional gel electrophoresis (2-DE) technology coupled with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis to identify differentially expressed proteins in the aganglionic (stenotic) and ganglionic (normal) colon segment tissues from patients with HSCR. We identified 15 proteins with different expression levels between the stenotic and the normal colon segment tissues from patients with HSCR. Nine proteins were upregulated and six proteins downregulated in the stenotic colon segment tissues compared to the normal colon segment tissues. Based on the biological functions, we selected the Hsp27 upregulated proteins and the PRDX3 downregulated proteins to confirm their expression in 20 patients. The protein and mRNA expressions of Hsp27 were statistically higher in the stenotic colon segment tissues than in the normal colon segment tissues, whereas the protein and mRNA expressions of PRDX3 were statistically lower in the stenotic colon segment tissues than in the normal colon segment tissues. These findings of changes in mRNA and protein in tissues from patients with HSCR provide information which may be helpful in understanding the pathomechanism that is implicated in the disease. © 2014 The Authors. International Journal of Experimental Pathology © 2014 International Journal of Experimental Pathology.

Inverse tissue mechanics of cell monolayer expansion.

PubMed

Kondo, Yohei; Aoki, Kazuhiro; Ishii, Shin

2018-03-01

Living tissues undergo deformation during morphogenesis. In this process, cells generate mechanical forces that drive the coordinated cell motion and shape changes. Recent advances in experimental and theoretical techniques have enabled in situ measurement of the mechanical forces, but the characterization of mechanical properties that determine how these forces quantitatively affect tissue deformation remains challenging, and this represents a major obstacle for the complete understanding of morphogenesis. Here, we proposed a non-invasive reverse-engineering approach for the estimation of the mechanical properties, by combining tissue mechanics modeling and statistical machine learning. Our strategy is to model the tissue as a continuum mechanical system and to use passive observations of spontaneous tissue deformation and force fields to statistically estimate the model parameters. This method was applied to the analysis of the collective migration of Madin-Darby canine kidney cells, and the tissue flow and force were simultaneously observed by the phase contrast imaging and traction force microscopy. We found that our monolayer elastic model, whose elastic moduli were reverse-engineered, enabled a long-term forecast of the traction force fields when given the tissue flow fields, indicating that the elasticity contributes to the evolution of the tissue stress. Furthermore, we investigated the tissues in which myosin was inhibited by blebbistatin treatment, and observed a several-fold reduction in the elastic moduli. The obtained results validate our framework, which paves the way to the estimation of mechanical properties of living tissues during morphogenesis.

The effect of partially exposed connective tissue graft on root-coverage outcomes: a systematic review and meta-analysis.

PubMed

Dodge, Austin; Garcia, Jeffrey; Luepke, Paul; Lai, Yu-Lin; Kassab, Moawia; Lin, Guo-Hao

2018-04-01

The aim of this systematic review was to compare the root-coverage outcomes of using a partially exposed connective tissue graft (CTG) technique with a fully covered CTG technique for root coverage. An electronic search up to February 28 th , 2017, was performed to identify human clinical studies with data comparing outcomes of root coverage using CTG, with and without a partially exposed graft. Five clinical studies were selected for inclusion in this review. For each study, the gain of keratinized gingiva, reduction of recession depth, number of surgical sites achieving complete root coverage, percentage of root coverage, gain of tissue thickness, and changes of probing depth and clinical attachment level were recorded. Meta-analysis for the comparison of complete root coverage between the two techniques presented no statistically significant differences. A statistically significant gain of keratinized tissue in favor of the sites with an exposed CTG and a tendency of greater reduction in recession depth were seen at the sites with a fully covered CTG. Based on the results, the use of a partially exposed CTG in root-coverage procedures could achieve greater gain in keratinized gingiva, while a fully covered CTG might be indicated for procedures aiming to reduce recession depth. © 2018 Eur J Oral Sci.

Mueller matrix mapping of biological polycrystalline layers using reference wave

NASA Astrophysics Data System (ADS)

Dubolazov, A.; Ushenko, O. G.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Grytsyuk, M.; Prysyazhnyuk, P. V.

2018-01-01

The paper consists of two parts. The first part is devoted to the short theoretical basics of the method of differential Mueller-matrix description of properties of partially depolarizing layers. It was provided the experimentally measured maps of differential matrix of the 1st order of polycrystalline structure of the histological section of brain tissue. It was defined the statistical moments of the 1st-4th orders, which characterize the distribution of matrix elements. In the second part of the paper it was provided the data of statistic analysis of birefringence and dichroism of the histological sections of mice liver tissue (normal and with diabetes). It were defined the objective criteria of differential diagnostics of diabetes.

Vascularized interpositional periosteal connective tissue flap: A modern approach to augment soft tissue

PubMed Central

Agarwal, Chitra; Deora, Savita; Abraham, Dennis; Gaba, Rohini; Kumar, Baron Tarun; Kudva, Praveen

2015-01-01

Context: Nowadays esthetics plays an important role in dentistry along with function of the prosthesis. Various soft tissue augmentation procedures are available to correct the ridge defects in the anterior region. The newer technique, vascularized interpositional periosteal connective tissue (VIP-CT) flap has been introduced, which has the potential to augment predictable amount of tissue and has many benefits when compared to other techniques. Aim: The study was designed to determine the efficacy of the VIP-CT flap in augmenting the ridge defect. Materials and Methods: Ten patients with Class III (Seibert's) ridge defects were treated with VIP-CT flap technique before fabricating fixed partial denture. Height and width of the ridge defects were measured before and after the procedure. Subsequent follow-up was done every 3 months for 1-year. Statistical Analysis Used: Paired t-test was performed to detect the significance of the procedure. Results: The surgical site healed uneventfully. The predictable amount of soft tissue augmentation had been achieved with the procedure. The increase in height and width of the ridge was statistically highly significant. Conclusion: The VIP-CT flap technique was effective in augmenting the soft tissue in esthetic area that remained stable over a long period. PMID:25810597

Immunohistochemical Analysis of the Role Connective Tissue Growth Factor in Drug-induced Gingival Overgrowth in Response to Phenytoin, Cyclosporine, and Nifedipine

PubMed Central

Anand, A. J.; Gopalakrishnan, Sivaram; Karthikeyan, R.; Mishra, Debasish; Mohapatra, Shreeyam

2018-01-01

Objective: To evaluate for the presence of connective tissue growth factor (CTGF) in drug (phenytoin, cyclosporine, and nifedipine)-induced gingival overgrowth (DIGO) and to compare it with healthy controls in the absence of overgrowth. Materials and Methods: Thirty-five patients were chosen for the study and segregated into study (25) and control groups (10). The study group consisted of phenytoin-induced (10), cyclosporine-induced (10), and nifedipine-induced (5) gingival overgrowth. After completing necessary medical evaluations, biopsy was done. The tissue samples were fixed in 10% formalin and then immunohistochemically evaluated for the presence of CTGF. The statistical analysis of the values was done using statistical package SPSS PC+ (Statistical Package for the Social Sciences, version 4.01). Results: The outcome of immunohistochemistry shows that DIGO samples express more CTGF than control group and phenytoin expresses more CTGF followed by nifedipine and cyclosporine. Conclusion: The study shows that there is an increase in the levels of CTGF in patients with DIGO in comparison to the control group without any gingival overgrowth. In the study, we compared the levels of CTGF in DIGO induced by three most commonly used drugs phenytoin, cyclosporine, and nifedipine. By comparing the levels of CTGF, we find that cyclosporine induces the production of least amount of CTGF. Therefore, it might be a more viable drug choice with reduced side effects. PMID:29629324

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

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

Zhou, Jian-Ying; Chen, Lijun; Zhang, Bai

The identification of protein biomarkers requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics strategy using one channel for universal normalization across all samples. A total of 307 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 107 one-dimensional (1D) LC-MS/MS datasets and 8 offline two-dimensional (2D) LC-MS/MS datasets (25 fractions for each set) for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assessmore » the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we developed a quantification confidence score based on the quality of each peptide-spectrum match (PSM) to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS datasets collected over a 16 month period.« less

Ontology-based, Tissue MicroArray oriented, image centered tissue bank

PubMed Central

Viti, Federica; Merelli, Ivan; Caprera, Andrea; Lazzari, Barbara; Stella, Alessandra; Milanesi, Luciano

2008-01-01

Background Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information. Results In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data. Conclusions Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes. PMID:18460177

Spatial cluster analysis of nanoscopically mapped serotonin receptors for classification of fixed brain tissue

NASA Astrophysics Data System (ADS)

Sams, Michael; Silye, Rene; Göhring, Janett; Muresan, Leila; Schilcher, Kurt; Jacak, Jaroslaw

2014-01-01

We present a cluster spatial analysis method using nanoscopic dSTORM images to determine changes in protein cluster distributions within brain tissue. Such methods are suitable to investigate human brain tissue and will help to achieve a deeper understanding of brain disease along with aiding drug development. Human brain tissue samples are usually treated postmortem via standard fixation protocols, which are established in clinical laboratories. Therefore, our localization microscopy-based method was adapted to characterize protein density and protein cluster localization in samples fixed using different protocols followed by common fluorescent immunohistochemistry techniques. The localization microscopy allows nanoscopic mapping of serotonin 5-HT1A receptor groups within a two-dimensional image of a brain tissue slice. These nanoscopically mapped proteins can be confined to clusters by applying the proposed statistical spatial analysis. Selected features of such clusters were subsequently used to characterize and classify the tissue. Samples were obtained from different types of patients, fixed with different preparation methods, and finally stored in a human tissue bank. To verify the proposed method, samples of a cryopreserved healthy brain have been compared with epitope-retrieved and paraffin-fixed tissues. Furthermore, samples of healthy brain tissues were compared with data obtained from patients suffering from mental illnesses (e.g., major depressive disorder). Our work demonstrates the applicability of localization microscopy and image analysis methods for comparison and classification of human brain tissues at a nanoscopic level. Furthermore, the presented workflow marks a unique technological advance in the characterization of protein distributions in brain tissue sections.

Accuracy comparison of guided surgery for dental implants according to the tissue of support: a systematic review and meta-analysis.

PubMed

Raico Gallardo, Yolanda Natali; da Silva-Olivio, Isabela Rodrigues Teixeira; Mukai, Eduardo; Morimoto, Susana; Sesma, Newton; Cordaro, Luca

2017-05-01

To systematically assess the current dental literature comparing the accuracy of computer-aided implant surgery when using different supporting tissues (tooth, mucosa, or bone). Two reviewers searched PubMed (1972 to January 2015) and the Cochrane Central Register of Controlled Trials (Central) (2002 to January 2015). For the assessment of accuracy, studies were included with the following outcome measures: (i) angle deviation, (ii) deviation at the entry point, and (iii) deviation at the apex. Eight clinical studies from the 1602 articles initially identified met the inclusion criteria for the qualitative analysis. Four studies (n = 599 implants) were evaluated using meta-analysis. The bone-supported guides showed a statistically significant greater deviation in angle (P < 0.001), entry point (P = 0.01), and the apex (P = 0.001) when compared to the tooth-supported guides. Conversely, when only retrospective studies were analyzed, not significant differences are revealed in the deviation of the entry point and apex. The mucosa-supported guides indicated a statistically significant greater reduction in angle deviation (P = 0.02), deviation at the entry point (P = 0.002), and deviation at the apex (P = 0.04) when compared to the bone-supported guides. Between the mucosa- and tooth-supported guides, there were no statistically significant differences for any of the outcome measures. It can be concluded that the tissue of the guide support influences the accuracy of computer-aided implant surgery. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Small-window parametric imaging based on information entropy for ultrasound tissue characterization

PubMed Central

Tsui, Po-Hsiang; Chen, Chin-Kuo; Kuo, Wen-Hung; Chang, King-Jen; Fang, Jui; Ma, Hsiang-Yang; Chou, Dean

2017-01-01

Constructing ultrasound statistical parametric images by using a sliding window is a widely adopted strategy for characterizing tissues. Deficiency in spatial resolution, the appearance of boundary artifacts, and the prerequisite data distribution limit the practicability of statistical parametric imaging. In this study, small-window entropy parametric imaging was proposed to overcome the above problems. Simulations and measurements of phantoms were executed to acquire backscattered radiofrequency (RF) signals, which were processed to explore the feasibility of small-window entropy imaging in detecting scatterer properties. To validate the ability of entropy imaging in tissue characterization, measurements of benign and malignant breast tumors were conducted (n = 63) to compare performances of conventional statistical parametric (based on Nakagami distribution) and entropy imaging by the receiver operating characteristic (ROC) curve analysis. The simulation and phantom results revealed that entropy images constructed using a small sliding window (side length = 1 pulse length) adequately describe changes in scatterer properties. The area under the ROC for using small-window entropy imaging to classify tumors was 0.89, which was higher than 0.79 obtained using statistical parametric imaging. In particular, boundary artifacts were largely suppressed in the proposed imaging technique. Entropy enables using a small window for implementing ultrasound parametric imaging. PMID:28106118

Small-window parametric imaging based on information entropy for ultrasound tissue characterization

NASA Astrophysics Data System (ADS)

Tsui, Po-Hsiang; Chen, Chin-Kuo; Kuo, Wen-Hung; Chang, King-Jen; Fang, Jui; Ma, Hsiang-Yang; Chou, Dean

2017-01-01

Constructing ultrasound statistical parametric images by using a sliding window is a widely adopted strategy for characterizing tissues. Deficiency in spatial resolution, the appearance of boundary artifacts, and the prerequisite data distribution limit the practicability of statistical parametric imaging. In this study, small-window entropy parametric imaging was proposed to overcome the above problems. Simulations and measurements of phantoms were executed to acquire backscattered radiofrequency (RF) signals, which were processed to explore the feasibility of small-window entropy imaging in detecting scatterer properties. To validate the ability of entropy imaging in tissue characterization, measurements of benign and malignant breast tumors were conducted (n = 63) to compare performances of conventional statistical parametric (based on Nakagami distribution) and entropy imaging by the receiver operating characteristic (ROC) curve analysis. The simulation and phantom results revealed that entropy images constructed using a small sliding window (side length = 1 pulse length) adequately describe changes in scatterer properties. The area under the ROC for using small-window entropy imaging to classify tumors was 0.89, which was higher than 0.79 obtained using statistical parametric imaging. In particular, boundary artifacts were largely suppressed in the proposed imaging technique. Entropy enables using a small window for implementing ultrasound parametric imaging.

Changes of statistical structural fluctuations unveils an early compacted degraded stage of PNS myelin

NASA Astrophysics Data System (ADS)

Poccia, Nicola; Campi, Gaetano; Ricci, Alessandro; Caporale, Alessandra S.; di Cola, Emanuela; Hawkins, Thomas A.; Bianconi, Antonio

2014-06-01

Degradation of the myelin sheath is a common pathology underlying demyelinating neurological diseases from Multiple Sclerosis to Leukodistrophies. Although large malformations of myelin ultrastructure in the advanced stages of Wallerian degradation is known, its subtle structural variations at early stages of demyelination remains poorly characterized. This is partly due to the lack of suitable and non-invasive experimental probes possessing sufficient resolution to detect the degradation. Here we report the feasibility of the application of an innovative non-invasive local structure experimental approach for imaging the changes of statistical structural fluctuations in the first stage of myelin degeneration. Scanning micro X-ray diffraction, using advances in synchrotron x-ray beam focusing, fast data collection, paired with spatial statistical analysis, has been used to unveil temporal changes in the myelin structure of dissected nerves following extraction of the Xenopus laevis sciatic nerve. The early myelin degeneration is a specific ordered compacted phase preceding the swollen myelin phase of Wallerian degradation. Our demonstration of the feasibility of the statistical analysis of SµXRD measurements using biological tissue paves the way for further structural investigations of degradation and death of neurons and other cells and tissues in diverse pathological states where nanoscale structural changes may be uncovered.

Cores Of Recurrent Events (CORE) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CORE is a statistically supported computational method for finding recurrently targeted regions in massive collections of genomic intervals, such as those arising from DNA copy number analysis of single tumor cells or bulk tumor tissues.

The differentiation of oral soft- and hard tissues using laser induced breakdown spectroscopy - a prospect for tissue specific laser surgery.

PubMed

Rohde, Maximilian; Mehari, Fanuel; Klämpfl, Florian; Adler, Werner; Neukam, Friedrich-Wilhelm; Schmidt, Michael; Stelzle, Florian

2017-10-01

Compared to conventional techniques, Laser surgery procedures provide a number of advantages, but may be associated with an increased risk of iatrogenic damage to important anatomical structures. The type of tissue ablated in the focus spot is unknown. Laser-Induced Breakdown-Spectroscopy (LIBS) has the potential to gain information about the type of material that is being ablated by the laser beam. This may form the basis for tissue selective laser surgery. In the present study, 7 different porcine tissues (cortical and cancellous bone, nerve, mucosa, enamel, dentine and pulp) from 6 animals were analyzed for their qualitative and semiquantitative molecular composition using LIBS. The so gathered data was used to first differentiate between the soft- and hard-tissues using a Calcium-Carbon emission based classifier. The tissues were then further classified using emission-ratio based analysis, principal component analysis (PCA) and linear discriminant analysis (LDA). The relatively higher concentration of Calcium in the hard tissues allows for an accurate first differentiation of soft- and hard tissues (100% sensitivity and specificity). The ratio based statistical differentiation approach yields results in the range from 65% (enamel-dentine pair) to 100% (nerve-pulp, cancellous bone-dentine, cancellous bone-enamel pairs) sensitivity and specificity. Experimental LIBS measuring setup. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small angle scattering polarization biopsy: a comparative analysis of various skin diseases

NASA Astrophysics Data System (ADS)

Zimnyakov, D. A.; Alonova, M. V.; Yermolenko, S. B.; Ivashko, P. V.; Reshetnikova, E. M.; Galkina, E. M.; Utz, S. R.

2013-12-01

An approach to differentiation of the morphological features of normal and pathological human epidermis on the base of statistical analysis of the local polarization states of laser light forward scattered by in-vitro tissue samples is discussed. The eccentricity and the azimuth angle of local polarization ellipses retrieved for various positions of the focused laser beam on the tissue surface, and the coefficient of collimated transmittance are considered as the diagnostic parameters for differentiation. The experimental data obtained with the psoriasis, discoid lupus erythematosus, alopecia, lichen planus, scabies, demodex, and normal skin samples are presented.

Hamstring autograft versus soft-tissue allograft in anterior cruciate ligament reconstruction: a systematic review and meta-analysis of randomized controlled trials.

PubMed

Cvetanovich, Gregory L; Mascarenhas, Randy; Saccomanno, Maristella F; Verma, Nikhil N; Cole, Brian J; Bush-Joseph, Charles A; Bach, Bernard R

2014-12-01

To compare outcomes of anterior cruciate ligament (ACL) reconstruction with hamstring autograft versus soft-tissue allograft by systematic review and meta-analysis. A systematic review of randomized controlled studies comparing hamstring autograft with soft-tissue allograft in ACL reconstruction was performed. Studies were identified by strict inclusion and exclusion criteria. Descriptive statistics were reported. Where possible, the data were pooled and a meta-analysis was performed using RevMan software (The Nordic Cochrane Centre, The Cochrane Collaboration, Copenhagen, Denmark). Dichotomous data were reported as risk ratios, whereas continuous data were reported as standardized mean differences and 95% confidence intervals. Heterogeneity was assessed by use of I(2) for each meta-analysis. Study methodologic quality was analyzed with the Modified Coleman Methodology Score and Jadad scale. Five studies with 504 combined patients (251 autograft and 253 allograft; 374 male and 130 female patients) with a mean age of 29.9 ± 2.2 years were included. The allografts used were fresh-frozen hamstring, irradiated hamstring, mixture of fresh-frozen and cryopreserved hamstring, fresh-frozen tibialis anterior, and fresh-frozen Achilles tendon grafts without bone blocks. The mean follow-up period was 47.4 ± 26.9 months, with a mean follow-up rate of 83.3% ± 8.6%. Two studies found a longer operative time with autograft than with allograft (77.1 ± 2.0 minutes v 59.9 ± 0.9 minutes, P = .008). Meta-analysis showed no statistically significant differences between autografts and allografts for any outcome measures (P > .05 for all tests). One study found significantly greater laxity for irradiated allograft than for autograft. The methodologic quality of the 5 studies was poor, with a mean Modified Coleman Methodology Score of 54.4 ± 6.9 and mean Jadad score of 1.6 ± 1.5. On the basis of this systematic review and meta-analysis of 5 randomized controlled trials, there is no statistically significant difference in outcome between patients undergoing ACL reconstruction with hamstring autograft and those undergoing ACL reconstruction with soft-tissue allograft. These results may not extrapolate to younger patient populations. The methodology of the available randomized controlled trials comparing hamstring autograft and soft-tissue allograft is poor. Level II, systematic review of Level I and II studies. Copyright © 2014 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

A Novel Candidate Molecule in Pathological Grading Of Gliomas: ELABELA.

PubMed

Artas, Gokhan; Ozturk, Sait; Kuloglu, Tuncay; Dagli, Adile Ferda; Gonen, Murat; Artas, Hakan; Aydin, Suleyman; Erol, Fatih Serhat

2018-04-06

This study aimed to investigate the possible role of ELABELA (ELA) in the histopathological grading of gliomas. We retrospectively assessed pathological specimens of patients who underwent surgery for intracranial space-occupying lesions. Only primary glioma specimens were included in this study. We enrolled 11 patients histologically diagnosed with low-grade glioma and 22 patients with high-grade glioma. The ELA antibody was applied to 4-6-µm-thick sections obtained from paraffin blocks. Histoscores were calculated using the distribution and intensity of staining immunoreactivity. An independent sample t-test was used for two-point inter-group assessments, whereas one-way analysis of variance was used for the other assessments. P 0.05 was considered statistically significant. The histoscores of the control brain, low-grade glioma, and high-grade glioma tissues were found to be 0.08, 0.37, and 0.92, respectively. The difference in ELA immunoreactivity between the control brain tissue and glioma tissue was statistically significant (p 0.05). In addition, a statistically significant increase was observed in ELA immunoreactivity in high-grade glioma tissues compared with that in low-grade glioma tissues (p 0.05). ELA has an angiogenetic role in the progression of glial tumors. ELA, which is an endogenous ligand of the apelin receptor, activates the apelinergic system and causes the progression of glial tumors. Further studies with a large number of patients are necessary to investigate the angiogenetic role of ELA in glial tumors.

Soft Tissue Response to Titanium Abutments with Different Surface Treatment: Preliminary Histologic Report of a Randomized Controlled Trial.

PubMed

Canullo, Luigi; Dehner, Jan Friedrich; Penarrocha, David; Checchi, Vittorio; Mazzoni, Annalisa; Breschi, Lorenzo

2016-01-01

The aim of this preliminary prospective RCT was to histologically evaluate peri-implant soft tissues around titanium abutments treated using different cleaning methods. Sixteen patients were randomized into three groups: laboratory customized abutments underwent Plasma of Argon treatment (Plasma Group), laboratory customized abutments underwent cleaning by steam (Steam Group), and abutments were used as they came from industry (Control Group). Seven days after the second surgery, soft tissues around abutments were harvested. Samples were histologically analyzed. Soft tissues surrounding Plasma Group abutments predominantly showed diffuse chronic infiltrate, almost no acute infiltrate, with presence of few polymorphonuclear neutrophil granulocytes, and a diffuse presence of collagenization bands. Similarly, in Steam Group, the histological analysis showed a high variability of inflammatory expression factors. Tissues harvested from Control Group showed presence of few neutrophil granulocytes, moderate presence of lymphocytes, and diffuse collagenization bands in some sections, while they showed absence of acute infiltrate in 40% of sections. However, no statistical difference was found among the tested groups for each parameter (p > 0.05). Within the limit of the present study, results showed no statistically significant difference concerning inflammation and healing tendency between test and control groups.

Dissolution of pulp tissue by aqueous solution of chlorhexidine digluconate and chlorhexidine digluconate gel.

PubMed

Okino, L A; Siqueira, E L; Santos, M; Bombana, A C; Figueiredo, J A P

2004-01-01

To evaluate the activity of various root canal irrigants on bovine pulp tissue. The irrigants tested were: 0.5, 1.0 and 2.5% sodium hypochlorite; 2% aqueous solution of chlorhexidine digluconate; 2% chlorhexidine digluconate gel (Natrosol); and distilled water as control. Bovine pulp fragments were weighed and placed in contact with 20 mL of each tested substance in a centrifuge at 150 r.p.m. until total dissolution. Dissolution speed was calculated by dividing pulp weight by dissolution time. Statistical analysis was performed using the Kruskal-Wallis test. Distilled water and both solutions of chlorhexidine did not dissolve the pulp tissue within 6 h. Mean dissolution speeds for 0.5, 1.0 and 2.5% sodium hypochlorite solutions were 0.31, 0.43 and 0.55 mg min(-1), respectively. The solvent ability of chlorhexidine solutions was similar to that of distilled water. The results for sodium hypochlorite solutions, chlorhexidine solutions and distilled water were statistically different (P>0.01). Both chlorhexidine preparations and distilled water were not able to dissolve pulp tissue. All sodium hypochlorite solutions were efficient in dissolving pulp tissue; the dissolution speed varied with the concentration of the solution.

Analysis of the optical characteristics of adipose tissue in vitro sensitized by indocyanine green and exposed to IR-laser irradiation

NASA Astrophysics Data System (ADS)

Yanina, I. Yu.; Doubrovski, V. A.; Tuchin, V. V.

2015-03-01

The effect of IR-laser irradiation on adipose tissue sensitized by indocyanine green is studied in vitro. Experiments and statistical analysis are used to show that wavelength-selective irradiation leads to an increase in the homogeneity of optical images of adipose cells with time. The transmission coefficient that is averaged over the image area weakly depends on the observation time. An increase in the homogeneity of images is interpreted as a result of immersion of optical inhomogeneities of tissue owing to the intracellular liquid that is released through the photochemically induced pores in cellular membranes. An increase in the optical homogeneity of the medium is compensated for by a decrease in the transmission coefficient of the sensitizer, which is manifested as a weak time dependence of the image-averaged transmittance of tissue.

Heavy Metal Content in Chilean Fish Related to Habitat Use, Tissue Type and River of Origin.

PubMed

Copaja, S V; Pérez, C A; Vega-Retter, C; Véliz, D

2017-12-01

In this study, we analyze the concentration of ten metals in two freshwater fish-the benthic catfish Trichomycterus areolatus and the limnetic silverside Basilichthys microlepidotus-in order to detect possible accumulation differences related to fish habitat (benthic or pelagic), tissue type (gill, liver and muscle), and the river of origin (four different rivers) in central Chile. The MANOVA performed with all variables and metals, revealed independent effects of fish, tissue and river. In the case of the fish factor, Cu, Cr, Mo and Zn showed statistically higher concentrations in catfish compared with silverside for all tissues and in all rivers (p < 0.05). In the case of the tissue factor, Al, Cr, Fe and Mn had statistically higher concentrations in liver and gills than in muscle (p  < 0.05). For the river effect, the analysis showed higher concentrations of Cr, Mn and Pb in the Cogoti river and the lower concentrations in the Recoleta river. These results suggest that not all metals have the same pattern of accumulation; however, some metals tend to accumulate more in readily catfish, probably due to their benthic habit, and in liver and gill tissue, probably as a result of accumulation from food sources and respiration.

Hierarchical patch-based co-registration of differently stained histopathology slides

NASA Astrophysics Data System (ADS)

Yigitsoy, Mehmet; Schmidt, Günter

2017-03-01

Over the past decades, digital pathology has emerged as an alternative way of looking at the tissue at subcellular level. It enables multiplexed analysis of different cell types at micron level. Information about cell types can be extracted by staining sections of a tissue block using different markers. However, robust fusion of structural and functional information from different stains is necessary for reproducible multiplexed analysis. Such a fusion can be obtained via image co-registration by establishing spatial correspondences between tissue sections. Spatial correspondences can then be used to transfer various statistics about cell types between sections. However, the multi-modal nature of images and sparse distribution of interesting cell types pose several challenges for the registration of differently stained tissue sections. In this work, we propose a co-registration framework that efficiently addresses such challenges. We present a hierarchical patch-based registration of intensity normalized tissue sections. Preliminary experiments demonstrate the potential of the proposed technique for the fusion of multi-modal information from differently stained digital histopathology sections.

Brain cancer probed by native fluorescence and stokes shift spectroscopy

NASA Astrophysics Data System (ADS)

Zhou, Yan; Liu, Cheng-hui; He, Yong; Pu, Yang; Li, Qingbo; Wang, Wei; Alfano, Robert R.

2012-12-01

Optical biopsy spectroscopy was applied to diagnosis human brain cancer in vitro. The spectra of native fluorescence, Stokes shift and excitation spectra were obtained from malignant meningioma, benign, normal meningeal tissues and acoustic neuroma benign tissues. The wide excitation wavelength ranges were used to establish the criterion for distinguishing brain diseases. The alteration of fluorescence spectra between normal and abnormal brain tissues were identified by the characteristic fluorophores under the excitation with UV to visible wavelength range. It was found that the ratios of the peak intensities and peak position in both spectra of fluorescence and Stokes shift may be used to diagnose human brain meninges diseases. The preliminary analysis of fluorescence spectral data from cancer and normal meningeal tissues by basic biochemical component analysis model (BBCA) and Bayes classification model based on statistical methods revealed the changes of components, and classified the difference between cancer and normal human brain meningeal tissues in a predictions accuracy rate is 0.93 in comparison with histopathology and immunohistochemistry reports (gold standard).

[Effect of overdose fluoride on expression of bone sialoprotein in developing dental tissues of rats].

PubMed

Xu, Zhi-ling; Wang, Qiang; Liu, Tian-lin; Guo, Li-ying; Jing, Feng-qiu; Liu, Hui

2006-04-01

To investigate the changes of bone sialoprotein (BSP) in developing dental tissues of rats exposed to fluoride. Twenty rats were randomly divided into two groups, one was with distilled water (control group), the other was with distilled water treated by fluoride (experimental group). When the fluorosis model was established, the changes of the expression of BSP were investigated and compared between the two groups. HE staining was used to observe the morphology of the cell, and immunohistochemisty assay was used to determine the expression of BSP in rat incisor. Student's t test was used for statistical analysis. The ameloblasts had normal morphology and arranged orderly. Immunoreactivitis of BSP was present in matured ameloblasts, dentinoblasts, cementoblasts, and the matrix in the control group. But in the experimental group the ameloblasts arranged in multiple layers, the enamel matrix was confused and the expression of BSP was significantly lower than that of the control group. Statistical analysis showed significant differences between the two groups (P<0.01). Fluoride can inhibit the expression of BSP in developing dental tissues of rats, and then inhibit differentiation of the tooth epithelial cells and secretion of matrix. This is a probable intracellular mechanism of dental fluorosis.

Statistical analysis of polarization interference images of biological fluids polycrystalline films in the tasks of optical anisotropy weak changes differentiation

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Dubolazov, O. V.; Ushenko, V. O.; Zhytaryuk, V. G.; Prydiy, O. G.; Pavlyukovich, N.; Pavlyukovich, O.

2018-01-01

In this paper, we present the results of a statistical analysis of polarization-interference images of optically thin histological sections of biological tissues and polycrystalline films of biological fluids of human organs. A new analytical parameter is introduced-the local contrast of the interference pattern in the plane of a polarizationinhomogeneous microscopic image of a biological preparation. The coordinate distributions of the given parameter and the sets of statistical moments of the first-fourth order that characterize these distributions are determined. On this basis, the differentiation of degenerative-dystrophic changes in the myocardium and the polycrystalline structure of the synovial fluid of the human knee with different pathologies is realized.

Intraoperative detection of 18F-FDG-avid tissue sites using the increased probe counting efficiency of the K-alpha probe design and variance-based statistical analysis with the three-sigma criteria

PubMed Central

2013-01-01

Background Intraoperative detection of 18F-FDG-avid tissue sites during 18F-FDG-directed surgery can be very challenging when utilizing gamma detection probes that rely on a fixed target-to-background (T/B) ratio (ratiometric threshold) for determination of probe positivity. The purpose of our study was to evaluate the counting efficiency and the success rate of in situ intraoperative detection of 18F-FDG-avid tissue sites (using the three-sigma statistical threshold criteria method and the ratiometric threshold criteria method) for three different gamma detection probe systems. Methods Of 58 patients undergoing 18F-FDG-directed surgery for known or suspected malignancy using gamma detection probes, we identified nine 18F-FDG-avid tissue sites (from amongst seven patients) that were seen on same-day preoperative diagnostic PET/CT imaging, and for which each 18F-FDG-avid tissue site underwent attempted in situ intraoperative detection concurrently using three gamma detection probe systems (K-alpha probe, and two commercially-available PET-probe systems), and then were subsequently surgical excised. Results The mean relative probe counting efficiency ratio was 6.9 (± 4.4, range 2.2–15.4) for the K-alpha probe, as compared to 1.5 (± 0.3, range 1.0–2.1) and 1.0 (± 0, range 1.0–1.0), respectively, for two commercially-available PET-probe systems (P < 0.001). Successful in situ intraoperative detection of 18F-FDG-avid tissue sites was more frequently accomplished with each of the three gamma detection probes tested by using the three-sigma statistical threshold criteria method than by using the ratiometric threshold criteria method, specifically with the three-sigma statistical threshold criteria method being significantly better than the ratiometric threshold criteria method for determining probe positivity for the K-alpha probe (P = 0.05). Conclusions Our results suggest that the improved probe counting efficiency of the K-alpha probe design used in conjunction with the three-sigma statistical threshold criteria method can allow for improved detection of 18F-FDG-avid tissue sites when a low in situ T/B ratio is encountered. PMID:23496877

Raman Spectroscopy Study of Prostatic Adenocarcinoma Bulk Tissues

NASA Astrophysics Data System (ADS)

Devpura, S.; Dai, H.; Thakur, J. S.; Naik, R.; Cao, A.; Pandya, A.; Auner, G. W.; Sarkar, F.; Sakr, W.; Naik, V.

2009-03-01

Prostate cancer is one of the most common types of cancer among men. The mortality rate for this disease can be dramatically reduced if it can be diagnosed in its early stages. Raman spectroscopy is one of the optical techniques which can provide fingerprints of a disease in terms of its molecular composition which changes due to the onset of disease. The aim of this project is to investigate the differences in the Raman spectra to identify benign epithelium (BE), prostatic intraepithelial neoplasia (PIN) and adenocarcinoma of various Gleason grades in archived bulk tissues embedded in paraffin wax. For each tissue, two adjacent tissue sections were cut and dewaxed, where one of the sections was stained using haematoxylin and eosin for histological examination and the other unstained adjacent section was used for Raman spectroscopic studies. We have collected Raman spectra from 10 prostatic adenocarcinoma dewaxed tissue sections using Raman microscope (785 nm excitation laser). The data were analyzed using statistical methods of principal component analysis and discriminant function analysis to classify the tissue regions. The results indicate that Raman Spectroscopy can differentiate between BE, PIN and Cancer regions.

Staging Liver Fibrosis with Statistical Observers

NASA Astrophysics Data System (ADS)

Brand, Jonathan Frieman

Chronic liver disease is a worldwide health problem, and hepatic fibrosis (HF) is one of the hallmarks of the disease. Pathology diagnosis of HF is based on textural change in the liver as a lobular collagen network that develops within portal triads. The scale of collagen lobules is characteristically on order of 1mm, which close to the resolution limit of in vivo Gd-enhanced MRI. In this work the methods to collect training and testing images for a Hotelling observer are covered. An observer based on local texture analysis is trained and tested using wet-tissue phantoms. The technique is used to optimize the MRI sequence based on task performance. The final method developed is a two stage model observer to classify fibrotic and healthy tissue in both phantoms and in vivo MRI images. The first stage observer tests for the presence of local texture. Test statistics from the first observer are used to train the second stage observer to globally sample the local observer results. A decision of the disease class is made for an entire MRI image slice using test statistics collected from the second observer. The techniques are tested on wet-tissue phantoms and in vivo clinical patient data.

Glycomics expression analysis of sulfated glycosaminoglycans of human colorectal cancer tissues and non-neoplastic mucosa by electrospray ionization mass spectrometry.

PubMed

Marolla, Ana Paula Cleto; Waisberg, Jaques; Saba, Gabriela Tognini; Waisberg, Daniel Reis; Margeotto, Fernando Beani; Pinhal, Maria Aparecida da Silva

2015-01-01

To determine the presence of glycosaminoglycans in the extracellular matrix of connective tissue from neoplastic and non-neoplastic colorectal tissues, since it has a central role in tumor development and progression. Tissue samples from neoplastic and non-neoplastic colorectal tissues were obtained from 64 operated patients who had colorectal carcinoma with no distant metastases. Expressions of heparan sulphate, chondroitin sulphate, dermatan sulphate and their fragments were analyzed by electrospray ionization mass spectrometry, with the technique for extraction and quantification of glycosaminoglycans after proteolysis and electrophoresis. The statistical analysis included mean, standard deviation, and Student'st test. The glycosaminoglycans extracted from colorectal tissue showed three electrophoretic bands in agarose gel. Electrospray ionization mass spectrometry showed characteristic disaccharide fragments from glycosaminoglycans, indicating their structural characterization in the tissues analyzed. Some peaks in the electrospray ionization mass spectrometry were not characterized as fragments of sugars, indicating the presence of fragments of the protein structure of proteoglycans generated during the glycosaminoglycan purification. The average amount of chondroitin and dermatan increased in the neoplastic tissue compared to normal tissue (p=0.01). On the other hand, the average amount of heparan decreased in the neoplastic tissue compared to normal tissue (p= 0.03). The method allowed the determination of the glycosaminoglycans structural profile in colorectal tissue from neoplastic and non-neoplastic colorectal tissue. Neoplastic tissues showed greater amounts of chondroitin sulphate and dermatan sulphate compared to non-neoplastic tissues, while heparan sulphate was decreased in neoplastic tissues.

Photoacoustic physio-chemical analysis for prostate cancer diagnosis (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Guan; Cheng, Qian; Huang, Shengsong; Qin, Ming; Hopkins, Thomas; Lee, Chang H.; Kopelman, Raoul; Chao, Wan-yu; Keller, Evan T.; Wu, Denglong; Wang, Xueding

2017-03-01

Photoacoustic physio-chemical analysis (PAPCA) is a recently developed technology capable of simultaneously quantifying the content of molecular components and the corresponding microarchitectures in biological tissue. We have successfully quantified the diagnostic information in livers with PAPCA. In this study, we implemented PAPCA to the diagnosis of prostate cancers. 4 human prostates were scanned ex vivo. The PA signals from normal and cancerous regions in the prostates were acquired by an interstitial needle PA probe. A total of 14 interstitial measurements, including 6 within the normal regions and 8 in the cancerous regions, were acquired. The observed changes in molecular components, including lipid, collagen and hemoglobin were consistent with the findings by other research groups. The changes were quantified by PA spectral analysis (PASA) at wavelengths where strong optical absorption of the relevant molecular components was found. Statistically significant differences among the PASA parameters were observed (p=0.025 at significance of 0.05). A support vector machine model for differentiating the normal and cancerous tissue was established. With the limited number of samples, an 85% diagnostic accuracy was found. The diagnostic information in the PCPCA can be further enriched by targeted optical contrast agents visualizing the microarchitecture in PCa tissues. F3 PAA-PEG nanoparticles was employed to stain the PCa cells in a transgenic mouse model, in which the microarchitectures of normal and cancerous prostate tissues are comparable to that in human. Statistically significant differences were observed between the contrast-enhanced normal and cancerous regions (p=0.038 at a significance of 0.05).

Automated tissue classification of intracardiac optical coherence tomography images (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gan, Yu; Tsay, David; Amir, Syed B.; Marboe, Charles C.; Hendon, Christine P.

2016-03-01

Remodeling of the myocardium is associated with increased risk of arrhythmia and heart failure. Our objective is to automatically identify regions of fibrotic myocardium, dense collagen, and adipose tissue, which can serve as a way to guide radiofrequency ablation therapy or endomyocardial biopsies. Using computer vision and machine learning, we present an automated algorithm to classify tissue compositions from cardiac optical coherence tomography (OCT) images. Three dimensional OCT volumes were obtained from 15 human hearts ex vivo within 48 hours of donor death (source, NDRI). We first segmented B-scans using a graph searching method. We estimated the boundary of each region by minimizing a cost function, which consisted of intensity, gradient, and contour smoothness. Then, features, including texture analysis, optical properties, and statistics of high moments, were extracted. We used a statistical model, relevance vector machine, and trained this model with abovementioned features to classify tissue compositions. To validate our method, we applied our algorithm to 77 volumes. The datasets for validation were manually segmented and classified by two investigators who were blind to our algorithm results and identified the tissues based on trichrome histology and pathology. The difference between automated and manual segmentation was 51.78 +/- 50.96 μm. Experiments showed that the attenuation coefficients of dense collagen were significantly different from other tissue types (P < 0.05, ANOVA). Importantly, myocardial fibrosis tissues were different from normal myocardium in entropy and kurtosis. The tissue types were classified with an accuracy of 84%. The results show good agreements with histology.

Transcriptomic and bioinformatics analysis of the early time-course of the response to prostaglandin F2 alpha in the bovine corpus luteum

USDA-ARS?s Scientific Manuscript database

RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069). Subsequent statistical ana...

Bibliography on Cold Regions Science and Technology. Volume 51, Part 1.

DTIC Science & Technology

1997-12-01

Loess, Plant ecology, Vegetation patterns, Revegeta- tion, Forestry, Soil conservation, Land reclamation, Regional planning, Statistical analysis...printing. Antikainen, M., Griffith, M., Zhang, J., Hon, W.C., Yang, D.S.C., Pihakaski-Maunsbach, K., Plant physi- ology. Mar. 1996, 110(1), p.845-857...65 refs. Plant physiology, Grasses, Plant tissues, Antifreezes, Acclimatization, Chemical analysis, Chemical prop- erties, Temperature effects

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

Ramos, Marcel; Schiffer, Lucas; Re, Angela; Azhar, Rimsha; Basunia, Azfar; Rodriguez, Carmen; Chan, Tiffany; Chapman, Phil; Davis, Sean R; Gomez-Cabrero, David; Culhane, Aedin C; Haibe-Kains, Benjamin; Hansen, Kasper D; Kodali, Hanish; Louis, Marie S; Mer, Arvind S; Riester, Markus; Morgan, Martin; Carey, Vince; Waldron, Levi

2017-11-01

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR . ©2017 American Association for Cancer Research.

[Microcytomorphometric video-image detection of nuclear chromatin in ovarian cancer].

PubMed

Grzonka, Dariusz; Kamiński, Kazimierz; Kaźmierczak, Wojciech

2003-09-01

Technology of detection of tissue preparates precisious evaluates contents of nuclear chromatine, largeness and shape of cellular nucleus, indicators of mitosis, DNA index, ploidy, phase-S fraction and other parameters. Methods of detection of picture are: microcytomorphometry video-image (MCMM-VI), flow, double flow and activated by fluorescence. Diagnostic methods of malignant neoplasm of ovary are still nonspecific and not precise, that is a reason of unsatisfied results of treatment. Evaluation of microcytomorphometric measurements of nuclear chromatine histopathologic tissue preparates (HP) of ovarian cancer and comparison to normal ovarian tissue. Estimated 10 paraffin embedded tissue preparates of serous ovarian cancer, 4 preparates mucinous cancer and 2 cases of tumor Kruckenberg patients operated in Clinic of Perinatology and Gynaecology Silesian Medical Academy in Zabrze in period 2001-2002, MCMM-VI estimation based on computer aided analysis system: microscope Axioscop 20, camera tv JVCTK-C 1380, CarlZeiss KS Vision 400 rel.3.0 software. Following MCMM-VI parameters assessed: count of pathologic nucleus, diameter of nucleus, area, min/max diameter ratio, equivalent circle diameter (Dcircle), mean of brightness (mean D), integrated optical density (IOD = area x mean D), DNA index and 2.5 c exceeding rate percentage (2.5 c ER%). MCMM-VI performed on the 160 areas of 16 preparates of cancer and 100 areas of normal ovarian tissue. Statistical analysis was performed by used t-Student test. We obtained stastistically significant higher values parameters of nuclear chromatine, DI, 2.5 c ER of mucinous cancer and tumor Kruckenberg comparison to serous cancer. MCMM-VI parameters of chromatine malignant ovarian neoplasm were statistically significantly higher than normal ovarian tissue. Cytometric and karyometric parametres of nuclear chromatine estimated MCMM-VI are useful in the diagnostics and prognosis of ovarian cancer.

Automatic characterization of neointimal tissue by intravascular optical coherence tomography.

PubMed

Ughi, Giovanni J; Steigerwald, Kristin; Adriaenssens, Tom; Desmet, Walter; Guagliumi, Giulio; Joner, Michael; D'hooge, Jan

2014-02-01

Intravascular optical coherence tomography (IVOCT) is rapidly becoming the method of choice for assessing vessel healing after stent implantation due to its unique axial resolution <20  μm. The amount of neointimal coverage is an important parameter. In addition, the characterization of neointimal tissue maturity is also of importance for an accurate analysis, especially in the case of drug-eluting and bioresorbable stent devices. Previous studies indicated that well-organized mature neointimal tissue appears as a high-intensity, smooth, and homogeneous region in IVOCT images, while lower-intensity signal areas might correspond to immature tissue mainly composed of acellular material. A new method for automatic neointimal tissue characterization, based on statistical texture analysis and a supervised classification technique, is presented. Algorithm training and validation were obtained through the use of 53 IVOCT images supported by histology data from atherosclerotic New Zealand White rabbits. A pixel-wise classification accuracy of 87% and a two-dimensional region-based analysis accuracy of 92% (with sensitivity and specificity of 91% and 93%, respectively) were found, suggesting that a reliable automatic characterization of neointimal tissue was achieved. This may potentially expand the clinical value of IVOCT in assessing the completeness of stent healing and speed up the current analysis methodologies (which are, due to their time- and energy-consuming character, not suitable for application in large clinical trials and clinical practice), potentially allowing for a wider use of IVOCT technology.

Quantization of liver tissue in dual kVp computed tomography using linear discriminant analysis

NASA Astrophysics Data System (ADS)

Tkaczyk, J. Eric; Langan, David; Wu, Xiaoye; Xu, Daniel; Benson, Thomas; Pack, Jed D.; Schmitz, Andrea; Hara, Amy; Palicek, William; Licato, Paul; Leverentz, Jaynne

2009-02-01

Linear discriminate analysis (LDA) is applied to dual kVp CT and used for tissue characterization. The potential to quantitatively model both malignant and benign, hypo-intense liver lesions is evaluated by analysis of portal-phase, intravenous CT scan data obtained on human patients. Masses with an a priori classification are mapped to a distribution of points in basis material space. The degree of localization of tissue types in the material basis space is related to both quantum noise and real compositional differences. The density maps are analyzed with LDA and studied with system simulations to differentiate these factors. The discriminant analysis is formulated so as to incorporate the known statistical properties of the data. Effective kVp separation and mAs relates to precision of tissue localization. Bias in the material position is related to the degree of X-ray scatter and partial-volume effect. Experimental data and simulations demonstrate that for single energy (HU) imaging or image-based decomposition pixel values of water-like tissues depend on proximity to other iodine-filled bodies. Beam-hardening errors cause a shift in image value on the scale of that difference sought between in cancerous and cystic lessons. In contrast, projection-based decomposition or its equivalent when implemented on a carefully calibrated system can provide accurate data. On such a system, LDA may provide novel quantitative capabilities for tissue characterization in dual energy CT.

Comparison of ferromagnetic induction and bipolar electrosurgery and suction in corticotomies in pig cerebrum.

PubMed

Bowers, Christian A; Burns, Greg; Salzman, Karen; McGill, Lawrence; MacDonald, Joel D

2015-04-01

The effects of newer energy-based surgical dissection and coagulation modalities on cerebral tissue have not been investigated. Several instruments have been developed to address the limitations of traditional electrosurgical instruments in the nervous system. We compared the effects of standard bipolar electrocautery and suction (BPS) with those of a new ferromagnetic induction (FMI) device in corticotomies of pig cerebral tissue as assessed by magnetic resonance imaging (MRI) and histological analysis. Three adult pigs underwent bilateral corticotomies (3 cm long×1 cm deep) using both FMI and BPS. The acute cerebral tissue edema created by each method was measured on coronal volumetric T2-weighted MRI sequences immediately after surgery. A lateral thermal "damage index" was calculated by dividing the width of the visible T2 tissue edema by the measured depth. The radiographic damage indices with each method were compared statistically. Histological analysis of each incision was conducted to compare the extent of tissue damage. MRI showed that the mean radiographic damage index of each corticotomy was significantly lower with the FMI (0.30 ± 0.02 (0.28-0.32)) than with the BPS method (0.54 ± 0.11 (0.42-0.64)) (p = 0.02). Histological analysis suggested a correlation with the radiographic findings as the FMI tissue samples demonstrated less adjacent tissue damage than BPS. FMI appeared to cause less adjacent tissue damage than the BPS method in pig cerebral tissue based on quantitative radiographic and qualitative histological analysis. Future studies are needed to investigate the clinical implications of energy-based surgical dissection on cerebral tissue. Copyright © 2015 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

PubMed Central

2012-01-01

Background Environmentally induced epigenetic transgenerational inheritance of adult onset disease involves a variety of phenotypic changes, suggesting a general alteration in genome activity. Results Investigation of different tissue transcriptomes in male and female F3 generation vinclozolin versus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes. The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Although each tissue transgenerational transcriptome was unique, common cellular pathways and processes were identified between the tissues. A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function. A large number of statistically significant over-represented clusters of genes were identified in the genome for both males and females. These gene clusters ranged from 2-5 megabases in size, and a number of them corresponded to the epimutations previously identified in sperm that transmit the epigenetic transgenerational inheritance of disease phenotypes. Conclusions Combined observations demonstrate that all tissues derived from the epigenetically altered germ line develop transgenerational transcriptomes unique to the tissue, but common epigenetic control regions in the genome may coordinately regulate these tissue-specific transcriptomes. This systems biology approach provides insight into the molecular mechanisms involved in the epigenetic transgenerational inheritance of a variety of adult onset disease phenotypes. PMID:23034163

Bladder radiotherapy treatment: A retrospective comparison of 3-dimensional conformal radiotherapy, intensity-modulated radiation therapy, and volumetric-modulated arc therapy plans

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

Pasciuti, Katia, E-mail: k.pasciuti@virgilio.it; Kuthpady, Shrinivas; Anderson, Anne

To examine tumor's and organ's response when different radiotherapy plan techniques are used. Ten patients with confirmed bladder tumors were first treated using 3-dimensional conformal radiotherapy (3DCRT) and subsequently the original plans were re-optimized using the intensity-modulated radiation treatment (IMRT) and volumetric-modulated arc therapy (VMAT)-techniques. Targets coverage in terms of conformity and homogeneity index, TCP, and organs' dose limits, including integral dose analysis were evaluated. In addition, MUs and treatment delivery times were compared. Better minimum target coverage (1.3%) was observed in VMAT plans when compared to 3DCRT and IMRT ones confirmed by a statistically significant conformity index (CI) results.more » Large differences were observed among techniques in integral dose results of the femoral heads. Even if no statistically significant differences were reported in rectum and tissue, a large amount of energy deposition was observed in 3DCRT plans. In any case, VMAT plans provided better organs and tissue sparing confirmed also by the normal tissue complication probability (NTCP) analysis as well as a better tumor control probability (TCP) result. Our analysis showed better overall results in planning using VMAT techniques. Furthermore, a total time reduction in treatment observed among techniques including gantry and collimator rotation could encourage using the more recent one, reducing target movements and patient discomfort.« less

Soft tissue thin-plate spline analysis of pre-pubertal Korean and European-Americans with untreated Angle's Class III malocclusions.

PubMed

Singh, G D; McNamara, J A; Lozanoff, S

1999-01-01

The purpose of this study was to assess soft tissue facial matrices in subjects of diverse ethnic origins with underlying dentoskeletal malocclusions. Pre-treatment lateral cephalographs of 71 Korean and 70 European-American children aged between 5 and 11 years with Angle's Class III malocclusions were traced, and 12 homologous, soft tissue landmarks digitized. Comparing mean Korean and European-American Class III soft tissue profiles, Procrustes analysis established statistical difference (P < 0.001) between the configurations, and this difference was also true at all seven age groups tested (P < 0.001). Comparing the overall European-American and Korean transformation, thin-plate spline analysis indicated that both affine and non-affine transformations contribute towards the total spline (deformation) of the averaged Class III soft tissue configurations. For non-affine transformations, partial warp (PW) 8 had the highest magnitude, indicating large-scale deformations visualized as labio-mental protrusion, predominantly. In addition, PW9, PW4, and PW5 also had high magnitudes, demonstrating labio-mental vertical compression and antero-posterior compression of the lower labio-mental soft tissues. Thus, Korean children with Class III malocclusions demonstrate antero-posterior and vertical deformations of the labio-mental soft tissue complex with respect to their European-American counterparts. Morphological heterogeneity of the soft tissue integument in subjects of diverse ethnic origin may obscure the underlying skeletal morphology, but the soft tissue integument appears to have minimal ontogenetic association with Class III malocclusions.

DNA methylation map in circulating leukocytes mirrors subcutaneous adipose tissue methylation pattern: a genome-wide analysis from non-obese and obese patients

PubMed Central

Crujeiras, A. B.; Diaz-Lagares, A.; Sandoval, J.; Milagro, F. I.; Navas-Carretero, S.; Carreira, M. C.; Gomez, A.; Hervas, D.; Monteiro, M. P.; Casanueva, F. F.; Esteller, M.; Martinez, J. A.

2017-01-01

The characterization of the epigenetic changes within the obesity-related adipose tissue will provide new insights to understand this metabolic disorder, but adipose tissue is not easy to sample in population-based studies. We aimed to evaluate the capacity of circulating leukocytes to reflect the adipose tissue-specific DNA methylation status of obesity susceptibility. DNA samples isolated from subcutaneous adipose tissue and circulating leukocytes were hybridized in the Infinium HumanMethylation 450 BeadChip. Data were compared between samples from obese (n = 45) and non-obese (n = 8–10) patients by Wilcoxon-rank test, unadjusted for cell type distributions. A global hypomethylation of the differentially methylated CpG sites (DMCpGs) was observed in the obese subcutaneous adipose tissue and leukocytes. The overlap analysis yielded a number of genes mapped by the common DMCpGs that were identified to reflect the obesity state in the leukocytes. Specifically, the methylation levels of FGFRL1, NCAPH2, PNKD and SMAD3 exhibited excellent and statistically significant efficiencies in the discrimination of obesity from non-obesity status (AUC > 0.80; p < 0.05) and a great correlation between both tissues. Therefore, the current study provided new and valuable DNA methylation biomarkers of obesity-related adipose tissue pathogenesis through peripheral blood analysis, an easily accessible and minimally invasive biological material instead of adipose tissue. PMID:28211912

Analysis of statistical properties of laser speckles, forming in skin and mucous of colon: potential application in laser surgery

NASA Astrophysics Data System (ADS)

Rubtsov, Vladimir; Kapralov, Sergey; Chalyk, Iuri; Ulianova, Onega; Ulyanov, Sergey

2013-02-01

Statistical properties of laser speckles, formed in skin and mucous of colon have been analyzed and compared. It has been demonstrated that first and second order statistics of "skin" speckles and "mucous" speckles are quite different. It is shown that speckles, formed in mucous, are not Gaussian one. Layered structure of colon mucous causes formation of speckled biospeckles. First- and second- order statistics of speckled speckles have been reviewed in this paper. Statistical properties of Fresnel and Fraunhofer doubly scattered and cascade speckles are described. Non-gaussian statistics of biospeckles may lead to high localization of intensity of coherent light in human tissue during the laser surgery. Way of suppression of highly localized non-gaussian speckles is suggested.

HPLC assisted Raman spectroscopic studies on bladder cancer

NASA Astrophysics Data System (ADS)

Zha, W. L.; Cheng, Y.; Yu, W.; Zhang, X. B.; Shen, A. G.; Hu, J. M.

2015-04-01

We applied confocal Raman spectroscopy to investigate 12 normal bladder tissues and 30 tumor tissues, and then depicted the spectral differences between the normal and the tumor tissues and the potential canceration mechanism with the aid of the high-performance liquid chromatographic (HPLC) technique. Normal tissues were demonstrated to contain higher tryptophan, cholesterol and lipid content, while bladder tumor tissues were rich in nucleic acids, collagen and carotenoids. In particular, β-carotene, one of the major types of carotenoids, was found through HPLC analysis of the extract of bladder tissues. The statistical software SPSS was applied to classify the spectra of the two types of tissues according to their differences. The sensitivity and specificity of 96.7 and 66.7% were obtained, respectively. In addition, different layers of the bladder wall including mucosa (lumps), muscle and adipose bladder tissue were analyzed by Raman mapping technique in response to previous Raman studies of bladder tissues. All of these will play an important role as a directive tool for the future diagnosis of bladder cancer in vivo.

Consistency of signal intensity and T2* in frozen ex vivo heart muscle, kidney, and liver tissue.

PubMed

Kaye, Elena A; Josan, Sonal; Lu, Aiming; Rosenberg, Jarrett; Daniel, Bruce L; Pauly, Kim Butts

2010-03-01

To investigate tissue dependence of the MRI-based thermometry in frozen tissue by quantification and comparison of signal intensity and T2* of ex vivo frozen tissue of three different types: heart muscle, kidney, and liver. Tissue samples were frozen and imaged on a 0.5 Tesla MRI scanner with ultrashort echo time (UTE) sequence. Signal intensity and T2* were determined as the temperature of the tissue samples was decreased from room temperature to approximately -40 degrees C. Statistical analysis was performed for (-20 degrees C, -5 degrees C) temperature interval. The findings of this study demonstrate that signal intensity and T2* are consistent across three types of tissue for (-20 degrees C, -5 degrees C) temperature interval. Both parameters can be used to calculate a single temperature calibration curve for all three types of tissue and potentially in the future serve as a foundation for tissue-independent MRI-based thermometry.

Histologic assessment of thermal injury to tonsillectomy specimens: a comparison of electrocautery, coblation, harmonic scalpel, and tonsillotome.

PubMed

Modi, Vikash K; Monforte, Hector; Geller, Kenneth A; Koempel, Jeffrey A

2009-11-01

To determine the extent of thermal injury to the tonsillar tissue following the use of various types of instrumentation. To determine if tonsillectomy specimens routinely contain tissue other than lymphoid tissue. Retrospective histologic analysis. A histologic analysis performed on 228 tonsillectomy specimens removed by use of an electrocautery in 132 specimens, harmonic scalpel in 46, coblation device in 24, and a tonsillotome in 26. The specimens were evaluated for presence and percentage of skeletal muscle and depth of thermal tissue injury. The mean percentage of skeletal muscle present in the specimens was 0.79% for electrocautery, 1.74% for harmonic scalpel, 0.97% for coblation device, and 1.66% for the tonsillotome. Skeletal muscle was absent in only 8 of 228 specimens (3.5%). Electrocautery has a statistically significant (P < .05) lower percentage of muscle tissue compared to harmonic scalpel and the tonsillotome. There was no statistically significant difference in the mean depth of thermal injury among the harmonic scalpel (0.68 mm), electrocautery (0.58 mm), and coblation device (0.71 mm) specimens. The tonsillotome specimens had no thermal injury. Attempts to remove the entire tonsil results in a similar depth of thermal injury to tonsillectomy specimens when using the harmonic scalpel, electrocautery, and coblation device. Skeletal muscle is a nearly ubiquitous finding in routine tonsillectomy specimens. The use of an electrocautery with a needle point may allow for a more precise dissection as it results in tonsillectomy specimens with a smaller percentage of muscle present.

Lewis x is highly expressed in normal tissues: a comparative immunohistochemical study and literature revision.

PubMed

Croce, María V; Isla-Larrain, Marina; Rabassa, Martín E; Demichelis, Sandra; Colussi, Andrea G; Crespo, Marina; Lacunza, Ezequiel; Segal-Eiras, Amada

2007-01-01

An immunohistochemical analysis was employed to determine the expression of carbohydrate antigens associated to mucins in normal epithelia. Tissue samples were obtained as biopsies from normal breast (18), colon (35) and oral cavity mucosa (8). The following carbohydrate epitopes were studied: sialyl-Lewis x, Lewis x, Lewis y, Tn hapten, sialyl-Tn and Thomsen-Friedenreich antigen. Mucins were also studied employing antibodies against MUC1, MUC2, MUC4, MUC5AC, MUC6 and also normal colonic glycolipid. Statistical analysis was performed and Kendall correlations were obtained. Lewis x showed an apical pattern mainly at plasma membrane, although cytoplasmic staining was also found in most samples. TF, Tn and sTn haptens were detected in few specimens, while sLewis x was found in oral mucosa and breast tissue. Also, normal breast expressed MUC1 at a high percentage, whereas MUC4 was observed in a small number of samples. Colon specimens mainly expressed MUC2 and MUC1, while most oral mucosa samples expressed MUC4 and MUC1. A positive correlation between MUC1VNTR and TF epitope (r=0.396) was found in breast samples, while in colon specimens MUC2 and colonic glycolipid versus Lewis x were statistically significantly correlated (r=0.28 and r=0.29, respectively). As a conclusion, a defined carbohydrate epitope expression is not exclusive of normal tissue or a determined localization, and it is possible to assume that different glycoproteins and glycolipids may be carriers of carbohydrate antigens depending on the tissue localization considered.

Pulp tissue dissolution capacity of QMix 2in1 irrigation solution.

PubMed

Arslan, Dilara; Guneser, Mehmet Burak; Kustarci, Alper; Er, Kursat; Siso, Seyda Herguner

2015-01-01

The aim of this study was to evaluate the tissue dissolution efficacy of four root canal irrigation solutions (sodium hypochlorite [NaOCl], chlorhexidine gluconate [CHX], Octenidine [OCT], and QMix 2in1) on bovine pulp tissue. Fifty bovine pulp tissue samples, each weighing 6.55 mg, were prepared and randomly divided into four experimental groups and one control group (n = 10) according to the dissolution irrigants used: (1) 5.25% NaOCl group; (2) 2% CHX group; (3) OCT group; (4) QMix 2in1 group; and (5) control group (saline solution). These samples were then placed into special bovine dentin reservoir models and immersed for 1 h with each test solution (0.1 mL of each) at room temperature. The pulp samples were then blotted dry and weighed again. The percentage of weight loss was calculated. Statistically analyzed with one-way analysis of variance and post-hoc Tukey tests (P = 0.05). Saline solution did not dissolve the bovine pulp tissue. All groups, except OCT, dissolved pulp samples more effectively than the control group (P < 0.05). The highest tissue dissolution was observed in 5.25% NaOCl group (P < 0.05). No statistically significant difference was found between the tissue-dissolving effect between QMix 2in1 and those of 2% CHX. Within the limitations of this in vitro study, NaOCl exhibited the best tissue-dissolving effect out of all solutions tested. CHX and QMix 2in1 were able to dissolve pulp tissue but less than NaOCl. OCT and saline solutions could not exhibit significantly tissue-dissolving effectiveness. This study shown that QMix 2in1 has little capacity to dissolve pulp tissue therefore used alone is not sufficient for this purpose.

Pulp tissue dissolution capacity of QMix 2in1 irrigation solution

PubMed Central

Arslan, Dilara; Guneser, Mehmet Burak; Kustarci, Alper; Er, Kursat; Siso, Seyda Herguner

2015-01-01

Objective: The aim of this study was to evaluate the tissue dissolution efficacy of four root canal irrigation solutions (sodium hypochlorite [NaOCl], chlorhexidine gluconate [CHX], Octenidine [OCT], and QMix 2in1) on bovine pulp tissue. Materials and Methods: Fifty bovine pulp tissue samples, each weighing 6.55 mg, were prepared and randomly divided into four experimental groups and one control group (n = 10) according to the dissolution irrigants used: (1) 5.25% NaOCl group; (2) 2% CHX group; (3) OCT group; (4) QMix 2in1 group; and (5) control group (saline solution). These samples were then placed into special bovine dentin reservoir models and immersed for 1 h with each test solution (0.1 mL of each) at room temperature. The pulp samples were then blotted dry and weighed again. The percentage of weight loss was calculated. Statistically analyzed with one-way analysis of variance and post-hoc Tukey tests (P = 0.05). Results: Saline solution did not dissolve the bovine pulp tissue. All groups, except OCT, dissolved pulp samples more effectively than the control group (P < 0.05). The highest tissue dissolution was observed in 5.25% NaOCl group (P < 0.05). No statistically significant difference was found between the tissue-dissolving effect between QMix 2in1 and those of 2% CHX. Conclusions: Within the limitations of this in vitro study, NaOCl exhibited the best tissue-dissolving effect out of all solutions tested. CHX and QMix 2in1 were able to dissolve pulp tissue but less than NaOCl. OCT and saline solutions could not exhibit significantly tissue-dissolving effectiveness. This study shown that QMix 2in1 has little capacity to dissolve pulp tissue therefore used alone is not sufficient for this purpose. PMID:26430374

Bone and Soft Tissue Response in Bone-Level Implants Restored with Platform Switching: A 5-Year Clinical Prospective Study.

PubMed

Lago, Laura; da Silva, Luis; Gude, Francisco; Rilo, Benito

The aim of this prospective study was to evaluate radiographic levels of peri-implant bone crest as well as soft tissue response, papilla height, and buccal mucosa recession, in bone-level implants restored with platform switching after 1-year and 5-year follow-ups. This prospective study called for the placement of 59 implants to obtain a target of 90% power. To compensate for possible dropouts, the sample size was adjusted to 67 implants. To assess marginal bone level changes, periapical radiographs were taken at baseline, 1 year, and 5 years after the definitive restorations. Peri-implant soft tissue modifications were evaluated by performing a photographic sequence at 15 days, 1 year, and 5 years after implant restoration. Parameters measured were: (1) distance from the tip of the papilla to the contact point and (2) apicocoronal crown length. A one-way analysis of variance (ANOVA rank test) was used to compare quantitative data among the three time points studied. Mean marginal bone level changes were as follows: -0.06 ± 0.32 mm from baseline to 1 year, -0.23 ± 0.38 mm from 1 to 5 years, and -0.28 ± 0.45 mm from baseline to 5 years. In bone-level outcomes, no statistically significant differences were found between baseline and 1 year, while the mean differences between 1 and 5 years and baseline and 5 years showed statistically significant differences. In the soft tissue analysis, the distance from the tip of the papilla to the contact point showed the following values: baseline, 2.08 mm; 1 year, 1.54 mm; 5 years, 1.31 mm. No statistically significant differences were found between baseline and 1 year, whereas statistically significant differences between 1 and 5 years and baseline and 5 years were found. Apicocoronal crown length measurements showed the following values: baseline, 9.44 mm; 1 year, 9.28 mm; 5 years, 9.81 mm. No significant differences were found between times studied. This prospective clinical study of 67 bone-level implants restored according to the platform-switching concept reported that radiographic levels of peri-implant bone crest were statistically significant between 1 and 5 years and baseline and 5 years. For the soft tissue response, the greatest reduction in the distance from the papilla to the contact point from 1 to 5 years and baseline to 5 years was observed. No significant differences were shown in the buccal margin.

Differential 3D Mueller-matrix mapping of optically anisotropic depolarizing biological layers

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Grytsyuk, M.; Ushenko, V. O.; Bodnar, G. B.; Vanchulyak, O.; Meglinskiy, I.

2018-01-01

The paper consists of two parts. The first part is devoted to the short theoretical basics of the method of differential Mueller-matrix description of properties of partially depolarizing layers. It was provided the experimentally measured maps of differential matrix of the 2nd order of polycrystalline structure of the histological section of rectum wall tissue. It was defined the values of statistical moments of the1st-4th orders, which characterize the distribution of matrix elements. In the second part of the paper it was provided the data of statistic analysis of birefringence and dichroism of the histological sections of connecting component of vagina wall tissue (normal and with prolapse). It were defined the objective criteria of differential diagnostics of pathologies of vagina wall.

Effect of citric acid, tetracycline, and doxycycline on instrumented periodontally involved root surfaces: A SEM study

PubMed Central

Chahal, Gurparkash Singh; Chhina, Kamalpreet; Chhabra, Vipin; Bhatnagar, Rakhi; Chahal, Amna

2014-01-01

Background: A surface smear layer consisting of organic and inorganic material is formed on the root surface following mechanical instrumentation and may inhibit the formation of new connective tissue attachment to the root surface. Modification of the tooth surface by root conditioning has resulted in improved connective tissue attachment and has advanced the goal of reconstructive periodontal treatment. Aim: The aim of this study was to compare the effects of citric acid, tetracycline, and doxycycline on the instrumented periodontally involved root surfaces in vitro using a scanning electron microscope. Settings and Design: A total of 45 dentin samples obtained from 15 extracted, scaled, and root planed teeth were divided into three groups. Materials and Methods: The root conditioning agents were applied with cotton pellets using the Passive burnishing technique for 5 minutes. The samples were then examined by the scanning electron microscope. Statistical Analysis Used: The statistical analysis was carried out using Statistical Package for Social Sciences (SPSS Inc., Chicago, IL, version 15.0 for Windows). For all quantitative variables means and standard deviations were calculated and compared. For more than two groups ANOVA was applied. For multiple comparisons post hoc tests with Bonferroni correction was used. Results: Upon statistical analysis the root conditioning agents used in this study were found to be effective in removing the smear layer, uncovering and widening the dentin tubules and unmasking the dentin collagen matrix. Conclusion: Tetracycline HCl was found to be the best root conditioner among the three agents used. PMID:24744541

Dynamic laser speckle angiography achieved by eigen-decomposition filtering.

PubMed

Li, Chenxi; Wang, Ruikang

2017-06-01

A new approach is proposed for statistically analysis of laser speckle signals emerged from a living biological tissue based on eigen-decomposition to separate the dynamic speckle signals due to moving blood cells from the static speckle signals due to static tissue components, upon which to achieve angiography of the interrogated tissue in vivo. The proposed approach is tested by imaging mouse ear pinna in vivo, demonstrating its capability of providing detailed microvascular networks with high contrast, and high temporal and spatial resolutions. It is expected to provide further opportunities for laser speckle imaging in the biomedical and clinical applications where microvascular response to certain stimulus or tissue injury is of interest. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transconjunctival penetration of mitomycin C.

PubMed

Velpandian, T; Sihota, Ramanjit; Sinha, Ankur; Gupta, Viney

2008-01-01

The study was performed to estimate transconjunctival penetration of mitomycin C (MMC) to Tenon's tissue following application over the intact conjunctiva before routine trabeculectomy. Institution-based case series. In 41 eyes of 41 patients, MMC (0.4 mg/ml for 3 min) was applied over the intact conjunctiva before beginning trabeculectomy. Tenon's capsule directly beneath the site of application was excised during trabeculectomy and was homogenized, centrifuged and MMC concentrations were analyzed using high-performance liquid chromatography (HPLC). Statistical analysis was performed using STATA 8.0 version software (STATA Corporation, Houston, TX, USA). In this study, P -values less than 0.05 were considered as statistically significant. The average weight of the sample of Tenon's tissue excised was 5.51+/-4.42 mg (range: 0.9-17.1) and the average estimated MMC concentration found to be present in Tenon's tissue using HPLC was 18.67+/-32.36 x 10(-6) moles/kg of the tissue (range: 0.38-197.05 x 10(-6)). In 36 of the 41 patients (87.80%), the MMC concentration reached above 2 x 10(-6) moles/kg of the tissue concentration required to inhibit human conjunctival fibroblasts. Mitomycin C does permeate into the subconjunctival tissue after supraconjunctival application for 3 min. Application of MMC over the conjunctiva may be a useful alternative to subconjunctival or subscleral application during routine trabeculectomy and as an adjunct for failing blebs.

Evaluation of clinical utility of BTC-2000 for measuring soft tissue fibrosis.

PubMed

Davis, Aileen M; Gerrand, Craig; Griffin, Anthony; O'Sullivan, Brian; Hill, Richard P; Wunder, Jay S; Abudu, Adesegun; Bell, Robert S

2004-09-01

To evaluate whether mechanical tissue parameters, specifically laxity (in millimeters) and energy absorption (millimeters of mercury multiplied by millimeters) as measured by the BTC-2000, could discriminate levels of fibrosis severity among patients treated for extremity soft tissue sarcoma by surgery alone; preoperative radiotherapy (RT) and surgery; and surgery followed by postoperative RT. A total of 41 patients were treated for extremity soft tissue sarcoma by surgery alone (n = 11); preoperative RT (50 Gy in 2-Gy daily fractions) and surgery (n = 15); and surgery followed by postoperative RT (66 Gy in 2-Gy daily fractions; n = 15). Serial fibrosis measurements were evaluated at equal intervals from the midpoint of the surgical incision along the length of the incision. On the basis of the average of these measurements, differences among the three groups were analyzed using analysis of variance. Pair-wise statistically significant differences were found among the three treatment groups for both laxity and energy absorption as determined by the average of all measurements. The treatment difference remained statistically significant even after adjusting for differences based on the untreated contralateral limb and anatomic site (p <0.001 and p = 0.002 for laxity and energy absorption, respectively). The biomechanical tissue parameters of laxity and energy absorption discriminated fibrosis severity in patients treated with different RT doses. The BTC-2000 may provide a useful quantitative measure of soft tissue fibrosis.

Personal Authentication Analysis Using Finger-Vein Patterns in Patients with Connective Tissue Diseases—Possible Association with Vascular Disease and Seasonal Change -

PubMed Central

Kono, Miyuki; Miura, Naoto; Fujii, Takao; Ohmura, Koichiro; Yoshifuji, Hajime; Yukawa, Naoichiro; Imura, Yoshitaka; Nakashima, Ran; Ikeda, Takaharu; Umemura, Shin-ichiro; Miyatake, Takafumi; Mimori, Tsuneyo

2015-01-01

Objective To examine how connective tissue diseases affect finger-vein pattern authentication. Methods The finger-vein patterns of 68 patients with connective tissue diseases and 24 healthy volunteers were acquired. Captured as CCD (charge-coupled device) images by transmitting near-infrared light through fingers, they were followed up in once in each season for one year. The similarity of the follow-up patterns and the initial one was evaluated in terms of their normalized cross-correlation C. Results The mean C values calculated for patients tended to be lower than those calculated for healthy volunteers. In midwinter (February in Japan) they showed statistically significant reduction both as compared with patients in other seasons and as compared with season-matched healthy controls, whereas the values calculated for healthy controls showed no significant seasonal changes. Values calculated for patients with systemic sclerosis (SSc) or mixed connective tissue disease (MCTD) showed major reductions in November and, especially, February. Patients with rheumatoid arthritis (RA) and patients with dermatomyositis or polymyositis (DM/PM) did not show statistically significant seasonal changes in C values. Conclusions Finger-vein patterns can be used throughout the year to identify patients with connective tissue diseases, but some attention is needed for patients with advanced disease such as SSc. PMID:26701644

Quantification of Nanoscale Density Fluctuations in Biological Cells/Tissues: Inverse Participation Ratio (IPR) Analysis of Transmission Electron Microscopy Images and Implications for Early-Stage Cancer Detection

NASA Astrophysics Data System (ADS)

Pradhan, Prabhakar; Damania, Dhwanil; Joshi, Hrushikesh; Taflove, Allen; Roy, Hemant; Dravid, Vinayak; Backman, Vadim

2010-03-01

We report a study of the nanoscale mass density fluctuations of biological cells and tissues by quantifying their nanoscale light-localization properties. Transmission electron microscope (TEM) images of human cells and tissues are used to construct corresponding effective disordered optical lattices. Light-localization properties are studied by statistical analysis of the inverse participation ratio (IPR) of the eigenfunctions of these optical lattices at the nanoscales. Our results indicate elevation of the nanoscale disorder strength (e.g., refractive index fluctuations) in early carcinogenesis. Importantly, our results demonstrate that the increase in the nanoscale disorder represents the earliest structural alteration in cells undergoing carcinogenesis known to-date. Potential applications of the technique for early stage cancer detection will be discussed.

Steady State Fluorescence Spectroscopy for Medical Diagnosis

NASA Astrophysics Data System (ADS)

Mahadevan-Jansen, Anita; Gebhart, Steven C.

Light can react with tissue in different ways and provide information for identifying the physiological state of tissue or detecting the presence of disease. The light used to probe tissue does so in a non-intrusive manner and typically uses very low levels of light far below the requirements for therapeutic applications. The use of fiber optics simplifies the delivery and collection of this light in a minimally invasive manner. Since tissue response is virtually instantaneous, the results are obtained in real-time and the use of data processing techniques and multi-variate statistical analysis allows for automated detection and therefore provides an objective estimation of the tissue state. These then form the fundamental basis for the application of optical techniques for the detection of tissue physiology as well as pathology. These distinct advantages have encouraged many researchers to pursue the development of the different optical interactions for biological and medical detection.

Brownian model of transcriptome evolution and phylogenetic network visualization between tissues.

PubMed

Gu, Xun; Ruan, Hang; Su, Zhixi; Zou, Yangyun

2017-09-01

While phylogenetic analysis of transcriptomes of the same tissue is usually congruent with the species tree, the controversy emerges when multiple tissues are included, that is, whether species from the same tissue are clustered together, or different tissues from the same species are clustered together. Recent studies have suggested that phylogenetic network approach may shed some lights on our understanding of multi-tissue transcriptome evolution; yet the underlying evolutionary mechanism remains unclear. In this paper we develop a Brownian-based model of transcriptome evolution under the phylogenetic network that can statistically distinguish between the patterns of species-clustering and tissue-clustering. Our model can be used as a null hypothesis (neutral transcriptome evolution) for testing any correlation in tissue evolution, can be applied to cancer transcriptome evolution to study whether two tumors of an individual appeared independently or via metastasis, and can be useful to detect convergent evolution at the transcriptional level. Copyright © 2017. Published by Elsevier Inc.

Risk factors for pedicled flap necrosis in hand soft tissue reconstruction: a multivariate logistic regression analysis.

PubMed

Gong, Xu; Cui, Jianli; Jiang, Ziping; Lu, Laijin; Li, Xiucun

2018-03-01

Few clinical retrospective studies have reported the risk factors of pedicled flap necrosis in hand soft tissue reconstruction. The aim of this study was to identify non-technical risk factors associated with pedicled flap perioperative necrosis in hand soft tissue reconstruction via a multivariate logistic regression analysis. For patients with hand soft tissue reconstruction, we carefully reviewed hospital records and identified 163 patients who met the inclusion criteria. The characteristics of these patients, flap transfer procedures and postoperative complications were recorded. Eleven predictors were identified. The correlations between pedicled flap necrosis and risk factors were analysed using a logistic regression model. Of 163 skin flaps, 125 flaps survived completely without any complications. The pedicled flap necrosis rate in hands was 11.04%, which included partial flap necrosis (7.36%) and total flap necrosis (3.68%). Soft tissue defects in fingers were noted in 68.10% of all cases. The logistic regression analysis indicated that the soft tissue defect site (P = 0.046, odds ratio (OR) = 0.079, confidence interval (CI) (0.006, 0.959)), flap size (P = 0.020, OR = 1.024, CI (1.004, 1.045)) and postoperative wound infection (P < 0.001, OR = 17.407, CI (3.821, 79.303)) were statistically significant risk factors for pedicled flap necrosis of the hand. Soft tissue defect site, flap size and postoperative wound infection were risk factors associated with pedicled flap necrosis in hand soft tissue defect reconstruction. © 2017 Royal Australasian College of Surgeons.

Glycomics expression analysis of sulfated glycosaminoglycans of human colorectal cancer tissues and non-neoplastic mucosa by electrospray ionization mass spectrometry

PubMed Central

Marolla, Ana Paula Cleto; Waisberg, Jaques; Saba, Gabriela Tognini; Waisberg, Daniel Reis; Margeotto, Fernando Beani; Pinhal, Maria Aparecida da Silva

2015-01-01

ABSTRACT Objective To determine the presence of glycosaminoglycans in the extracellular matrix of connective tissue from neoplastic and non-neoplastic colorectal tissues, since it has a central role in tumor development and progression. Methods Tissue samples from neoplastic and non-neoplastic colorectal tissues were obtained from 64 operated patients who had colorectal carcinoma with no distant metastases. Expressions of heparan sulphate, chondroitin sulphate, dermatan sulphate and their fragments were analyzed by electrospray ionization mass spectrometry, with the technique for extraction and quantification of glycosaminoglycans after proteolysis and electrophoresis. The statistical analysis included mean, standard deviation, and Student’s t test. Results The glycosaminoglycans extracted from colorectal tissue showed three electrophoretic bands in agarose gel. Electrospray ionization mass spectrometry showed characteristic disaccharide fragments from glycosaminoglycans, indicating their structural characterization in the tissues analyzed. Some peaks in the electrospray ionization mass spectrometry were not characterized as fragments of sugars, indicating the presence of fragments of the protein structure of proteoglycans generated during the glycosaminoglycan purification. The average amount of chondroitin and dermatan increased in the neoplastic tissue compared to normal tissue (p=0.01). On the other hand, the average amount of heparan decreased in the neoplastic tissue compared to normal tissue (p= 0.03). Conclusion The method allowed the determination of the glycosaminoglycans structural profile in colorectal tissue from neoplastic and non-neoplastic colorectal tissue. Neoplastic tissues showed greater amounts of chondroitin sulphate and dermatan sulphate compared to non-neoplastic tissues, while heparan sulphate was decreased in neoplastic tissues. PMID:26761548

Measurement of the hyperelastic properties of 44 pathological ex vivo breast tissue samples

NASA Astrophysics Data System (ADS)

O'Hagan, Joseph J.; Samani, Abbas

2009-04-01

The elastic and hyperelastic properties of biological soft tissues have been of interest to the medical community. There are several biomedical applications where parameters characterizing such properties are critical for a reliable clinical outcome. These applications include surgery planning, needle biopsy and brachtherapy where tissue biomechanical modeling is involved. Another important application is interpreting nonlinear elastography images. While there has been considerable research on the measurement of the linear elastic modulus of small tissue samples, little research has been conducted for measuring parameters that characterize the nonlinear elasticity of tissues included in tissue slice specimens. This work presents hyperelastic measurement results of 44 pathological ex vivo breast tissue samples. For each sample, five hyperelastic models have been used, including the Yeoh, N = 2 polynomial, N = 1 Ogden, Arruda-Boyce, and Veronda-Westmann models. Results show that the Yeoh, polynomial and Ogden models are the most accurate in terms of fitting experimental data. The results indicate that almost all of the parameters corresponding to the pathological tissues are between two times to over two orders of magnitude larger than those of normal tissues, with C11 showing the most significant difference. Furthermore, statistical analysis indicates that C02 of the Yeoh model, and C11 and C20 of the polynomial model have very good potential for cancer classification as they show statistically significant differences for various cancer types, especially for invasive lobular carcinoma. In addition to the potential for use in cancer classification, the presented data are very important for applications such as surgery planning and virtual reality based clinician training systems where accurate nonlinear tissue response modeling is required.

Classification of coronary artery tissues using optical coherence tomography imaging in Kawasaki disease

NASA Astrophysics Data System (ADS)

Abdolmanafi, Atefeh; Prasad, Arpan Suravi; Duong, Luc; Dahdah, Nagib

2016-03-01

Intravascular imaging modalities, such as Optical Coherence Tomography (OCT) allow nowadays improving diagnosis, treatment, follow-up, and even prevention of coronary artery disease in the adult. OCT has been recently used in children following Kawasaki disease (KD), the most prevalent acquired coronary artery disease during childhood with devastating complications. The assessment of coronary artery layers with OCT and early detection of coronary sequelae secondary to KD is a promising tool for preventing myocardial infarction in this population. More importantly, OCT is promising for tissue quantification of the inner vessel wall, including neo intima luminal myofibroblast proliferation, calcification, and fibrous scar deposits. The goal of this study is to classify the coronary artery layers of OCT imaging obtained from a series of KD patients. Our approach is focused on developing a robust Random Forest classifier built on the idea of randomly selecting a subset of features at each node and based on second- and higher-order statistical texture analysis which estimates the gray-level spatial distribution of images by specifying the local features of each pixel and extracting the statistics from their distribution. The average classification accuracy for intima and media are 76.36% and 73.72% respectively. Random forest classifier with texture analysis promises for classification of coronary artery tissue.

Evaluation of implant osseointegration with different regeneration techniques in the treatment of bone defects around implants: an experimental study in a rabbit model.

PubMed

Guerra, Isabel; Morais Branco, Fernando; Vasconcelos, Mário; Afonso, Américo; Figueiral, Helena; Zita, Raquel

2011-03-01

The aim of this study was to evaluate the osseointegration of implants placed in areas with artificially created bone defects, using three bone regeneration techniques. The experimental model was the rabbit femur (16), where bone defects were created and implants were placed. The peri-implant bone defects were filled with a deproteinized bovine bone mineral, NuOss™ (N), NuOss™ combined with plasma rich in growth factors (PRGF) (N+PRGF), NuOss™ covered by an RCM(6) membrane (N+M), or remained unfilled (control group [C]). After 4 and 8 weeks, the animals were euthanized and bone tissue blocks with the implants and the surrounding bone tissue were removed and processed according to a histological protocol for hard tissues on non-decalcified ground sections. The samples were studied by light and electron scanning microscopy, histometric analysis was performed to assess the percentage of bone in direct contact with the implant surface and a statistical analysis of the results was performed. In the samples analyzed 4 weeks after implantation, the percentage of bone tissue in direct contact with the implant surface for the four groups were 57.66±24.39% (N), 58.62±20.37% (N+PRGF), 70.82±20.34 % (N+M) and 33.07±5.49% (C). In the samples with 8 weeks of implantation time, the percentage of bone in direct contact was 63.35±27.69% (N), 58.42±24.77% (N+PRGF), 78.02±15.13% (N+M) and 40.28±27.32% (C). In terms of the percentage of bone contact, groups N and N+M presented statistically significant differences from group C in the 4-week trial test (P<0.05; ANOVA). For the 8-week results, only group N+M showed statistically significant differences when compared with group C (P<0.05; ANOVA). In conclusion, the NuOss™ granules/RCM(6) membrane combination presented a percentage of bone contact with the implant surface statistically greater than in the other groups. © 2010 John Wiley & Sons A/S.

Correlations between iron content in knee joint tissues and chosen indices of peripheral blood morphology.

PubMed

Brodziak-Dopierała, Barbara; Roczniak, Wojciech; Jakóbik-Kolon, Agata; Kluczka, Joanna; Koczy, Bogdan; Kwapuliński, Jerzy; Babuśka-Roczniak, Magdalena

2017-10-01

Iron as a cofactor of enzymes takes part in the synthesis of the bone matrix. Severe deficiency of iron reduces the strength and mineral density of bones, whereas its excess may increase oxidative stress. In this context, it is essential to determine the iron content in knee joint tissues. The study objective was to determine the level of iron in the tissues of the knee joint, i.e., in the femoral bone, tibia and meniscus. Material for analysis was obtained during endoprosthetic surgery of the knee joint. Within the knee joint, the tibia, femur and meniscus were analyzed. Samples were collected from 50 patients, including 36 women and 14 men. The determination of iron content was performed with the ICP-AES method, using Varian 710-ES. The lowest iron content was in the tibia (27.04 μg/g), then in the meniscus (38.68 μg/g) and the highest in the femur (41.93 μg/g). Statistically significant differences were noted in the content of iron in knee joint tissues. In patients who underwent endoprosthesoplasty of the knee joint, statistically significant differences were found in the levels of iron in various components of the knee joint. The highest iron content was found in the femoral bone of the knee joint and then in the meniscus, the lowest in the tibia. The differences in iron content in the knee joint between women and men were not statistically significant.

Morphological and histomorphometric evaluation of the ventral rectus sheath of the rectus abdominis muscle, fascia lata and pectoral fascia. The beginning of a morphological information bank of human fascias.

PubMed

Morales-Avalos, Rodolfo; Soto-Domínguez, Adolfo; García-Juárez, Jaime; Cardenas-Serna, Marcela; Esparza-Hernández, Claudia N; Carreño-Salcedo, Sofía Alejandra; Montes-de-Oca-Luna, Roberto; Loera-Arias, María de Jesús; Saucedo-Cárdenas, Odila; Elizondo-Omaña, Rodrigo E; Guzmán-López, Santos

2017-03-01

The aim of this study was to characterize and compare the morphological and histomorphometric characteristics of the pectoral fascia, fascia lata and ventral rectus sheath. Twenty cadaveric samples of these fascias were analyzed and stained with hematoxylin and eosin, orcein, Van Gieson, Masson's trichrome and Verhoeff¨s stain (1200 slides in total). Morphological evaluation, semiquantitative, morphometric and microdensitometric analysis of elastic fibers present in each of the tissues and a morphometrical analysis of tissue thickness were performed. The mean value of the pectoral fascia thickness was 612±68.13 μm; 84±246 μm for the fascia lata and 584±92 μm for the ventral rectus sheath. The area occupied by the elastic fibers in the pectoral fascia was 12.24±5.84%; 6,54±3.85% for the fascia lata and 11.11±5.26% for the ventral rectus sheath. There were no statistically significant differences when comparing the mean values between the pectoral fascia and the ventral rectus sheath (p=0.07). There were statistically significant differences when comparing the fascia lata to the pectoral fascia and the ventral rectus sheath (p≤0.001). This study reports other morphological characteristics not described in previous histological studies of the analyzed tissues. The results of the morphometric and densitometric analysis in this study reveal that the fascia lata has the fewest elastic fibers of all the tissues analyzed, and the pectoral fascia has the most. These results will be useful for the beginning of a morphological information bank of human fascias.

Prognostic relevance of Centromere protein H expression in esophageal carcinoma.

PubMed

Guo, Xian-Zhi; Zhang, Ge; Wang, Jun-Ye; Liu, Wan-Li; Wang, Fang; Dong, Ju-Qin; Xu, Li-Hua; Cao, Jing-Yan; Song, Li-Bing; Zeng, Mu-Sheng

2008-08-13

Many kinetochore proteins have been shown to be associated with human cancers. The aim of the present study was to clarify the expression of Centromere protein H (CENP-H), one of the fundamental components of the human active kinetochore, in esophageal carcinoma and its correlation with clinicopathological features. We examined the expression of CENP-H in immortalized esophageal epithelial cells as well as in esophageal carcinoma cells, and in 12 cases of esophageal carcinoma tissues and the paired normal esophageal tissues by RT-PCR and Western blot analysis. In addition, we analyzed CENP-H protein expression in 177 clinicopathologically characterized esophageal carcinoma cases by immunohistochemistry. Statistical analyses were applied to test for prognostic and diagnostic associations. The level of CENP-H mRNA and protein were higher in the immortalized cells, cancer cell lines and most cancer tissues than in normal control tissues. Immunohistochemistry showed that CENP-H was expressed in 127 of 171 ESCC cases (74.3%) and in 3 of 6 esophageal adenocarcinoma cases (50%). Statistical analysis of ESCC cases showed that there was a significant difference of CENP-H expression in patients categorized according to gender (P = 0.013), stage (P = 0.023) and T classification (P = 0.019). Patients with lower CENP-H expression had longer overall survival time than those with higher CENP-H expression. Multivariate analysis suggested that CENP-H expression was an independent prognostic marker for esophageal carcinoma patients. A prognostic value of CENP-H was also found in the subgroup of T3 approximately T4 and N0 tumor classification. Our results suggest that CENP-H protein is a valuable marker of esophageal carcinoma progression. CENP-H might be used as a valuable prognostic marker for esophageal carcinoma patients.

Optical coherence tomography angiography-based capillary velocimetry

NASA Astrophysics Data System (ADS)

Wang, Ruikang K.; Zhang, Qinqin; Li, Yuandong; Song, Shaozhen

2017-06-01

Challenge persists in the field of optical coherence tomography (OCT) when it is required to quantify capillary blood flow within tissue beds in vivo. We propose a useful approach to statistically estimate the mean capillary flow velocity using a model-based statistical method of eigendecomposition (ED) analysis of the complex OCT signals obtained with the OCT angiography (OCTA) scanning protocol. ED-based analysis is achieved by the covariance matrix of the ensemble complex OCT signals, upon which the eigenvalues and eigenvectors that represent the subsets of the signal makeup are calculated. From this analysis, the signals due to moving particles can be isolated by employing an adaptive regression filter to remove the eigencomponents that represent static tissue signals. The mean frequency (MF) of moving particles can be estimated by the first lag-one autocorrelation of the corresponding eigenvectors. Three important parameters are introduced, including the blood flow signal power representing the presence of blood flow (i.e., OCTA signals), the MF indicating the mean velocity of blood flow, and the frequency bandwidth describing the temporal flow heterogeneity within a scanned tissue volume. The proposed approach is tested using scattering phantoms, in which microfluidic channels are used to simulate the functional capillary vessels that are perfused with the scattering intralipid solution. The results indicate a linear relationship between the MF and mean flow velocity. In vivo animal experiments are also conducted by imaging mouse brain with distal middle cerebral artery ligation to test the capability of the method to image the changes in capillary flows in response to an ischemic insult, demonstrating the practical usefulness of the proposed method for providing important quantifiable information about capillary tissue beds in the investigations of neurological conditions in vivo.

Clinicopathological significance of c-MYC in esophageal squamous cell carcinoma.

PubMed

Lian, Yu; Niu, Xiangdong; Cai, Hui; Yang, Xiaojun; Ma, Haizhong; Ma, Shixun; Zhang, Yupeng; Chen, Yifeng

2017-07-01

Esophageal squamous cell carcinoma is one of the most common malignant tumors. The oncogene c-MYC is thought to be important in the initiation, promotion, and therapy resistance of cancer. In this study, we aim to investigate the clinicopathologic roles of c-MYC in esophageal squamous cell carcinoma tissue. This study is aimed at discovering and analyzing c-MYC expression in a series of human esophageal tissues. A total of 95 esophageal squamous cell carcinoma samples were analyzed by the western blotting and immunohistochemistry techniques. Then, correlation of c-MYC expression with clinicopathological features of esophageal squamous cell carcinoma patients was statistically analyzed. In most esophageal squamous cell carcinoma cases, the c-MYC expression was positive in tumor tissues. The positive rate of c-MYC expression in tumor tissues was 61.05%, obviously higher than the adjacent normal tissues (8.42%, 8/92) and atypical hyperplasia tissues (19.75%, 16/95). There was a statistical difference among adjacent normal tissues, atypical hyperplasia tissues, and tumor tissues. Overexpression of the c-MYC was detected in 61.05% (58/95) esophageal squamous cell carcinomas, which was significantly correlated with the degree of differentiation (p = 0.004). The positive rate of c-MYC expression was 40.0% in well-differentiated esophageal tissues, with a significantly statistical difference (p = 0.004). The positive rate of c-MYC was 41.5% in T1 + T2 esophageal tissues and 74.1% in T3 + T4 esophageal tissues, with a significantly statistical difference (p = 0.001). The positive rate of c-MYC was 45.0% in I + II esophageal tissues and 72.2% in III + IV esophageal tissues, with a significantly statistical difference (p = 0.011). The c-MYC expression strongly correlated with clinical staging (p = 0.011), differentiation degree (p = 0.004), lymph node metastasis (p = 0.003), and invasion depth (p = 0.001) of patients with esophageal squamous cell carcinoma. The c-MYC was differentially expressed in a series of human esophageal tissues, and the aberrant c-MYC expression could be a potential factor in carcinogenesis and progression of esophageal squamous cell carcinoma. There was a statistical signification for c-MYC in esophageal squamous cell carcinoma patients to analyze clinicopathological features. It possibly becomes a new diagnostic indicator of esophageal squamous cell carcinoma.

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

PubMed

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

2015-09-01

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

Risk factors for hydrocephalus and neurological deficit in children born with an encephalocele.

PubMed

Da Silva, Stephanie L; Jeelani, Yasser; Dang, Ha; Krieger, Mark D; McComb, J Gordon

2015-04-01

There is a known association of hydrocephalus with encephaloceles. Risk factors for hydrocephalus and neurological deficit were ascertained in a series of patients born with an encephalocele. A retrospective analysis was undertaken of patients treated for encephaloceles at Children's Hospital Los Angeles between 1994 and 2012. The following factors were evaluated for their prognostic value: age at presentation, sex, location of encephalocele, size, contents, microcephaly, presence of hydrocephalus, CSF leak, associated cranial anomalies, and neurological outcome. Seventy children were identified, including 38 girls and 32 boys. The median age at presentation was 2 months. The mean follow-up duration was 3.7 years. Encephalocele location was classified as anterior (n = 14) or posterior (n = 56) to the coronal suture. The average maximum encephalocele diameter was 4 cm (range 0.5-23 cm). Forty-seven encephaloceles contained neural tissue. Eight infants presented at birth with CSF leaking from the encephalocele, with 1 being infected. Six patients presented with hydrocephalus, while 11 developed progressive hydrocephalus postoperatively. On univariate analysis, the presence of neural tissue, cranial anomalies, encephalocele size of at least 2 cm, seizure disorder, and microcephaly were each positively associated with hydrocephalus. On multivariate logistic regression modeling, the single prognostic factor for hydrocephalus of borderline statistical significance was the presence of neural tissue (odds ratio [OR] = 5.8, 95% confidence interval [CI] = 0.8-74.0). Fourteen patients had severe developmental delay, 28 had mild/moderate delay, and 28 were neurologically normal. On univariate analysis, the presence of cranial anomalies, larger size of encephalocele, hydrocephalus, and microcephaly were positively associated with neurological deficit. In the multivariable model, the only statistically significant prognostic factor for neurological deficit was presence of hydrocephalus (OR 17.2, 95% CI 1.7-infinity). In multivariate models, the presence of neural tissue was borderline significantly associated with hydrocephalus and the presence of hydrocephalus was significantly associated with neurological deficit. The location of the encephalocele did not have a statistically significant association with incidence of hydrocephalus or neurological deficit. In contrast to modestly good/fair neurological outcome in children with an encephalocele without hydrocephalus, the presence of hydrocephalus resulted in a far worse neurological outcome.

Dielectric properties of human normal, malignant and cirrhotic liver tissue: in vivo and ex vivo measurements from 0.5 to 20 GHz using a precision open-ended coaxial probe.

PubMed

O'Rourke, Ann P; Lazebnik, Mariya; Bertram, John M; Converse, Mark C; Hagness, Susan C; Webster, John G; Mahvi, David M

2007-08-07

Hepatic malignancies have historically been treated with surgical resection. Due to the shortcomings of this technique, there is interest in other, less invasive, treatment modalities, such as microwave hepatic ablation. Crucial to the development of this technique is the accurate knowledge of the dielectric properties of human liver tissue at microwave frequencies. To this end, we characterized the dielectric properties of in vivo and ex vivo normal, malignant and cirrhotic human liver tissues from 0.5 to 20 GHz. Analysis of our data at 915 MHz and 2.45 GHz indicates that the dielectric properties of ex vivo malignant liver tissue are 19 to 30% higher than normal tissue. The differences in the dielectric properties of in vivo malignant and normal liver tissue are not statistically significant (with the exception of effective conductivity at 915 MHz, where malignant tissue properties are 16% higher than normal). Also, the dielectric properties of in vivo normal liver tissue at 915 MHz and 2.45 GHz are 16 to 43% higher than ex vivo. No statistically significant differences were found between the dielectric properties of in vivo and ex vivo malignant tissue (with the exception of effective conductivity at 915 MHz, where malignant tissue properties are 28% higher than normal). We report the one-pole Cole-Cole parameters for ex vivo normal, malignant and cirrhotic liver tissue in this frequency range. We observe that wideband dielectric properties of in vivo liver tissue are different from the wideband dielectric properties of ex vivo liver tissue, and that the in vivo data cannot be represented in terms of a Cole-Cole model. Further work is needed to uncover the mechanisms responsible for the observed wideband trends in the in vivo liver data.

Integrative analysis for identification of shared markers from various functional cells/tissues for rheumatoid arthritis.

PubMed

Xia, Wei; Wu, Jian; Deng, Fei-Yan; Wu, Long-Fei; Zhang, Yong-Hong; Guo, Yu-Fan; Lei, Shu-Feng

2017-02-01

Rheumatoid arthritis (RA) is a systemic autoimmune disease. So far, it is unclear whether there exist common RA-related genes shared in different tissues/cells. In this study, we conducted an integrative analysis on multiple datasets to identify potential shared genes that are significant in multiple tissues/cells for RA. Seven microarray gene expression datasets representing various RA-related tissues/cells were downloaded from the Gene Expression Omnibus (GEO). Statistical analyses, testing both marginal and joint effects, were conducted to identify significant genes shared in various samples. Followed-up analyses were conducted on functional annotation clustering analysis, protein-protein interaction (PPI) analysis, gene-based association analysis, and ELISA validation analysis in in-house samples. We identified 18 shared significant genes, which were mainly involved in the immune response and chemokine signaling pathway. Among the 18 genes, eight genes (PPBP, PF4, HLA-F, S100A8, RNASEH2A, P2RY6, JAG2, and PCBP1) interact with known RA genes. Two genes (HLA-F and PCBP1) are significant in gene-based association analysis (P = 1.03E-31, P = 1.30E-2, respectively). Additionally, PCBP1 also showed differential protein expression levels in in-house case-control plasma samples (P = 2.60E-2). This study represented the first effort to identify shared RA markers from different functional cells or tissues. The results suggested that one of the shared genes, i.e., PCBP1, is a promising biomarker for RA.

[GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value].

PubMed

Skorodumova, L O; Babalyan, K A; Sultanov, R; Vasiliev, A O; Govorov, A V; Pushkar, D Y; Prilepskaya, E A; Danilenko, S A; Generozov, E V; Larin, A K; Kostryukova, E S; Sharova, E I

2016-11-01

There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

Analysis of heavy metals from water, sediment, and tissues of Labeo angra (Hamilton, 1822), from an Ox-box lake- an wetland site from Assam, India.

PubMed

Das, Suchismita; Choudhury, Shamim Sultana

2016-01-01

The aim of this study was to assess the regional impacts of heavy metals (Mn, Fe, Mg, Ca, Cu, Zn, Cd, Cr, Pb and Ni) on water, sediment and a native, teleost fish species, Labeo angra, inhabiting a flood plain wetland of Barak River in Assam, India. Heavy metal concentrations in the water, sediments and fish were measured; bioaccumulation factor, metal pollution index as well as condition indices were calculated, to assess the pollution load and health status of the fish. Multivariate statistical analysis was used on wetland water and sediment heavy metals to ascertain the possible sources and seasonal variations of the pollutants. Results showed that most heavy metals in the wetland water and sediments exceeded the water (drinking and irrigation) and sediment quality guidelines, respectively. Seasonal variations were observed for geogenic heavy metals, Mn, Fe, Mg and Ca while no seasonal variations were observed for anthropogenic heavy metals, Cu, Cd, Cr, Pb and Ni. Multivariate statistical analysis showed that there was strong correlation between geogenic and anthropogenic heavy metals in water and sediment, both originating from the common anthropogenic sources. Accumulation of most of the metals in all the tissues was above the safe limits as recommended by the Food and Agriculture Organization. High bioaccumulation factors and metal pollution index for these metals in the different tissues revealed that metals were extensively bio-accumulated and bioconcentrated. Condition indices in fish from the wetland suggested metabolic abnormalities.

Soils element activities for the period October 1973--September 1974

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

Fowler, E.B.; Essington, E.H.; White, M.G.

Soils Element activities were conducted on behalf of the U. S. Atomic Energy Commission's Nevada Applied Ecology Group (NAEG) program to provide source term information for the other program elements and maintain continuous cognizance of program requirements for sampling, sample preparation, and analysis. Activities included presentation of papers; participation in workshops; analysis of soil, vegetation, and animal tissue samples for $sup 238$Pu, $sup 239-240$Pu, $sup 241$Am, $sup 137$Cs, $sup 60$Co, and gamma scan for routine and laboratory quality control purposes; preparation and analysis of animal tissue samples for NAEG laboratory certification; studies on a number of analytical, sample preparation, andmore » sample collection procedures; and contributions to the evaluation of procedures for calculation of specialized counting statistics. (auth)« less

Gram-Negative Bacterial Wound Infections

DTIC Science & Technology

2014-05-01

shows an effect with increasing concentration, however survival analysis does not show a significant difference between treatment groups and controls ...with 3 dead larvae in the 25 mM group compared to a single dead larva in the control group (Fig. 7). Probit analysis estimates the lethal...statistically differ- ent from that of the control group . The levels (CFU/g) of bacteria in lung tissue correlated with the survival curves. The median

Optimization method of superpixel analysis for multi-contrast Jones matrix tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Miyazawa, Arata; Hong, Young-Joo; Makita, Shuichi; Kasaragod, Deepa K.; Miura, Masahiro; Yasuno, Yoshiaki

2017-02-01

Local statistics are widely utilized for quantification and image processing of OCT. For example, local mean is used to reduce speckle, local variation of polarization state (degree-of-polarization-uniformity (DOPU)) is used to visualize melanin. Conventionally, these statistics are calculated in a rectangle kernel whose size is uniform over the image. However, the fixed size and shape of the kernel result in a tradeoff between image sharpness and statistical accuracy. Superpixel is a cluster of pixels which is generated by grouping image pixels based on the spatial proximity and similarity of signal values. Superpixels have variant size and flexible shapes which preserve the tissue structure. Here we demonstrate a new superpixel method which is tailored for multifunctional Jones matrix OCT (JM-OCT). This new method forms the superpixels by clustering image pixels in a 6-dimensional (6-D) feature space (spatial two dimensions and four dimensions of optical features). All image pixels were clustered based on their spatial proximity and optical feature similarity. The optical features are scattering, OCT-A, birefringence and DOPU. The method is applied to retinal OCT. Generated superpixels preserve the tissue structures such as retinal layers, sclera, vessels, and retinal pigment epithelium. Hence, superpixel can be utilized as a local statistics kernel which would be more suitable than a uniform rectangle kernel. Superpixelized image also can be used for further image processing and analysis. Since it reduces the number of pixels to be analyzed, it reduce the computational cost of such image processing.

Progress in the detection of neoplastic progress and cancer by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Bakker Schut, Tom C.; Stone, Nicholas; Kendall, Catherine A.; Barr, Hugh; Bruining, Hajo A.; Puppels, Gerwin J.

2000-05-01

Early detection of cancer is important because of the improved survival rates when the cancer is treated early. We study the application of NIR Raman spectroscopy for detection of dysplasia because this technique is sensitive to the small changes in molecular invasive in vivo detection using fiber-optic probes. The result of an in vitro study to detect neoplastic progress of esophageal Barrett's esophageal tissue will be presented. Using multivariate statistics, we developed three different linear discriminant analysis classification models to predict tissue type on the basis of the measured spectrum. Spectra of normal, metaplastic and dysplasia tissue could be discriminated with an accuracy of up to 88 percent. Therefore Raman spectroscopy seems to be a very suitable technique to detect dysplasia in Barrett's esophageal tissue.

Histological comparison of alendronate, calcium hydroxide and formocresol in amputated rat molar.

PubMed

Cengiz, S Burcak; Batirbaygil, Yildiz; Onur, Mehmet Ali; Atilla, Pergin; Asan, Esin; Altay, Nil; Cehreli, Zafer C

2005-10-01

The purpose of this study was to evaluate the potential of alendronate sodium (ALN), a biphosohonate to stimulate hard tissue formation in pulpotomized (amputated) rat molars. Two commonly used pulpotomy materials, calcium hydroxide (CH) and formocresol (FC) were utilized for comparisons. Histological evaluations were performed by observers blinded to treatment allocation on days 7, 15, 30 and 60, followed by statistical analysis of selected histological criteria. In all evaluation periods, hard tissue deposition was evident along the radicular dentin in ALN and CH groups. In days 30 and 60, the latter two groups showed no differences in inflammatory cell response and hard tissue deposition scores (P > 0.05). ALN appears to be capable of maintaining pulpal vitality, while promoting hard tissue formation, similar to CH.

Metabolomic and Lipidomic Analysis of the Heart of Peroxisome Proliferator-Activated Receptor-γ Coactivator 1-β Knock Out Mice on a High Fat Diet.

PubMed

McCombie, Gregor; Medina-Gomez, Gema; Lelliott, Christopher J; Vidal-Puig, Antonio; Griffin, Julian L

2012-06-18

The peroxisome proliferator-activated receptor-γ coactivators (PGC-1) are transcriptional coactivators with an important role in mitochondrial biogenesis and regulation of genes involved in the electron transport chain and oxidative phosphorylation in oxidative tissues including cardiac tissue. These coactivators are thought to play a key role in the development of obesity, type 2 diabetes and the metabolic syndrome. In this study we have used a combined metabolomic and lipidomic analysis of cardiac tissue from the PGC-1β null mouse to examine the effects of a high fat diet on this organ. Multivariate statistics readily separated tissue from PGC-1β null mice from their wild type controls either in gender specific models or in combined datasets. This was associated with an increase in creatine and a decrease in taurine in the null mouse, and an increase in myristic acid and a reduction in long chain polyunsaturated fatty acids for both genders. The most profound changes were detected by liquid chromatography mass spectrometry analysis of intact lipids with the tissue from the null mouse having a profound increase in a number of triglycerides. The metabolomic and lipodomic changes indicate PGC-1β has a profound influence on cardiac metabolism.

Fractal analysis of scatter imaging signatures to distinguish breast pathologies

NASA Astrophysics Data System (ADS)

Eguizabal, Alma; Laughney, Ashley M.; Krishnaswamy, Venkataramanan; Wells, Wendy A.; Paulsen, Keith D.; Pogue, Brian W.; López-Higuera, José M.; Conde, Olga M.

2013-02-01

Fractal analysis combined with a label-free scattering technique is proposed for describing the pathological architecture of tumors. Clinicians and pathologists are conventionally trained to classify abnormal features such as structural irregularities or high indices of mitosis. The potential of fractal analysis lies in the fact of being a morphometric measure of the irregular structures providing a measure of the object's complexity and self-similarity. As cancer is characterized by disorder and irregularity in tissues, this measure could be related to tumor growth. Fractal analysis has been probed in the understanding of the tumor vasculature network. This work addresses the feasibility of applying fractal analysis to the scattering power map (as a physical modeling) and principal components (as a statistical modeling) provided by a localized reflectance spectroscopic system. Disorder, irregularity and cell size variation in tissue samples is translated into the scattering power and principal components magnitude and its fractal dimension is correlated with the pathologist assessment of the samples. The fractal dimension is computed applying the box-counting technique. Results show that fractal analysis of ex-vivo fresh tissue samples exhibits separated ranges of fractal dimension that could help classifier combining the fractal results with other morphological features. This contrast trend would help in the discrimination of tissues in the intraoperative context and may serve as a useful adjunct to surgeons.

Dominant factor analysis of B-flow twinkling sign with phantom and simulation data.

PubMed

Lu, Weijia; Haider, Bruno

2017-01-01

The twinkling sign in B-flow imaging (BFI-TS) has been reported in the literature to increase both specificity and sensitivity compared to the traditional gray-scale imaging. Unfortunately, there has been no conclusive study on the mechanism of this effect. In the study presented here, a comparative test on phantoms is introduced, where the variance of a phase estimator is used to quantify the motion amplitude. The statistical inference is employed later to find the dominate factor for the twinkling sign, which is proven by computer simulation. Through the analysis, it is confirmed that the tissue viscoelasticity is closely coupled with the twinkling sign. Moreover, the acoustic radiation force caused by tissue attenuation is found to be the trigger of the twinkling sign. Based on these findings, the BFI-TS is interpreted as a tissue movement triggering vibration of microcalcifications particle.

Components of soft tissue deformations in subjects with untreated angle's Class III malocclusions: thin-plate spline analysis.

PubMed

Singh, G D; McNamara, J A; Lozanoff, S

1998-01-01

While the dynamics of maxillo-mandibular allometry associated with treatment modalities available for the management of Class III malocclusions currently are under investigation, developmental aberration of the soft tissues in untreated Class III malocclusions requires specification. In this study, lateral cephalographs of 124 prepubertal European-American children (71 with untreated Class III malocclusion; 53 with Class I occlusion) were traced, and 12 soft-tissue landmarks digitized. Resultant geometries were scaled to an equivalent size and mean Class III and Class I configurations compared. Procrustes analysis established statistical difference (P < 0.001) between the mean configurations. Comparing the overall untreated Class III and Class I configurations, thin-plate spline (TPS) analysis indicated that both affine and non-affine transformations contribute towards the deformation (total spline) of the averaged Class III soft tissue configuration. For non-affine transformations, partial warp 8 had the highest magnitude, indicating large-scale deformations visualized as a combination of columellar retrusion and lower labial protrusion. In addition, partial warp 5 also had a high magnitude, demonstrating upper labial vertical compression with antero-inferior elongation of the lower labio-mental soft tissue complex. Thus, children with Class III malocclusions demonstrate antero-posterior and vertical deformations of the maxillary soft tissue complex in combination with antero-inferior mandibular soft tissue elongation. This pattern of deformations may represent gene-environment interactions, resulting in Class III malocclusions with characteristic phenotypes, that are amenable to orthodontic and dentofacial orthopedic manipulations.

Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies

PubMed Central

Zhang, Shujun

2018-01-01

Genome-wide association studies (GWASs) have identified many disease associated loci, the majority of which have unknown biological functions. Understanding the mechanism underlying trait associations requires identifying trait-relevant tissues and investigating associations in a trait-specific fashion. Here, we extend the widely used linear mixed model to incorporate multiple SNP functional annotations from omics studies with GWAS summary statistics to facilitate the identification of trait-relevant tissues, with which to further construct powerful association tests. Specifically, we rely on a generalized estimating equation based algorithm for parameter inference, a mixture modeling framework for trait-tissue relevance classification, and a weighted sequence kernel association test constructed based on the identified trait-relevant tissues for powerful association analysis. We refer to our analytic procedure as the Scalable Multiple Annotation integration for trait-Relevant Tissue identification and usage (SMART). With extensive simulations, we show how our method can make use of multiple complementary annotations to improve the accuracy for identifying trait-relevant tissues. In addition, our procedure allows us to make use of the inferred trait-relevant tissues, for the first time, to construct more powerful SNP set tests. We apply our method for an in-depth analysis of 43 traits from 28 GWASs using tissue-specific annotations in 105 tissues derived from ENCODE and Roadmap. Our results reveal new trait-tissue relevance, pinpoint important annotations that are informative of trait-tissue relationship, and illustrate how we can use the inferred trait-relevant tissues to construct more powerful association tests in the Wellcome trust case control consortium study. PMID:29377896

The electromagnetic-trait imaging computation of traveling wave method in breast tumor microwave sensor system.

PubMed

Tao, Zhi-Fu; Han, Zhong-Ling; Yao, Meng

2011-01-01

Using the difference of dielectric constant between malignant tumor tissue and normal breast tissue, breast tumor microwave sensor system (BRATUMASS) determines the detected target of imaging electromagnetic trait by analyzing the properties of target tissue back wave obtained after near-field microwave radicalization (conelrad). The key of obtained target properties relationship and reconstructed detected space is to analyze the characteristics of the whole process from microwave transmission to back wave reception. Using traveling wave method, we derive spatial transmission properties and the relationship of the relation detected points distances, and valuate the properties of each unit by statistical valuation theory. This chapter gives the experimental data analysis results.

Mueller-matrix mapping of biological tissues in differential diagnosis of optical anisotropy mechanisms of protein networks

NASA Astrophysics Data System (ADS)

Ushenko, V. A.; Sidor, M. I.; Marchuk, Yu F.; Pashkovskaya, N. V.; Andreichuk, D. R.

2015-03-01

We report a model of Mueller-matrix description of optical anisotropy of protein networks in biological tissues with allowance for the linear birefringence and dichroism. The model is used to construct the reconstruction algorithms of coordinate distributions of phase shifts and the linear dichroism coefficient. In the statistical analysis of such distributions, we have found the objective criteria of differentiation between benign and malignant tissues of the female reproductive system. From the standpoint of evidence-based medicine, we have determined the operating characteristics (sensitivity, specificity and accuracy) of the Mueller-matrix reconstruction method of optical anisotropy parameters and demonstrated its effectiveness in the differentiation of benign and malignant tumours.

Quantification of hemoglobin and its derivatives in oral cancer diagnosis by diffuse reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Kaniyappan, Udayakumar; Gnanatheepam, Einstein; Aruna, Prakasarao; Dornadula, Koteeswaran; Ganesan, Singaravelu

2017-02-01

Cancer is one of the most common threat to human beings and it increases at an alarming level around the globe. In recent years, due to the advancements in opto-electronic technology, various optical spectroscopy techniques have emerged to assess the photophysicochemical and morphological conditions of normal and malignant tissues in micro as well as in macroscopic scale. In this regard, diffuse reflectance spectroscopy is considered to be the simplest, cost effective and rapid technique in diagnosis of cancerous tissues. In the present study, the hemoglobin concentration in normal and cancerous oral tissues was quantified and subsequent statistical analysis has been carried out to verify the diagnostic potentiality of the technique.

Evaluation of specimen preparation techniques for micro-PIXE localisation of elements in hyperaccumulating plants

NASA Astrophysics Data System (ADS)

Kachenko, Anthony G.; Siegele, Rainer; Bhatia, Naveen P.; Singh, Balwant; Ionescu, Mihail

2008-04-01

Hybanthus floribundus subsp. floribundus, a rare Australian Ni-hyperaccumulating shrub and Pityrogramma calomelanos var. austroamericana, an Australian naturalized As-hyperaccumulating fern are promising species for use in phytoremediation of contaminated sites. Micro-proton-induced X-ray emission (μ-PIXE) spectroscopy was used to map the elemental distribution of the accumulated metal(loid)s, Ca and K in leaf or pinnule tissues of the two plant species. Samples were prepared by two contrasting specimen preparation techniques: freeze-substitution in tetrahydrofuran (THF) and freeze-drying. The specimens were analysed to compare the suitability of each technique in preserving (i) the spatial elemental distribution and (ii) the tissue structure of the specimens. Further, the μ-PIXE results were compared with concentration of elements in the bulk tissue obtained by ICP-AES analysis. In H. floribundus subsp. floribundus, μ-PIXE analysis revealed Ni, Ca and K concentrations in freeze-dried leaf tissues were at par with bulk tissue concentrations. Elemental distribution maps illustrated that Ni was preferentially localised in the adaxial epidermal tissues (1% DW) and least concentration was found in spongy mesophyll tissues (0.53% DW). Conversely, elemental distribution maps of THF freeze-substituted tissues indicated significantly lower Ni, Ca and K concentrations than freeze-dried specimens and bulk tissue concentrations. Moreover, Ni concentrations were uniform across the whole specimen and no localisation was observed. In P. calomelanos var. austroamericana freeze-dried pinnule tissues, μ-PIXE revealed statistically similar As, Ca and K concentrations as compared to bulk tissue concentrations. Elemental distribution maps showed that As localisation was relatively uniform across the whole specimen. Once again, THF freeze-substituted tissues revealed a significant loss of As compared to freeze-dried specimens and the concentrations obtained by bulk tissue analysis. The results demonstrate that freeze-drying is a suitable sample preparation technique to study elemental distribution of ions in H. floribundus and P. calomelanos plant tissues using μ-PIXE spectroscopy. Furthermore, cellular structure was preserved in samples prepared using this technique.

Detecting discordance enrichment among a series of two-sample genome-wide expression data sets.

PubMed

Lai, Yinglei; Zhang, Fanni; Nayak, Tapan K; Modarres, Reza; Lee, Norman H; McCaffrey, Timothy A

2017-01-25

With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene set enrichment analysis have been frequently conducted. Integrative analysis can be conducted when multiple data sets are available. In practice, discordant molecular behaviors among a series of data sets can be of biological and clinical interest. In this study, a statistical method is proposed for detecting discordance gene set enrichment. Our method is based on a two-level multivariate normal mixture model. It is statistically efficient with linearly increased parameter space when the number of data sets is increased. The model-based probability of discordance enrichment can be calculated for gene set detection. We apply our method to a microarray expression data set collected from forty-five matched tumor/non-tumor pairs of tissues for studying pancreatic cancer. We divided the data set into a series of non-overlapping subsets according to the tumor/non-tumor paired expression ratio of gene PNLIP (pancreatic lipase, recently shown it association with pancreatic cancer). The log-ratio ranges from a negative value (e.g. more expressed in non-tumor tissue) to a positive value (e.g. more expressed in tumor tissue). Our purpose is to understand whether any gene sets are enriched in discordant behaviors among these subsets (when the log-ratio is increased from negative to positive). We focus on KEGG pathways. The detected pathways will be useful for our further understanding of the role of gene PNLIP in pancreatic cancer research. Among the top list of detected pathways, the neuroactive ligand receptor interaction and olfactory transduction pathways are the most significant two. Then, we consider gene TP53 that is well-known for its role as tumor suppressor in cancer research. The log-ratio also ranges from a negative value (e.g. more expressed in non-tumor tissue) to a positive value (e.g. more expressed in tumor tissue). We divided the microarray data set again according to the expression ratio of gene TP53. After the discordance enrichment analysis, we observed overall similar results and the above two pathways are still the most significant detections. More interestingly, only these two pathways have been identified for their association with pancreatic cancer in a pathway analysis of genome-wide association study (GWAS) data. This study illustrates that some disease-related pathways can be enriched in discordant molecular behaviors when an important disease-related gene changes its expression. Our proposed statistical method is useful in the detection of these pathways. Furthermore, our method can also be applied to genome-wide expression data collected by the recent RNA-seq technology.

[Histologic assessment of tissue healing of hyaline cartilage by use of semiquantitative evaluation scale].

PubMed

Vukasović, Andreja; Ivković, Alan; Jezek, Davor; Cerovecki, Ivan; Vnuk, Drazen; Kreszinger, Mario; Hudetz, Damir; Pećina, Marko

2011-01-01

Articular cartilage is an avascular and aneural tissue lacking lymph drainage, hence its inability of spontaneous repair following injury. Thus, it offers an interesting model for scientific research. A number of methods have been suggested to enhance cartilage repair, but none has yet produced significant success. The possible application of the aforementioned methods has brought about the necessity to evaluate their results. The objective of this study was to analyze results of a study of the effects of the use of TGF-beta gene transduced bone marrow clot on articular cartilage defects using ICRS visual histological assessment scale. The research was conducted on 28 skeletally mature sheep that were randomly assigned to four groups and surgically inflicted femoral chondral defects. The articular surfaces were then treated with TGF-beta1 gene transduced bone marrow clot (TGF group), GFP transduced bone marrow clot (GFP group), untransduced bone marrow clot (BM group) or left untreated (NC group). The analysis was performed by visual examination of cartilage samples and results were obtained using ICRS visual histological assessment scale. The results were subsequently subjected to statistical assessment using Kruskal-Wallis and Mann-Whitney tests. Kruskal-Wallis test yielded statistically significant difference with respect to cell distribution. Mann-Whitney test showed statistically significant difference between TGF and NC groups (P = 0.002), as well as between BM and NC groups (P = 0.002 with Bonferroni correction). Twenty-six of the twenty-eight samples were subjected to histologic and subsequent statistical analysis; two were discarded due to faulty histology technique. Our results indicated a level of certainty as to the positive effect of TGF-beta1 gene transduced bone marrow clot in restoration of articular cartilage defects. However, additional research is necessary in the field. One of the significant drawbacks on histologic assessment of cartilage samples were the errors in histologic preparation, for which some samples had to be discarded and significantly impaired the analytical quality of the others. Defects of structures surrounding the articular cartilage, e.g., subchondral bone or connective tissue, might also impair the quality of histologic analysis. Additional analyses, i.e. polarizing microscopy should be performed to determine the degree of integration of the newly formed tissue with the surrounding cartilage. The semiquantitative ICRS scale, although of great practical value, has limitations as to the objectivity of the assessment, taking into account the analytical ability of the evaluator, as well as the accuracy of semiquantitative analysis in comparison to the methods of quantitative analysis. Overall results of histologic analysis indicated that the application of TGF-beta1 gene transduced bone marrow clot could have measurable clinical effects on articular cartilage repair. The ICRS visual histological assessment scale is a valuable analytical method for cartilage repair evaluation. In this respect, further analyses of the method value would be of great importance.

Elevated expression of matrix metalloproteinase-9 is associated with bladder cancer pathogenesis.

PubMed

Wu, Gong-Jin; Bao, Jun-Sheng; Yue, Zhong-Jin; Zeng, Fan-Chang; Cen, Song; Tang, Zheng-Yan; Kang, Xin-Li

2018-01-01

This study investigated the association between abnormal matrix metalloproteinase-9 (MMP-9) expression and bladder cancer (BC) development. In a retrospective analysis, this study used tissue samples derived from 92 patients pathologically diagnosed with BC (experimental group), who were hospitalized between September 2012 and June 2014 at the Urinary Surgery of Department of Urology, Lanzhou University Second Hospital. As controls (control group), 63 normal pericancerous bladder mucosal tissues (3 cm distant form edge of BC foci) with confirmed pathology were selected from the same time period. Immunohistochemistry was employed to detect MMP-9 protein expression in the tissues and enzyme-linked immunosorbent assay was performed to measure MMP-9 protein levels in tissue samples of patients and control subjects. Finally, a meta-analysis was conducted to understand the overall impact of MMP-9 on BC pathogenesis. STATA 12.0 software (Stata Corp, College Station, TX, USA) was used for all statistical analyses. The MMP-9 positive expression rate in tissue samples and MMP-9 levels were significantly greater in the experimental group compared to the control group (both P < 0.001). The frequency of MMP-9 positive status showed statistically significant differences between G1 (low-grade) and G3 (high-grade) (P < 0.001), between G2 and G3 (P < 0.05), and between G1/G2 and G3 (P = 0.001). Our meta-analysis findings provided further evidence that MMP-9 positive expression status and MMP-9 levels in the experimental group were significantly higher than the control group (positive expressions: Odds ratio [OR] = 18.59, 95% confidence interval [95% CI] = 11.63-29.71, P < 0.001; expression levels: Standard mean difference = 1.51, 95%CI = 0.63-2.39, P = 0.001). The positive expression status of MMP-9 was notably lower in G1/G2 compared to G3 (OR = 0.24, 95%CI = 0.15-0.36, P < 0.001). Our study demonstrated that both positive expression status in tumor tissue and expression levels of MMP-9 are significantly elevated in BC patients and correlate with disease progression. Thus, MMP-9 can serve as a biomarker to determine the degree of BC malignancy.

Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach.

PubMed

Mridula, Meenu R; Nair, Ashalatha S; Kumar, K Satheesh

2018-02-01

In this paper, we compared the efficacy of observation based modeling approach using a genetic algorithm with the regular statistical analysis as an alternative methodology in plant research. Preliminary experimental data on in vitro rooting was taken for this study with an aim to understand the effect of charcoal and naphthalene acetic acid (NAA) on successful rooting and also to optimize the two variables for maximum result. Observation-based modelling, as well as traditional approach, could identify NAA as a critical factor in rooting of the plantlets under the experimental conditions employed. Symbolic regression analysis using the software deployed here optimised the treatments studied and was successful in identifying the complex non-linear interaction among the variables, with minimalistic preliminary data. The presence of charcoal in the culture medium has a significant impact on root generation by reducing basal callus mass formation. Such an approach is advantageous for establishing in vitro culture protocols as these models will have significant potential for saving time and expenditure in plant tissue culture laboratories, and it further reduces the need for specialised background.

Changes in rat respiratory system produced by exposure to exhaust gases of combustion of glycerol.

PubMed

Serra, Daniel Silveira; Evangelista, Janaína Serra Azul Monteiro; Zin, Walter Araujo; Leal-Cardoso, José Henrique; Cavalcante, Francisco Sales Ávila

2017-08-01

The combustion of residual glycerol to generate heat in industrial processes has been suggested as a cost-effective solution for disposal of this environmental liability. Thus, we investigated the effects of exposure to the exhaust gases of glycerol combustion in the rat respiratory system. We used 2 rats groups, one exposed to the exhaust gases from glycerol combustion (Glycerol), and the other exposed to ambient air (Control). Exposure occurred 5h a day, 5days a week for 13 weeks. We observed statistically changes in all parameters of respiratory system mechanics in vivo. This results was supported by histological analysis and morphometric data, confirming narrower airways and lung parenchimal changes. Variables related to airway resistance (ΔR N ) and elastic properties of the tissue (ΔH), increased after challenge with methacholine. Finally, analysis of lung tissue micromechanics showed statistically increases in all parameters (R, E and hysteresivity). In conclusion, exhaust gases from glycerol combustion were harmful to the respiratory system. Copyright © 2017 Elsevier B.V. All rights reserved.

The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue.

PubMed

Wan, Yinan; Almeida, Alexandra D; Rulands, Steffen; Chalour, Naima; Muresan, Leila; Wu, Yunmin; Simons, Benjamin D; He, Jie; Harris, William A

2016-04-01

Clonal analysis is helping us understand the dynamics of cell replacement in homeostatic adult tissues (Simons and Clevers, 2011). Such an analysis, however, has not yet been achieved for continuously growing adult tissues, but is essential if we wish to understand the architecture of adult organs. The retinas of lower vertebrates grow throughout life from retinal stem cells (RSCs) and retinal progenitor cells (RPCs) at the rim of the retina, called the ciliary marginal zone (CMZ). Here, we show that RSCs reside in a niche at the extreme periphery of the CMZ and divide asymmetrically along a radial (peripheral to central) axis, leaving one daughter in the peripheral RSC niche and the other more central where it becomes an RPC. We also show that RPCs of the CMZ have clonal sizes and compositions that are statistically similar to progenitor cells of the embryonic retina and fit the same stochastic model of proliferation. These results link embryonic and postembryonic cell behaviour, and help to explain the constancy of tissue architecture that has been generated over a lifetime. © 2016. Published by The Company of Biologists Ltd.

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

PubMed

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

Ridge preservation using a composite bone graft and a bioabsorbable membrane with and without primary wound closure: a comparative clinical trial.

PubMed

Engler-Hamm, Daniel; Cheung, Wai S; Yen, Alec; Stark, Paul C; Griffin, Terrence

2011-03-01

The aim of this single-masked, randomized controlled clinical trial is to compare hard and soft tissue changes after ridge preservation performed with (control, RPc) and without (test, RPe) primary soft tissue closure in a split-mouth design. Eleven patients completed this 6-month trial. Extraction and ridge preservation were performed using a composite bone graft of inorganic bovine-derived hydroxyapatite matrix and cell binding peptide P-15 (ABM/P-15), demineralized freeze-dried bone allograft, and a copolymer bioabsorbable membrane. Primary wound closure was achieved on the control sites (RPc), whereas test sites (RPe) left the membrane exposed. Pocket probing depth on adjacent teeth, repositioning of the mucogingival junction, bone width, bone fill, and postoperative discomfort were assessed. Bone cores were obtained for histological examination. Intragroup analyses for both groups demonstrated statistically significant mean reductions in probing depth (RPc: 0.42 mm, P = 0.012; RPe: 0.25 mm, P = 0.012) and bone width (RPc: 3 mm, P = 0.002; RPe: 3.42 mm, P <0.001). However, intergroup analysis did not find these parameters to be statistically different at 6 months. The test group showed statistically significant mean change in bone fill (7.21 mm; P <0.001). Compared to the control group, the test group showed statistically significant lower mean postoperative discomfort (RPc 4 versus RPe 2; P = 0.002). Histomorphometric analysis showed presence of 0% to 40% of ABM/P-15 and 5% to 20% of new bone formation in both groups. Comparison of clinical variables between the two groups at 6 months revealed that the mucogingival junction was statistically significantly more coronally displaced in the control group than in the test group, with a mean of 3.83 mm versus 1.21 mm (P = 0.002). Ridge preservation without flap advancement preserves more keratinized tissue and has less postoperative discomfort and swelling. Although ridge preservation is performed with either method, ≈27% to 30% of bone width is lost.

Relationship between histological diagnosis and evolution of 70 periapical lesions at 12 months, treated by periapical surgery.

PubMed

Carrillo, Celia; Peñarrocha, Miguel; Bagán, José Vicente; Vera, Francisco

2008-08-01

To relate the histologic diagnosis and radiographic size with the prognosis of 70 biopsies obtained via periapical surgery. Seventy biopsies obtained during periapical surgery were histologically analyzed following curettage of the tissue, establishing the diagnosis as either apical granuloma, radicular cyst, or scar tissue. The radiographic size of the lesion (area in mm(2)) before surgery and after 1 year of follow-up was measured. The evolution at 12 months after surgery was evaluated according to the criteria of von Arx and Kurt. A statistical study was made, the inter-variable relationships were studied using analysis of variance with subsequent Tukey testing and calculation of Pearson correlation coefficient. Results indicated that 65.7% of lesions were granulomas, 25.7% scar tissue, and 8.6% cysts. The larger lesions had the worst prognosis. Cysts had the worst evolution at 12 months after surgery, this result being statistically significant. The prognosis for the periapical lesion depended on the type of lesion and its radiographic size, with cysts and larger lesions having the worst evolution.

Research of second harmonic generation images based on texture analysis

NASA Astrophysics Data System (ADS)

Liu, Yao; Li, Yan; Gong, Haiming; Zhu, Xiaoqin; Huang, Zufang; Chen, Guannan

2014-09-01

Texture analysis plays a crucial role in identifying objects or regions of interest in an image. It has been applied to a variety of medical image processing, ranging from the detection of disease and the segmentation of specific anatomical structures, to differentiation between healthy and pathological tissues. Second harmonic generation (SHG) microscopy as a potential noninvasive tool for imaging biological tissues has been widely used in medicine, with reduced phototoxicity and photobleaching. In this paper, we clarified the principles of texture analysis including statistical, transform, structural and model-based methods and gave examples of its applications, reviewing studies of the technique. Moreover, we tried to apply texture analysis to the SHG images for the differentiation of human skin scar tissues. Texture analysis method based on local binary pattern (LBP) and wavelet transform was used to extract texture features of SHG images from collagen in normal and abnormal scars, and then the scar SHG images were classified into normal or abnormal ones. Compared with other texture analysis methods with respect to the receiver operating characteristic analysis, LBP combined with wavelet transform was demonstrated to achieve higher accuracy. It can provide a new way for clinical diagnosis of scar types. At last, future development of texture analysis in SHG images were discussed.

Orthodontic soft-tissue parameters: a comparison of cone-beam computed tomography and the 3dMD imaging system.

PubMed

Metzger, Tasha E; Kula, Katherine S; Eckert, George J; Ghoneima, Ahmed A

2013-11-01

Orthodontists rely heavily on soft-tissue analysis to determine facial esthetics and treatment stability. The aim of this retrospective study was to determine the equivalence of soft-tissue measurements between the 3dMD imaging system (3dMD, Atlanta, Ga) and the segmented skin surface images derived from cone-beam computed tomography. Seventy preexisting 3dMD facial photographs and cone-beam computed tomography scans taken within minutes of each other for the same subjects were registered in 3 dimensions and superimposed using Vultus (3dMD) software. After reliability studies, 28 soft-tissue measurements were recorded with both imaging modalities and compared to analyze their equivalence. Intraclass correlation coefficients and Bland-Altman plots were used to assess interexaminer and intraexaminer repeatability and agreement. Summary statistics were calculated for all measurements. To demonstrate equivalence of the 2 methods, the difference needed a 95% confidence interval contained entirely within the equivalence limits defined by the repeatability results. Statistically significant differences were reported for the vermilion height, mouth width, total facial width, mouth symmetry, soft-tissue lip thickness, and eye symmetry. There are areas of nonequivalence between the 2 imaging methods; however, the differences are clinically acceptable from the orthodontic point of view. Copyright © 2013 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Quantitative analysis of tissue deformation dynamics reveals three characteristic growth modes and globally aligned anisotropic tissue deformation during chick limb development.

PubMed

Morishita, Yoshihiro; Kuroiwa, Atsushi; Suzuki, Takayuki

2015-05-01

Tissue-level characterization of deformation dynamics is crucial for understanding organ morphogenetic mechanisms, especially the interhierarchical links among molecular activities, cellular behaviors and tissue/organ morphogenetic processes. Limb development is a well-studied topic in vertebrate organogenesis. Nevertheless, there is still little understanding of tissue-level deformation relative to molecular and cellular dynamics. This is mainly because live recording of detailed cell behaviors in whole tissues is technically difficult. To overcome this limitation, by applying a recently developed Bayesian approach, we here constructed tissue deformation maps for chick limb development with high precision, based on snapshot lineage tracing using dye injection. The precision of the constructed maps was validated with a clear statistical criterion. From the geometrical analysis of the map, we identified three characteristic tissue growth modes in the limb and showed that they are consistent with local growth factor activity and cell cycle length. In particular, we report that SHH signaling activity changes dynamically with developmental stage and strongly correlates with the dynamic shift in the tissue growth mode. We also found anisotropic tissue deformation along the proximal-distal axis. Morphogenetic simulation and experimental studies suggested that this directional tissue elongation, and not local growth, has the greatest impact on limb shaping. This result was supported by the novel finding that anisotropic tissue elongation along the proximal-distal axis occurs independently of cell proliferation. Our study marks a pivotal point for multi-scale system understanding in vertebrate development. © 2015. Published by The Company of Biologists Ltd.

A high-throughput comparative characterization of laser-induced soft tissue damage using 3D digital microscopy.

PubMed

Das, Debobrato; Reed, Stephanie; Klokkevold, Perry R; Wu, Benjamin M

2013-02-01

3D digital microscopy was used to develop a rapid alternative approach to quantify the effects of specific laser parameters on soft tissue ablation and charring in vitro without the use of conventional tissue processing techniques. Two diode lasers operating at 810 and 980 nm wavelengths were used to ablate three tissue types (bovine liver, turkey breast, and bovine muscle) at varying laser power (0.3, 1.0, and 2.0 W) and velocities (1-50 mm/s). Spectrophotometric analyses were performed on each tissue to determine tissue-specific absorption coefficients and were considered in creating wavelength-dependent energy attenuation models to evaluate minimum heat of tissue ablations. 3D surface contour profiles characterizing tissue damage revealed that ablation depth and tissue charring increased with laser power and decreased with lateral velocity independent of wavelength and tissue type. While bovine liver ablation and charring were statistically higher at 810 than 980 nm (p < 0.05), turkey breast and bovine muscle ablated and charred more at 980 than 810 nm (p < 0.05). Spectrophotometric analysis revealed that bovine liver tissue had a greater tissue-specific absorption coefficient at 810 than 980 nm, while turkey breast and bovine muscle had a larger absorption coefficient at 980 nm (p < 0.05). This rapid 3D microscopic analysis of robot-driven laser ablation yielded highly reproducible data that supported well-defined trends related to laser-tissue interactions and enabled high throughput characterization of many laser-tissue permutations. Since 3D microscopy quantifies entire lesions without altering the tissue specimens, conventional and immunohistologic techniques can be used, if desired, to further interrogate specific sections of the digitized lesions.

Results of Li-Tho trial: a prospective randomized study on effectiveness of LigaSure® in lung resections.

PubMed

Bertolaccini, Luca; Viti, Andrea; Cavallo, Antonio; Terzi, Alberto

2014-04-01

The role of electro-thermal bipolar tissue sealing system (LigaSure(®), (LS); Covidien, Inc., CO, USA) in thoracic surgery is still undefined. Reports of its use are still limited. The objective of the trial was to evaluate the cost and benefits of LS in major lung resection surgery. A randomized blinded study of a consecutive series of 100 patients undergoing lobectomy was undertaken. After muscle-sparing thoracotomy and classification of lung fissures according to Craig-Walker, patients with fissure Grade 2-4 were randomized to Stapler group or LS group fissure completion. Recorded parameters were analysed for differences in selected intraoperative and postoperative outcomes. Statistical analysis was performed with the bootstrap method. Pearson's χ(2) test and Fisher's exact test were used to calculate probability value for dichotomous variables comparison. Cost-benefit evaluation was performed using Pareto optimal analysis. There were no significant differences between groups, regarding demographic and baseline characteristics. No patient was withdrawn from the study; no adverse effect was recorded. There was no mortality or major complications in both groups. There were no statistically significant differences as to operative time or morbidity between patients in the LS group compared with the Stapler group. In the LS group, there was a not statistically significant increase of postoperative air leaks in the first 24 postoperative hours, while a statistically significant increase of drainage amount was observed in the LS group. No statistically significant difference in hospital length of stay was observed. Overall, the LS group had a favourable multi-criteria analysis of cost/benefit ratio with a good 'Pareto optimum'. LS is a safe device for thoracic surgery and can be a valid alternative to Staplers. In this setting, LS allows functional lung tissue preservation. As to costs, LS seems equivalent to Staplers.

A mixture model-based approach to the clustering of microarray expression data.

PubMed

McLachlan, G J; Bean, R W; Peel, D

2002-03-01

This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of t distributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes. The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets. EMMIX-GENE is available at http://www.maths.uq.edu.au/~gjm/emmix-gene/

Expression of FOXP3, CD68, and CD20 at Diagnosis in the Microenvironment of Classical Hodgkin Lymphoma Is Predictive of Outcome

PubMed Central

Greaves, Paul; Clear, Andrew; Coutinho, Rita; Wilson, Andrew; Matthews, Janet; Owen, Andrew; Shanyinde, Milensu; Lister, T. Andrew; Calaminici, Maria; Gribben, John G.

2013-01-01

Purpose The immune microenvironment is key to the pathophysiology of classical Hodgkin lymphoma (CHL). Twenty percent of patients experience failure of their initial treatment, and others receive excessively toxic treatment. Prognostic scores and biomarkers have yet to influence outcomes significantly. Previous biomarker studies have been limited by the extent of tissue analyzed, statistical inconsistencies, and failure to validate findings. We aimed to overcome these limitations by validating recently identified microenvironment biomarkers (CD68, FOXP3, and CD20) in a new patient cohort with a greater extent of tissue and by using rigorous statistical methodology. Patients and Methods Diagnostic tissue from 122 patients with CHL was microarrayed and stained, and positive cells were counted across 10 to 20 high-powered fields per patient by using an automated system. Two statistical analyses were performed: a categorical analysis with test/validation set-defined cut points and Kaplan-Meier estimated outcome measures of 5-year overall survival (OS), disease-specific survival (DSS), and freedom from first-line treatment failure (FFTF) and an independent multivariate analysis of absolute uncategorized counts. Results Increased CD20 expression confers superior OS. Increased FOXP3 expression confers superior OS, and increased CD68 confers inferior FFTF and OS. FOXP3 varies independently of CD68 expression and retains significance when analyzed as a continuous variable in multivariate analysis. A simple score combining FOXP3 and CD68 discriminates three groups: FFTF 93%, 62%, and 47% (P < .001), DSS 93%, 82%, and 63% (P = .03), and OS 93%, 82%, and 59% (P = .002). Conclusion We have independently validated CD68, FOXP3, and CD20 as prognostic biomarkers in CHL, and we demonstrate, to the best of our knowledge for the first time, that combining FOXP3 and CD68 may further improve prognostic stratification. PMID:23045593

Sample processing, protocol, and statistical analysis of the time-of-flight secondary ion mass spectrometry (ToF-SIMS) of protein, cell, and tissue samples.

PubMed

Barreto, Goncalo; Soininen, Antti; Sillat, Tarvo; Konttinen, Yrjö T; Kaivosoja, Emilia

2014-01-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly being used in analysis of biological samples. For example, it has been applied to distinguish healthy and osteoarthritic human cartilage. This chapter discusses ToF-SIMS principle and instrumentation including the three modes of analysis in ToF-SIMS. ToF-SIMS sets certain requirements for the samples to be analyzed; for example, the samples have to be vacuum compatible. Accordingly, sample processing steps for different biological samples, i.e., proteins, cells, frozen and paraffin-embedded tissues and extracellular matrix for the ToF-SIMS are presented. Multivariate analysis of the ToF-SIMS data and the necessary data preprocessing steps (peak selection, data normalization, mean-centering, and scaling and transformation) are discussed in this chapter.

Decreased expression of dual specificity phosphatase 22 in colorectal cancer and its potential prognostic relevance for stage IV CRC patients.

PubMed

Yu, Dan; Li, Zhenli; Gan, Meifu; Zhang, Hanyun; Yin, Xiaoyang; Tang, Shunli; Wan, Ledong; Tian, Yiping; Zhang, Shuai; Zhu, Yimin; Lai, Maode; Zhang, Dandan

2015-11-01

Dual specificity phosphatase 22 (DUSP22) is a novel dual specificity phosphatase that has been demonstrated to be a cancer suppressor gene associated with numerous biological and pathological processes. However, little is known of DUSP22 expression profiling in colorectal cancer and its prognostic value. Our study aims to investigate the role of DUSP22 expression in the prognosis of colorectal cancer. We detected the mRNA expression in 92 paired primary colorectal cancer tissues and the corresponding adjacent normal tissues by using QuantiGenePlex assay. The Friedman test was used to determine the statistical difference of gene expression. Kaplan-Meier survival analysis was performed. Mann-Whitney test and Kruskal-Wallis test were used to conduct data analyses to determine the prognostic value. Statistical significance was set at P < 0.05. In 74 of 92 cases, DUSP22 mRNA was reduced in primary colorectal cancer tissues, compared to the adjacent normal tissues. The mRNA levels of DUSP22 were significantly lower in colorectal cancer tissues than in adjacent normal tissues (0.0290 vs. 0.0658; P < 0.001). Low expression of DUSP22 correlated significantly with large tumor size (P = 0.013). No association was observed between DUSP22 mRNA expression and differentiation, histopathological type, tumor invasion, lymph node metastases, metastases, TNM stage, and Duke's phase (all P > 0.05). Kaplan-Meier analysis indicated that DUSP22 expression had no significant relationship with overall survival in all patients (P > 0.05). Interestingly, low expression level of DUSP22 in stage IV patients had a poor survival measures with a marginal P value (P = 0.07). Reduced DUSP22 expression was found in colorectal cancer specimens. Low expression level of DUSP22 in stage IV patients had a poor survival outcome. Further study is required for the investigation of the role of DUSP22 in colorectal cancer.

New bone formation in a bone defect associated to dental implant using absorbable or non-absorbable membrane in a dog model

PubMed Central

Lopez, Maria de Almeida; Olate, Sergio; Lanata-Flores, Antonio; Pozzer, Leandro; Cavalieri-Pereira, Lucas; Cantín, Mario; Vásquez, Bélgica; de Albergaria-Barbosa, José

2013-01-01

The aim of this research was to determine the bone formation capacity in fenestration defects associated with dental implants using absorbable and non-absorbable membranes. Six dogs were used in the study. In both tibias of each animal 3 implants were installed, and around these 5 mm circular defects were created. The defects were covered with absorbable membranes (experimental group 1), non-absorbable membranes (experimental group 2), and the third defect was not covered (control group). At 3 and 8 weeks post-surgery, the animals were euthanized and the membranes with the bone tissue around the implants were processed for histological analysis. The statistical analysis was conducted with Tukey’s test, considering statistical significance when p<0.1. Adequate bone repair was observed in the membrane-covered defects. At 3 weeks, organization of the tissue, bone formation from the periphery of the defect and the absence of inflammatory infiltrate were observed in both experimental groups, but the defect covered with absorbable membrane presented statistically greater bone formation. At 8 weeks, both membrane-covered defects showed adequate bone formation without significant differences, although they did in fact present differences with the control defect in both periods (p>0.1). In the defects without membrane, continuous connective tissue invasions and bone repair deficiency were observed. There were no significant differences in the characteristics and volume of the neoformed bone in the defects around the implants covered by the different membranes, whereas the control defects produced significantly less bone. The use of biological membranes contributes to bone formation in three-wall defects. PMID:24228090

Novel biomarker identification using metabolomic profiling to differentiate radiation necrosis and recurrent tumor following Gamma Knife radiosurgery.

PubMed

Lu, Alex Y; Turban, Jack L; Damisah, Eyiyemisi C; Li, Jie; Alomari, Ahmed K; Eid, Tore; Vortmeyer, Alexander O; Chiang, Veronica L

2017-08-01

OBJECTIVE Following an initial response of brain metastases to Gamma Knife radiosurgery, regrowth of the enhancing lesion as detected on MRI may represent either radiation necrosis (a treatment-related inflammatory change) or recurrent tumor. Differentiation of radiation necrosis from tumor is vital for management decision making but remains difficult by imaging alone. In this study, gas chromatography with time-of-flight mass spectrometry (GC-TOF) was used to identify differential metabolite profiles of the 2 tissue types obtained by surgical biopsy to find potential targets for noninvasive imaging. METHODS Specimens of pure radiation necrosis and pure tumor obtained from patient brain biopsies were flash-frozen and validated histologically. These formalin-free tissue samples were then analyzed using GC-TOF. The metabolite profiles of radiation necrosis and tumor samples were compared using multivariate and univariate statistical analysis. Statistical significance was defined as p ≤ 0.05. RESULTS For the metabolic profiling, GC-TOF was performed on 7 samples of radiation necrosis and 7 samples of tumor. Of the 141 metabolites identified, 17 (12.1%) were found to be statistically significantly different between comparison groups. Of these metabolites, 6 were increased in tumor, and 11 were increased in radiation necrosis. An unsupervised hierarchical clustering analysis found that tumor had elevated levels of metabolites associated with energy metabolism, whereas radiation necrosis had elevated levels of metabolites that were fatty acids and antioxidants/cofactors. CONCLUSIONS To the authors' knowledge, this is the first tissue-based metabolomics study of radiation necrosis and tumor. Radiation necrosis and recurrent tumor following Gamma Knife radiosurgery for brain metastases have unique metabolite profiles that may be targeted in the future to develop noninvasive metabolic imaging techniques.

Preliminary assessment of facial soft tissue thickness utilizing three-dimensional computed tomography models of living individuals.

PubMed

Parks, Connie L; Richard, Adam H; Monson, Keith L

2014-04-01

Facial approximation is the technique of developing a representation of the face from the skull of an unknown individual. Facial approximation relies heavily on average craniofacial soft tissue depths. For more than a century, researchers have employed a broad array of tissue depth collection methodologies, a practice which has resulted in a lack of standardization in craniofacial soft tissue depth research. To combat such methodological inconsistencies, Stephan and Simpson 2008 [15] examined and synthesized a large number of previously published soft tissue depth studies. Their comprehensive meta-analysis produced a pooled dataset of averaged tissue depths and a simplified methodology, which the researchers suggest be utilized as a minimum standard protocol for future craniofacial soft tissue depth research. The authors of the present paper collected craniofacial soft tissue depths using three-dimensional models generated from computed tomography scans of living males and females of four self-identified ancestry groups from the United States ranging in age from 18 to 62 years. This paper assesses the differences between: (i) the pooled mean tissue depth values from the sample utilized in this paper and those published by Stephan 2012 [21] and (ii) the mean tissue depth values of two demographically similar subsets of the sample utilized in this paper and those published by Rhine and Moore 1984 [16]. Statistical test results indicate that the tissue depths collected from the sample evaluated in this paper are significantly and consistently larger than those published by Stephan 2012 [21]. Although a lack of published variance data by Rhine and Moore 1984 [16] precluded a direct statistical assessment, a substantive difference was also concluded. Further, the dataset presented in this study is representative of modern American adults and is, therefore, appropriate for use in constructing contemporary facial approximations. Published by Elsevier Ireland Ltd.

A Next-generation Tissue Microarray (ngTMA) Protocol for Biomarker Studies

PubMed Central

Zlobec, Inti; Suter, Guido; Perren, Aurel; Lugli, Alessandro

2014-01-01

Biomarker research relies on tissue microarrays (TMA). TMAs are produced by repeated transfer of small tissue cores from a ‘donor’ block into a ‘recipient’ block and then used for a variety of biomarker applications. The construction of conventional TMAs is labor intensive, imprecise, and time-consuming. Here, a protocol using next-generation Tissue Microarrays (ngTMA) is outlined. ngTMA is based on TMA planning and design, digital pathology, and automated tissue microarraying. The protocol is illustrated using an example of 134 metastatic colorectal cancer patients. Histological, statistical and logistical aspects are considered, such as the tissue type, specific histological regions, and cell types for inclusion in the TMA, the number of tissue spots, sample size, statistical analysis, and number of TMA copies. Histological slides for each patient are scanned and uploaded onto a web-based digital platform. There, they are viewed and annotated (marked) using a 0.6-2.0 mm diameter tool, multiple times using various colors to distinguish tissue areas. Donor blocks and 12 ‘recipient’ blocks are loaded into the instrument. Digital slides are retrieved and matched to donor block images. Repeated arraying of annotated regions is automatically performed resulting in an ngTMA. In this example, six ngTMAs are planned containing six different tissue types/histological zones. Two copies of the ngTMAs are desired. Three to four slides for each patient are scanned; 3 scan runs are necessary and performed overnight. All slides are annotated; different colors are used to represent the different tissues/zones, namely tumor center, invasion front, tumor/stroma, lymph node metastases, liver metastases, and normal tissue. 17 annotations/case are made; time for annotation is 2-3 min/case. 12 ngTMAs are produced containing 4,556 spots. Arraying time is 15-20 hr. Due to its precision, flexibility and speed, ngTMA is a powerful tool to further improve the quality of TMAs used in clinical and translational research. PMID:25285857

Texture analysis of MR images of patients with Mild Traumatic Brain Injury

PubMed Central

2010-01-01

Background Our objective was to study the effect of trauma on texture features in cerebral tissue in mild traumatic brain injury (MTBI). Our hypothesis was that a mild trauma may cause microstructural changes, which are not necessarily perceptible by visual inspection but could be detected with texture analysis (TA). Methods We imaged 42 MTBI patients by using 1.5 T MRI within three weeks of onset of trauma. TA was performed on the area of mesencephalon, cerebral white matter at the levels of mesencephalon, corona radiata and centrum semiovale and in different segments of corpus callosum (CC) which have been found to be sensitive to damage. The same procedure was carried out on a control group of ten healthy volunteers. Patients' TA data was compared with the TA results of the control group comparing the amount of statistically significantly differing TA parameters between the left and right sides of the cerebral tissue and comparing the most discriminative parameters. Results There were statistically significant differences especially in several co-occurrence and run-length matrix based parameters between left and right side in the area of mesencephalon, in cerebral white matter at the level of corona radiata and in the segments of CC in patients. Considerably less difference was observed in the healthy controls. Conclusions TA revealed significant changes in texture parameters of cerebral tissue between hemispheres and CC segments in TBI patients. TA may serve as a novel additional tool for detecting the conventionally invisible changes in cerebral tissue in MTBI and help the clinicians to make an early diagnosis. PMID:20462439

Stable phenotype of B-cell subsets following cryopreservation and thawing of normal human lymphocytes stored in a tissue biobank.

PubMed

Rasmussen, Simon Mylius; Bilgrau, Anders Ellern; Schmitz, Alexander; Falgreen, Steffen; Bergkvist, Kim Steve; Tramm, Anette Mai; Baech, John; Jacobsen, Chris Ladefoged; Gaihede, Michael; Kjeldsen, Malene Krag; Bødker, Julie Støve; Dybkaer, Karen; Bøgsted, Martin; Johnsen, Hans Erik

2015-01-01

Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are no phenotypic differences between cryopreserved and fresh B-cell subsets." Subsequently, we performed an uncontrolled comparison of tonsil tissue samples. By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue-specific comparative analysis. © 2014 Clinical Cytometry Society.

Stable Phenotype Of B-Cell Subsets Following Cryopreservation and Thawing of Normal Human Lymphocytes Stored in a Tissue Biobank.

PubMed

Rasmussen, Simon Mylius; Bilgrau, Anders Ellern; Schmitz, Alexander; Falgreen, Steffen; Bergkvist, Kim Steve; Tramm, Anette Mai; Baech, John; Jacobsen, Chris Ladefoged; Gaihede, Michael; Kjeldsen, Malene Krag; Bødker, Julie Støve; Dybkaer, Karen; Bøgsted, Martin; Johnsen, Hans Erik

2014-09-20

Background Cryopreservation is an acknowledged procedure to store vital cells for future biomarker analyses. Few studies, however, have analyzed the impact of the cryopreservation on phenotyping. Methods We have performed a controlled comparison of cryopreserved and fresh cellular aliquots prepared from individual healthy donors. We studied circulating B-cell subset membrane markers and global gene expression, respectively by multiparametric flow cytometry and microarray data. Extensive statistical analysis of the generated data tested the concept that "overall, there are phenotypic differences between cryopreserved and fresh B-cell subsets". Subsequently, we performed a consecutive uncontrolled comparison of tonsil tissue samples. Results By multiparametric flow analysis, we documented no significant changes following cryopreservation of subset frequencies or membrane intensity for the differentiation markers CD19, CD20, CD22, CD27, CD38, CD45, and CD200. By gene expression profiling following cryopreservation, across all samples, only 16 out of 18708 genes were significantly up or down regulated, including FOSB, KLF4, RBP7, ANXA1 or CLC, DEFA3, respectively. Implementation of cryopreserved tissue in our research program allowed us to present a performance analysis, by comparing cryopreserved and fresh tonsil tissue. As expected, phenotypic differences were identified, but to an extent that did not affect the performance of the cryopreserved tissue to generate specific B-cell subset associated gene signatures and assign subset phenotypes to independent tissue samples. Conclusions We have confirmed our working concept and illustrated the usefulness of vital cryopreserved cell suspensions for phenotypic studies of the normal B-cell hierarchy; however, storage procedures need to be delineated by tissue specific comparative analysis. © 2014 Clinical Cytometry Society. Copyright © 2014 Clinical Cytometry Society.

Germinal center texture entropy as possible indicator of humoral immune response: immunophysiology viewpoint.

PubMed

Pantic, Igor; Pantic, Senka

2012-10-01

In this article, we present the results indicating that spleen germinal center (GC) texture entropy determined by gray-level co-occurrence matrix (GLCM) method is related to humoral immune response. Spleen tissue was obtained from eight outbred male short-haired guinea pigs previously immunized by sheep red blood cells (SRBC). A total of 312 images from 39 germinal centers (156 GC light zone images and 156 GC dark zone images) were acquired and analyzed by GLCM method. Angular second moment, contrast, correlation, entropy, and inverse difference moment were calculated for each image. Humoral immune response to SRBC was measured using T cell-dependent antibody response (TDAR) assay. Statistically highly significant negative correlation was detected between light zone entropy and the number of TDAR plaque-forming cells (r (s) = -0.86, p < 0.01). The entropy decreased as the plaque-forming cells increased and vice versa. A statistically significant negative correlation was also detected between dark zone entropy values and the number of plaque-forming cells (r (s) = -0.69, p < 0.05). Germinal center texture entropy may be a powerful indicator of humoral immune response. This study is one of the first to point out the potential scientific value of GLCM image texture analysis in lymphoid tissue cytoarchitecture evaluation. Lymphoid tissue texture analysis could become an important and affordable addition to the conventional immunophysiology techniques.

Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

DOE PAGES

Yu, Peiqiang

2006-01-01

Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in biological tissues at ultraspatial resolutions.« less

Coherent light depolarization by multiple scattering media and tissues: some fundamentals and applications

NASA Astrophysics Data System (ADS)

Zimnyakov, Dmitry A.; Tuchin, Valery V.; Yodh, Arjun G.; Mishin, Alexey A.; Peretochkin, Igor S.

1998-04-01

Relationships between decorrelation and depolarization of coherent light scattered by disordered media are examined by using the conception of the photon paths distribution functions. Analysis of behavior of the autocorrelation functions of the scattered field fluctuations and their polarization properties allows us to introduce generalized parameter of scattering media such as specific correlation time. Determination of specific correlation time has been carried out for phantom scattering media (water suspensions of polystyrene spheres). Results of statistical, correlation and polarization analysis of static and dynamic speckle patterns carried out in the experiments with human sclera with artificially controlled optical transmittance are presented. Some possibilities of applications of such polarization- correlation technique for monitoring and visualization of non- single scattering tissue structures are discussed.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis.

PubMed

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence.

Texture-preserved penalized weighted least-squares reconstruction of low-dose CT image via image segmentation and high-order MRF modeling

NASA Astrophysics Data System (ADS)

Han, Hao; Zhang, Hao; Wei, Xinzhou; Moore, William; Liang, Zhengrong

2016-03-01

In this paper, we proposed a low-dose computed tomography (LdCT) image reconstruction method with the help of prior knowledge learning from previous high-quality or normal-dose CT (NdCT) scans. The well-established statistical penalized weighted least squares (PWLS) algorithm was adopted for image reconstruction, where the penalty term was formulated by a texture-based Gaussian Markov random field (gMRF) model. The NdCT scan was firstly segmented into different tissue types by a feature vector quantization (FVQ) approach. Then for each tissue type, a set of tissue-specific coefficients for the gMRF penalty was statistically learnt from the NdCT image via multiple-linear regression analysis. We also proposed a scheme to adaptively select the order of gMRF model for coefficients prediction. The tissue-specific gMRF patterns learnt from the NdCT image were finally used to form an adaptive MRF penalty for the PWLS reconstruction of LdCT image. The proposed texture-adaptive PWLS image reconstruction algorithm was shown to be more effective to preserve image textures than the conventional PWLS image reconstruction algorithm, and we further demonstrated the gain of high-order MRF modeling for texture-preserved LdCT PWLS image reconstruction.

Identification of organ tissue types and skin from forensic samples by microRNA expression analysis.

PubMed

Sauer, Eva; Extra, Antje; Cachée, Philipp; Courts, Cornelius

2017-05-01

The identification of organ tissues in traces recovered from scenes and objects with regard to violent crimes involving serious injuries can be of considerable relevance in forensic investigations. Molecular genetic approaches are provably superior to histological and immunological assays in characterizing organ tissues, and micro-RNAs (miRNAs), due to their cell type specific expression patterns and stability against degradation, emerged as a promising molecular species for forensic analyses, with a range of tried and tested indicative markers. Thus, herein we present the first miRNA based approach for the forensic identification of organ tissues. Using quantitative PCR employing an empirically derived strategy for data normalization and unbiased statistical decision making, we assessed the differential expression of 15 preselected miRNAs in tissues of brain, kidney, lung, liver, heart muscle, skeletal muscle and skin. We show that not only can miRNA expression profiling be used to reliably differentiate between organ tissues but also that this method, which is compatible with and complementary to forensic DNA analysis, is applicable to realistic forensic samples e.g. mixtures, aged and degraded material as well as traces generated by mock stabbings and experimental shootings at ballistic models. Copyright © 2017 Elsevier B.V. All rights reserved.

Metabolic effects of large-volume liposuction for obese healthy women: a meta-analysis of fasting insulin levels.

PubMed

Boriani, Filippo; Villani, Riccardo; Morselli, Paolo Giovanni

2014-10-01

Obesity is increasingly frequent in our society and is associated closely with metabolic disorders. As some studies have suggested, removal of fat tissue through liposuction and dermolipectomies may be of some benefit in the improvement of metabolic indices. This article aimed to review the published literature on this topic and to evaluate metabolic variations meta-analytically after liposuction, dermolipectomy, or both. Through a literature search with the PubMed/Medline database, 14 studies were identified. All articles were analyzed, and several metabolic variables were chosen in the attempt to meta-analyze the effect of adipose tissue removal through the various studies. All statistical calculations were performed with Review Manager (RevMan), version 5.0. Several cardiovascular and metabolic variables are described as prone to variations after body-contouring procedures when a significant amount of adipose tissue has been excised. Four of the studies included in the analysis reported improvements in all the parameters examined. Seven articles showed improvement in some variables and no improvement in others, whereas three studies showed no beneficial variation in any of the considered indicators after body-contouring procedures. Fasting plasma insulin was identified as the only variable for which a meta-analysis of five included studies was possible. The meta-analysis showed a statistically significant reduction in fasting plasma insulin resulting from large-volume liposuction in obese healthy women. Many beneficial metabolic effects resulting from dermolipectomy and liposuction procedures are described in the literature. In particular, fasting plasma insulin and thus insulin sensitivity seem to be positively influenced. Further research, including prospective clinical studies, is necessary for better exploration of the effects that body-contouring plastic surgery procedures have on metabolic parameters.

Biphasic cellular and tissue response of rat lungs after eight-day aerosol exposure to the silicon dioxide cristobalite.

PubMed Central

Absher, M. P.; Trombley, L.; Hemenway, D. R.; Mickey, R. M.; Leslie, K. O.

1989-01-01

Cristobalite is a crystalline silicon dioxide that elicits pulmonary inflammation and fibrosis in humans and experimental animals. Exposure of rats to aerosols of respirable cristobalite for 8 days led to a rapid influx of neutrophils and macrophages into alveolar and tissue compartments of the lung followed by a more gradual accumulation of T lymphocytes. This inflammatory response persisted throughout 52 weeks after the end of the exposure. For some variables studied there appeared to be a cyclical nature to the response. Statistical analysis of alveolar cell populations and lung tissue weight, protein, and hydroxyproline showed significant time-dependent fluctuations. Histologic analysis revealed a progressive deposition of collagen and type II cell hyperplasia centered on airways, however, there appeared to be some correlation between fluctuations in alveolar cell populations and overall tissue pathology. The observed cellular and biochemical fluctuations and the persistence of the inflammatory response may be due to the presence of silica in the lung, which serves as a source of repetitive stimulation of lung cells. Images Figure 4 Figure 5 PMID:2547319

Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology⋆

PubMed Central

Fu, Wenjiang J.; Stromberg, Arnold J.; Viele, Kert; Carroll, Raymond J.; Wu, Guoyao

2009-01-01

Over the past two decades, there have been revolutionary developments in life science technologies characterized by high throughput, high efficiency, and rapid computation. Nutritionists now have the advanced methodologies for the analysis of DNA, RNA, protein, low-molecular-weight metabolites, as well as access to bioinformatics databases. Statistics, which can be defined as the process of making scientific inferences from data that contain variability, has historically played an integral role in advancing nutritional sciences. Currently, in the era of systems biology, statistics has become an increasingly important tool to quantitatively analyze information about biological macromolecules. This article describes general terms used in statistical analysis of large, complex experimental data. These terms include experimental design, power analysis, sample size calculation, and experimental errors (type I and II errors) for nutritional studies at population, tissue, cellular, and molecular levels. In addition, we highlighted various sources of experimental variations in studies involving microarray gene expression, real-time polymerase chain reaction, proteomics, and other bioinformatics technologies. Moreover, we provided guidelines for nutritionists and other biomedical scientists to plan and conduct studies and to analyze the complex data. Appropriate statistical analyses are expected to make an important contribution to solving major nutrition-associated problems in humans and animals (including obesity, diabetes, cardiovascular disease, cancer, ageing, and intrauterine fetal retardation). PMID:20233650

Adverse effects of metallic artifacts on voxel-wise analysis and tract-based spatial statistics in diffusion tensor imaging.

PubMed

Goto, Masami; Abe, Osamu; Hata, Junichi; Fukunaga, Issei; Shimoji, Keigo; Kunimatsu, Akira; Gomi, Tsutomu

2017-02-01

Background Diffusion tensor imaging (DTI) is a magnetic resonance imaging (MRI) technique that reflects the Brownian motion of water molecules constrained within brain tissue. Fractional anisotropy (FA) is one of the most commonly measured DTI parameters, and can be applied to quantitative analysis of white matter as tract-based spatial statistics (TBSS) and voxel-wise analysis. Purpose To show an association between metallic implants and the results of statistical analysis (voxel-wise group comparison and TBSS) for fractional anisotropy (FA) mapping, in DTI of healthy adults. Material and Methods Sixteen healthy volunteers were scanned with 3-Tesla MRI. A magnetic keeper type of dental implant was used as the metallic implant. DTI was acquired three times in each participant: (i) without a magnetic keeper (FAnon1); (ii) with a magnetic keeper (FAimp); and (iii) without a magnetic keeper (FAnon2) as reproducibility of FAnon1. Group comparisons with paired t-test were performed as FAnon1 vs. FAnon2, and as FAnon1 vs. FAimp. Results Regions of significantly reduced and increased local FA values were revealed by voxel-wise group comparison analysis (a P value of less than 0.05, corrected with family-wise error), but not by TBSS. Conclusion Metallic implants existing outside the field of view produce artifacts that affect the statistical analysis (voxel-wise group comparisons) for FA mapping. When statistical analysis for FA mapping is conducted by researchers, it is important to pay attention to any dental implants present in the mouths of the participants.

Altered Molecular Expression of the TLR4/NF-κB Signaling Pathway in Mammary Tissue of Chinese Holstein Cattle with Mastitis

PubMed Central

Wu, Jie; Li, Lian; Sun, Yu; Huang, Shuai; Tang, Juan; Yu, Pan; Wang, Genlin

2015-01-01

Toll-like receptor 4 (TLR4) mediated activation of the nuclear transcription factor κB (NF-κB) signaling pathway by mastitis initiates expression of genes associated with inflammation and the innate immune response. In this study, the profile of mastitis-induced differential gene expression in the mammary tissue of Chinese Holstein cattle was investigated by Gene-Chip microarray and bioinformatics. The microarray results revealed that 79 genes associated with the TLR4/NF-κB signaling pathway were differentially expressed. Of these genes, 19 were up-regulated and 29 were down-regulated in mastitis tissue compared to normal, healthy tissue. Statistical analysis of transcript and protein level expression changes indicated that 10 genes, namely TLR4, MyD88, IL-6, and IL-10, were up-regulated, while, CD14, TNF-α, MD-2, IL-β, NF-κB, and IL-12 were significantly down-regulated in mastitis tissue in comparison with normal tissue. Analyses using bioinformatics database resources, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and the Gene Ontology Consortium (GO) for term enrichment analysis, suggested that these differently expressed genes implicate different regulatory pathways for immune function in the mammary gland. In conclusion, our study provides new evidence for better understanding the differential expression and mechanisms of the TLR4 /NF-κB signaling pathway in Chinese Holstein cattle with mastitis. PMID:25706977

Altered molecular expression of the TLR4/NF-κB signaling pathway in mammary tissue of Chinese Holstein cattle with mastitis.

PubMed

Wu, Jie; Li, Lian; Sun, Yu; Huang, Shuai; Tang, Juan; Yu, Pan; Wang, Genlin

2015-01-01

Toll-like receptor 4 (TLR4) mediated activation of the nuclear transcription factor κB (NF-κB) signaling pathway by mastitis initiates expression of genes associated with inflammation and the innate immune response. In this study, the profile of mastitis-induced differential gene expression in the mammary tissue of Chinese Holstein cattle was investigated by Gene-Chip microarray and bioinformatics. The microarray results revealed that 79 genes associated with the TLR4/NF-κB signaling pathway were differentially expressed. Of these genes, 19 were up-regulated and 29 were down-regulated in mastitis tissue compared to normal, healthy tissue. Statistical analysis of transcript and protein level expression changes indicated that 10 genes, namely TLR4, MyD88, IL-6, and IL-10, were up-regulated, while, CD14, TNF-α, MD-2, IL-β, NF-κB, and IL-12 were significantly down-regulated in mastitis tissue in comparison with normal tissue. Analyses using bioinformatics database resources, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and the Gene Ontology Consortium (GO) for term enrichment analysis, suggested that these differently expressed genes implicate different regulatory pathways for immune function in the mammary gland. In conclusion, our study provides new evidence for better understanding the differential expression and mechanisms of the TLR4 /NF-κB signaling pathway in Chinese Holstein cattle with mastitis.

Potential for autoimmune pathogenesis of Rift Valley Fever virus retinitis.

PubMed

Newman-Gerhardt, Shoshana; Muiruri, Samuel; Muchiri, Eric; Peters, Clarence J; Morrill, John; Lucas, Alexander H; King, Charles H; Kazura, James; LaBeaud, Angelle Desiree

2013-09-01

Rift Valley Fever (RVF) is a significant threat to human health because it can progress to retinitis, encephalitis, and hemorrhagic fever. The timing of onset of Rift Valley Fever virus (RVFV) retinitis suggests an autoimmune origin. To determine whether RVFV retinitis is associated with increased levels of IgG against retinal tissue, we measured and compared levels of IgG against healthy human eye tissue by immunohistochemical analysis. We found that serum samples from RVFV-exposed Kenyans with retinitis (n = 8) were slightly more likely to have antibodies against retinal tissue than control populations, but the correlation was not statistically significant. Further investigation into the possible immune pathogenesis of RVFV retinitis could lead to improved therapies to prevent or treat this severe complication.

Potential for Autoimmune Pathogenesis of Rift Valley Fever Virus Retinitis

PubMed Central

Newman-Gerhardt, Shoshana; Muiruri, Samuel; Muchiri, Eric; Peters, Clarence J.; Morrill, John; Lucas, Alexander H.; King, Charles H.; Kazura, James; LaBeaud, Angelle Desiree

2013-01-01

Rift Valley Fever (RVF) is a significant threat to human health because it can progress to retinitis, encephalitis, and hemorrhagic fever. The timing of onset of Rift Valley Fever virus (RVFV) retinitis suggests an autoimmune origin. To determine whether RVFV retinitis is associated with increased levels of IgG against retinal tissue, we measured and compared levels of IgG against healthy human eye tissue by immunohistochemical analysis. We found that serum samples from RVFV-exposed Kenyans with retinitis (n = 8) were slightly more likely to have antibodies against retinal tissue than control populations, but the correlation was not statistically significant. Further investigation into the possible immune pathogenesis of RVFV retinitis could lead to improved therapies to prevent or treat this severe complication. PMID:23918215

Tissue multifractality and hidden Markov model based integrated framework for optimum precancer detection

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Sabyasachi; Das, Nandan K.; Kurmi, Indrajit; Pradhan, Asima; Ghosh, Nirmalya; Panigrahi, Prasanta K.

2017-10-01

We report the application of a hidden Markov model (HMM) on multifractal tissue optical properties derived via the Born approximation-based inverse light scattering method for effective discrimination of precancerous human cervical tissue sites from the normal ones. Two global fractal parameters, generalized Hurst exponent and the corresponding singularity spectrum width, computed by multifractal detrended fluctuation analysis (MFDFA), are used here as potential biomarkers. We develop a methodology that makes use of these multifractal parameters by integrating with different statistical classifiers like the HMM and support vector machine (SVM). It is shown that the MFDFA-HMM integrated model achieves significantly better discrimination between normal and different grades of cancer as compared to the MFDFA-SVM integrated model.

Spectral region optimization for Raman-based optical biopsy of inflammatory lesions.

PubMed

de Carvalho, Luis Felipe das Chagas E Silva; Bitar, Renata Andrade; Arisawa, Emília Angela Loschiavo; Brandão, Adriana Aigotti Haberbeck; Honório, Kathia Maria; Cabral, Luiz Antônio Guimarães; Martin, Airton Abrahão; Martinho, Herculano da Silva; Almeida, Janete Dias

2010-08-01

The biochemical alterations between inflammatory fibrous hyperplasia (IFH) and normal tissues of buccal mucosa were probed by using the FT-Raman spectroscopy technique. The aim was to find the minimal set of Raman bands that would furnish the best discrimination. Raman-based optical biopsy is a widely recognized potential technique for noninvasive real-time diagnosis. However, few studies had been devoted to the discrimination of very common subtle or early pathologic states as inflammatory processes that are always present on, for example, cancer lesion borders. Seventy spectra of IFH from 14 patients were compared with 30 spectra of normal tissues from six patients. The statistical analysis was performed with principal components analysis and soft independent modeling class analogy cross-validated, leave-one-out methods. Bands close to 574, 1,100, 1,250 to 1,350, and 1,500 cm(-1) (mainly amino acids and collagen bands) showed the main intragroup variations that are due to the acanthosis process in the IFH epithelium. The 1,200 (C-C aromatic/DNA), 1,350 (CH(2) bending/collagen 1), and 1,730 cm(-1) (collagen III) regions presented the main intergroup variations. This finding was interpreted as originating in an extracellular matrix-degeneration process occurring in the inflammatory tissues. The statistical analysis results indicated that the best discrimination capability (sensitivity of 95% and specificity of 100%) was found by using the 530-580 cm(-1) spectral region. The existence of this narrow spectral window enabling normal and inflammatory diagnosis also had useful implications for an in vivo dispersive Raman setup for clinical applications.

Effects of pH, lactate, hematocrit and potassium level on the accuracy of continuous glucose monitoring (CGM) in pediatric intensive care unit.

PubMed

Marics, Gábor; Koncz, Levente; Eitler, Katalin; Vatai, Barbara; Szénási, Boglárka; Zakariás, David; Mikos, Borbála; Körner, Anna; Tóth-Heyn, Péter

2015-03-19

Continuous glucose monitoring (CGM) originally was developed for diabetic patients and it may be a useful tool for monitoring glucose changes in pediatric intensive care unit (PICU). Its use is, however, limited by the lack of sufficient data on its reliability at insufficient peripheral perfusion. We aimed to correlate the accuracy of CGM with laboratory markers relevant to disturbed tissue perfusion. In 38 pediatric patients (age range, 0-18 years) requiring intensive care we tested the effect of pH, lactate, hematocrit and serum potassium on the difference between CGM and meter glucose measurements. Guardian® (Medtronic®) CGM results were compared to GEM 3000 (Instrumentation laboratory®) and point-of-care measurements. The clinical accuracy of CGM was evaluated by Clarke Error Grid -, Bland-Altman analysis and Pearson's correlation. We used Friedman test for statistical analysis (statistical significance was established as a p < 0.05). CGM values exhibited a considerable variability without any correlation with the examined laboratory parameters. Clarke, Bland-Altman analysis and Pearson's correlation coefficient demonstrated a good clinical accuracy of CGM (zone A and B = 96%; the mean difference between reference and CGM glucose was 1,3 mg/dL, 48 from the 780 calibration pairs overrunning the 2 standard deviation; Pearson's correlation coefficient: 0.83). The accuracy of CGM measurements is independent of laboratory parameters relevant to tissue hypoperfusion. CGM may prove a reliable tool for continuous monitoring of glucose changes in PICUs, not much influenced by tissue perfusion, but still not appropriate for being the base for clinical decisions.

Comparison of imaging value for diabetic lower extremity arterial disease between FBI and CE-MRA.

PubMed

Yi, C-Y; Zhou, D-X; Li, H-H; Wang, Y; Chen, K; Chen, J; Huang, B-C; Xu, X-L

2016-07-01

This study adopted self-control study method to assess the efficacy of fresh blood imaging (FBI) and contrast-enhanced MR angiography (CE-MRA) for patients with diabetic lower extremity arterial disease (DLEAD) (Fontaine stage I to IV), and to evaluate the imaging of lower extremity peripheral arterial disease (PAD) in different stages of diabetes mellitus (DM). 1. This study recruited 44 diabetic patients with suspected lower extremity PAD to take both FBI and CE-MRA. 2. Two experienced cardiovascular radiologists assessed the image quality, the detection of lower extremity arterial branches, and tissue contamination (veins, arteries, and soft tissues) of FBI and CE-MRA, as well as the presence and severity of stenotic lesions. 3. Statistical differences of the quality of FBI and CE-MRA were determined using paired t-test. 4. Correlation analysis was adopted for determining the direction and strength of the relationship between the changes of the indexes of FBI and the different Fontaine stages. 1. The quality evaluation results of the image of lower extremity arteries from the 44 diabetic patients indicated no statistically significant difference between FBI and CE-MRA in the patients with Fontaine stage I-III (p >0.05). However, a statistically significant difference was observed in the patients with Fontaine stage IV (p <0.05), and the quality of FBI was slightly worse. 2. Arterial branches that observed from FBI and CE-MRA were 885 and 904, respectively. There was no statistically significant difference for the arterial branches between FBI and CE-MRA in the patients with Fontaine stage I-III (p >0.05). However, a statistically significant difference was observed in the patients with Fontaine stage IV (p <0.05), and CE-MRA indicated more artery branches than FBI. 3. There was a statistically significant difference for the evaluation of venous contamination between FBI and CE-MRA (p <0.05), and there was less venous contamination using FBI. 4. The study results indicated that with Fontaine stages going on the FBI's image quality and arterial branches reduced gradually, and the degree of tissue interference and arteriostenosis was rising gradually. The results of this study indicated that using FBI in lower extremity PAD of diabetics had good quality and high diagnostic accurancy, and the tissue contamination (veins and soft tissues of calf) was effectively avoided. Especially in Fontaine stage I-III, FBI can be used as an alternative technique of CE-MRA, and it also can be used in diabetic patients with renal impairment in Fontaine IV.

Label-free monitoring of inflammatory tissue conditions using a carrageenan-induced acute inflammation rat model.

PubMed

Lee, Seung Ho; Lee, Sang Hwa; Shin, Jae-Ho; Choi, Samjin

2018-06-01

Although the confirmation of inflammatory changes within tissues at the onset of various diseases is critical for the early detection of disease and selection of appropriate treatment, most therapies are based on complex and time-consuming diagnostic procedures. Raman spectroscopy has the ability to provide non-invasive, real-time, chemical bonding analysis through the inelastic scattering of photons. In this study, we evaluate the feasibility of Raman spectroscopy as a new, easy, fast, and accurate diagnostic method to support diagnostic decisions. The molecular changes in carrageenan-induced acute inflammation rat tissues were assessed by Raman spectroscopy. Volumes of 0 (control), 100, 150, and 200 µL of 1% carrageenan were administered to rat hind paws to control the degree of inflammation. The prominent peaks at [1,062, 1,131] cm -1 and [2,847, 2,881] cm -1 were selected as characteristic measurements corresponding to the C-C stretching vibrational modes and the symmetric and asymmetric C-H (CH 2 ) stretching vibrational modes, respectively. Principal component analysis of the inflammatory Raman spectra enabled graphical representation of the degree of inflammation through principal component loading profiles of inflammatory tissues on a two-dimensional plot. Therefore, Raman spectroscopy with multivariate statistical analysis represents a promising method for detecting biomolecular responses based on different types of inflammatory tissues. © 2018 Wiley Periodicals, Inc.

Expression analysis of URI/RMP gene in endometrioid adenocarcinoma by tissue microarray immunohistochemistry.

PubMed

Gu, Junxia; Liang, Yuting; Qiao, Longwei; Li, Xiaoyun; Li, Xingang; Lu, Yaojuan; Zheng, Qiping

2013-01-01

Multiple studies have recently demonstrated the oncogenic property of URI (or RMP, a member of the prefoldin family of molecular chaperones) during progression of hepatocellular carcinoma, ovarian cancer, and possibly prostate cancer. Most recently, we have shown that URI/RMP is up-regulated in cervical cancer, another reproductive system tumor beside ovarian and prostate cancers. To investigate if URI/RMP also plays a role in other reproductive system tumors, especially in endometrioid adenocarcinoma, we analyzed URI/RMP expression in a TMA (tissue microarray) containing tissues from 30 cases of endometrioid adenocarcinoma (which covers tumor tissues from Grade I through Grade III) and adjacent endometrium by immunohistochemistry (IHC) and densitometry analysis using image-pro plus 6.0 software. Our results showed that the mean density of URI/RMP expression in cancerous tissue is slightly higher than that of the adjacent endometrial tissue, though not statistically significant (p>0.05). There is no significant difference either between the mean density of Grade III cancerous tissue and that of Grade I and II cancers. Notably, we detected significantly higher signal intensity in cancerous tissue of all 7 Grade III cases than that of their adjacent endometrial tissue (p<0.05), suggesting a correlation of URI/RMP expression with the differentiation and pathological classification of endometrioid adenocarcinoma. Together, our results demonstrate the heterogeneous expression of URI/RMP in endometrioid adenocarcinoma. The higher level of URI/RMP expression in high-grade endometrioid adenocarcinomas compared to tissues of adjacent endometrium or gland suggests a diagnostic and possibly, a prognostic value of URI/RMP in endometrioid adenocarcinoma.

Expression analysis of URI/RMP gene in endometrioid adenocarcinoma by tissue microarray immunohistochemistry

PubMed Central

Gu, Junxia; Liang, Yuting; Qiao, Longwei; Li, Xiaoyun; Li, Xingang; Lu, Yaojuan; Zheng, Qiping

2013-01-01

Multiple studies have recently demonstrated the oncogenic property of URI (or RMP, a member of the prefoldin family of molecular chaperones) during progression of hepatocellular carcinoma, ovarian cancer, and possibly prostate cancer. Most recently, we have shown that URI/RMP is up-regulated in cervical cancer, another reproductive system tumor beside ovarian and prostate cancers. To investigate if URI/RMP also plays a role in other reproductive system tumors, especially in endometrioid adenocarcinoma, we analyzed URI/RMP expression in a TMA (tissue microarray) containing tissues from 30 cases of endometrioid adenocarcinoma (which covers tumor tissues from Grade I through Grade III) and adjacent endometrium by immunohistochemistry (IHC) and densitometry analysis using image-pro plus 6.0 software. Our results showed that the mean density of URI/RMP expression in cancerous tissue is slightly higher than that of the adjacent endometrial tissue, though not statistically significant (p>0.05). There is no significant difference either between the mean density of Grade III cancerous tissue and that of Grade I and II cancers. Notably, we detected significantly higher signal intensity in cancerous tissue of all 7 Grade III cases than that of their adjacent endometrial tissue (p<0.05), suggesting a correlation of URI/RMP expression with the differentiation and pathological classification of endometrioid adenocarcinoma. Together, our results demonstrate the heterogeneous expression of URI/RMP in endometrioid adenocarcinoma. The higher level of URI/RMP expression in high-grade endometrioid adenocarcinomas compared to tissues of adjacent endometrium or gland suggests a diagnostic and possibly, a prognostic value of URI/RMP in endometrioid adenocarcinoma. PMID:24228101

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

PubMed Central

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

2012-01-01

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

Cartilaginous Metabolomic Study Reveals Potential Mechanisms of Osteophyte Formation in Osteoarthritis.

PubMed

Xu, Zhongwei; Chen, Tingmei; Luo, Jiao; Ding, Shijia; Gao, Sichuan; Zhang, Jian

2017-04-07

Osteophyte is one of the inevitable consequences of progressive osteoarthritis with the main characteristics of cartilage degeneration and endochondral ossification. The pathogenesis of osteophyte formation is not fully understood to date. In this work, metabolomic approaches were employed to explore potential mechanisms of osteophyte formation by detecting metabolic variations between extracts of osteophyte cartilage tissues (n = 32) and uninvolved control cartilage tissues (n = 34), based on the platform of ultraperformance liquid chromatography tandem quadrupole time-of-flight mass spectrometry, as well as the use of multivariate statistic analysis and univariate statistic analysis. The osteophyte group was significantly separated from the control group by the orthogonal partial least-squares discriminant analysis models, indicating that metabolic state of osteophyte cartilage had been changed. In total, 28 metabolic variations further validated by mass spectrum (MS) match, tandom mass spectrum (MS/MS) match, and standards match mainly included amino acids, sulfonic acids, glycerophospholipids, and fatty acyls. These metabolites were related to some specific physiological or pathological processes (collagen dissolution, boundary layers destroyed, self-restoration triggered, etc.) which might be associated with the procedure of osteophyte formation. Pathway analysis showed phenylalanine metabolism (PI = 0.168, p = 0.004) was highly correlative to this degenerative process. Our findings provided a direction for targeted metabolomic study and an insight into further reveal the molecular mechanisms of ostophyte formation.

Nondestructive tissue analysis for ex vivo and in vivo cancer diagnosis using a handheld mass spectrometry system

PubMed Central

Zhang, Jialing; Rector, John; Lin, John Q.; Young, Jonathan H.; Sans, Marta; Katta, Nitesh; Giese, Noah; Yu, Wendong; Nagi, Chandandeep; Suliburk, James; Liu, Jinsong; Bensussan, Alena; DeHoog, Rachel J.; Garza, Kyana Y.; Ludolph, Benjamin; Sorace, Anna G.; Syed, Anum; Zahedivash, Aydin; Milner, Thomas E.; Eberlin, Livia S.

2018-01-01

Conventional methods for histopathologic tissue diagnosis are labor- and time-intensive and can delay decision-making during diagnostic and therapeutic procedures. We report the development of an automated and biocompatible handheld mass spectrometry device for rapid and nondestructive diagnosis of human cancer tissues. The device, named MasSpec Pen, enables controlled and automated delivery of a discrete water droplet to a tissue surface for efficient extraction of biomolecules. We used the MasSpec Pen for ex vivo molecular analysis of 20 human cancer thin tissue sections and 253 human patient tissue samples including normal and cancerous tissues from breast, lung, thyroid, and ovary. The mass spectra obtained presented rich molecular profiles characterized by a variety of potential cancer biomarkers identified as metabolites, lipids, and proteins. Statistical classifiers built from the histologically validated molecular database allowed cancer prediction with high sensitivity (96.4%), specificity (96.2%), and overall accuracy (96.3%), as well as prediction of benign and malignant thyroid tumors and different histologic subtypes of lung cancer. Notably, our classifier allowed accurate diagnosis of cancer in marginal tumor regions presenting mixed histologic composition. Last, we demonstrate that the MasSpec Pen is suited for in vivo cancer diagnosis during surgery performed in tumor-bearing mouse models, without causing any observable tissue harm or stress to the animal. Our results provide evidence that the MasSpec Pen could potentially be used as a clinical and intraoperative technology for ex vivo and in vivo cancer diagnosis. PMID:28878011

Software phantom with realistic speckle modeling for validation of image analysis methods in echocardiography

NASA Astrophysics Data System (ADS)

Law, Yuen C.; Tenbrinck, Daniel; Jiang, Xiaoyi; Kuhlen, Torsten

2014-03-01

Computer-assisted processing and interpretation of medical ultrasound images is one of the most challenging tasks within image analysis. Physical phenomena in ultrasonographic images, e.g., the characteristic speckle noise and shadowing effects, make the majority of standard methods from image analysis non optimal. Furthermore, validation of adapted computer vision methods proves to be difficult due to missing ground truth information. There is no widely accepted software phantom in the community and existing software phantoms are not exible enough to support the use of specific speckle models for different tissue types, e.g., muscle and fat tissue. In this work we propose an anatomical software phantom with a realistic speckle pattern simulation to _ll this gap and provide a exible tool for validation purposes in medical ultrasound image analysis. We discuss the generation of speckle patterns and perform statistical analysis of the simulated textures to obtain quantitative measures of the realism and accuracy regarding the resulting textures.

Non-Immunogenic Structurally and Biologically Intact Tissue Matrix Grafts for the Immediate Repair of Ballistic-Induced Vascular and Nerve Tissue Injury in Combat Casualty Care

DTIC Science & Technology

2005-07-01

as an access graft is addressed using statistical methods below. Graft consistency can be defined statistically as the variance associated with the...addressed using statistical methods below. Graft consistency can be defined statistically as the variance associated with the sample of grafts tested in...measured using a refractometer (Brix % method). The equilibration data are shown in Graph 1. The results suggest the following equilibration scheme: 40% v/v

Subperiosteal preparation using a new piezoelectric device: a histological examination.

PubMed

Stoetzer, Marcus; Magel, Anja; Kampmann, Andreas; Lemound, Juliana; Gellrich, Nils-Claudius; von See, Constantin

2014-01-01

Subperiosteal preparation using a periosteal elevator leads to disturbances of local immunohistochemistry and periosteal histology due to a microtrauma. Usually soft-tissue damage can be considerably reduced by using piezoelectric technology. For this reason, the effects of a novel piezoelectric device on immunohistochemistry and periosteal histology were examined and compared to conventional preparation of the periosteum using a periosteal elevator. Lewis rats were randomly assigned to one of five groups (n=50). Subperiosteal preparation was performed using either a piezoelectric device or a periosteal elevator. Immunohistochemical and histological analyses were performed immediately after preparation as well as three and eight days postoperatively. A statistical analysis of the histological colouring was performed offline using analysis of variance (ANOVA) on ranks (p<0.05). At all times, immunohistochemical and histological analysis demonstrated a significantly more homogenous tissue structure in the group of rats that underwent piezosurgery than in the group of rats that underwent treatment with a periosteal elevator. The use of a piezoelectric device for subperiosteal preparation is associated with more harmonious immunohistochemical and histological results for the periosteum than the use of a conventional periosteal elevator. As a result, piezoelectric devices can be expected to have a positive effect primarily on soft tissue, in particular of the periosteal as well as on surrounding tissues.

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PubMed Central

Galfalvy, Hanga C; Erraji-Benchekroun, Loubna; Smyrniotopoulos, Peggy; Pavlidis, Paul; Ellis, Steven P; Mann, J John; Sibille, Etienne; Arango, Victoria

2003-01-01

Background Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods. Results Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA]), to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression. Conclusion In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex, supporting the notion of a putative direct role of sex-chromosome genes in differentiation and maintenance of sexual dimorphism of the central nervous system. Importantly, these analytical approaches are applicable to all microarray studies that include male and female human or animal subjects. PMID:12962547

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PubMed

Galfalvy, Hanga C; Erraji-Benchekroun, Loubna; Smyrniotopoulos, Peggy; Pavlidis, Paul; Ellis, Steven P; Mann, J John; Sibille, Etienne; Arango, Victoria

2003-09-08

Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods. Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA]), to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression. In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex, supporting the notion of a putative direct role of sex-chromosome genes in differentiation and maintenance of sexual dimorphism of the central nervous system. Importantly, these analytical approaches are applicable to all microarray studies that include male and female human or animal subjects.

Quantitative photoacoustic assessment of ex-vivo lymph nodes of colorectal cancer patients

NASA Astrophysics Data System (ADS)

Sampathkumar, Ashwin; Mamou, Jonathan; Saegusa-Beercroft, Emi; Chitnis, Parag V.; Machi, Junji; Feleppa, Ernest J.

2015-03-01

Staging of cancers and selection of appropriate treatment requires histological examination of multiple dissected lymph nodes (LNs) per patient, so that a staggering number of nodes require histopathological examination, and the finite resources of pathology facilities create a severe processing bottleneck. Histologically examining the entire 3D volume of every dissected node is not feasible, and therefore, only the central region of each node is examined histologically, which results in severe sampling limitations. In this work, we assess the feasibility of using quantitative photoacoustics (QPA) to overcome the limitations imposed by current procedures and eliminate the resulting under sampling in node assessments. QPA is emerging as a new hybrid modality that assesses tissue properties and classifies tissue type based on multiple estimates derived from spectrum analysis of photoacoustic (PA) radiofrequency (RF) data and from statistical analysis of envelope-signal data derived from the RF signals. Our study seeks to use QPA to distinguish cancerous from non-cancerous regions of dissected LNs and hence serve as a reliable means of imaging and detecting small but clinically significant cancerous foci that would be missed by current methods. Dissected lymph nodes were placed in a water bath and PA signals were generated using a wavelength-tunable (680-950 nm) laser. A 26-MHz, f-2 transducer was used to sense the PA signals. We present an overview of our experimental setup; provide a statistical analysis of multi-wavelength classification parameters (mid-band fit, slope, intercept) obtained from the PA signal spectrum generated in the LNs; and compare QPA performance with our established quantitative ultrasound (QUS) techniques in distinguishing metastatic from non-cancerous tissue in dissected LNs. QPA-QUS methods offer a novel general means of tissue typing and evaluation in a broad range of disease-assessment applications, e.g., cardiac, intravascular, musculoskeletal, endocrine-gland, etc.

Trend Analysis of Organ and Tissue Donation for Transplantation.

PubMed

Dos Santos, M J; Leal de Moraes, E; Santini Martins, M; Carlos de Almeida, E; Borges de Barros E Silva, L; Urias, V; Silvano Corrêa Pacheco Furtado, M C; Brito Nunes, Á; El Hage, S

2018-03-01

The goal of this study was to identify the tendency toward donations of tissue and organs from donors with brain death between 2001 and 2016 as registered by an organ procurement organization in São Paulo City. This quantitative, retrospective, exploratory study encompassed all Tissue and Organ Donation Terms signed between 2001 and 2016. A logistic regression model was applied to verify whether there was an upward or downward trend in donation. After statistical analysis, a significant change trend was identified in skin, bones, valve, vessel, heart, lung, and pancreas donations, indicating an increase in the donation rate through the years. The donation rate did not show changes over the years for donations of liver, kidneys, and corneas. The decision-making process regarding organ and tissue donation is restricted not only to the dilemma of whether to donate but another question then arises as well: which organs and tissues are to be donated? The discrepancy between the authorization for organ donation and the authorization for tissue donation, as well as the option for one or another organ and/or tissue, must be thoroughly examined because these factors directly affect the number of transplants and acquirements effectively accomplished. These factors may be related to explaining to one's relatives aspects of the surgery, body reassembling, and usage of such organs and/or tissues. They may also be related to the lack of knowledge concerning organ donation and the symbolism represented by the organ and/or tissue, among other factors. Copyright © 2018 Elsevier Inc. All rights reserved.

Effect of intravenous gadolinium-DTPA on diffusion-weighted imaging of brain tumors: a short temporal interval assessment.

PubMed

Li, Xiang; Qu, Jin-Rong; Luo, Jun-Peng; Li, Jing; Zhang, Hong-Kai; Shao, Nan-Nan; Kwok, Keith; Zhang, Shou-Ning; Li, Yan-le; Liu, Cui-Cui; Zee, Chi-Shing; Li, Hai-Liang

2014-09-01

To determine the effect of intravenous administration of gadolinium (Gd) contrast medium (Gd-DTPA) on diffusion-weighted imaging (DWI) for the evaluation of normal brain parenchyma vs. brain tumor following a short temporal interval. Forty-four DWI studies using b values of 0 and 1000 s/mm(2) were performed before, immediately after, 1 min after, 3 min after, and 5 min after the administration of Gd-DTPA on 62 separate lesions including 15 meningioma, 17 glioma and 30 metastatic lesions. The signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and apparent diffusion coefficient (ADC) values of the brain tumor lesions and normal brain tissues were measured on pre- and postcontrast images. Statistical analysis using paired t-test between precontrast and postcontrast data were obtained on three brain tumors and normal brain tissue. The SNR and CNR of brain tumors and the SNR of normal brain tissue showed no statistical differences between pre- and postcontrast (P > 0.05). The ADC values on the three cases of brain tumors demonstrated significant initial increase on the immediate time point (P < 0.01) and decrease on following the 1 min time point (P < 0.01) after contrast. Significant decrease of ADC value was still found at 3min and 5min time point in the meningioma group (P < 0.01) with gradual normalization over time. The ADC values of normal brain tissues demonstrated significant initial elevation on the immediately postcontrast DWI sequence (P < 0.01). Contrast medium can cause a slight but statistically significant change on the ADC value within a short temporal interval after the contrast administration. The effect is both time and lesion-type dependent. © 2013 Wiley Periodicals, Inc.

A comparative clinical study of the efficacy of subepithelial connective tissue graft and acellular dermal matrix graft in root coverage: 6-month follow-up observation

PubMed Central

Thomas, Libby John; Emmadi, Pamela; Thyagarajan, Ramakrishnan; Namasivayam, Ambalavanan

2013-01-01

Aims: The purpose of this study was to compare the clinical efficacy of subepithelial connective tissue graft and acellular dermal matrix graft associated with coronally repositioned flap in the treatment of Miller's class I and II gingival recession, 6 months postoperatively. Settings and Design: Ten patients with bilateral Miller's class I or class II gingival recession were randomly divided into two groups using a split-mouth study design. Materials and Methods: Group I (10 sites) was treated with subepithelial connective tissue graft along with coronally repositioned flap and Group II (10 sites) treated with acellular dermal matrix graft along with coronally repositioned flap. Clinical parameters like recession height and width, probing pocket depth, clinical attachment level, and width of keratinized gingiva were evaluated at baseline, 90th day, and 180th day for both groups. The percentage of root coverage was calculated based on the comparison of the recession height from 0 to 180th day in both Groups I and II. Statistical Analysis Used: Intragroup parameters at different time points were measured using the Wilcoxon signed rank test and Mann–Whitney U test was employed to analyze the differences between test and control groups. Results: There was no statistically significant difference in recession height and width, gain in CAL, and increase in the width of keratinized gingiva between the two groups on the 180th day. Both procedures showed clinically and statistically significant root coverage (Group I 96%, Group II 89.1%) on the 180th day. Conclusions: The results indicate that coverage of denuded root with both subepithelial connective tissue autograft and acellular dermal matrix allograft are very predictable procedures, which were stable for 6 months postoperatively. PMID:24174728

Morphological and biochemical examination of Cosmos 1887 rat heart tissue. Part 1: Ultrastructure

NASA Technical Reports Server (NTRS)

Philpott, D. E.; Popova, I. A.; Kato, K.; Stevenson, J.; Miquel, J.; Sapp, W.

1990-01-01

Morphological changes were observed in the left ventricle of rat heart tissue from animals flown on the Cosmos 1887 biosatellite for 12.5 days. These tissues were compared to the synchronous and vivarium control hearts. While many normal myofibrils were observed, others exhibited ultrastructural alterations, i.e., damaged and irregular-shaped mitochondria and generalized myofibrillar edema. Analysis of variance (ANOVA) of the volume density data revealed a statistically significant increase in glycogen and a significant decrease in mitochondria compared to the synchronous and vivarium controls. Point counting indicated an increase in lipid and myeloid bodies and a decrease in microtubules, but these changes were not statistically significant. In addition, the flight animals exhibited some patchy loss of protofibrils (actin and myosin filaments) and some abnormal supercontracted myofibrils that were not seen in the controls. This study was undertaken to gain insight into the mechanistic aspects of cardiac changes in both animals and human beings as a consequence of space travel. Cardiac hypotrophy and fluid shifts have been observed after actual or simulated weightlessness and raise concerns about the functioning of the heart and circulatory system during and after travel in space.

Soy consumption and histopathologic markers in breast tissue using tissue microarrays.

PubMed

Maskarinec, Gertraud; Erber, Eva; Verheus, Martijn; Hernandez, Brenda Y; Killeen, Jeffrey; Cashin, Suzanne; Cline, J Mark

2009-01-01

This study examined the relation of soy intake with hormonal and proliferation markers in benign and malignant breast tissue using tissue microarrays (TMAs). TMAs with up to 4 malignant and 4 benign tissue samples for 268 breast cancer cases were constructed. Soy intake in early life and in adulthood was assessed by questionnaire. The TMAs were stained for estrogen receptor (ER) alpha, ERbeta, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2/neu), proliferating cell nuclear antigen (PCNA), and Ki-67 using standard immunohistochemical methods. Logistic regression was applied for statistical analysis. A higher percentage of women showed positive marker expression in malignant than in benign tissue. With one exception, HER2/neu, no significant associations between soy intake and pathologic markers were observed. Early life soy intake was associated with lower HER2/neu and PCNA staining of malignant tissue. In benign tissue, early life soy intake showed higher ER and PR expression, but no difference in proliferation markers. The results of this investigation provide some assurance that soy intake does not adversely affect markers of proliferation. TMAs were shown to be a useful tool for epidemiologic research.

The effect of silymarin on hepatic regeneration after partial hepatectomy: is silymarin effective in hepatic regeneration?

PubMed Central

Cetinkunar, Suleyman; Tokgoz, Serhat; Bilgin, Bulent Caglar; Erdem, Hasan; Aktimur, Recep; Can, Serpil; Erol, Huseyin Serkan; Isgoren, Atilla; Sozen, Selim; Polat, Yilmaz

2015-01-01

Aim: Silymarin from Silybum marianum was found to reduce liver injury. The aim of the present study was to investigate the effects of silymarin on hepatic regeneration in partially hepatectomized rats. Methods: Thirty Wistar-Albino rats were divided into 3 groups of 10 animals as sham, control and experimental groups. In the sham group (n=10) abdominal incision was closed after laparotomy. In the control group (n=10), the rats underwent 70% hepatectomy after laparotomy. In the experimental group (n=10) after partial 70% hepatectomy, silymarin (200 mg/kg/d) were given to rats for 10 days. Rats in three groups were sacrificed on 10 days. Aspartate (AST) and alanine transaminase (ALT), gamma glutamyl transferase (GGT), ALP, LDH and total bilirubin levels were measured using intracardiac blood samples. Tissue malondialdehyde (MDA) and tissue glutathion (GSH) and Superoxide dismutase (SOD) levels were measured. To reveal the increase in the mass of the remnant liver tissue in the control and experimental groups relative weight of the liver was calculated. Histopathological analysis of the liver was performed using a semi-quantitative scoring system. Results: A statistically significant difference among three groups was not shown for AST and ALT levels. A statistically significant difference was found between the groups as for total bilirubin and gamma glutamyl transferase levels. Increases in relative liver weights were seen with time in Groups 2 and 3. A statistically significant difference was not found for tissue malondialdehyde, Glutathion and Superoxide dismutase levels between hepatectomy and hepatectomy + silymarin groups. On liver tissue sections of the rats in the hepatectomy + silymarin group, increased regeneration and lipid peroxidation were observed accompanied by decreased antioxidant response. Conclusion: It has been observed that silymarin with many established functions such as antiproliferative, anti-inflammatory and energy antioxidant effects, does not contributed to proliferative regeneration of the liver-which has very important metabolic functions -after partial hepatectomy; instead it will decrease serum levels of transaminases. PMID:25932204

A large-scale study of the ultrawideband microwave dielectric properties of normal breast tissue obtained from reduction surgeries.

PubMed

Lazebnik, Mariya; McCartney, Leah; Popovic, Dijana; Watkins, Cynthia B; Lindstrom, Mary J; Harter, Josephine; Sewall, Sarah; Magliocco, Anthony; Booske, John H; Okoniewski, Michal; Hagness, Susan C

2007-05-21

The efficacy of emerging microwave breast cancer detection and treatment techniques will depend, in part, on the dielectric properties of normal breast tissue. However, knowledge of these properties at microwave frequencies has been limited due to gaps and discrepancies in previously reported small-scale studies. To address these issues, we experimentally characterized the wideband microwave-frequency dielectric properties of a large number of normal breast tissue samples obtained from breast reduction surgeries at the University of Wisconsin and University of Calgary hospitals. The dielectric spectroscopy measurements were conducted from 0.5 to 20 GHz using a precision open-ended coaxial probe. The tissue composition within the probe's sensing region was quantified in terms of percentages of adipose, fibroconnective and glandular tissues. We fit a one-pole Cole-Cole model to the complex permittivity data set obtained for each sample and determined median Cole-Cole parameters for three groups of normal breast tissues, categorized by adipose tissue content (0-30%, 31-84% and 85-100%). Our analysis of the dielectric properties data for 354 tissue samples reveals that there is a large variation in the dielectric properties of normal breast tissue due to substantial tissue heterogeneity. We observed no statistically significant difference between the within-patient and between-patient variability in the dielectric properties.

Long-term outcomes of tissue-based ACTH-antibody assay-guided transsphenoidal resection of pituitary adenomas in Cushing disease.

PubMed

Erfe, J Mark; Perry, Avital; McClaskey, John; Inzucchi, Silvio E; James, Whitney Sheen; Eid, Tore; Bronen, Richard A; Mahajan, Amit; Huttner, Anita; Santos, Florecita; Spencer, Dennis

2017-10-13

OBJECTIVE Cushing disease is caused by a pituitary micro- or macroadenoma that hypersecretes adrenocorticotropic hormone (ACTH), resulting in hypercortisolemia. For decades, transsphenoidal resection (TSR) has been an efficacious treatment but with certain limitations, namely precise tumor localization and complete excision. The authors evaluated the novel use of a double-antibody sandwich assay for the real-time quantitation of ACTH in resected pituitary specimens with the goals of augmenting pathological diagnosis and ultimately improving long-term patient outcome. METHODS This study involved a retrospective review of records and an analysis of assay values, pathology slides, and MRI studies of patients with Cushing disease who had undergone TSR in the period from 2009 to 2014 and had at least 1 year of follow-up in coordination with an endocrinologist. In the operating room, biopsy specimens from the patients had been analyzed for tissue ACTH concentration. Additional samples were simultaneously sent for frozen-section pathological analysis. The ACTH assay performance was compared against pathology assessments of surgical tumor samples using receiver operating characteristic (ROC) analysis and against pre- and postoperative MRI studies. RESULTS Fourteen patients underwent TSR with guidance by ACTH-antibody assay and pathological assessment of 127 biopsy samples and were followed up for an average of 3 years. The ACTH threshold for discriminating adenomatous from normal tissue was 290,000 pg/mg of tissue, based on jointly maximized sensitivity (95.0%) and specificity (71.3%). Lateralization discordance between preoperative MRI studies and surgical visualization was noted in 3 patients, confirming the impression that MRI alone may not achieve optimal localization. A majority of the patients (85.7%) attained long-term disease remission based on urinary free cortisol levels, plasma cortisol levels, and long-term corticosteroid therapy. Comparisons of patient-months of remission and treatment failure showed that the remission rate in the study sample statistically exceeds the rate in historical controls (71.9%; p = 0.0007, Fisher's exact test). Long-term unexpected hormonal deficiencies were statistically similar between study patients (29%) and those in a meta-analysis (25%; p = 0.7596, Fisher's exact test). CONCLUSIONS These preliminary findings reflect the promising potential of tissue-based ACTH-antibody-guided assay for improving the cure rates of Cushing disease patients undergoing TSR. Further studies with larger sample sizes, further refinements of assay interpretation, and longer-term follow-ups are needed.

[Tissue engineered bone scaffold material in restoration of alveolar socket after extraction of lower impacted third molar].

PubMed

Chen, Zhi-fang

2011-02-01

To investigate the effects of tissue engineered bone scaffold material in the restoration of alveolar socket after extraction of lower impacted third molar. Thirteen patients were immediately implanted with Bio-oss or PerioGlas® in the alveolar cavity after impacted mandibular third molar extraction. Clinical observation and X-ray were taken 1 to 12 weeks after operation. Paired t test was used for statistical analysis by SPSS10.0 software package. Thirteen patients did not experience postoperative complications. The distal alveolar height of the second molar and the gingival attachment did decrease significantly 1 to 12 weeks after operation(P < 0.05). Tissue engineered bone scaffold material is helpful in the restoration of alveolar socket after impacted third molar extraction.

A comparison study of different facial soft tissue analysis methods.

PubMed

Kook, Min-Suk; Jung, Seunggon; Park, Hong-Ju; Oh, Hee-Kyun; Ryu, Sun-Youl; Cho, Jin-Hyoung; Lee, Jae-Seo; Yoon, Suk-Ja; Kim, Min-Soo; Shin, Hyo-Keun

2014-07-01

The purpose of this study was to evaluate several different facial soft tissue measurement methods. After marking 15 landmarks in the facial area of 12 mannequin heads of different sizes and shapes, facial soft tissue measurements were performed by the following 5 methods: Direct anthropometry, Digitizer, 3D CT, 3D scanner, and DI3D system. With these measurement methods, 10 measurement values representing the facial width, height, and depth were determined twice with a one week interval by one examiner. These data were analyzed with the SPSS program. The position created based on multi-dimensional scaling showed that direct anthropometry, 3D CT, digitizer, 3D scanner demonstrated relatively similar values, while the DI3D system showed slightly different values. All 5 methods demonstrated good accuracy and had a high coefficient of reliability (>0.92) and a low technical error (<0.9 mm). The measured value of the distance between the right and left medial canthus obtained by using the DI3D system was statistically significantly different from that obtained by using the digital caliper, digitizer and laser scanner (p < 0.05), but the other measured values were not significantly different. On evaluating the reproducibility of measurement methods, two measurement values (Ls-Li, G-Pg) obtained by using direct anthropometry, one measurement value (N'-Prn) obtained by using the digitizer, and four measurement values (EnRt-EnLt, AlaRt-AlaLt, ChRt-ChLt, Sn-Pg) obtained by using the DI3D system, were statistically significantly different. However, the mean measurement error in every measurement method was low (<0.7 mm). All measurement values obtained by using the 3D CT and 3D scanner did not show any statistically significant difference. The results of this study show that all 3D facial soft tissue analysis methods demonstrate favorable accuracy and reproducibility, and hence they can be used in clinical practice and research studies. Copyright © 2013 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Near-infrared Raman spectroscopy for estimating biochemical changes associated with different pathological conditions of cervix

NASA Astrophysics Data System (ADS)

Daniel, Amuthachelvi; Prakasarao, Aruna; Ganesan, Singaravelu

2018-02-01

The molecular level changes associated with oncogenesis precede the morphological changes in cells and tissues. Hence molecular level diagnosis would promote early diagnosis of the disease. Raman spectroscopy is capable of providing specific spectral signature of various biomolecules present in the cells and tissues under various pathological conditions. The aim of this work is to develop a non-linear multi-class statistical methodology for discrimination of normal, neoplastic and malignant cells/tissues. The tissues were classified as normal, pre-malignant and malignant by employing Principal Component Analysis followed by Artificial Neural Network (PC-ANN). The overall accuracy achieved was 99%. Further, to get an insight into the quantitative biochemical composition of the normal, neoplastic and malignant tissues, a linear combination of the major biochemicals by non-negative least squares technique was fit to the measured Raman spectra of the tissues. This technique confirms the changes in the major biomolecules such as lipids, nucleic acids, actin, glycogen and collagen associated with the different pathological conditions. To study the efficacy of this technique in comparison with histopathology, we have utilized Principal Component followed by Linear Discriminant Analysis (PC-LDA) to discriminate the well differentiated, moderately differentiated and poorly differentiated squamous cell carcinoma with an accuracy of 94.0%. And the results demonstrated that Raman spectroscopy has the potential to complement the good old technique of histopathology.

Efficient Cancer Detection Using Multiple Neural Networks.

PubMed

Shell, John; Gregory, William D

2017-01-01

The inspection of live excised tissue specimens to ascertain malignancy is a challenging task in dermatopathology and generally in histopathology. We introduce a portable desktop prototype device that provides highly accurate neural network classification of malignant and benign tissue. The handheld device collects 47 impedance data samples from 1 Hz to 32 MHz via tetrapolar blackened platinum electrodes. The data analysis was implemented with six different backpropagation neural networks (BNN). A data set consisting of 180 malignant and 180 benign breast tissue data files in an approved IRB study at the Aurora Medical Center, Milwaukee, WI, USA, were utilized as a neural network input. The BNN structure consisted of a multi-tiered consensus approach autonomously selecting four of six neural networks to determine a malignant or benign classification. The BNN analysis was then compared with the histology results with consistent sensitivity of 100% and a specificity of 100%. This implementation successfully relied solely on statistical variation between the benign and malignant impedance data and intricate neural network configuration. This device and BNN implementation provides a novel approach that could be a valuable tool to augment current medical practice assessment of the health of breast, squamous, and basal cell carcinoma and other excised tissue without requisite tissue specimen expertise. It has the potential to provide clinical management personnel with a fast non-invasive accurate assessment of biopsied or sectioned excised tissue in various clinical settings.

Efficient Cancer Detection Using Multiple Neural Networks

PubMed Central

Gregory, William D.

2017-01-01

The inspection of live excised tissue specimens to ascertain malignancy is a challenging task in dermatopathology and generally in histopathology. We introduce a portable desktop prototype device that provides highly accurate neural network classification of malignant and benign tissue. The handheld device collects 47 impedance data samples from 1 Hz to 32 MHz via tetrapolar blackened platinum electrodes. The data analysis was implemented with six different backpropagation neural networks (BNN). A data set consisting of 180 malignant and 180 benign breast tissue data files in an approved IRB study at the Aurora Medical Center, Milwaukee, WI, USA, were utilized as a neural network input. The BNN structure consisted of a multi-tiered consensus approach autonomously selecting four of six neural networks to determine a malignant or benign classification. The BNN analysis was then compared with the histology results with consistent sensitivity of 100% and a specificity of 100%. This implementation successfully relied solely on statistical variation between the benign and malignant impedance data and intricate neural network configuration. This device and BNN implementation provides a novel approach that could be a valuable tool to augment current medical practice assessment of the health of breast, squamous, and basal cell carcinoma and other excised tissue without requisite tissue specimen expertise. It has the potential to provide clinical management personnel with a fast non-invasive accurate assessment of biopsied or sectioned excised tissue in various clinical settings. PMID:29282435

Infrared spectral imaging as a novel approach for histopathological recognition in colon cancer diagnosis

NASA Astrophysics Data System (ADS)

Nallala, Jayakrupakar; Gobinet, Cyril; Diebold, Marie-Danièle; Untereiner, Valérie; Bouché, Olivier; Manfait, Michel; Sockalingum, Ganesh Dhruvananda; Piot, Olivier

2012-11-01

Innovative diagnostic methods are the need of the hour that could complement conventional histopathology for cancer diagnosis. In this perspective, we propose a new concept based on spectral histopathology, using IR spectral micro-imaging, directly applied to paraffinized colon tissue array stabilized in an agarose matrix without any chemical pre-treatment. In order to correct spectral interferences from paraffin and agarose, a mathematical procedure is implemented. The corrected spectral images are then processed by a multivariate clustering method to automatically recover, on the basis of their intrinsic molecular composition, the main histological classes of the normal and the tumoral colon tissue. The spectral signatures from different histological classes of the colonic tissues are analyzed using statistical methods (Kruskal-Wallis test and principal component analysis) to identify the most discriminant IR features. These features allow characterizing some of the biomolecular alterations associated with malignancy. Thus, via a single analysis, in a label-free and nondestructive manner, main changes associated with nucleotide, carbohydrates, and collagen features can be identified simultaneously between the compared normal and the cancerous tissues. The present study demonstrates the potential of IR spectral imaging as a complementary modern tool, to conventional histopathology, for an objective cancer diagnosis directly from paraffin-embedded tissue arrays.

Uninduced adipose-derived stem cells repair the defect of full-thickness hyaline cartilage.

PubMed

Zhang, Hai-Ning; Li, Lei; Leng, Ping; Wang, Ying-Zhen; Lv, Cheng-Yu

2009-04-01

To testify the effect of the stem cells derived from the widely distributed fat tissue on repairing full-thickness hyaline cartilage defects. Adipose-derived stem cells (ADSCs) were derived from adipose tissue and cultured in vitro. Twenty-seven New Zealand white rabbits were divided into three groups randomly. The cultured ADSCs mixed with calcium alginate gel were used to fill the full-thickness hyaline cartilage defects created at the patellafemoral joint, and the defects repaired with gel or without treatment served as control groups. After 4, 8 and 12 weeks, the reconstructed tissue was evaluated macroscopically and microscopically. Histological analysis and qualitative scoring were also performed to detect the outcome. Full thickness hyaline cartilage defects were repaired completely with ADSCs-derived tissue. The result was better in ADSCs group than the control ones. The microstructure of reconstructed tissue with ADSCs was similar to that of hyaline cartilage and contained more cells and regular matrix fibers, being better than other groups. Plenty of collagen fibers around cells could be seen under transmission electron microscopy. Statistical analysis revealed a significant difference in comparison with other groups at each time point (t equal to 4.360, P less than 0.01). These results indicate that stem cells derived from mature adipose without induction possess the ability to repair cartilage defects.

The lipid-reactive oxygen species phenotype of breast cancer. Raman spectroscopy and mapping, PCA and PLSDA for invasive ductal carcinoma and invasive lobular carcinoma. Molecular tumorigenic mechanisms beyond Warburg effect.

PubMed

Surmacki, Jakub; Brozek-Pluska, Beata; Kordek, Radzislaw; Abramczyk, Halina

2015-04-07

Vibrational signatures of human breast tissue (invasive ductal carcinoma and invasive lobular carcinoma) were used to identify, characterize and discriminate structures in normal (noncancerous) and cancerous tissues by confocal Raman imaging, Raman spectroscopy and IR spectroscopy. The most important differences between normal and cancerous tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives. K-means clustering and basis analysis followed by PCA and PLSDA is employed to analyze Raman spectroscopic maps of human breast tissue and for a statistical analysis of the samples (82 patients, 164 samples). Raman maps successfully identify regions of carotenoids, fatty acids, and proteins. The intensities, frequencies and profiles of the average Raman spectra differentiate the biochemical composition of normal and cancerous tissues. The paper demonstrates that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The sensitivity and specificity obtained directly from PLSLD and cross validation are equal to 90.5% and 84.8% for calibration and 84.7% and 71.9% for cross-validation respectively.

Analysis of energy dispersive x-ray diffraction profiles for material identification, imaging and system control

NASA Astrophysics Data System (ADS)

Cook, Emily Jane

2008-12-01

This thesis presents the analysis of low angle X-ray scatter measurements taken with an energy dispersive system for substance identification, imaging and system control. Diffraction measurements were made on illicit drugs, which have pseudo- crystalline structures and thus produce diffraction patterns comprising a se ries of sharp peaks. Though the diffraction profiles of each drug are visually characteristic, automated detection systems require a substance identification algorithm, and multivariate analysis was selected as suitable. The software was trained with measured diffraction data from 60 samples covering 7 illicit drugs and 5 common cutting agents, collected with a range of statistical qual ities and used to predict the content of 7 unknown samples. In all cases the constituents were identified correctly and the contents predicted to within 15%. Soft tissues exhibit broad peaks in their diffraction patterns. Diffraction data were collected from formalin fixed breast tissue samples and used to gen erate images. Maximum contrast between healthy and suspicious regions was achieved using momentum transfer windows 1.04-1.10 and 1.84-1.90 nm_1. The resulting images had an average contrast of 24.6% and 38.9% compared to the corresponding transmission X-ray images (18.3%). The data was used to simulate the feedback for an adaptive imaging system and the ratio of the aforementioned momentum transfer regions found to be an excellent pa rameter. Investigation into the effects of formalin fixation on human breast tissue and animal tissue equivalents indicated that fixation in standard 10% buffered formalin does not alter the diffraction profiles of tissue in the mo mentum transfer regions examined, though 100% unbuffered formalin affects the profile of porcine muscle tissue (a substitute for glandular and tumourous tissue), though fat is unaffected.

Biochemical and molecular characterization of thyroid tissue by micro-Raman spectroscopy and gene expression analysis

NASA Astrophysics Data System (ADS)

Neto, Lázaro P. M.; Martin, Aírton A.; Soto, Claudio A. T.; Santos, André B. O.; Mello, Evandro S.; Pereira, Marina A.; Cernea, Cláudio R.; Brandão, Lenine G.; Canevari, Renata A.

2016-02-01

Thyroid carcinomas represent the main endocrine malignancy and their diagnosis may produce inconclusive results. Raman spectroscopy and gene expression analysis have shown excellent results on the differentiation of carcinomas. This study aimed to improve the discrimination between different thyroid pathologies combining of both analyses. A total of 35 thyroid tissues samples including normal tissue (n=10), goiter (n=10), papillary (n=10) and follicular carcinomas (n=5) were analyzed. Confocal Raman spectra was obtain by using a Rivers Diagnostic System, 785 nm laser excitation and CCD detector. The data was processed by the software Labspec5 and Origin 8.5 and analyzed by Minitab® program. The gene expression analysis was performed by qRT-PCR technique for TG, TPO, PDGFB, SERPINA1, LGALS3 and TFF3 genes and statistically analyzed by Mann-Whitney test. The confocal Raman spectroscopy allowed a maximum discrimination of 91.1% between normal and tumor tissues, 84.8% between benign and malignant pathologies and 84.6% among carcinomas analyzed. Significant differences was observed for TG, LGALS3, SERPINA1 and TFF3 genes between benign lesions and carcinomas, and SERPINA1 and TFF3 genes between papillary and follicular carcinomas. Principal component analysis was performed using PC1 and PC2 in the papillary carcinoma samples that showed over gene expression when compared with normal sample, where 90% of discrimination was observed at the Amide 1 (1655 cm-1), and at the tyrosine spectra region (856 cm-1). The discrimination of tissues thyroid carried out by confocal Raman spectroscopy and gene expression analysis indicate that these techniques are promising tools to be used in the diagnosis of thyroid lesions.

Epstein-Barr Virus and Gastric Cancer Risk: A Meta-analysis With Meta-regression of Case-control Studies.

PubMed

Bae, Jong-Myon; Kim, Eun Hee

2016-03-01

Research on how the risk of gastric cancer increases with Epstein-Barr virus (EBV) infection is lacking. In a systematic review that investigated studies published until September 2014, the authors did not calculate the summary odds ratio (SOR) due to heterogeneity across studies. Therefore, we include here additional studies published until October 2015 and conduct a meta-analysis with meta-regression that controls for the heterogeneity among studies. Using the studies selected in the previously published systematic review, we formulated lists of references, cited articles, and related articles provided by PubMed. From the lists, only case-control studies that detected EBV in tissue samples were selected. In order to control for the heterogeneity among studies, subgroup analysis and meta-regression were performed. In the 33 case-control results with adjacent non-cancer tissue, the total number of test samples in the case and control groups was 5280 and 4962, respectively. In the 14 case-control results with normal tissue, the total number of test samples in case and control groups was 1393 and 945, respectively. Upon meta-regression, the type of control tissue was found to be a statistically significant variable with regard to heterogeneity. When the control tissue was normal tissue of healthy individuals, the SOR was 3.41 (95% CI, 1.78 to 6.51; I-squared, 65.5%). The results of the present study support the argument that EBV infection increases the risk of gastric cancer. In the future, age-matched and sex-matched case-control studies should be conducted.

A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients

PubMed Central

Zhong, Qing; Guo, Tiannan; Rechsteiner, Markus; Rüschoff, Jan H.; Rupp, Niels; Fankhauser, Christian; Saba, Karim; Mortezavi, Ashkan; Poyet, Cédric; Hermanns, Thomas; Zhu, Yi; Moch, Holger; Aebersold, Ruedi; Wild, Peter J.

2017-01-01

Microscopy image data of human cancers provide detailed phenotypes of spatially and morphologically intact tissues at single-cell resolution, thus complementing large-scale molecular analyses, e.g., next generation sequencing or proteomic profiling. Here we describe a high-resolution tissue microarray (TMA) image dataset from a cohort of 71 prostate tissue samples, which was hybridized with bright-field dual colour chromogenic and silver in situ hybridization probes for the tumour suppressor gene PTEN. These tissue samples were digitized and supplemented with expert annotations, clinical information, statistical models of PTEN genetic status, and computer source codes. For validation, we constructed an additional TMA dataset for 424 prostate tissues, hybridized with FISH probes for PTEN, and performed survival analysis on a subset of 339 radical prostatectomy specimens with overall, disease-specific and recurrence-free survival (maximum 167 months). For application, we further produced 6,036 image patches derived from two whole slides. Our curated collection of prostate cancer data sets provides reuse potential for both biomedical and computational studies. PMID:28291248

Development of Tissue to Total Mass Correction Factor for Porites divaricata in Calcification Rate Studies

NASA Astrophysics Data System (ADS)

Cannone, T. C.; Kelly, S. K.; Foster, K.

2013-05-01

One anticipated result of ocean acidification is lower calcification rates of corals. Many studies currently use the buoyant weights of coral nubbins as a means of estimating skeletal weight during non-destructive experiments. The objectives of this study, conducted at the Little Cayman Research Centre, were twofold: (1) to determine whether the purple and yellow color variations of Porites divaricata had similar tissue mass to total mass ratios; and (2) to determine a correction factor for tissue mass based on the total coral mass. T-test comparisons indicated that the tissue to total mass ratios were statistically similar for purple and yellow cohorts, thus allowing them to be grouped together within a given sample population. Linear regression analysis provided a correction factor (r2 = 0.69) to estimate the tissue mass from the total mass, which may eliminate the need to remove tissue during studies and allow subsequent testing on the same nubbins or their return to the natural environment. Additional work is needed in the development of a correction factor for P. divaricata with a higher prediction accuracy.

Evaluation of fluid absorption during holmium laser enucleation of prostate by breath ethanol technique.

PubMed

Shah, Hemendra N; Kausik, Vikram; Hegde, Sunil; Shah, Jignesh N; Bansal, Manish B

2006-02-01

In a prospective manner we studied various factors affecting fluid absorption during HoLEP. We also simultaneously evaluated changes in serum electrolytes and hemoglobin decrease during HoLEP. This prospective study comprised of 53 patients who underwent HoLEP at our institute. Irrigation fluid was normal saline tagged with ethanol (1% w/v). Intraoperatively a standard breath analyzer was used to monitor expired breath ethanol levels during the procedure at 10-minute intervals. Patients who absorbed irrigating fluid as indicated by positive intraoperative breath tests were considered absorbers. Serum electrolyte and hemoglobin estimations were done before and after surgery. Total irrigation time, amount of irrigation fluid used, weight of resected tissue and presence of capsular perforation were recorded. Statistical analysis was performed to observe the effects of various factors on the amount of intraoperative fluid absorption. Of 53 patients studied 14 (26.41%) demonstrated fluid absorption in the range of 213 to 930 ml (mean 459). Preoperative prostate weight, total irrigation time, amount of irrigation fluid used and resected tissue weight were all significantly greater in absorbers. Similarly, absorbers had a statistically significant decrease in hemoglobin level postoperatively. There was no statistically significant change in serum electrolytes between absorbers and nonabsorbers. Preoperative weight of prostate, total irrigation time, amount of irrigation fluid used and weight of resected tissue all directly influence the amount of fluid absorption during HoLEP. There is no significant change in serum electrolytes and no risk of the transurethral resection syndrome.

Statistical parametric mapping of the regional distribution and ontogenetic scaling of foot pressures during walking in Asian elephants (Elephas maximus).

PubMed

Panagiotopoulou, Olga; Pataky, Todd C; Hill, Zoe; Hutchinson, John R

2012-05-01

Foot pressure distributions during locomotion have causal links with the anatomical and structural configurations of the foot tissues and the mechanics of locomotion. Elephant feet have five toes bound in a flexible pad of fibrous tissue (digital cushion). Does this specialized foot design control peak foot pressures in such giant animals? And how does body size, such as during ontogenetic growth, influence foot pressures? We addressed these questions by studying foot pressure distributions in elephant feet and their correlation with body mass and centre of pressure trajectories, using statistical parametric mapping (SPM), a neuro-imaging technology. Our results show a positive correlation between body mass and peak pressures, with the highest pressures dominated by the distal ends of the lateral toes (digits 3, 4 and 5). We also demonstrate that pressure reduction in the elephant digital cushion is a complex interaction of its viscoelastic tissue structure and its centre of pressure trajectories, because there is a tendency to avoid rear 'heel' contact as an elephant grows. Using SPM, we present a complete map of pressure distributions in elephant feet during ontogeny by performing statistical analysis at the pixel level across the entire plantar/palmar surface. We hope that our study will build confidence in the potential clinical and scaling applications of mammalian foot pressures, given our findings in support of a link between regional peak pressures and pathogenesis in elephant feet.

An investigation into the effects of temporal resolution on hepatic dynamic contrast-enhanced MRI in volunteers and in patients with hepatocellular carcinoma

NASA Astrophysics Data System (ADS)

Gill, Andrew B.; Black, Richard T.; Bowden, David J.; Priest, Andrew N.; Graves, Martin J.; Lomas, David J.

2014-06-01

This study investigated the effect of temporal resolution on the dual-input pharmacokinetic (PK) modelling of dynamic contrast-enhanced MRI (DCE-MRI) data from normal volunteer livers and from patients with hepatocellular carcinoma. Eleven volunteers and five patients were examined at 3 T. Two sections, one optimized for the vascular input functions (VIF) and one for the tissue, were imaged within a single heart-beat (HB) using a saturation-recovery fast gradient echo sequence. The data was analysed using a dual-input single-compartment PK model. The VIFs and/or uptake curves were then temporally sub-sampled (at interval ▵t = [2-20] s) before being subject to the same PK analysis. Statistical comparisons of tumour and normal tissue PK parameter values using a 5% significance level gave rise to the same study results when temporally sub-sampling the VIFs to HB < ▵t <4 s. However, sub-sampling to ▵t > 4 s did adversely affect the statistical comparisons. Temporal sub-sampling of just the liver/tumour tissue uptake curves at ▵t ≤ 20 s, whilst using high temporal resolution VIFs, did not substantially affect PK parameter statistical comparisons. In conclusion, there is no practical advantage to be gained from acquiring very high temporal resolution hepatic DCE-MRI data. Instead the high temporal resolution could be usefully traded for increased spatial resolution or SNR.

Effects of thread size in the implant neck area on peri-implant hard and soft tissues: an animal study.

PubMed

Choi, Jay-Yong; Moon, Ik-Sang; Yun, Jeong-Ho; Park, Kwang-Ho; Huh, Jong-Ki; Lee, Dong-Won

2016-09-01

The aim of this animal study was to examine the effects of thread size in the implant neck area on peri-implant tissues in terms of BIC and hard- and soft-tissue dimensions. Six Beagle dogs received experimental implants in the mandible 3 month after the removal of premolars and first molars (P2, P3, P4, and M1). Two different types of implants were installed in each animal: Anyone microthread(®) as Group 1 and Anyone(®) as Group 2. Resonance frequency test, intraoral radiography, micro-CT, and histomorphometry were used to evaluate peri-implant tissue after implantation periods of 4 and 8 weeks. No remarkable complication was observed during the healing period in either group. Resonance frequency testing revealed no significant difference between groups. In radiographic evaluation, Group 2 showed more bone loss than Group 1. However, this difference was not statistically significant. In the micro-CT analysis, BIC and BIV values and soft-tissue height were not significant in both groups. Histological analysis revealed no significant difference in BIC ratio, bone density, or bone loss between groups. However, soft-tissue height was significantly greater in Group 2 than in Group 1 (P = 0.0004). No difference in peri-implant hard or soft tissues was observed according to thread size in the implant neck area. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Soft tissue volume alterations after connective tissue grafting at teeth: the subepithelial autologous connective tissue graft versus a porcine collagen matrix - a pre-clinical volumetric analysis.

PubMed

Schmitt, Christian M; Matta, Ragai E; Moest, Tobias; Humann, Julia; Gammel, Lisa; Neukam, Friedrich W; Schlegel, Karl A

2016-07-01

This study evaluates a porcine collagen matrix (CM) for soft tissue thickening in comparison to the subepithelial connective tissue graft (SCTG). In eight beagle dogs, soft tissue thickening was performed at the buccal aspects of the upper canines (SCTG and CM). Impressions were taken before augmentation (i1), after surgery (i2), after one (i3), three (i4) and ten month (i5). Casts were optically scanned with a 3D scanner and each augmented region (unit of analysis) evaluated (primary outcome variable: volume increase in mm(3) ; secondary outcome variables: volume increase in percent, mean and maximum thickness increases in mm). 3D tissue measurements after surgery revealed a significant higher volume increase in the CM (86.37 mm(3)  ± 35.16 mm(3) ) than in the SCTG group (47.65 mm(3)  ± 17.90 mm(3) ). After 10 months, volume increase was non-significant between groups (SCTG:11.36 mm(3)  ± 9.26 mm(3) ; CM: 8.67 mm(3)  ± 13.67 mm(3) ). Maximum soft tissue thickness increase (i1-i5) was 0.66 mm ± 0.29 mm (SCTG) and 0.79 mm ± 0.37 mm (CM) with no significant difference. Ten months after soft tissue thickening, the CM is statistically non-inferior to the SCTG in terms of soft tissue volume and thickness increase. Further 3D studies are needed to confirm the data. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Vascular endothelial growth factor (VEGF) expression in locally advanced prostate cancer: secondary analysis of radiation therapy oncology group (RTOG) 8610.

PubMed

Pan, Larry; Baek, Seunghee; Edmonds, Pamela R; Roach, Mack; Wolkov, Harvey; Shah, Satish; Pollack, Alan; Hammond, M Elizabeth; Dicker, Adam P

2013-04-25

Angiogenesis is a key element in solid-tumor growth, invasion, and metastasis. VEGF is among the most potent angiogenic factor thus far detected. The aim of the present study is to explore the potential of VEGF (also known as VEGF-A) as a prognostic and predictive biomarker among men with locally advanced prostate cancer. The analysis was performed using patients enrolled on RTOG 8610, a phase III randomized control trial of radiation therapy alone (Arm 1) versus short-term neoadjuvant and concurrent androgen deprivation and radiation therapy (Arm 2) in men with locally advanced prostate carcinoma. Tissue samples were obtained from the RTOG tissue repository. Hematoxylin and eosin slides were reviewed, and paraffin blocks were immunohistochemically stained for VEGF expression and graded by Intensity score (0-3). Cox or Fine and Gray's proportional hazards models were used. Sufficient pathologic material was available from 103 (23%) of the 456 analyzable patients enrolled in the RTOG 8610 study. There were no statistically significant differences in the pre-treatment characteristics between the patient groups with and without VEGF intensity data. Median follow-up for all surviving patients with VEGF intensity data is 12.2 years. Univariate and multivariate analyses demonstrated no statistically significant correlation between the intensity of VEGF expression and overall survival, distant metastasis, local progression, disease-free survival, or biochemical failure. VEGF expression was also not statistically significantly associated with any of the endpoints when analyzed by treatment arm. This study revealed no statistically significant prognostic or predictive value of VEGF expression for locally advanced prostate cancer. This analysis is among one of the largest sample bases with long-term follow-up in a well-characterized patient population. There is an urgent need to establish multidisciplinary initiatives for coordinating further research in the area of human prostate cancer biomarkers.

Association between pathology and texture features of multi parametric MRI of the prostate

NASA Astrophysics Data System (ADS)

Kuess, Peter; Andrzejewski, Piotr; Nilsson, David; Georg, Petra; Knoth, Johannes; Susani, Martin; Trygg, Johan; Helbich, Thomas H.; Polanec, Stephan H.; Georg, Dietmar; Nyholm, Tufve

2017-10-01

The role of multi-parametric (mp)MRI in the diagnosis and treatment of prostate cancer has increased considerably. An alternative to visual inspection of mpMRI is the evaluation using histogram-based (first order statistics) parameters and textural features (second order statistics). The aims of the present work were to investigate the relationship between benign and malignant sub-volumes of the prostate and textures obtained from mpMR images. The performance of tumor prediction was investigated based on the combination of histogram-based and textural parameters. Subsequently, the relative importance of mpMR images was assessed and the benefit of additional imaging analyzed. Finally, sub-structures based on the PI-RADS classification were investigated as potential regions to automatically detect maligned lesions. Twenty-five patients who received mpMRI prior to radical prostatectomy were included in the study. The imaging protocol included T2, DWI, and DCE. Delineation of tumor regions was performed based on pathological information. First and second order statistics were derived from each structure and for all image modalities. The resulting data were processed with multivariate analysis, using PCA (principal component analysis) and OPLS-DA (orthogonal partial least squares discriminant analysis) for separation of malignant and healthy tissue. PCA showed a clear difference between tumor and healthy regions in the peripheral zone for all investigated images. The predictive ability of the OPLS-DA models increased for all image modalities when first and second order statistics were combined. The predictive value reached a plateau after adding ADC and T2, and did not increase further with the addition of other image information. The present study indicates a distinct difference in the signatures between malign and benign prostate tissue. This is an absolute prerequisite for automatic tumor segmentation, but only the first step in that direction. For the specific identified signature, DCE did not add complementary information to T2 and ADC maps.

Peri-implant soft tissue colour around titanium and zirconia abutments: a prospective randomized controlled clinical study.

PubMed

Cosgarea, Raluca; Gasparik, Cristina; Dudea, Diana; Culic, Bogdan; Dannewitz, Bettina; Sculean, Anton

2015-05-01

To objectively determine the difference in colour between the peri-implant soft tissue at titanium and zirconia abutments. Eleven patients, each with two contralaterally inserted osteointegrated dental implants, were included in this study. The implants were restored either with titanium abutments and porcelain-fused-to-metal crowns, or with zirconia abutments and ceramic crowns. Prior and after crown cementation, multi-spectral images of the peri-implant soft tissues and the gingiva of the neighbouring teeth were taken with a colorimeter. The colour parameters L*, a*, b*, c* and the colour differences ΔE were calculated. Descriptive statistics, including non-parametric tests and correlation coefficients, were used for statistical analyses of the data. Compared to the gingiva of the neighbouring teeth, the peri-implant soft tissue around titanium and zirconia (test group), showed distinguishable ΔE both before and after crown cementation. Colour differences around titanium were statistically significant different (P = 0.01) only at 1 mm prior to crown cementation compared to zirconia. Compared to the gingiva of the neighbouring teeth, statistically significant (P < 0.01) differences were found for all colour parameter, either before or after crown cementation for both abutments; more significant differences were registered for titanium abutments. Tissue thickness correlated positively with c*-values for titanium at 1 mm and 2 mm from the gingival margin. Within their limits, the present data indicate that: (i) The peri-implant soft tissue around titanium and zirconia showed colour differences when compared to the soft tissue around natural teeth, and (ii) the peri-implant soft tissue around zirconia demonstrated a better colour match to the soft tissue at natural teeth than titanium. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data.

PubMed

Trede, Dennis; Kobarg, Jan Hendrik; Oetjen, Janina; Thiele, Herbert; Maass, Peter; Alexandrov, Theodore

2012-03-21

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 10⁸ to 10⁹ intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

On the Importance of Mathematical Methods for Analysis of MALDI-Imaging Mass Spectrometry Data.

PubMed

Trede, Dennis; Kobarg, Jan Hendrik; Oetjen, Janina; Thiele, Herbert; Maass, Peter; Alexandrov, Theodore

2012-03-01

In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 108 to 109 intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.

Network Analysis of Rodent Transcriptomes in Spaceflight

NASA Technical Reports Server (NTRS)

Ramachandran, Maya; Fogle, Homer; Costes, Sylvain

2017-01-01

Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

Age dependence of dielectric properties of bovine brain and ocular tissues in the frequency range of 400 MHz to 18 GHz

NASA Astrophysics Data System (ADS)

Schmid, Gernot; Überbacher, Richard

2005-10-01

In order to identify possible age-dependent dielectric properties of brain and eye tissues in the frequency range of 400 MHz to 18 GHz, measurements on bovine grey and white matter as well as on cornea, lens (cortical) and the vitreous body were performed using a commercially available open-ended coaxial probe and a computer-controlled vector network analyser. Freshly excised tissues of 52 animals of two age groups (42 adult animals, i.e. 16-24 month old and 10 young animals, i.e. 4-6 month old calves) were examined within 8 min (brain tissue) and 15 min (eye tissue), respectively, of the animals' death. Tissue temperatures for the measurements were 32 ± 1 °C and 25 ± 1 °C for brain and eye tissues, respectively. Statistical analysis of the measured data revealed significant differences in the dielectric properties of white matter and cortical lens tissue between the adult and the young group. In the case of white matter the mean values of conductivity and permittivity of young tissue were 15%-22% and 12%-15%, respectively, higher compared to the adult tissue in the considered frequency range. Similarly, young cortical lens tissue was 25%-76% higher in conductivity and 27%-39% higher in permittivity than adult cortical lens tissue.

Grading of cervical intraepithelial neoplasia using spatial frequency for optical histology

NASA Astrophysics Data System (ADS)

Pu, Yang; Jagtap, Jaidip; Pradhan, Asima; Alfano, Robert R.

2014-03-01

It is important to detect cervical dysplasia, Cervical Intraepithelial Neoplasia (CIN). CIN is the potentially premalignant and abnormal squamous cells on surface of cervix. In this study, the spatial frequency spectra of pre-cancer cervical tissues are used to detect differences among different grades of human cervical tissues. Seven sets of thick tissue sections of human cervix of normal, CIN 1, CIN 2, and CIN 3 tissues are studied. The confocal microscope images of the stromal region of normal and CIN human tissues were analyzed using Fast Fourier Transform (FFT) to generate the spatial spectra. It is observed that higher frequency components exist in CIN tissues than those in normal tissue, as well as those in higher grade CIN tissue than those in lower grade CIN tissue. The width of the spatial frequency of different types of tissues is used to create a criterion for CIN grading by training a support vector machine (SVM) classifier. The results show that the randomness of tissue structures from normal to different stages of precancer in cervical tissue can be recognized by fingerprints of the spatial frequency. The efficacy of spatial frequency analysis for CIN grading is evaluated as excellent since high AUC (area under the ROC curve), sensitivity and specificity are obtained by the statistics study. This works lays the foundation of using spatial frequency spectra for a histology evaluation.

Status quo of management of the human tissue banks in Taiwan.

PubMed

Chou, Ching-Pang; Chou, Szu-Cheng; Chen, Ying-Hua; Chen, Yu-Hsuan; Lee, Ming-Shin

2017-03-01

As the technologies associated with transplantation and biological tissue engineering continue to advance, human cells and tissues form an integral part to the practice of regenerative medicine. The patient's use of tissues entails the risk of introducing, transmitting and spreading communicable diseases. To prevent such risk and to ensure that the human organs, tissues and cells remain intact and functional after being handled and processed, the transplanted tissues must be subject to good management standards through all stages of collection, screening, processing, storage and distribution as the safety of the users is of the utmost importance. On February 2009, the government of Taiwan promulgated the Regulations for Administration on Human Organ Bank that requires all human tissues banks to adhere to the Good Tissue Practice for Human Organ, Tissue and Cell in terms of establishment and operation in order to cope with the international management trend and the development and management need of the domestic industry. Six years have passed since the law became effective. This article seeks to introduce the current management mechanism and status quo of management of human tissue banks in Taiwan. We also conducted statistical analysis of the data relating to the tissue banks to identify potential risks and the room for improvement. The study concludes that human tissue banks in Taiwan are on the right track with their management practice, leading to a state of steady development and progress.

Ambient Ionization Mass Spectrometry for Cancer Diagnosis and Surgical Margin Evaluation

PubMed Central

Ifa, Demian R.; Eberlin, Livia S.

2017-01-01

Background There is a clinical need for new technologies that would enable rapid disease diagnosis based on diagnostic molecular signatures. Ambient ionization mass spectrometry has revolutionized the means by which molecular information can be obtained from tissue samples in real time and with minimal sample pretreatment. New developments in ambient ionization techniques applied to clinical research suggest that ambient ionization mass spectrometry will soon become a routine medical tool for tissue diagnosis. Content This review summarizes the main developments in ambient ionization techniques applied to tissue analysis, with focus on desorption electrospray ionization mass spectrometry, probe electrospray ionization, touch spray, and rapid evaporative ionization mass spectrometry. We describe their applications to human cancer research and surgical margin evaluation, highlighting integrated approaches tested for ex vivo and in vivo human cancer tissue analysis. We also discuss the challenges for clinical implementation of these tools and offer perspectives on the future of the field. Summary A variety of studies have showcased the value of ambient ionization mass spectrometry for rapid and accurate cancer diagnosis. Small molecules have been identified as potential diagnostic biomarkers, including metabolites, fatty acids, and glycerophospholipids. Statistical analysis allows tissue discrimination with high accuracy rates (>95%) being common. This young field has challenges to overcome before it is ready to be broadly accepted as a medical tool for cancer diagnosis. Growing research in new, integrated ambient ionization mass spectrometry technologies and the ongoing improvements in the existing tools make this field very promising for future translation into the clinic. PMID:26555455

Spectroscopic characterization of bone tissue of experimental animals after glucocorticoid treatment and recovery period

NASA Astrophysics Data System (ADS)

Mitić, Žarko J.; Najman, Stevo J.; Cakić, Milorad D.; Ajduković, Zorica R.; Ignjatović, Nenad L.; Nikolić, Ružica S.; Nikolić, Goran M.; Stojanović, Sanja T.; Vukelić, Marija Đ.; Trajanović, Miroslav D.

2014-09-01

The influence of glucocorticoids on the composition and mineral/organic content of the mandible in tested animals after recovery and healing phase was investigated in this work. The results of FTIR analysis demonstrated that bone tissue composition was changed after glucocorticoid treatment. The increase of calcium, magnesium, phosphorus content and mineral part of bones was statistically significant in recovery phase and in treatment phase that included calcitonin and thymus extract. Some changes also happened in the organic part of the matrix, as indicated by intensity changes for already present IR bands and the appearance of new IR bands in the region 3500-1300 cm-1.

Peripheral intravenous and central catheter algorithm: a proactive quality initiative.

PubMed

Wilder, Kerry A; Kuehn, Susan C; Moore, James E

2014-12-01

Peripheral intravenous (PIV) infiltrations causing tissue damage is a global issue surrounded by situations that make vascular access decisions difficult. The purpose of this quality improvement project was to develop an algorithm and assess its effectiveness in reducing PIV infiltrations in neonates. The targeted subjects were all infants in our neonatal intensive care unit (NICU) with a PIV catheter. We completed a retrospective chart review of the electronic medical record to collect 4th quarter 2012 baseline data. Following adoption of the algorithm, we also performed a daily manual count of all PIV catheters in the 1st and 2nd quarters 2013. Daily PIV days were defined as follows: 1 patient with a PIV catheter equals 1 PIV day. An infant with 2 PIV catheters in place was counted as 2 PIV days. Our rate of infiltration or tissue damage was determined by counting the number of events and dividing by the number of PIV days. The rate of infiltration or tissue damage was reported as the number of events per 100 PIV days. The number of infiltrations and PIV catheters was collected from the electronic medical record and also verified manually by daily assessment after adoption of the algorithm. To reduce the rate of PIV infiltrations leading to grade 4 infiltration and tissue damage by at least 30% in the NICU population. Incidence of PIV infiltrations/100 catheter days. The baseline rate for total infiltrations increased slightly from 5.4 to 5.68/100 PIV days (P = .397) for the NICU. We attributed this increase to heightened awareness and better reporting. Grade 4 infiltrations decreased from 2.8 to 0.83/100 PIV catheter days (P = .00021) after the algorithm was implemented. Tissue damage also decreased from 0.68 to 0.3/100 PIV days (P = .11). Statistical analysis used the Fisher exact test and reported as statistically significant at P < .05. Our findings suggest that utilization of our standardized decision pathway was instrumental in providing guidance for problem solving related to vascular access decisions. We feel this contributed to the overall reduction in grade 4 intravenous infiltration and tissue damage rates. Grade 4 infiltration reductions were highly statistically significant (P = .00021).

Linking Mechanics and Statistics in Epidermal Tissues

NASA Astrophysics Data System (ADS)

Kim, Sangwoo; Hilgenfeldt, Sascha

2015-03-01

Disordered cellular structures, such as foams, polycrystals, or living tissues, can be characterized by quantitative measurements of domain size and topology. In recent work, we showed that correlations between size and topology in 2D systems are sensitive to the shape (eccentricity) of the individual domains: From a local model of neighbor relations, we derived an analytical justification for the famous empirical Lewis law, confirming the theory with experimental data from cucumber epidermal tissue. Here, we go beyond this purely geometrical model and identify mechanical properties of the tissue as the root cause for the domain eccentricity and thus the statistics of tissue structure. The simple model approach is based on the minimization of an interfacial energy functional. Simulations with Surface Evolver show that the domain statistics depend on a single mechanical parameter, while parameter fluctuations from cell to cell play an important role in simultaneously explaining the shape distribution of cells. The simulations are in excellent agreement with experiments and analytical theory, and establish a general link between the mechanical properties of a tissue and its structure. The model is relevant to diagnostic applications in a variety of animal and plant tissues.

Joint learning of ultrasonic backscattering statistical physics and signal confidence primal for characterizing atherosclerotic plaques using intravascular ultrasound.

PubMed

Sheet, Debdoot; Karamalis, Athanasios; Eslami, Abouzar; Noël, Peter; Chatterjee, Jyotirmoy; Ray, Ajoy K; Laine, Andrew F; Carlier, Stephane G; Navab, Nassir; Katouzian, Amin

2014-01-01

Intravascular Ultrasound (IVUS) is a predominant imaging modality in interventional cardiology. It provides real-time cross-sectional images of arteries and assists clinicians to infer about atherosclerotic plaques composition. These plaques are heterogeneous in nature and constitute fibrous tissue, lipid deposits and calcifications. Each of these tissues backscatter ultrasonic pulses and are associated with a characteristic intensity in B-mode IVUS image. However, clinicians are challenged when colocated heterogeneous tissue backscatter mixed signals appearing as non-unique intensity patterns in B-mode IVUS image. Tissue characterization algorithms have been developed to assist clinicians to identify such heterogeneous tissues and assess plaque vulnerability. In this paper, we propose a novel technique coined as Stochastic Driven Histology (SDH) that is able to provide information about co-located heterogeneous tissues. It employs learning of tissue specific ultrasonic backscattering statistical physics and signal confidence primal from labeled data for predicting heterogeneous tissue composition in plaques. We employ a random forest for the purpose of learning such a primal using sparsely labeled and noisy samples. In clinical deployment, the posterior prediction of different lesions constituting the plaque is estimated. Folded cross-validation experiments have been performed with 53 plaques indicating high concurrence with traditional tissue histology. On the wider horizon, this framework enables learning of tissue-energy interaction statistical physics and can be leveraged for promising clinical applications requiring tissue characterization beyond the application demonstrated in this paper. Copyright © 2013 Elsevier B.V. All rights reserved.

Bone histomorphometry using free and commonly available software.

PubMed

Egan, Kevin P; Brennan, Tracy A; Pignolo, Robert J

2012-12-01

Histomorphometric analysis is a widely used technique to assess changes in tissue structure and function. Commercially available programs that measure histomorphometric parameters can be cost-prohibitive. In this study, we compared an inexpensive method of histomorphometry to a current proprietary software program. Image J and Adobe Photoshop(®) were used to measure static and kinetic bone histomorphometric parameters. Photomicrographs of Goldner's trichrome-stained femurs were used to generate black-and-white image masks, representing bone and non-bone tissue, respectively, in Adobe Photoshop(®) . The masks were used to quantify histomorphometric parameters (bone volume, tissue volume, osteoid volume, mineralizing surface and interlabel width) in Image J. The resultant values obtained using Image J and the proprietary software were compared and differences found to be statistically non-significant. The wide-ranging use of histomorphometric analysis for assessing the basic morphology of tissue components makes it important to have affordable and accurate measurement options available for a diverse range of applications. Here we have developed and validated an approach to histomorphometry using commonly and freely available software that is comparable to a much more costly, commercially available software program. © 2012 Blackwell Publishing Limited.

Bone histomorphometry using free and commonly available software

PubMed Central

Egan, Kevin P.; Brennan, Tracy A.; Pignolo, Robert J.

2012-01-01

Aims Histomorphometric analysis is a widely used technique to assess changes in tissue structure and function. Commercially-available programs that measure histomorphometric parameters can be cost prohibitive. In this study, we compared an inexpensive method of histomorphometry to a current proprietary software program. Methods and results Image J and Adobe Photoshop® were used to measure static and kinetic bone histomorphometric parameters. Photomicrographs of Goldner’s Trichrome stained femurs were used to generate black and white image masks, representing bone and non-bone tissue, respectively, in Adobe Photoshop®. The masks were used to quantify histomorphometric parameters (bone volume, tissue volume, osteoid volume, mineralizing surface, and interlabel width) in Image J. The resultant values obtained using Image J and the proprietary software were compared and found to be statistically non-significant. Conclusions The wide ranging use of histomorphometric analysis for assessing the basic morphology of tissue components makes it important to have affordable and accurate measurement options that are available for a diverse range of applications. Here we have developed and validated an approach to histomorphometry using commonly and freely available software that is comparable to a much more costly, commercially-available software program. PMID:22882309

Comparison of destructive and nondestructive sampling techniques of retail chicken carcasses for enumeration of hygiene indicator microorganisms.

PubMed

Cossi, Marcus Vinícius Coutinho; de Almeida, Michelle Vieira; Dias, Mariane Rezende; de Arruda Pinto, Paulo Sérgiode; Nero, Luís Augusto

2012-01-01

The type of sampling technique used to obtain food samples is fundamental to the success of microbiological analysis. Destructive and nondestructive techniques, such as tissue excision and rinsing, respectively, are widely employed in obtaining samples from chicken carcasses. In this study, four sampling techniques used for chicken carcasses were compared to evaluate their performances in the enumeration of hygiene indicator microorganisms. Sixty fresh chicken carcasses were sampled by rinsing, tissue excision, superficial swabbing, and skin excision. All samples were submitted for enumeration of mesophilic aerobes, Enterobacteriaceae, coliforms, and Escherichia coli. The results were compared to determine the statistical significance of differences and correlation (P < 0.05). Tissue excision provided the highest microbial counts compared with the other procedures, with significant differences obtained only for coliforms and E. coli (P < 0.05). Significant correlations (P < 0.05) were observed for all the sampling techniques evaluated for most of the hygiene indicators. Despite presenting a higher recovery ability, tissue excision did not present significant differences for microorganism enumeration compared with other nondestructive techniques, such as rinsing, indicating its adequacy for microbiological analysis of chicken carcasses.

Using independent component analysis for electrical impedance tomography

NASA Astrophysics Data System (ADS)

Yan, Peimin; Mo, Yulong

2004-05-01

Independent component analysis (ICA) is a way to resolve signals into independent components based on the statistical characteristics of the signals. It is a method for factoring probability densities of measured signals into a set of densities that are as statistically independent as possible under the assumptions of a linear model. Electrical impedance tomography (EIT) is used to detect variations of the electric conductivity of the human body. Because there are variations of the conductivity distributions inside the body, EIT presents multi-channel data. In order to get all information contained in different location of tissue it is necessary to image the individual conductivity distribution. In this paper we consider to apply ICA to EIT on the signal subspace (individual conductivity distribution). Using ICA the signal subspace will then be decomposed into statistically independent components. The individual conductivity distribution can be reconstructed by the sensitivity theorem in this paper. Compute simulations show that the full information contained in the multi-conductivity distribution will be obtained by this method.

Pulp calcification in traumatized primary teeth: prevalence and associated factors.

PubMed

Mello-Moura, A C V; Bonini, G A V C; Zardetto, C G D C; Rodrigues, C R M D; Wanderley, M T

2011-01-01

To establish the prevalence of pulp calcifications in 946 patients at the Research and Clinical Center of Dental Trauma in Primary Teeth. The clinical and radiographic records of l675 traumatized primary teeth were evaluated. Statistical analysis was performed using chi-square and univariate logistic regression. 197 (20.8%) patients showed pulp calcification (PC). A total of 250 (14.9%) calcified teeth were observed In most teeth, PC appeared within the first 12 months following trauma. PC prevalence was higher in cases of repeated trauma (29.6%) than in single trauma (16.4%), p < 0.05, with a 2.14 chance of showing pulp calcification when a child suffered recurrent trauma. Most teeth showing calcified pulp, suffered trauma to the supportive tissue (67.4%), being statistically significant in relation to the trauma to dental tissue (p < 0.05). PC is a sequelae in cases of trauma to the primary dentition; teeth that suffered recurrent traumatic injuries show higher risk of presenting.

Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

PubMed

Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

2017-08-01

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

Resonance Raman of BCC and normal skin

NASA Astrophysics Data System (ADS)

Liu, Cheng-hui; Sriramoju, Vidyasagar; Boydston-White, Susie; Wu, Binlin; Zhang, Chunyuan; Pei, Zhe; Sordillo, Laura; Beckman, Hugh; Alfano, Robert R.

2017-02-01

The Resonance Raman (RR) spectra of basal cell carcinoma (BCC) and normal human skin tissues were analyzed using 532nm laser excitation. RR spectral differences in vibrational fingerprints revealed skin normal and cancerous states tissues. The standard diagnosis criterion for BCC tissues are created by native RR biomarkers and its changes at peak intensity. The diagnostic algorithms for the classification of BCC and normal were generated based on SVM classifier and PCA statistical method. These statistical methods were used to analyze the RR spectral data collected from skin tissues, yielding a diagnostic sensitivity of 98.7% and specificity of 79% compared with pathological reports.

Early Assessment of Treatment Responses During Radiation Therapy for Lung Cancer Using Quantitative Analysis of Daily Computed Tomography

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

Paul, Jijo; Yang, Cungeng; Wu, Hui

Purpose: To investigate early tumor and normal tissue responses during the course of radiation therapy (RT) for lung cancer using quantitative analysis of daily computed tomography (CT) scans. Methods and Materials: Daily diagnostic-quality CT scans acquired using CT-on-rails during CT-guided RT for 20 lung cancer patients were quantitatively analyzed. On each daily CT set, the contours of the gross tumor volume (GTV) and lungs were generated and the radiation dose delivered was reconstructed. The changes in CT image intensity (Hounsfield unit [HU]) features in the GTV and the multiple normal lung tissue shells around the GTV were extracted from themore » daily CT scans. The associations between the changes in the mean HUs, GTV, accumulated dose during RT delivery, and patient survival rate were analyzed. Results: During the RT course, radiation can induce substantial changes in the HU histogram features on the daily CT scans, with reductions in the GTV mean HUs (dH) observed in the range of 11 to 48 HU (median 30). The dH is statistically related to the accumulated GTV dose (R{sup 2} > 0.99) and correlates weakly with the change in GTV (R{sup 2} = 0.3481). Statistically significant increases in patient survival rates (P=.038) were observed for patients with a higher dH in the GTV. In the normal lung, the 4 regions proximal to the GTV showed statistically significant (P<.001) HU reductions from the first to last fraction. Conclusion: Quantitative analysis of the daily CT scans indicated that the mean HUs in lung tumor and surrounding normal tissue were reduced during RT delivery. This reduction was observed in the early phase of the treatment, is patient specific, and correlated with the delivered dose. A larger HU reduction in the GTV correlated significantly with greater patient survival. The changes in daily CT features, such as the mean HU, can be used for early assessment of the radiation response during RT delivery for lung cancer.« less

Early Assessment of Treatment Responses During Radiation Therapy for Lung Cancer Using Quantitative Analysis of Daily Computed Tomography.

PubMed

Paul, Jijo; Yang, Cungeng; Wu, Hui; Tai, An; Dalah, Entesar; Zheng, Cheng; Johnstone, Candice; Kong, Feng-Ming; Gore, Elizabeth; Li, X Allen

2017-06-01

To investigate early tumor and normal tissue responses during the course of radiation therapy (RT) for lung cancer using quantitative analysis of daily computed tomography (CT) scans. Daily diagnostic-quality CT scans acquired using CT-on-rails during CT-guided RT for 20 lung cancer patients were quantitatively analyzed. On each daily CT set, the contours of the gross tumor volume (GTV) and lungs were generated and the radiation dose delivered was reconstructed. The changes in CT image intensity (Hounsfield unit [HU]) features in the GTV and the multiple normal lung tissue shells around the GTV were extracted from the daily CT scans. The associations between the changes in the mean HUs, GTV, accumulated dose during RT delivery, and patient survival rate were analyzed. During the RT course, radiation can induce substantial changes in the HU histogram features on the daily CT scans, with reductions in the GTV mean HUs (dH) observed in the range of 11 to 48 HU (median 30). The dH is statistically related to the accumulated GTV dose (R 2  > 0.99) and correlates weakly with the change in GTV (R 2  = 0.3481). Statistically significant increases in patient survival rates (P=.038) were observed for patients with a higher dH in the GTV. In the normal lung, the 4 regions proximal to the GTV showed statistically significant (P<.001) HU reductions from the first to last fraction. Quantitative analysis of the daily CT scans indicated that the mean HUs in lung tumor and surrounding normal tissue were reduced during RT delivery. This reduction was observed in the early phase of the treatment, is patient specific, and correlated with the delivered dose. A larger HU reduction in the GTV correlated significantly with greater patient survival. The changes in daily CT features, such as the mean HU, can be used for early assessment of the radiation response during RT delivery for lung cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

PubMed Central

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Effects of bacterial infestation caused by human wastes on the skin structures of Mugil platanus Günther, 1880 (Mugilidae).

PubMed

Langer, S L; Vargas, V M F; Flores-Lopes, F; Malabarba, L R

2009-05-01

Manifestation of infectious pathologies in fishes usually increases in environments where organic wastes are disposed. Specimens of Mugil platanus Günther, 1880 and water samples collected at three points of the Tramandaí river were analyzed during a one year period. The macroscopic observation revealed ulcerations in the caudal peduncle area covered with a mass of amorphous and whitened tissues. Histopathologic analysis showed the presence of negative gram bacteria, probably responsible for alterations of the normal structure of the epidermic tissues. Non-parametric statistical analysis for ammonia concentration showed a significant variation among the three collected spots as well as in the multiple comparison between two spots. In this study, we describe cutaneous lesions observed in Mugil platanus specimens and tested their correlation with environmental ammonia concentration.

Transcriptional expression analysis of survivin splice variants reveals differential expression of survivin-3α in breast cancer.

PubMed

Moniri Javadhesari, Solmaz; Gharechahi, Javad; Hosseinpour Feizi, Mohammad Ali; Montazeri, Vahid; Halimi, Monireh

2013-04-01

Survivin, which is a novel member of the inhibitor of apoptosis family proteins, is known to play an important role in the regulation of cell cycle and apoptosis. Differential expression of survivin in tumor tissues introduces it as a new candidate molecular marker for cancer. Here we investigated the expression of survivin and its splice variants in breast tumors, as well as normal adjacent tissues obtained from the same patients. Thirty five tumors and 17 normal adjacent tissues from women diagnosed with breast cancer were explored in this study. Differential expression of different survivin splice variants was detected and semiquantitatively analyzed using reverse transcription-polymerase chain reaction. Results showed that survivin and its splice variants were differentially expressed in tumor specimens compared with normal adjacent tissues. The expression of survivin-3B and survivin-3α was specifically detected in tumor tissues compared with normal adjacent ones (53% in tumor tissues compared to 5% in normal adjacent for survivin-3B and 65% in tumor tissues and 0.0% in normal adjacent tissues for survivin-3α). Statistical analysis showed that survivin and survivin-ΔEx3 were upregulated in benign (90%, p<0.034) and malignant (76%, p<0.042) tumors, respectively. On the other hand, our results showed that survivin-2α (100% of the cases) was the dominant expressed variant of survivin in breast cancer. The data presented here showed that survivin splice variants were differentially expressed in benign and malignant breast cancer tissues, suggesting their potential role in breast cancer development. Differential expression of survivin-2α and survivin-3α splice variants highlights their usefulness as new candidate markers for breast cancer diagnosis and prognosis.

Penetration and pharmacokinetics of non-steroidal anti-inflammatory drugs in rat prostate tissue.

PubMed

Yellepeddi, Venkata K; Radhakrishnan, Jayashree; Radhakrishnan, Rajan

2018-02-01

Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) involves inflammation of the prostate and affects the quality of life of men of all ages. It is well reported in clinical studies that the treatment for CP/CPPS using nonsteroidal anti-inflammatory drugs (NSAIDs) produced favorable outcomes. However, currently, there are no guidelines on choice of the NSAIDs for the treatment of CP/CPPS. Therefore, in the current research study, we evaluated the prostate tissue penetration of four NSAIDs in rats to provide guidance on choice of NSAIDs for the treatment of CP/CPPS. Male Sprague-Dawley rats were administered orally with four NSAIDs viz. celecoxib, diclofenac, ibuprofen, and naproxen at 500 mg/kg dose. The animals were then sacrificed at various time points, and their prostate tissues were harvested. The NSAIDs were then extracted from the prostate tissues using liquid extraction technique, and their concentration in prostate tissue was quantified using high-performance liquid chromatography (HPLC). The prostate tissue penetration and related pharmacokinetic parameters were evaluated by non-compartmental analysis. The HPLC method for quantifying NSAIDs in prostate tissue resulted in single, sharp peaks without any interference and all validation parameters were within limits. Celecoxib showed the highest area under the curve (AUC) [146.50 ± 2.75 μg/mL*h] of all NSAID's. A two-factor analysis of variance (ANOVA) with replication indicated an overall statistically significant difference in the pharmacokinetic parameters for celecoxib, diclofenac, ibuprofen, and naproxen. This study for the first time reported the relative prostate tissue penetration of four NSAIDs. The pharmacokinetic data indicated that celecoxib has the highest penetration and retention in rat prostate tissues. Therefore, celecoxib may be considered as a better choice for the treatment CP/CPPS involving NSAIDs. © 2017 Wiley Periodicals, Inc.

Polarimetry based partial least square classification of ex vivo healthy and basal cell carcinoma human skin tissues.

PubMed

Ahmad, Iftikhar; Ahmad, Manzoor; Khan, Karim; Ikram, Masroor

2016-06-01

Optical polarimetry was employed for assessment of ex vivo healthy and basal cell carcinoma (BCC) tissue samples from human skin. Polarimetric analyses revealed that depolarization and retardance for healthy tissue group were significantly higher (p<0.001) compared to BCC tissue group. Histopathology indicated that these differences partially arise from BCC-related characteristic changes in tissue morphology. Wilks lambda statistics demonstrated the potential of all investigated polarimetric properties for computer assisted classification of the two tissue groups. Based on differences in polarimetric properties, partial least square (PLS) regression classified the samples with 100% accuracy, sensitivity and specificity. These findings indicate that optical polarimetry together with PLS statistics hold promise for automated pathology classification. Copyright © 2016 Elsevier B.V. All rights reserved.

An Observation-Driven Agent-Based Modeling and Analysis Framework for C. elegans Embryogenesis.

PubMed

Wang, Zi; Ramsey, Benjamin J; Wang, Dali; Wong, Kwai; Li, Husheng; Wang, Eric; Bao, Zhirong

2016-01-01

With cutting-edge live microscopy and image analysis, biologists can now systematically track individual cells in complex tissues and quantify cellular behavior over extended time windows. Computational approaches that utilize the systematic and quantitative data are needed to understand how cells interact in vivo to give rise to the different cell types and 3D morphology of tissues. An agent-based, minimum descriptive modeling and analysis framework is presented in this paper to study C. elegans embryogenesis. The framework is designed to incorporate the large amounts of experimental observations on cellular behavior and reserve data structures/interfaces that allow regulatory mechanisms to be added as more insights are gained. Observed cellular behaviors are organized into lineage identity, timing and direction of cell division, and path of cell movement. The framework also includes global parameters such as the eggshell and a clock. Division and movement behaviors are driven by statistical models of the observations. Data structures/interfaces are reserved for gene list, cell-cell interaction, cell fate and landscape, and other global parameters until the descriptive model is replaced by a regulatory mechanism. This approach provides a framework to handle the ongoing experiments of single-cell analysis of complex tissues where mechanistic insights lag data collection and need to be validated on complex observations.

The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.

PubMed

Fasoli, Marianna; Dal Santo, Silvia; Zenoni, Sara; Tornielli, Giovanni Battista; Farina, Lorenzo; Zamboni, Anita; Porceddu, Andrea; Venturini, Luca; Bicego, Manuele; Murino, Vittorio; Ferrarini, Alberto; Delledonne, Massimo; Pezzotti, Mario

2012-09-01

We developed a genome-wide transcriptomic atlas of grapevine (Vitis vinifera) based on 54 samples representing green and woody tissues and organs at different developmental stages as well as specialized tissues such as pollen and senescent leaves. Together, these samples expressed ∼91% of the predicted grapevine genes. Pollen and senescent leaves had unique transcriptomes reflecting their specialized functions and physiological status. However, microarray and RNA-seq analysis grouped all the other samples into two major classes based on maturity rather than organ identity, namely, the vegetative/green and mature/woody categories. This division represents a fundamental transcriptomic reprogramming during the maturation process and was highlighted by three statistical approaches identifying the transcriptional relationships among samples (correlation analysis), putative biomarkers (O2PLS-DA approach), and sets of strongly and consistently expressed genes that define groups (topics) of similar samples (biclustering analysis). Gene coexpression analysis indicated that the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of clusters of neighboring genes and global regulation based on codon preference. This global transcriptomic reprogramming during maturation has not been observed in herbaceous annual species and may be a defining characteristic of perennial woody plants.

The choice of statistical methods for comparisons of dosimetric data in radiotherapy.

PubMed

Chaikh, Abdulhamid; Giraud, Jean-Yves; Perrin, Emmanuel; Bresciani, Jean-Pierre; Balosso, Jacques

2014-09-18

Novel irradiation techniques are continuously introduced in radiotherapy to optimize the accuracy, the security and the clinical outcome of treatments. These changes could raise the question of discontinuity in dosimetric presentation and the subsequent need for practice adjustments in case of significant modifications. This study proposes a comprehensive approach to compare different techniques and tests whether their respective dose calculation algorithms give rise to statistically significant differences in the treatment doses for the patient. Statistical investigation principles are presented in the framework of a clinical example based on 62 fields of radiotherapy for lung cancer. The delivered doses in monitor units were calculated using three different dose calculation methods: the reference method accounts the dose without tissues density corrections using Pencil Beam Convolution (PBC) algorithm, whereas new methods calculate the dose with tissues density correction for 1D and 3D using Modified Batho (MB) method and Equivalent Tissue air ratio (ETAR) method, respectively. The normality of the data and the homogeneity of variance between groups were tested using Shapiro-Wilks and Levene test, respectively, then non-parametric statistical tests were performed. Specifically, the dose means estimated by the different calculation methods were compared using Friedman's test and Wilcoxon signed-rank test. In addition, the correlation between the doses calculated by the three methods was assessed using Spearman's rank and Kendall's rank tests. The Friedman's test showed a significant effect on the calculation method for the delivered dose of lung cancer patients (p <0.001). The density correction methods yielded to lower doses as compared to PBC by on average (-5 ± 4.4 SD) for MB and (-4.7 ± 5 SD) for ETAR. Post-hoc Wilcoxon signed-rank test of paired comparisons indicated that the delivered dose was significantly reduced using density-corrected methods as compared to the reference method. Spearman's and Kendall's rank tests indicated a positive correlation between the doses calculated with the different methods. This paper illustrates and justifies the use of statistical tests and graphical representations for dosimetric comparisons in radiotherapy. The statistical analysis shows the significance of dose differences resulting from two or more techniques in radiotherapy.

Time to significant pain reduction following DETP application vs placebo for acute soft tissue injuries.

PubMed

Yanchick, J; Magelli, M; Bodie, J; Sjogren, J; Rovati, S

2010-08-01

Nonsteroidal anti-inflammatory drugs (NSAIDs) provide fast and effective acute pain relief, but systemic administration has increased risk for some adverse reactions. The diclofenac epolamine 1.3% topical patch (DETP) is a topical NSAID with demonstrated safety and efficacy in treatment of acute pain from minor soft tissue injuries. Significant pain reduction has been observed in clinical trials within several hours following DETP application, suggesting rapid pain relief; however, this has not been extensively studied for topical NSAIDs in general. This retrospective post-hoc analysis examined time to onset of significant pain reduction after DETP application compared to a placebo patch for patients with mild-to-moderate acute ankle sprain, evaluating the primary efficacy endpoint from two nearly identical studies. Data from two double-blind, randomized, parallel-group, placebo-controlled studies (N = 274) of safety and efficacy of the DETP applied once daily for 7 days for acute ankle sprain were evaluated post-hoc using statistical modeling to estimate time to onset of significant pain reduction following DETP application. Pain on active movement on a 100 mm Visual Analog Scale (VAS) recorded in patient diaries; physician- and patient-assessed tolerability; and adverse events. DETP treatment resulted in significant pain reduction within approximately 3 hours compared to placebo. Within-treatment post-hoc analysis based on a statistical model suggested significant pain reduction occurred as early as 1.27 hours for the DETP group. The study may have been limited by the retrospective nature of the analyses. In both studies, the DETP was well tolerated with few adverse events, limited primarily to application site skin reactions. The DETP is an effective treatment for acute minor soft tissue injury, providing pain relief as rapidly as 1.27 hours post-treatment. Statistical modeling may be useful in estimating time to onset of pain relief for comparison of topical and oral NSAIDs.

Statistical and fractal analysis of autofluorescent myocardium images in posthumous diagnostics of acute coronary insufficiency

NASA Astrophysics Data System (ADS)

Boichuk, T. M.; Bachinskiy, V. T.; Vanchuliak, O. Ya.; Minzer, O. P.; Garazdiuk, M.; Motrich, A. V.

2014-08-01

This research presents the results of investigation of laser polarization fluorescence of biological layers (histological sections of the myocardium). The polarized structure of autofluorescence imaging layers of biological tissues was detected and investigated. Proposed the model of describing the formation of polarization inhomogeneous of autofluorescence imaging biological optically anisotropic layers. On this basis, analytically and experimentally tested to justify the method of laser polarimetry autofluorescent. Analyzed the effectiveness of this method in the postmortem diagnosis of infarction. The objective criteria (statistical moments) of differentiation of autofluorescent images of histological sections myocardium were defined. The operational characteristics (sensitivity, specificity, accuracy) of these technique were determined.

MALDI Orbitrap Mass Spectrometry Profiling of Dysregulated Sulfoglycosphingolipids in Renal Cell Carcinoma Tissues

NASA Astrophysics Data System (ADS)

Jirásko, Robert; Holčapek, Michal; Khalikova, Maria; Vrána, David; Študent, Vladimír; Prouzová, Zuzana; Melichar, Bohuslav

2017-08-01

Matrix-assisted laser desorption/ionization coupled with Orbitrap mass spectrometry (MALDI-Orbitrap-MS) is used for the clinical study of patients with renal cell carcinoma (RCC), as the most common type of kidney cancer. Significant changes in sulfoglycosphingolipid abundances between tumor and autologous normal kidney tissues are observed. First, sulfoglycosphingolipid species in studied RCC samples are identified using high mass accuracy full scan and tandem mass spectra. Subsequently, optimization, method validation, and statistical evaluation of MALDI-MS data for 158 tissues of 80 patients are discussed. More than 120 sulfoglycosphingolipids containing one to five hexosyl units are identified in human RCC samples based on the systematic study of their fragmentation behavior. Many of them are recorded here for the first time. Multivariate data analysis (MDA) methods, i.e., unsupervised principal component analysis (PCA) and supervised orthogonal partial least square discriminant analysis (OPLS-DA), are used for the visualization of differences between normal and tumor samples to reveal the most up- and downregulated lipids in tumor tissues. Obtained results are closely correlated with MALDI mass spectrometry imaging (MSI) and histologic staining. Important steps of the present MALDI-Orbitrap-MS approach are also discussed, such as the selection of best matrix, correct normalization, validation for semiquantitative study, and problems with possible isobaric interferences on closed masses in full scan mass spectra.

Resonance Raman spectroscopy for human cancer detection of key molecules with clinical diagnosis

NASA Astrophysics Data System (ADS)

Zhou, Yan; Liu, Cheng-hui; Li, Jiyou; Zhou, Lixin; He, Jingsheng; Sun, Yi; Pu, Yang; Zhu, Ke; Liu, Yulong; Li, Qingbo; Cheng, Gangge; Alfano, Robert R.

2013-03-01

Resonance Raman (RR) has the potential to reveal the differences between cancerous and normal breast and brain tissues in vitro. This differences caused by the changes of specific biomolecules in the tissues were displayed in resonance enhanced of vibrational fingerprints. It observed that the changes of reduced collagen contents and the number of methyl may show the sub-methylation of DNA in cancer cells. Statistical theoretical models of Bayesian, principal component analysis (PCA) and support vector machine (SVM) were used for distinguishing cancer from normal based on the RR spectral data of breast and meninges tissues yielding the diagnostic sensitivity of 80% and 90.9%, and specificity of 100% and 100%, respectively. The results demonstrated that the RR spectroscopic technique could be applied as clinical optical pathology tool with a high accuracy and reliability.

Detergent-enzymatic decellularization of swine blood vessels: insight on mechanical properties for vascular tissue engineering.

PubMed

Pellegata, Alessandro F; Asnaghi, M Adelaide; Stefani, Ilaria; Maestroni, Anna; Maestroni, Silvia; Dominioni, Tommaso; Zonta, Sandro; Zerbini, Gianpaolo; Mantero, Sara

2013-01-01

Small caliber vessels substitutes still remain an unmet clinical need; few autologous substitutes are available, while synthetic grafts show insufficient patency in the long term. Decellularization is the complete removal of all cellular and nuclear matters from a tissue while leaving a preserved extracellular matrix representing a promising tool for the generation of acellular scaffolds for tissue engineering, already used for various tissues with positive outcomes. The aim of this work is to investigate the effect of a detergent-enzymatic decellularization protocol on swine arteries in terms of cell removal, extracellular matrix preservation, and mechanical properties. Furthermore, the effect of storage at -80°C on the mechanical properties of the tissue is evaluated. Swine arteries were harvested, frozen, and decellularized; histological analysis revealed complete cell removal and preserved extracellular matrix. Furthermore, the residual DNA content in decellularized tissues was far low compared to native one. Mechanical testings were performed on native, defrozen, and decellularized tissues; no statistically significant differences were reported for Young's modulus, ultimate stress, compliance, burst pressure, and suture retention strength, while ultimate strain and stress relaxation of decellularized vessels were significantly different from the native ones. Considering the overall results, the process was confirmed to be suitable for the generation of acellular scaffolds for vascular tissue engineering.

Recovery of low volumes of wear debris from rat stifle joint tissues using a novel particle isolation method.

PubMed

Patel, J; Lal, S; Nuss, K; Wilshaw, S P; von Rechenberg, B; Hall, R M; Tipper, J L

2018-04-15

Less than optimal particle isolation techniques have impeded analysis of orthopaedic wear debris in vivo. The purpose of this research was to develop and test an improved method for particle isolation from tissue. A volume of 0.018 mm 3 of clinically relevant CoCrMo, Ti-6Al-4V or Si 3 N 4 particles was injected into rat stifle joints for seven days of in vivo exposure. Following sacrifice, particles were located within tissues using histology. The particles were recovered by enzymatic digestion of periarticular tissue with papain and proteinase K, followed by ultracentrifugation using a sodium polytungstate density gradient. Particles were recovered from all samples, observed using SEM and the particle composition was verified using EDX, which demonstrated that all isolated particles were free from contamination. Particle size, aspect ratio and circularity were measured using image analysis software. There were no significant changes to the measured parameters of CoCrMo or Si 3 N 4 particles before and after the recovery process (KS tests, p > 0.05). Titanium particles were too few before and after isolation to analyse statistically, though size and morphologies were similar. Overall the method demonstrated a significant improvement to current particle isolation methods from tissue in terms of sensitivity and efficacy at removal of protein, and has the potential to be used for the isolation of ultra-low wearing total joint replacement materials from periprosthetic tissues. This research presents a novel method for the isolation of wear particles from tissue. Methodology outlined in this work would be a valuable resource for future researchers wishing to isolate particles from tissues, either as part of preclinical testing, or from explants from patients for diagnostic purposes. It is increasingly recognised that analysis of wear particles is critical to evaluating the safety of an orthopaedic device. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Identical mitochondrial somatic mutations unique to chronic periodontitis and coronary artery disease

PubMed Central

Pallavi, Tokala; Chandra, Rampalli Viswa; Reddy, Aileni Amarender; Reddy, Bavigadda Harish; Naveen, Anumala

2016-01-01

Context: The inflammatory processes involved in chronic periodontitis and coronary artery diseases (CADs) are similar and produce reactive oxygen species that may result in similar somatic mutations in mitochondrial deoxyribonucleic acid (mtDNA). Aims: The aims of the present study were to identify somatic mtDNA mutations in periodontal and cardiac tissues from subjects undergoing coronary artery bypass surgery and determine what fraction was identical and unique to these tissues. Settings and Design: The study population consisted of 30 chronic periodontitis subjects who underwent coronary artery surgery after an angiogram had indicated CAD. Materials and Methods: Gingival tissue samples were taken from the site with deepest probing depth; coronary artery tissue samples were taken during the coronary artery bypass grafting procedures, and blood samples were drawn during this surgical procedure. These samples were stored under aseptic conditions and later transported for mtDNA analysis. Statistical Analysis Used: Complete mtDNA sequences were obtained and aligned with the revised Cambridge reference sequence (NC_012920) using sequence analysis and auto assembler tools. Results: Among the complete mtDNA sequences, a total of 162 variations were spread across the whole mitochondrial genome and present only in the coronary artery and the gingival tissue samples but not in the blood samples. Among the 162 variations, 12 were novel and four of the 12 novel variations were found in mitochondrial NADH dehydrogenase subunit 5 complex I gene (33.3%). Conclusions: Analysis of mtDNA mutations indicated 162 variants unique to periodontitis and CAD. Of these, 12 were novel and may have resulted from destructive oxidative forces common to these two diseases. PMID:27041832

Validation of a free software for unsupervised assessment of abdominal fat in MRI.

PubMed

Maddalo, Michele; Zorza, Ivan; Zubani, Stefano; Nocivelli, Giorgio; Calandra, Giulio; Soldini, Pierantonio; Mascaro, Lorella; Maroldi, Roberto

2017-05-01

To demonstrate the accuracy of an unsupervised (fully automated) software for fat segmentation in magnetic resonance imaging. The proposed software is a freeware solution developed in ImageJ that enables the quantification of metabolically different adipose tissues in large cohort studies. The lumbar part of the abdomen (19cm in craniocaudal direction, centered in L3) of eleven healthy volunteers (age range: 21-46years, BMI range: 21.7-31.6kg/m 2 ) was examined in a breath hold on expiration with a GE T1 Dixon sequence. Single-slice and volumetric data were considered for each subject. The results of the visceral and subcutaneous adipose tissue assessments obtained by the unsupervised software were compared to supervised segmentations of reference. The associated statistical analysis included Pearson correlations, Bland-Altman plots and volumetric differences (VD % ). Values calculated by the unsupervised software significantly correlated with corresponding supervised segmentations of reference for both subcutaneous adipose tissue - SAT (R=0.9996, p<0.001) and visceral adipose tissue - VAT (R=0.995, p<0.001). Bland-Altman plots showed the absence of systematic errors and a limited spread of the differences. In the single-slice analysis, VD % were (1.6±2.9)% for SAT and (4.9±6.9)% for VAT. In the volumetric analysis, VD % were (1.3±0.9)% for SAT and (2.9±2.7)% for VAT. The developed software is capable of segmenting the metabolically different adipose tissues with a high degree of accuracy. This free add-on software for ImageJ can easily have a widespread and enable large-scale population studies regarding the adipose tissue and its related diseases. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Robust tissue-air volume segmentation of MR images based on the statistics of phase and magnitude: Its applications in the display of susceptibility-weighted imaging of the brain.

PubMed

Du, Yiping P; Jin, Zhaoyang

2009-10-01

To develop a robust algorithm for tissue-air segmentation in magnetic resonance imaging (MRI) using the statistics of phase and magnitude of the images. A multivariate measure based on the statistics of phase and magnitude was constructed for tissue-air volume segmentation. The standard deviation of first-order phase difference and the standard deviation of magnitude were calculated in a 3 x 3 x 3 kernel in the image domain. To improve differentiation accuracy, the uniformity of phase distribution in the kernel was also calculated and linear background phase introduced by field inhomogeneity was corrected. The effectiveness of the proposed volume segmentation technique was compared to a conventional approach that uses the magnitude data alone. The proposed algorithm was shown to be more effective and robust in volume segmentation in both synthetic phantom and susceptibility-weighted images of human brain. Using our proposed volume segmentation method, veins in the peripheral regions of the brain were well depicted in the minimum-intensity projection of the susceptibility-weighted images. Using the additional statistics of phase, tissue-air volume segmentation can be substantially improved compared to that using the statistics of magnitude data alone. (c) 2009 Wiley-Liss, Inc.

Fourier Transform Infrared Imaging analysis of dental pulp inflammatory diseases.

PubMed

Giorgini, E; Sabbatini, S; Conti, C; Rubini, C; Rocchetti, R; Fioroni, M; Memè, L; Orilisi, G

2017-05-01

Fourier Transform Infrared microspectroscopy let characterize the macromolecular composition and distribution of tissues and cells, by studying the interaction between infrared radiation and matter. Therefore, we hypothesize to exploit this analytical tool in the analysis of inflamed pulps, to detect the different biochemical features related to various degrees of inflammation. IR maps of 13 irreversible and 12 hyperplastic pulpitis, together with 10 normal pulps, were acquired, compared with histological findings and submitted to multivariate (HCA, PCA, SIMCA) and statistical (one-way ANOVA) analysis. The fit of convoluted bands let calculate meaningful band area ratios (means ± s.d., P < 0.05). The infrared imaging analysis pin-pointed higher amounts of water and lower quantities of type I collagen in all inflamed pulps. Specific vibrational markers were defined for irreversible pulpitis (Lipids/Total Biomass, PhII/Total Biomass, CH 2 /CH 3 , and Ty/AII) and hyperplastic ones (OH/Total Biomass, Collagen/Total Biomass, and CH 3 Collagen/Total Biomass). The study confirmed that FTIR microspectroscopy let discriminate tissues' biological features. The infrared imaging analysis evidenced, in inflamed pulps, alterations in tissues' structure and composition. Changes in lipid metabolism, increasing amounts of tyrosine, and the occurrence of phosphorylative processes were highlighted in irreversible pulpitis, while high amounts of water and low quantities of type I collagen were detected in hyperplastic samples. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Wavelet analysis of myocardium polarization images in problems of diagnostic of necrotic changes

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Vanchuliak, O.; Bodnar, G. B.; Ushenko, V. O.; Pavlyukovich, N.; Pavlyukovich, O. V.; Antonyuk, O.

2017-08-01

The paper presents the results of polarization manifestations of small - and Large-scale phase anisotropy of dead in consequence of ischemic heart disease (IHD) and acute coronary insufficiency (ACI) people myocardial tissue structures to differentiate information, the wavelet analysis method is used. The resulting maps of the of the polarizationcorrelation parameters distributions (the phase of the two-point first and second parameters of the Stokes vector) are analyzed in the framework of statistical approach. On this basis, the criteria for differential diagnosis of IHD and ACI cases have been determined.

Connective tissue growth factor immunohistochemical expression is associated with gallbladder cancer progression.

PubMed

Garcia, Patricia; Leal, Pamela; Alvarez, Hector; Brebi, Priscilla; Ili, Carmen; Tapia, Oscar; Roa, Juan C

2013-02-01

Gallbladder cancer (GBC) is an aggressive neoplasia associated with late diagnosis, unsatisfactory treatment, and poor prognosis. Molecular mechanisms involved in GBC pathogenesis remain poorly understood. Connective tissue growth factor (CTGF) is thought to play a role in the pathologic processes and is overexpressed in several human cancers, including GBC. No information is available about CTGF expression in early stages of gallbladder carcinogenesis. Objective.- To evaluate the expression level of CTGF in benign and malignant lesions of gallbladder and its correlation with clinicopathologic features and GBC prognosis. Connective tissue growth factor protein was examined by immunohistochemistry on tissue microarrays containing tissue samples of chronic cholecystitis (n = 51), dysplasia (n = 15), and GBC (n = 169). The samples were scored according to intensity of staining as low/absent and high CTGF expressers. Statistical analysis was performed using the χ(2) test or Fisher exact probability test with a significance level of P < .05. Survival analysis was assessed by the Kaplan-Meier method and the log-rank test. Connective tissue growth factor expression showed a progressive increase from chronic cholecystitis to dysplasia and then to early and advanced carcinoma. Immunohistochemical expression (score ≥2) was significantly higher in advanced tumors, in comparison with chronic cholecystitis (P < .001) and dysplasia (P = .03). High levels of CTGF expression correlated with better survival (P = .04). Our results suggest a role for CTGF in GBC progression and a positive association with better prognosis. In addition, they underscore the importance of considering the involvement of inflammation on GBC development.

Role of inflammatory mediators in patients with recurrent pregnancy loss.

PubMed

Comba, Cihan; Bastu, Ercan; Dural, Ozlem; Yasa, Cenk; Keskin, Gulsah; Ozsurmeli, Mehmet; Buyru, Faruk; Serdaroglu, Hasan

2015-12-01

To examine interleukin-12 (IL-12), IL-18, IFN-γ, intracellular adhesion molecule-1 (ICAM-1), leukemia inhibitory factor (LIF), and migration inhibitory factor (MIF) levels in precisely-timed blood and endometrial tissue samples from women with idiopathic recurrent pregnancy loss (RPL). Case-control study. University hospital. Twenty-one women with RPL and 20 women with proven fertility (controls). Primary endometrial cells and blood samples during the midsecretory phase (days 19-23). Detection of IL-12, IL-18, IFN-γ, ICAM-1, LIF, and MIF via enzyme-linked immunosorbent assay in both blood and endometrial tissue samples. The blood and tissue levels of IL-12, IL-18, and IFN-γ were statistically significantly higher, and the blood and tissue levels of LIF and MIF were statistically significantly lower in patients with RPL. Only the level of tissue ICAM-1 was higher in patients with RPL. There was a strong correlation between blood and tissue level measurements of IL-12, IL-18, LIF, and MIF. Our findings support the hypothesis that inflammatory processes may contribute to pregnancy loss, possibly through their role in implantation. We found that blood and tissue levels of IL-18, LIF, and MIF, and tissue levels of IL-12, IFN-γ, and ICAM-1 have statistically significant prognostic relevance. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Histologic and photonic evaluation of a pulsed Nd:YAG laser for ablation of subcutaneous adipose tissue.

PubMed

Ichikawa, Kota; Tanino, Ryuzaburo; Wakaki, Moriaki

2006-12-20

Although various lasers are available, few of them are applicable in liposculpture. Laser interaction with fat tissue has not also been well documented. The aim of our study was to gather basic data on laser absorption in fat tissue and to analyze the relationship between laser energy and lipolysis for development of a more effective laser system. The transmittance rate in human fat specimens was measured by a spectrophotometer to determine the optimum wavelength. The absorption coefficient was used to evaluate laser absorption at a wavelength of 1064 nm. Areas of heat degeneration and evaporation were measured by scanning electron microscopy. The relation between laser energy and the areas was analyzed statistically among low-power and high-power groups and controls. Energy dispersion at the fiber tip was investigated and analyzed statistically using the far field pattern. A graph of the absorption rate at wavelengths from 400 to 2400 nm showed a peak near 1700 nm and increases at wavelengths over 2000 nm. The formula gave as an absorption coefficient of 0.4 cm(-1), and involvement of the photo-acoustic effect and non-linear effect with short-pulse and high-peak energy was suggested. Findings of tissue evaporation, destruction, heat coagulation, and rupture of cell membrane were more frequently seen in irradiated specimens than in controls in scanning electron microscopy. The destroyed area in the low-power irradiated groups was significantly larger than that of controls in the statistical analysis. The affected area in the high-power irradiated groups was significantly larger than that of low-power specimens. Energy was concentrated at the tip with laser coherency. Energy at the oblique-cut tip was statistically lower than that at the normal tip, revealing that durability and maintenance of the fiber tip is essential to maintain energy levels in clinical practice. This study is the first to demonstrate the histologic and photonic relationship of energy absorption and lipolysis using a pulsed Nd:YAG laser. The results will be useful for research and development of a more effective laser system for liposculpture.

Effects of glutamine on wound healing.

PubMed

Kesici, Ugur; Kesici, Sevgi; Ulusoy, Hulya; Yucesan, Fulya; Turkmen, Aygen U; Besir, Ahmet; Tuna, Verda

2015-06-01

Studies reporting the need for replacing amino acids such as glutamine (Gln), hydroxymethyl butyrate (HMB) and arginine (Arg) to accelerate wound healing are available in the literature. The primary objective of this study was to present the effects of Gln on tissue hydroxyproline (OHP) levels in wound healing. This study was conducted on 30 female Sprague Dawley rats with a mean weight of 230 ± 20 g. Secondary wounds were formed by excising 2 × 1 cm skin subcutaneous tissue on the back of the rats. The rats were divided into three equal groups. Group C (Control): the group received 1 ml/day isotonic solution by gastric gavage after secondary wound was formed. Group A (Abound): the group received 0·3 g/kg/day/ml Gln, 0·052 g/kg/day/ml HMB and 0·3 g/kg/day/ml Arg by gastric gavage after secondary wound was formed. Group R (Resource): the group received 0·3 g/kg/day/ml Gln by gastric gavage after secondary wound was formed. The OHP levels of the tissues obtained from the upper half region on the 8th day and the lower half region on the 21st day from the same rats in the groups were examined. Statistical analysis was performed using the statistics program SPSS version 17.0. No statistically significant differences were reported with regard to the OHP measurements on the 8th and 21st days (8th day: F = 0·068, P = 0·935 > 0·05; 21st day: F = 0·018, P = 0·983 > 0·05). The increase in mean OHP levels on the 8th and 21st days within each group was found to be statistically significant (F = 1146·34, P = 0·000 < 0·001). We conclude that in adults who eat healthy food, who do not have any factor that can affect wound healing negatively and who do not have large tissue loss at critical level, Gln, Arg and HMB support would not be required to accelerate secondary wound healing. © 2013 The Authors. International Wound Journal © 2013 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

Retained structural integrity of collagen and elastin within cryopreserved human heart valve tissue as detected by two-photon laser scanning confocal microscopy.

PubMed

Gerson, Cindy J; Goldstein, Steven; Heacox, Albert E

2009-10-01

Cryopreservation is commonly used for the long-term storage of heart valve allografts. Despite the excellent hemodynamic performance and durability of cryopreserved allografts, reports have questioned whether cryopreservation affects the valvular structural proteins, collagen and elastin. This study uses two-photon laser scanning confocal microscopy (LSCM) to evaluate the effect of cryopreservation on collagen and elastin integrity within the leaflet and conduit of aortic and pulmonary human heart valves. To permit pairwise comparisons of fresh and cryopreserved tissue, test valves were bisected longitudinally with one segment imaged fresh and the other imaged after cryopreservation and brief storage in liquid nitrogen. Collagen was detected by second harmonic generation (SHG) stimulation and elastin by autofluorescence excitation. Qualitative analysis of all resultant images indicated the maintenance of collagen and elastin structure within leaflet and conduit post-cryopreservation. Analysis of the optimized percent laser transmission (OPLT) required for full dynamic range imaging of collagen and elastin showed that OPLT observations were highly variable among both fresh and cryopreserved samples. Changes in donor-specific average OPLT in response to cryopreservation exhibited no consistent directional trend. The donor-aggregated results predominantly showed no statistically significant change in collagen and elastin average OPLT due to cryopreservation. Since OPLT has an inverse relationship with structural signal intensity, these results indicate that there was largely no statistical difference in collagen and elastin signal strength between fresh and cryopreserved tissue. Overall, this study indicates that the conventional cryopreservation of human heart valve allografts does not detrimentally affect their collagen and elastin structural integrity.

Analysis of elemental concentration censored distributions in breast malignant and breast benign neoplasm tissues

NASA Astrophysics Data System (ADS)

Kubala-Kukuś, A.; Banaś, D.; Braziewicz, J.; Góźdź, S.; Majewska, U.; Pajek, M.

2007-07-01

The total reflection X-ray fluorescence method was applied to study the trace element concentrations in human breast malignant and breast benign neoplasm tissues taken from the women who were patients of Holycross Cancer Centre in Kielce (Poland). These investigations were mainly focused on the development of new possibilities of cancer diagnosis and therapy monitoring. This systematic comparative study was based on relatively large (˜ 100) population studied, namely 26 samples of breast malignant and 68 samples of breast benign neoplasm tissues. The concentrations, being in the range from a few ppb to 0.1%, were determined for thirteen elements (from P to Pb). The results were carefully analysed to investigate the concentration distribution of trace elements in the studied samples. The measurements of concentration of trace elements by total reflection X-ray fluorescence were limited, however, by the detection limit of the method. It was observed that for more than 50% of elements determined, the concentrations were not measured in all samples. These incomplete measurements were treated within the statistical concept called left-random censoring and for the estimation of the mean value and median of censored concentration distributions, the Kaplan-Meier estimator was used. For comparison of concentrations in two populations, the log-rank test was applied, which allows to compare the censored total reflection X-ray fluorescence data. Found statistically significant differences are discussed in more details. It is noted that described data analysis procedures should be the standard tool to analyze the censored concentrations of trace elements analysed by X-ray fluorescence methods.

Clinical Usefulness of Real-Time Polymerase Chain Reaction for the Diagnosis of Vibrio vulnificus Infection Using Skin and Soft Tissues.

PubMed

Lee, Jun-Young; Kim, Seok Won; Kim, Dong-Min; Yun, Na Ra; Kim, Choon-Mee; Lee, Sang-Hong

2017-08-01

Vibrio vulnificus is a halophilic gram-negative bacillus isolated in seawater, fish, and shellfish. Infection by V. vulnificus is the most severe food-borne infection reported in the United States of America. Here, we aimed to examine the clinical usefulness of polymerase chain reaction (PCR) using tissue specimens other than blood samples as a diagnostic tool for V. vulnificus infection. A retrospective study was conducted with patients who underwent real-time PCR of toxR in both blood and skin tissues, including serum, bullae, swab, and operation room specimens, between 2006 and 2009. The median V. vulnificus DNA load of 14 patients in real-time PCR analysis of serum at the time of admission was 638.5 copies/mL blood, which was within the interquartile range (IQR: 37-3,225). In contrast, the median value by real-time PCR using the first tissue specimen at the time of admission was 16,650 copies/mL tissue fluid (IQR: 4,419-832,500). This difference was statistically significant ( P = 0.022). DNA copy numbers in tissues were less affected by short-term antibiotic administration than that in blood samples, and antibiotic administration increased the DNA copy number in some patients. We found, for the first time, that DNA copy numbers in tissues of patients infected by V. vulnificus were higher than those in blood samples. Additionally, skin lesions were more useful than blood samples as specimens for PCR analysis in patients administered antibiotics for V. vulnificus infection before admission.

Probabilistic atlas and geometric variability estimation to drive tissue segmentation.

PubMed

Xu, Hao; Thirion, Bertrand; Allassonnière, Stéphanie

2014-09-10

Computerized anatomical atlases play an important role in medical image analysis. While an atlas usually refers to a standard or mean image also called template, which presumably represents well a given population, it is not enough to characterize the observed population in detail. A template image should be learned jointly with the geometric variability of the shapes represented in the observations. These two quantities will in the sequel form the atlas of the corresponding population. The geometric variability is modeled as deformations of the template image so that it fits the observations. In this paper, we provide a detailed analysis of a new generative statistical model based on dense deformable templates that represents several tissue types observed in medical images. Our atlas contains both an estimation of probability maps of each tissue (called class) and the deformation metric. We use a stochastic algorithm for the estimation of the probabilistic atlas given a dataset. This atlas is then used for atlas-based segmentation method to segment the new images. Experiments are shown on brain T1 MRI datasets. Copyright © 2014 John Wiley & Sons, Ltd.

Pomegranate vinegar attenuates adiposity in obese rats through coordinated control of AMPK signaling in the liver and adipose tissue

PubMed Central

2013-01-01

Background The effect of pomegranate vinegar (PV) on adiposity was investigated in high-fat diet (HF)-induced obese rats. Methods The rats were divided into 5 groups and treated with HF with PV or acetic acid (0, 6.5 or 13% w/w) for 16 weeks. Statistical analyses were performed by the Statistical Analysis Systems package, version 9.2. Results Compared to control, PV supplementation increased phosphorylation of AMP-activated protein kinase (AMPK), leading to changes in mRNA expressions: increases for hormone sensitive lipase and mitochondrial uncoupling protein 2 and decreases for sterol regulatory element binding protein-1c (SREBP-1c) and peroxisome proliferator-activated receptorγ (PPARγ) in adipose tissue; increases for PPARα and carnitinepalmitoyltransferase-1a (CPT-1a) and decrease for SREBP-1c in the liver. Concomitantly, PV reduced increases of body weight (p = 0.048), fat mass (p = 0.033), hepatic triglycerides (p = 0.005), and plasma triglycerides (p = 0.001). Conclusions These results suggest that PV attenuates adiposity through the coordinated control of AMPK, which leads to promotion of lipolysis in adipose tissue and stimulation of fatty acid oxidation in the liver. PMID:24180378

The effects of 2.45 GHz radio frequency energy on neurological tissue genes using an unrestrained murine model in vivo

NASA Astrophysics Data System (ADS)

Stevens, Brandon William

The effects that radio frequency (RF) energy has on the body is currently an inconclusive and controversial topic. This is in part due to the differences and issues that can be found in previous studies. This thesis describes a study on the effect of continuous RF energy on the genome of in vivo mouse brain tissue for a duration of 31 days. To address the issues found in previous studies a new standardized procedure was followed. The genome of the brain tissue was quantified using RNA-seq and then analyzed using statistical combinations and empirical p-values. Transcripts with their respective p-values were uploaded into Integrity Pathway Analysis® to determine genes associated disease and function within the brain tissue. The results from this study provided evidence that supports RF energy induces changes in the genome. Additionally, the results provided evidence of the first reported case of a potential RF-controlled genetic transistor.

Rapid Detection of Necrosis in Breast Cancer with Desorption Electrospray Ionization Mass Spectrometry

PubMed Central

Tata, Alessandra; Woolman, Michael; Ventura, Manuela; Bernards, Nicholas; Ganguly, Milan; Gribble, Adam; Shrestha, Bindesh; Bluemke, Emma; Ginsberg, Howard J.; Vitkin, Alex; Zheng, Jinzi; Zarrine-Afsar, Arash

2016-01-01

Identification of necrosis in tumors is of prognostic value in treatment planning, as necrosis is associated with aggressive forms of cancer and unfavourable outcomes. To facilitate rapid detection of necrosis with Mass Spectrometry (MS), we report the lipid MS profile of necrotic breast cancer with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) imaging validated with statistical analysis and correlating pathology. This MS profile is characterized by (1) the presence of the ion of m/z 572.48 [Cer(d34:1) + Cl]− which is a ceramide absent from the viable cancer subregions; (2) the absence of the ion of m/z 391.25 which is present in small abundance only in viable cancer subregions; and (3) a slight increase in the relative intensity of known breast cancer biomarker ions of m/z 281.25 [FA(18:1)-H]− and 303.23 [FA(20:4)-H]−. Necrosis is accompanied by alterations in the tissue optical depolarization rate, allowing tissue polarimetry to guide DESI-MS analysis for rapid MS profiling or targeted MS imaging. This workflow, in combination with the MS profile of necrosis, may permit rapid characterization of necrotic tumors from tissue slices. Further, necrosis-specific biomarker ions are detected in seconds with single MS scans of necrotic tumor tissue smears, which further accelerates the identification workflow by avoiding tissue sectioning and slide preparation. PMID:27734938

Analysis of plastic deformation in cortical bone after insertion of coated and non-coated self-tapping orthopaedic screws.

PubMed

Koistinen, A P; Korhonen, H; Kiviranta, I; Kröger, H; Lappalainen, R

2011-07-01

Insertion of internal fracture fixation devices, such as screws, mechanically weakens the bone. Diamond-like carbon has outstanding tribology properties which may decrease the amount of damage in tissue. The purpose of this study was to investigate methods for quantification of cortical bone damage after orthopaedic bone screw insertion and to evaluate the effect of surface modification on tissue damage. In total, 48 stainless steel screws were inserted into cadaver bones. Half of the screws were coated with a smooth amorphous diamond coating. Geometrical data of the bones was determined by peripheral quantitative computed tomography. Thin sections of the bone samples were prepared after screw insertion, and histomorphometric evaluation of damage was performed on images obtained using light microscopy. Micro-computed tomography and scanning electron microscopy were also used to examine tissue damage. A positive correlation was found between tissue damage and the geometric properties of the bone. The age of the cadaver significantly affected the bone mineral density, as well as the damage perimeter and diameter of the screw hole. However, the expected positive effect of surface modification was probably obscured by large variations in the results and, thus, statistically significant differences were not found in this study. This can be explained by natural variability in bone tissue, which also made automated image analysis difficult.

In-Depth Characterization and Validation of Human Urine Metabolomes Reveal Novel Metabolic Signatures of Lower Urinary Tract Symptoms

NASA Astrophysics Data System (ADS)

Hao, Ling; Greer, Tyler; Page, David; Shi, Yatao; Vezina, Chad M.; Macoska, Jill A.; Marker, Paul C.; Bjorling, Dale E.; Bushman, Wade; Ricke, William A.; Li, Lingjun

2016-08-01

Lower urinary tract symptoms (LUTS) are a range of irritative or obstructive symptoms that commonly afflict aging population. The diagnosis is mostly based on patient-reported symptoms, and current medication often fails to completely eliminate these symptoms. There is a pressing need for objective non-invasive approaches to measure symptoms and understand disease mechanisms. We developed an in-depth workflow combining urine metabolomics analysis and machine learning bioinformatics to characterize metabolic alterations and support objective diagnosis of LUTS. Machine learning feature selection and statistical tests were combined to identify candidate biomarkers, which were statistically validated with leave-one-patient-out cross-validation and absolutely quantified by selected reaction monitoring assay. Receiver operating characteristic analysis showed highly-accurate prediction power of candidate biomarkers to stratify patients into disease or non-diseased categories. The key metabolites and pathways may be possibly correlated with smooth muscle tone changes, increased collagen content, and inflammation, which have been identified as potential contributors to urinary dysfunction in humans and rodents. Periurethral tissue staining revealed a significant increase in collagen content and tissue stiffness in men with LUTS. Together, our study provides the first characterization and validation of LUTS urinary metabolites and pathways to support the future development of a urine-based diagnostic test for LUTS.

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

PubMed

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

2016-01-01

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. 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. 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. 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.

Selenium and mining in the Powder River Basin, Wyoming: Phase III - a preliminary survey of selenium concentrations in deer mice (Peromyscus maniculatus) livers

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

Raisbeck, M.L.; Vance, G.F.; Steward, D.G.

1995-09-01

Samples of liver tissue from deer mice trapped on not-yet-mined areas and reclaimed areas at five surface coal mines in the Powder River Basin of northeastern Wyoming were analyzed for selenium. The overall mean concentration of selenium in wet weight liver tissue was 1.685 ppm. The mean value from not-yet-mined areas was 1.437 ppm; the mean value from reclaimed areas was 1.910 ppm (significant at p<0.1016). When one not-yet-mined outlier was removed, significance rose to p<0.0004. Mine-to-mine comparison of samples stratified by type (that is, by not-yet-mined or reclaimed), showed average tissue concentrations from the reclaimed area of Mine 1more » were also higher (p<0.0143) then not-yet-mined area samples at Mine 1. No statistically significant differences were found between mines for samples from not-yet-mined areas, and no statistically significant differences were found between Mines 2, 3, 4, and 5 for samples from reclaimed areas. Multiple analysis of variance using the factors: site (mine) and type (not-yet-mined or reclaimed) was not significantly significant (p<0.2115). Simple linear regression showed that selenium concentrations in dry tissue could easily be predicted from wet tissue selenium (r2=0.9775), demonstrating that percent water in the samples was relatively constant. Animal body weight in general was not a predictor for either wet or dry tissue selenium concentrations, but was related to body weight at the higher tissue concentrations of selenium encountered in samples from the reclaimed area at Mine 1. Mouse body weights at Mine 1 were higher on the reclaimed area than mouse body weights from the not-yet-mined area.« less

Comparative analysis of arthroscopic debridement in osseous versus soft tissue anterior ankle impingement.

PubMed

Devgan, Ashish; Rohilla, Rajesh; Tanwar, Milind; Jain, Aditya; Siwach, Karan; Devgan, Radika

2016-01-01

Arthroscopic debridement has been a gold standard procedure for anterior ankle impingement, both in cases of osseous and soft tissue impingement. There is sparse literature on comparative outcome with respect to functional results between the two types of impingement post-arthroscopic debridement. Our study included 14 patients diagnosed as cases of anterior ankle impingement on the basis of clinical and radiological examination. They were segregated into two groups (on the basis of cause of impingement (osseous versus soft tissue)). Both groups were treated by arthroscopic debridement. Primary outcome was patient satisfaction, which was assessed by Likert scale and clinical outcomes were measured using AOFAS ankle-hind foot scale, VAS score, range of motion and time to return to pre-injury activity level in both groups. Mean follow-up was of 15 months where eleven patients reported an excellent recovery, two patients had good recovery while one patient reported poor outcome. Mean AOFAS ankle hind foot scale improved from 50.5 preoperatively to 85.71 postoperatively (statistically significant; p value - 0.0001). Mean Likert scale value post-operative was 4.21. VAS score showed significant improvement in patients of both the groups. Range of motion was slightly better in soft tissue impingement type with a relatively shorter time to return to sports or preinjury activity level as compared to osseous impingement group. The patients in both the groups had comparable outcomes with no statistically significant difference with regard to patient satisfaction and clinical outcome.

Mineral Trioxide Aggregate and Portland Cement for Direct Pulp Capping in Dog: A Histopathological Evaluation

PubMed Central

Bidar, Maryam; Naghavi, Neda; Mohtasham, Nooshin; Sheik-Nezami, Mahshid; Fallahrastegar, Amir; Afkhami, Farzaneh; Attaran Mashhadi, Negin; Nargesi, Iman

2014-01-01

Background and aims. Mineral trioxide aggregate and calcium hydroxide are considered the gold standard pulp-capping materials. Recently, Portland cement has been introduced with properties similar to those of mineral trioxide aggregate. Histopathological effects of direct pulp capping using mineral trioxide aggregate and Portland cements on dog dental pulp tissue were evaluated in the present study. Materials and methods. This histopatological study was carried out on 64 dog premolars. First, the pulp was exposed with a sterile bur. Then, the exposed pulp was capped with white or gray mineral trioxide aggregates and white or gray Portland cements in each quadrant and sealed with glass-ionomer. The specimens were evaluated under a light microscope after 6 months. Statistical analysis was carried out using Kruskal-Wallis test. Statistical significance was defined at α=5%. Results. There was no acute inflammation in any of the specimens. Chronic inflammation in white and gray mineral trioxide aggregates and white and gray Portland cements was reported to be 45.5%, 27.3%, 57.1% and 34.1%, respectively. Although the differences were not statistically significant, severe inflammation was observed mostly adjacent to white mineral trioxide aggregate. The largest extent of increased vascularization (45%) and the least increase in fibrous tissue were observed adjacent to white mineral trioxide aggregate, with no significant differences. In addition, the least calcified tissue formed adjacent to white mineral trioxide aggregate, although the difference was not significant. Conclusion. The materials used in this study were equally effective as pulp protection materials following direct pulp capping in dog teeth. PMID:25346831

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

High-Throughput Analysis of Age-Dependent Protein Changes in Layer II/III of the Human Orbitofrontal Cortex

NASA Astrophysics Data System (ADS)

Kapadia, Fenika

Studies on the orbitofrontal cortex (OFC) during normal aging have shown a decline in cognitive functions, a loss of spines/synapses in layer III and gene expression changes related to neural communication. Biological changes during the course of normal aging are summarized into 9 hallmarks based on aging in peripheral tissue. Whether these hallmarks apply to non-dividing brain tissue is not known. Therefore, we opted to perform large-scale proteomic profiling of the OFC layer II/III during normal aging from 15 young and 18 old male subjects. MaxQuant was utilized for label-free quantification and statistical analysis by the Random Intercept Model (RIM) identified 118 differentially expressed (DE) age-related proteins. Altered neural communication was the most represented hallmark of aging (54% of DE proteins), highlighting the importance of communication in the brain. Functional analysis showed enrichment in GABA/glutamate signaling and pro-inflammatory responses. The former may contribute to alterations in excitation/inhibition, leading to cognitive decline during aging.

Abutment Material Effect on Peri-implant Soft Tissue Color and Perceived Esthetics.

PubMed

Kim, Aram; Campbell, Stephen D; Viana, Marlos A G; Knoernschild, Kent L

2016-12-01

The purpose of this study was to evaluate the effect of implant abutment material on peri-implant soft tissue color using intraoral spectrophotometric analysis and to compare the clinical outcomes with patient and clinician perception and satisfaction. Thirty patients and four prosthodontic faculty members participated. Abutments were zirconia, gold-hued titanium, and titanium. Peri-implant mucosa color of a single anterior implant restoration was compared to the patient's control tooth. Spectrophotometric analysis using SpectroShade TM Micro data determined the color difference (ΔE, ΔL*, Δa*, Δb*) between the midfacial peri-implant soft tissue for each abutment material and the marginal gingiva of the control tooth. Color difference values of the abutment groups were compared using ANOVA (α = 0.05). Patient and clinician satisfaction surveys were also conducted using a color-correcting light source. The results of each patient and clinician survey question were compared using chi-square analysis (α = 0.05). Pearson correlation analyses identified the relationship between the total color difference (ΔE) and the patient/clinician perception and satisfaction, as well as between ΔE and tissue thickness. Zirconia abutments displayed significantly smaller spectrophotometric gingival color difference (ΔE) compared to titanium and gold-hued titanium abutments (respectively, 3.98 ± 0.99; 7.22 ± 3.31; 5.65 ± 2.11; p < 0.05). Among ΔL*, Δa*, and Δb*, only Δa* (red-green spectrum) showed significant difference between groups. There was no significant correlation between measured soft tissue thickness and ΔE, but thick gingival phenotype, determined by a probe test, demonstrated a smaller ΔE than thin phenotype (4.82 ± 1.49; 6.41 ± 3.27; p = 0.097). There was no statistical difference in patient or clinician satisfaction among abutment materials, and no correlation between ΔE and the patient and clinician satisfaction. Patient satisfaction was significantly higher than clinician, and patient-perceived differences were lower than clinicians' (p < 0.01). Clinicians' satisfaction was higher for gingival (pink) esthetics than crown (white) esthetics (p < 0.05). Peri-implant mucosa with zirconia abutments demonstrated significantly lower mean color difference compared to titanium or gold-hued titanium abutments as measured spectrophotometrically; however, no statistical difference in patient or clinician perception/satisfaction among abutment materials was demonstrated. Patients were significantly more satisfied than clinicians. © 2015 by the American College of Prosthodontists.

Mounting ground sections of teeth: Cyanoacrylate adhesive versus Canada balsam

PubMed Central

Vangala, Manogna RL; Rudraraju, Amrutha; Subramanyam, RV

2016-01-01

Introduction: Hard tissues can be studied by either decalcification or by preparing ground sections. Various mounting media have been tried and used for ground sections of teeth. However, there are very few studies on the use of cyanoacrylate adhesive as a mounting medium. Aims: The aim of our study was to evaluate the efficacy of cyanoacrylate adhesive (Fevikwik™) as a mounting medium for ground sections of teeth and to compare these ground sections with those mounted with Canada balsam. Materials and Methods: Ground sections were prepared from twenty extracted teeth. Each section was divided into two halves and mounted on one slide, one with cyanoacrylate adhesive (Fevikwik™) and the other with Canada balsam. Scoring for various features in the ground sections was done by two independent observers. Statistical Analysis Used: Statistical analysis using Student's t-test (unpaired) of average scores was performed for each feature observed. Results: No statistically significant difference was found between the two for most of the features. However, cyanoacrylate was found to be better than Canada balsam for observing striae of Retzius (P < 0.0205), enamel lamellae (P < 0.036), dentinal tubules (P < 0.0057), interglobular dentin (P < 0.0001), sclerotic dentin – transmitted light (P < 0.00001), sclerotic dentin – polarized light (P < 0.0002) and Sharpey's fibers (P < 0.0004). Conclusions: This initial study shows that cyanoacrylate is better than Canada balsam for observing certain features of ground sections of teeth. However, it remains to be seen whether it will be useful for studying undecalcified sections of carious teeth and for soft tissue sections. PMID:27194857

In vitro chemotaxis and tissue remodeling assays quantitatively characterize foreign body reaction.

PubMed

Jannasch, Maren; Weigel, Tobias; Engelhardt, Lisa; Wiezoreck, Judith; Gaetzner, Sabine; Walles, Heike; Schmitz, Tobias; Hansmann, Jan

2017-01-01

Surgical implantation of a biomaterial triggers foreign-body-induced fibrous encapsulation. Two major mechanisms of this complex physiological process are (I) chemotaxis of fibroblasts from surrounding tissue to the implant region, followed by (II) tissue remodeling. As an alternative to animal studies, we here propose a process-aligned in vitro test platform to investigate the material dependency of fibroblast chemotaxis and tissue remodeling mediated by material-resident macrophages. Embedded in a biomimetic three-dimensional collagen hydrogel, chemotaxis of fibroblasts in the direction of macrophage-material-conditioned cell culture supernatant was analyzed by live cell imaging. A combination of statistical analysis with a complementary parameterized random walk model allowed quantitative and qualitative characterization of the cellular walk process. We thereby identified an increasing macrophage-mediated chemotactic potential ranking of biomaterials from glass over polytetrafluorethylene to titanium. To address long-term effects of bio-material-resident macrophages on fibroblasts in a three-dimensional microenvironment, we further studied tissue remodeling by applying macrophage-material-conditioned medium on fibrous in vitro tissue models. A high correlation of the in vitro tissue model to state of the art in vivo study data was found. Titanium exhibited a significantly lower tissue remodeling capacity compared to polytetrafluorethylene. With this approach, we identified a material dependency of both chemotaxis and tissue remodeling processes, strengthening knowledge on their specific contribution to the foreign body reaction.

Multi-tissue partial volume quantification in multi-contrast MRI using an optimised spectral unmixing approach.

PubMed

Collewet, Guylaine; Moussaoui, Saïd; Deligny, Cécile; Lucas, Tiphaine; Idier, Jérôme

2018-06-01

Multi-tissue partial volume estimation in MRI images is investigated with a viewpoint related to spectral unmixing as used in hyperspectral imaging. The main contribution of this paper is twofold. It firstly proposes a theoretical analysis of the statistical optimality conditions of the proportion estimation problem, which in the context of multi-contrast MRI data acquisition allows to appropriately set the imaging sequence parameters. Secondly, an efficient proportion quantification algorithm based on the minimisation of a penalised least-square criterion incorporating a regularity constraint on the spatial distribution of the proportions is proposed. Furthermore, the resulting developments are discussed using empirical simulations. The practical usefulness of the spectral unmixing approach for partial volume quantification in MRI is illustrated through an application to food analysis on the proving of a Danish pastry. Copyright © 2018 Elsevier Inc. All rights reserved.

Histogram analysis parameters identify multiple associations between DWI and DCE MRI in head and neck squamous cell carcinoma.

PubMed

Meyer, Hans Jonas; Leifels, Leonard; Schob, Stefan; Garnov, Nikita; Surov, Alexey

2018-01-01

Nowadays, multiparametric investigations of head and neck squamous cell carcinoma (HNSCC) are established. These approaches can better characterize tumor biology and behavior. Diffusion weighted imaging (DWI) can by means of apparent diffusion coefficient (ADC) quantitatively characterize different tissue compartments. Dynamic contrast-enhanced magnetic resonance imaging (DCE MRI) reflects perfusion and vascularization of tissues. Recently, a novel approach of data acquisition, namely histogram analysis of different images is a novel diagnostic approach, which can provide more information of tissue heterogeneity. The purpose of this study was to analyze possible associations between DWI, and DCE parameters derived from histogram analysis in patients with HNSCC. Overall, 34 patients, 9 women and 25 men, mean age, 56.7±10.2years, with different HNSCC were involved in the study. DWI was obtained by using of an axial echo planar imaging sequence with b-values of 0 and 800s/mm 2 . Dynamic T1w DCE sequence after intravenous application of contrast medium was performed for estimation of the following perfusion parameters: volume transfer constant (K trans ), volume of the extravascular extracellular leakage space (Ve), and diffusion of contrast medium from the extravascular extracellular leakage space back to the plasma (Kep). Both ADC and perfusion parameters maps were processed offline in DICOM format with custom-made Matlab-based application. Thereafter, polygonal ROIs were manually drawn on the transferred maps on each slice. For every parameter, mean, maximal, minimal, and median values, as well percentiles 10th, 25th, 75th, 90th, kurtosis, skewness, and entropy were estimated. Сorrelation analysis identified multiple statistically significant correlations between the investigated parameters. Ve related parameters correlated well with different ADC values. Especially, percentiles 10 and 75, mode, and median values showed stronger correlations in comparison to other parameters. Thereby, the calculated correlation coefficients ranged from 0.62 to 0.69. Furthermore, K trans related parameters showed multiple slightly to moderate significant correlations with different ADC values. Strongest correlations were identified between ADC P75 and K trans min (p=0.58, P=0.0007), and ADC P75 and K trans P10 (p=0.56, P=0.001). Only four K ep related parameters correlated statistically significant with ADC fractions. Strongest correlation was found between K ep max and ADC mode (p=-0.47, P=0.008). Multiple statistically significant correlations between, DWI and DCE MRI parameters derived from histogram analysis were identified in HNSCC. Copyright © 2017 Elsevier Inc. All rights reserved.

Tissue angiotensin-converting enzyme inhibitors for the prevention of cardiovascular disease in patients with diabetes mellitus without left ventricular systolic dysfunction or clinical evidence of heart failure: a pooled meta-analysis of randomized placebo-controlled clinical trials.

PubMed

Saha, S A; Molnar, J; Arora, R R

2008-01-01

The aim of this study was to determine the role of tissue angiotensin-converting enzyme (ACE) inhibitors in the prevention of cardiovascular disease in patients with diabetes mellitus without left ventricular systolic dysfunction or clinical evidence of heart failure in randomized placebo-controlled clinical trials using pooled meta-analysis techniques. Randomized placebo-controlled clinical trials of at least 12 months duration in patients with diabetes mellitus without left ventricular systolic dysfunction or heart failure who had experienced a prior cardiovascular event or were at high cardiovascular risk were selected. A total of 10 328 patients (43 517 patient-years) from four selected trials were used for meta-analysis. Relative risk estimations were made using data pooled from the selected trials and statistical significance was determined using the Chi-squared test (two-sided alpha error <0.05). The number of patients needed to treat was also calculated. Tissue ACE inhibitors significantly reduced the risk of cardiovascular mortality by 14.9% (p = 0.022), myocardial infarction by 20.8% (p = 0.002) and the need for invasive coronary revascularization by 14% (p = 0.015) when compared to placebo. The risk of all-cause mortality also tended to be lower among patients randomized to tissue ACE inhibitors, whereas the risks of stroke and hospitalization for heart failure were not significantly affected. Treating about 65 patients with tissue ACE inhibitors for about 4.2 years would prevent one myocardial infarction, whereas treating about 85 patients would prevent one cardiovascular death. Pooled meta-analysis of randomized placebo-controlled trials suggests that tissue ACE inhibitors modestly reduce the risk of myocardial infarction and cardiovascular death and tend to reduce overall mortality in diabetic patients without left ventricular systolic dysfunction or heart failure.

The Effect of Estrogen Usage on Eccentric Exercise-Induced Damage in Rat Testes

PubMed Central

Can, Serpil; Selli, Jale; Buyuk, Basak; Aydin, Sergulen; Kocaaslan, Ramazan; Guvendi, Gulname Findik

2015-01-01

Background: Recent years, lots of scientific studies are focused on the possible mechanism of inflammatory response and oxidative stress which are the mechanism related with tissue damage and exercise fatigue. It is well-known that free oxygen radicals may be induced under invitro conditions as well as oxidative stress by exhaustive physical exercise. Objectives: The aim of this study was to investigate the effects of anabolic steroids in conjunction with exercise in the process of spermatogenesis in the testes, using histological and stereological methods. Materials and Methods: Thirty-six male Sprague Dawley rats were divided to six groups, including the control group, the eccentric exercise administered group, the estrogen applied group, the estrogen applied and dissected one hour after eccentric exercise group, the no estrogen applied and dissected 48 hours after eccentric exercise group and the estrogen applied and dissected 48 hours after eccentric exercise group. Eccentric exercise was performed on a motorized rodent treadmill and the estrogen applied groups received daily physiological doses by subcutaneous injections. Testicular tissues were examined using specific histopathological, immunohistochemical and stereological methods. Sections of the testes tissue were stained using the TUNEL method to identify apoptotic cells. Apoptosis was calculated as the percentage of positive cells, using stereological analysis. A statistical analysis of the data was carried out with one-way analysis of variance (ANOVA) for the data obtained from stereological analysis. Results: Conventional light microscopic results revealed that testes tissues of the eccentric exercise administered group and the estrogen supplemented group exhibited slight impairment. In groups that were both eccentrically exercised and estrogen supplemented, more deterioration was detected in testes tissues. Likewise, immunohistochemistry findings were also more prominent in the eccentrically exercised and estrogen supplemented groups. Conclusions: The findings suggest that estrogen supplementation increases damage in testicular tissue due to eccentric exercise. PMID:26023337

Evidence-based knowledge on the aesthetics and maintenance of peri-implant soft tissues: Osteology Foundation Consensus Report Part 1-Effects of soft tissue augmentation procedures on the maintenance of peri-implant soft tissue health.

PubMed

Giannobile, William V; Jung, Ronald E; Schwarz, Frank

2018-03-01

The goal of Working Group 1 at the 2nd Consensus Meeting of the Osteology Foundation was to comprehensively assess the effects of soft tissue augmentation procedures on peri-implant health or disease. A systematic review and meta-analysis on the effects of soft tissue augmentation procedures included a total of 10 studies (mucosal thickness: n = 6; keratinized tissue: n = 4). Consensus statements, clinical recommendations, and implications for future research were based on structured group discussions and a plenary session approval. Soft tissue grafting to increase the width of keratinized tissue around implants was associated with greater reductions in gingival and plaque indices when compared to non-augmented sites. Statistically significant differences were noted for final marginal bone levels in favor of an apically positioned flap plus autogenous graft vs. all standard-of-care control treatments investigated. Soft tissue grafting (i.e., autogenous connective tissue) to increase the mucosal thickness around implants in the aesthetic zone was associated with significantly less marginal bone loss over time, but no significant changes in bleeding on probing, probing depths, or plaque scores when compared to sites without grafting. The limited evidence available supports the use of soft tissue augmentation procedures to promote peri-implant health. © 2018 The Authors. Clinical Oral Implants Research Published by John Wiley & Sons Ltd.

A taxonomy of epithelial human cancer and their metastases

PubMed Central

2009-01-01

Background Microarray technology has allowed to molecularly characterize many different cancer sites. This technology has the potential to individualize therapy and to discover new drug targets. However, due to technological differences and issues in standardized sample collection no study has evaluated the molecular profile of epithelial human cancer in a large number of samples and tissues. Additionally, it has not yet been extensively investigated whether metastases resemble their tissue of origin or tissue of destination. Methods We studied the expression profiles of a series of 1566 primary and 178 metastases by unsupervised hierarchical clustering. The clustering profile was subsequently investigated and correlated with clinico-pathological data. Statistical enrichment of clinico-pathological annotations of groups of samples was investigated using Fisher exact test. Gene set enrichment analysis (GSEA) and DAVID functional enrichment analysis were used to investigate the molecular pathways. Kaplan-Meier survival analysis and log-rank tests were used to investigate prognostic significance of gene signatures. Results Large clusters corresponding to breast, gastrointestinal, ovarian and kidney primary tissues emerged from the data. Chromophobe renal cell carcinoma clustered together with follicular differentiated thyroid carcinoma, which supports recent morphological descriptions of thyroid follicular carcinoma-like tumors in the kidney and suggests that they represent a subtype of chromophobe carcinoma. We also found an expression signature identifying primary tumors of squamous cell histology in multiple tissues. Next, a subset of ovarian tumors enriched with endometrioid histology clustered together with endometrium tumors, confirming that they share their etiopathogenesis, which strongly differs from serous ovarian tumors. In addition, the clustering of colon and breast tumors correlated with clinico-pathological characteristics. Moreover, a signature was developed based on our unsupervised clustering of breast tumors and this was predictive for disease-specific survival in three independent studies. Next, the metastases from ovarian, breast, lung and vulva cluster with their tissue of origin while metastases from colon showed a bimodal distribution. A significant part clusters with tissue of origin while the remaining tumors cluster with the tissue of destination. Conclusion Our molecular taxonomy of epithelial human cancer indicates surprising correlations over tissues. This may have a significant impact on the classification of many cancer sites and may guide pathologists, both in research and daily practice. Moreover, these results based on unsupervised analysis yielded a signature predictive of clinical outcome in breast cancer. Additionally, we hypothesize that metastases from gastrointestinal origin either remember their tissue of origin or adapt to the tissue of destination. More specifically, colon metastases in the liver show strong evidence for such a bimodal tissue specific profile. PMID:20017941

Applications of Mass Spectrometry Imaging for Safety Evaluation.

PubMed

Bonnel, David; Stauber, Jonathan

2017-01-01

Mass spectrometry imaging (MSI) was first derived from techniques used in physics, which were then incorporated into chemistry followed by application in biology. Developed over 50 years ago, and with different principles to detect and map compounds on a sample surface, MSI supports modern biology questions by detecting biological compounds within tissue sections. MALDI (matrix-assisted laser desorption/ionization) imaging trend analysis in this field shows an important increase in the number of publications since 2005, especially with the development of the MALDI imaging technique and its applications in biomarker discovery and drug distribution. With recent improvements of statistical tools, absolute and relative quantification protocols, as well as quality and reproducibility evaluations, MALDI imaging has become one of the most reliable MSI techniques to support drug discovery and development phases. MSI allows to potentially address important questions in drug development such as "What is the localization of the drug and its metabolites in the tissues?", "What is the pharmacological effect of the drug in this particular region of interest?", or "Is the drug and its metabolites related to an atypical finding?" However, prior to addressing these questions using MSI techniques, expertise needs to be developed to become proficient at histological procedures (tissue preparation with frozen of fixed tissues), analytical chemistry, matrix application, instrumentation, informatics, and mathematics for data analysis and interpretation.

Multiscale strain analysis of tissue equivalents using a custom-designed biaxial testing device.

PubMed

Bell, B J; Nauman, E; Voytik-Harbin, S L

2012-03-21

Mechanical signals transferred between a cell and its extracellular matrix play an important role in regulating fundamental cell behavior. To further define the complex mechanical interactions between cells and matrix from a multiscale perspective, a biaxial testing device was designed and built. Finite element analysis was used to optimize the cruciform specimen geometry so that stresses within the central region were concentrated and homogenous while minimizing shear and grip effects. This system was used to apply an equibiaxial loading and unloading regimen to fibroblast-seeded tissue equivalents. Digital image correlation and spot tracking were used to calculate three-dimensional strains and associated strain transfer ratios at macro (construct), meso, matrix (collagen fibril), cell (mitochondria), and nuclear levels. At meso and matrix levels, strains in the 1- and 2-direction were statistically similar throughout the loading-unloading cycle. Interestingly, a significant amplification of cellular and nuclear strains was observed in the direction perpendicular to the cell axis. Findings indicate that strain transfer is dependent upon local anisotropies generated by the cell-matrix force balance. Such multiscale approaches to tissue mechanics will assist in advancement of modern biomechanical theories as well as development and optimization of preconditioning regimens for functional engineered tissue constructs. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Association between promoter hypermethylation of the DACT2 gene and tumor stages in breast cancer.

PubMed

Marusa Borgonio-Cuadra, Veronica; Miranda-Duarte, Antonio; Rojas-Toledo, Xochitl; Garcia-Hernandez, Normand; Alfredo Sierra-Ramirez, Jose; Cardenas-Garcia, Maura; Elena Hernandez-Caballero, Marta

2018-01-01

Aberrant methylation of CpG islands in the promoter is a hallmark of cancer, leading to transcriptional silencing of tumor suppressor genes. The aim of this work was to evaluate the promoter methylation status of the DACT2 gene in breast cancer (BC) tissue and to analyze its possible effect on tumor type or grade. CpG island from the DACT2 promoter in region -240 to -14 from transcriptional start site (TSS) were obtained. Through the use of sodium bisulfite DNA conversion analysis, followed by detection with MSP (methylation specific PCR), we analyzed 79 BC and 15 adjacent healthy samples. T he c ases a nalyzed w ere i n s tage I ( 2.5%), I I (38%), or III (59.5%). The most frequent tumor type was invasive ductal carcinoma (71.4%). Methylation analysis comparing tumor tissues with adjacent non-cancerous tissues showed statistical significance. Methylation was observed in 32.9% (26/79) of the samples; no methylation was found in adjacent healthy tissue. DACT2 methylation was associated with tumor stage I-II (p=0.03) and stage III (p=0.004). An association was found of DACT2 promoter methylation with advanced tumor stages. This gene has been suggested as a potential biomarker, however, more investigation is required to validate this function.

Up-regulated expression of type II very low density lipoprotein receptor correlates with cancer metastasis and has a potential link to β-catenin in different cancers.

PubMed

He, Lei; Lu, Yanjun; Wang, Peng; Zhang, Jun; Yin, Chuanchang; Qu, Shen

2010-11-03

Very low density lipoprotein receptor (VLDLR) has been considered as a multiple function receptor due to binding numerous ligands, causing endocytosis and regulating cellular signaling. Our group previously reported that enhanced activity of type II VLDLR (VLDLR II), one subtype of VLDLR, promotes adenocarcinoma SGC7901 cells proliferation and migration. The aim of this study is to explore the expression levels of VLDLR II in human gastric, breast and lung cancer tissues, and to investigate its relationship with clinical characteristics and β-catenin expression status. VLDLR II expression was examined using immunohistochemistry (IHC) and Western blot in tumor tissues from 213 gastric, breast and lung cancer patients, tumor adjacent noncancerous tissues by same methods. Correlations between VLDLR II and clinical features, as well as β-catenin expression status were evaluated by statistical analysis. The immunohistochemical staining of VLDLR II showed statistical difference between tumor tissues and tumor adjacent noncancerous tissues in gastric, breast and lung cancers (P = 0.034, 0.018 and 0.043, respectively). Moreover, using Western, we found higher VLDLR II expression levels were associated with lymph node and distant metastasis in gastric and breast cancer (P < 0.05). Furthermore, highly significant positive correlations were found between VLDLR II and β-catenin in gastric cancer (r = 0.689; P < 0.001)breast cancer (r = 0.594; P < 0.001). According to the results of the current study, high VLDLR II expression is correlated with lymph node and distant metastasis in gastric and breast cancer patients, the data suggest that VLDLR II may be a clinical marker in cancers, and has a potential link with β-catenin signaling pathway. This is the first to reveal the closer relationship of VLDLR II with clinical information.

An analytical poroelastic model for ultrasound elastography imaging of tumors

NASA Astrophysics Data System (ADS)

Tauhidul Islam, Md; Chaudhry, Anuj; Unnikrishnan, Ginu; Reddy, J. N.; Righetti, Raffaella

2018-01-01

The mechanical behavior of biological tissues has been studied using a number of mechanical models. Due to the relatively high fluid content and mobility, many biological tissues have been modeled as poroelastic materials. Diseases such as cancers are known to alter the poroelastic response of a tissue. Tissue poroelastic properties such as compressibility, interstitial permeability and fluid pressure also play a key role for the assessment of cancer treatments and for improved therapies. At the present time, however, a limited number of poroelastic models for soft tissues are retrievable in the literature, and the ones available are not directly applicable to tumors as they typically refer to uniform tissues. In this paper, we report the analytical poroelastic model for a non-uniform tissue under stress relaxation. Displacement, strain and fluid pressure fields in a cylindrical poroelastic sample containing a cylindrical inclusion during stress relaxation are computed. Finite element simulations are then used to validate the proposed theoretical model. Statistical analysis demonstrates that the proposed analytical model matches the finite element results with less than 0.5% error. The availability of the analytical model and solutions presented in this paper may be useful to estimate diagnostically relevant poroelastic parameters such as interstitial permeability and fluid pressure, and, in general, for a better interpretation of clinically-relevant ultrasound elastography results.

Robust demarcation of basal cell carcinoma by dependent component analysis-based segmentation of multi-spectral fluorescence images.

PubMed

Kopriva, Ivica; Persin, Antun; Puizina-Ivić, Neira; Mirić, Lina

2010-07-02

This study was designed to demonstrate robust performance of the novel dependent component analysis (DCA)-based approach to demarcation of the basal cell carcinoma (BCC) through unsupervised decomposition of the red-green-blue (RGB) fluorescent image of the BCC. Robustness to intensity fluctuation is due to the scale invariance property of DCA algorithms, which exploit spectral and spatial diversities between the BCC and the surrounding tissue. Used filtering-based DCA approach represents an extension of the independent component analysis (ICA) and is necessary in order to account for statistical dependence that is induced by spectral similarity between the BCC and surrounding tissue. This generates weak edges what represents a challenge for other segmentation methods as well. By comparative performance analysis with state-of-the-art image segmentation methods such as active contours (level set), K-means clustering, non-negative matrix factorization, ICA and ratio imaging we experimentally demonstrate good performance of DCA-based BCC demarcation in two demanding scenarios where intensity of the fluorescent image has been varied almost two orders of magnitude. Copyright 2010 Elsevier B.V. All rights reserved.

Texture analysis of pulmonary parenchyma in normal and emphysematous lung

NASA Astrophysics Data System (ADS)

Uppaluri, Renuka; Mitsa, Theophano; Hoffman, Eric A.; McLennan, Geoffrey; Sonka, Milan

1996-04-01

Tissue characterization using texture analysis is gaining increasing importance in medical imaging. We present a completely automated method for discriminating between normal and emphysematous regions from CT images. This method involves extracting seventeen features which are based on statistical, hybrid and fractal texture models. The best subset of features is derived from the training set using the divergence technique. A minimum distance classifier is used to classify the samples into one of the two classes--normal and emphysema. Sensitivity and specificity and accuracy values achieved were 80% or greater in most cases proving that texture analysis holds great promise in identifying emphysema.

Biomechanical influence of crown-to-implant ratio on stress distribution over internal hexagon short implant: 3-D finite element analysis with statistical test.

PubMed

Ramos Verri, Fellippo; Santiago Junior, Joel Ferreira; de Faria Almeida, Daniel Augusto; de Oliveira, Guilherme Bérgamo Brandão; de Souza Batista, Victor Eduardo; Marques Honório, Heitor; Noritomi, Pedro Yoshito; Pellizzer, Eduardo Piza

2015-01-02

The study of short implants is relevant to the biomechanics of dental implants, and research on crown increase has implications for the daily clinic. The aim of this study was to analyze the biomechanical interactions of a singular implant-supported prosthesis of different crown heights under vertical and oblique force, using the 3-D finite element method. Six 3-D models were designed with Invesalius 3.0, Rhinoceros 3D 4.0, and Solidworks 2010 software. Each model was constructed with a mandibular segment of bone block, including an implant supporting a screwed metal-ceramic crown. The crown height was set at 10, 12.5, and 15 mm. The applied force was 200 N (axial) and 100 N (oblique). We performed an ANOVA statistical test and Tukey tests; p<0.05 was considered statistically significant. The increase of crown height did not influence the stress distribution on screw prosthetic (p>0.05) under axial load. However, crown heights of 12.5 and 15 mm caused statistically significant damage to the stress distribution of screws and to the cortical bone (p<0.001) under oblique load. High crown to implant (C/I) ratio harmed microstrain distribution on bone tissue under axial and oblique loads (p<0.001). Crown increase was a possible deleterious factor to the screws and to the different regions of bone tissue. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spatial-frequency Fourier polarimetry of the complex degree of mutual anisotropy of linear and circular birefringence in the diagnostics of oncological changes in morphological structure of biological tissues

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

Ushenko, Yu A; Gorskii, M P; Dubolazov, A V

2012-08-31

Theory of polarisation-correlation analysis of laser images of histological sections of biopsy material from cervix tissue based on spatial frequency selection of linear and circular birefringence mechanisms is formulated. Comparative results of measuring the coordinate distributions of the complex degree of mutual anisotropy (CDMA), produced by fibrillar networks formed by myosin and collagen fibres of cervix tissue in different pathological conditions, namely, pre-cancer (dysplasia) and cancer (adenocarcinoma), are presented. The values and variation ranges of statistical (moments of the first - fourth order), correlation (excess-autocorrelation functions), and fractal (slopes of approximating curves and dispersion of extrema of logarithmic dependences ofmore » power spectra) parameters of the CDMA coordinate distributions are studied. Objective criteria for pathology diagnostics and differentiation of its severity degree are determined. (image processing)« less

Spatial-frequency Fourier polarimetry of the complex degree of mutual anisotropy of linear and circular birefringence in the diagnostics of oncological changes in morphological structure of biological tissues

NASA Astrophysics Data System (ADS)

Ushenko, Yu A.; Gorskii, M. P.; Dubolazov, A. V.; Motrich, A. V.; Ushenko, V. A.; Sidor, M. I.

2012-08-01

Theory of polarisation-correlation analysis of laser images of histological sections of biopsy material from cervix tissue based on spatial frequency selection of linear and circular birefringence mechanisms is formulated. Comparative results of measuring the coordinate distributions of the complex degree of mutual anisotropy (CDMA), produced by fibrillar networks formed by myosin and collagen fibres of cervix tissue in different pathological conditions, namely, pre-cancer (dysplasia) and cancer (adenocarcinoma), are presented. The values and variation ranges of statistical (moments of the first — fourth order), correlation (excess-autocorrelation functions), and fractal (slopes of approximating curves and dispersion of extrema of logarithmic dependences of power spectra) parameters of the CDMA coordinate distributions are studied. Objective criteria for pathology diagnostics and differentiation of its severity degree are determined.

PTEN Loss as Determined by Clinical-grade Immunohistochemistry Assay Is Associated with Worse Recurrence-free Survival in Prostate Cancer

PubMed Central

Lotan, Tamara L.; Wei, Wei; Morais, Carlos L.; Hawley, Sarah T.; Fazli, Ladan; Hurtado-Coll, Antonio; Troyer, Dean; McKenney, Jesse K.; Simko, Jeffrey; Carroll, Peter R.; Gleave, Martin; Lance, Raymond; Lin, Daniel W.; Nelson, Peter S.; Thompson, Ian M.; True, Lawrence D.; Feng, Ziding; Brooks, James D.

2015-01-01

Background PTEN is the most commonly deleted tumor suppressor gene in primary prostate cancer (PCa) and its loss is associated with poor clinical outcomes and ERG gene rearrangement. Objective We tested whether PTEN loss is associated with shorter recurrence-free survival (RFS) in surgically treated PCa patients with known ERG status. Design, setting, and participants A genetically validated, automated PTEN immunohistochemistry (IHC) protocol was used for 1275 primary prostate tumors from the Canary Foundation retrospective PCa tissue microarray cohort to assess homogeneous (in all tumor tissue sampled) or heterogeneous (in a subset of tumor tissue sampled) PTEN loss. ERG status as determined by a genetically validated IHC assay was available for a subset of 938 tumors. Outcome measurements and statistical analysis Associations between PTEN and ERG status were assessed using Fisher’s exact test. Kaplan-Meier and multivariate weighted Cox proportional models for RFS were constructed. Results and limitations When compared to intact PTEN, homogeneous (hazard ratio [HR] 1.66, p = 0.001) but not heterogeneous (HR 1.24, p = 0.14) PTEN loss was significantly associated with shorter RFS in multivariate models. Among ERG-positive tumors, homogeneous (HR 3.07, p < 0.0001) but not heterogeneous (HR 1.46, p = 0.10) PTEN loss was significantly associated with shorter RFS. Among ERG-negative tumors, PTEN did not reach significance for inclusion in the final multivariate models. The interaction term for PTEN and ERG status with respect to RFS did not reach statistical significance (p = 0.11) for the current sample size. Conclusions These data suggest that PTEN is a useful prognostic biomarker and that there is no statistically significant interaction between PTEN and ERG status for RFS. Patient summary We found that loss of the PTEN tumor suppressor gene in prostate tumors as assessed by tissue staining is correlated with shorter time to prostate cancer recurrence after radical prostatectomy. PMID:27617307

[Treating high angle bimaxillary protrusion with three kinds of extraction method: a clinical study].

PubMed

Dai, Jia-Yin; Zhang, Miao-Miao; Sun, Miao; Ni, Hui

2009-06-01

To compare the effect of three kinds of extraction model on high angle bimaxillary protrusion patients. A total of 30 patients with Class I malocclusion and bimaxillary protrusion, aged 14-25 years old, were selected and divided into three groups. Four first premolars were extracted in the first group. The two maxillary first premolars and two mandibular first molars were extracted in the second group. The two maxillary first premolars and two mandibular first molars were extracted in the third group, and two additional micro-implants used as orthodontic anchorage in maxilla. Three groups were all treated with MBT appliance. Cephalometric analysis were carried out before and after treatment, and the results were analyzed with statistics. 1) About the hard tissues, compared with the first group, there were statistically significant differences of N-Me, SGo/NMe, ANS-Me, FH/MP, SN/MP, and ODI in the second and the third group after treatment (P<0.01). 2) About the soft tissues, the teeth and the alveolar bone, compared with the first group, there were statistically significant differences of Pg-Pos, Li-SnPos, Si-LiPos, LL-E, L1-NB, L1/NB, U1/L1, L7-MP in the second and the third group after treatment (P<0.01). 3) All patients received consummate orthodontic treatment and obtained fine occlusion. Facial profiles were improved significantly after orthodontic treatment. 1) After orthodontic treatment with mandibular first molars extraction, FH/MP, SN/MP, N-Me, ANS-Me, L1-NB and L1/NB decreased respectively, and soft tissue profiles were improved significantly. 2) Additional micro-implant used as orthodontic anchorage in maxilla significantly contributed to the maxillary incisor retraction and subsequent soft tissue change. 3) The first molars extraction and additional micro-implant used as orthodontic anchorage are efficient in improving the facial profiles for high angle bimaxillary protrusion patients.

Morphological texture assessment of oral bone as a screening tool for osteoporosis

NASA Astrophysics Data System (ADS)

Analoui, Mostafa; Eggertsson, Hafsteinn; Eckert, George

2001-07-01

Three classes of texture analysis approaches have been employed to assess the textural characteristic of oral bone. A set of linear structuring elements was used to compute granulometric features of trabecular bone. Multifractal analysis was also used to compute the fractal dimension of the corresponding tissues. In addition, some statistical features and histomorphometric parameters were computed. To assess the proposed approach we acquired digital intraoral radiographs of 47 subjects (14 males and 33 females). All radiographs were captured at 12 bits/pixel. Images were converted to binary form through a sliding locally adaptive thresholding approach. Each subject was scanned by DEXA for bone dosimetry. Subject were classified into one of the following three categories according World Health Organization (WHO) standard (1) healthy, (2) with osteopenia and (3) osteoporosis. In this study fractal dimension showed very low correlation with bone mineral density (BMD) measurements, which did not reach a level of statistical significance (p<0.5). However, entropy of pattern spectrum (EPS), along with statistical features and histomorphometric parameters, has shown correlation coefficients ranging from low to high, with statistical significance for both males and females. The results of this study indicate the utility of this approach for bone texture analysis. It is conjectured that designing a 2-D structuring element, specially tuned to trabecular bone texture, will increase the efficacy of the proposed method.

Modelling short time series in metabolomics: a functional data analysis approach.

PubMed

Montana, Giovanni; Berk, Maurice; Ebbels, Tim

2011-01-01

Metabolomics is the study of the complement of small molecule metabolites in cells, biofluids and tissues. Many metabolomic experiments are designed to compare changes observed over time under two or more experimental conditions (e.g. a control and drug-treated group), thus producing time course data. Models from traditional time series analysis are often unsuitable because, by design, only very few time points are available and there are a high number of missing values. We propose a functional data analysis approach for modelling short time series arising in metabolomic studies which overcomes these obstacles. Our model assumes that each observed time series is a smooth random curve, and we propose a statistical approach for inferring this curve from repeated measurements taken on the experimental units. A test statistic for detecting differences between temporal profiles associated with two experimental conditions is then presented. The methodology has been applied to NMR spectroscopy data collected in a pre-clinical toxicology study.

Expression of survivin and clinical correlation in patients with breast cancer.

PubMed

Sohn, Doo Min; Kim, Sung Yong; Baek, Moo Jun; Lim, Cheol Wan; Lee, Min Hyuk; Cho, Moo Sik; Kim, Tae Yoon

2006-07-01

Survivin is a member of the inhibitor of apoptosis (IAP) family, which is also involved in the regulation of cell division and is also overexpressed and associated with parameters of poor prognosis in most human cancers, including carcinomas of the lung, breast, colon, stomach, esophagus and pancreas. This study examined the expression patterns of survivin in normal breast tissue, atypical hyperplasia, primary breast cancer and lymph node tissues involved in breast cancer and determined whether the expression of survivin is associated with the characteristics and prognosis of breast cancer. Formalin-fixed paraffin-embedded samples from 80 breast cancer, 20 atypical hyperplasia and 20 malignant lymph node tissue cases were immunostained using polyclonal survivin (Novus Biologicals, CO, USA). The degree of immunostaining was recorded on a scale of 0-3 according to the percentages of staining and distributions within the cytoplasm and nucleus. Survivin was expressed in 52, 14 and 17 of the 80 breast cancer (65%), atypical hyperplasia (70%) and breast cancer lymphoid (85%) specimens, respectively. Among those expressing cancer, 11.3%, 31.3% and 22.5% demonstrated only nuclear staining, only cytoplasmic staining and both nuclear and cytoplasmic staining, respectively. A statistical analysis revealed that cytoplasmic survivin expression was correlated with the stage, histological grade and L/N metastasis. In a Cox proportional hazard model analysis, the expression of survivin was not identified as a significant independent predictor of overall survival (P=0.168), although the decrease in the survival rate of survivin-positive patients did reach statistical significance (P=0.048). our results show that survivin is frequently overexpressed in primary breast cancer and its expression gradually increased from normal breast tissue to malignant lymph nodes. The expression of cytoplasmic survivin was common in breast cancer and could be both a useful diagnostic marker and an important source of prognostic information.

Immunohistochemical evaluation of myofibroblasts in odontogenic cysts and tumors: A comparative study

PubMed Central

Syamala, Deepa; Suresh, Rakesh; Janardhanan, Mahija; Savithri, Vindhya; Anand, Prem P; Jose, Amrutha

2016-01-01

Context: Myofibroblasts are fibroblasts with smooth muscle-like features characterized by the presence of a contractile apparatus and found in the connective tissue stroma of normal tissues such as blood vessels and lymph nodes. They are now thought to play a role in the synthesis and reorganization of extracellular matrix, which could contribute to the aggressive biologic behavior of the lesions. Aims: To compare the mean number of stromal myofibroblasts in dentigerous cysts (DCs), keratocystic odontogenic tumor (KCOT) and ameloblastoma; and to derive a correlation between the stromal myofibroblasts and the known biologic behavior of the lesions. Settings and Design: A cross-sectional immunohistochemical analysis of cases of DC, KCOT and ameloblastoma. Materials and Methods: Twenty paraffin-embedded tissue blocks each of DC, KCOT and multicystic ameloblastoma were selected for the study and diagnosis confirmed through hematoxylin and eosin staining. Tissue sections were analyzed for the number of myofibroblasts using alpha smooth muscle actin (α-SMA) immunostaining. Statistical Analysis: Differences in the mean number of α-SMA positive cells in each group were analyzed using one-way ANOVA test. Intergroup comparisons of mean values of α-SMA positive cells were performed using Mann-Whitney U-test. Results: Ameloblastoma showed the highest number of myofibroblasts, whereas DC showed the lowest. Among the groups, there were significant differences between the myofibroblast counts among DC and KCOT and between DC and ameloblastoma, whereas the difference in counts was not statistically significant between KCOT and ameloblastoma. A positive correlation was observed between the myofibroblast count and the known biologic behavior of the lesions. Conclusion: Myofibroblasts may act in close association with the epithelial cells to bring about changes in stromal microenvironment, favorable to the growth and progression of the lesion. They may be of great value in predicting the biologic behavior and growth potential of such lesions. PMID:27601810

Is CD147 a New Biomarker Reflecting Histological Malignancy of Gliomas?

PubMed

Kong, Xiangyi; Wang, Yu; Dai, Congxin; Ma, Wenbin; Wang, Renzhi

2017-03-01

CD147 belongs to immunoglobulin superfamily and can stimulate the surrounding fibroblasts to secret matrix metalloproteinases (MMPs). Studies showed that when compared with their normal counterparts, CD47 expression level increased in lung carcinoma tissue, breast cancer tissue, and bladder cancer tissue. They increase in line with a tumor's malignant progression, invasiveness, and metastasis. However, the precise implications and utility of the presence of CD147 in the WHO grading system for gliomas have rarely been reported; in addition, the signal transduction pathways regarding CD147 remain unclear and controversial. Thus, in performing a meta-analysis, it is essential to reach a reliable conclusion. The related literatures were incorporated into the present meta-analysis after careful assessment, and odds ratios (ORs) with 95 % confidence intervals (95 % CIs) were calculated. Heterogeneity evaluation was estimated. Ten studies involving 615 patients were found to be eligible, nine of which were conducted in China and the remaining one in Japan. Analysis of eight studies involving dichotomous data revealed that CD147 overexpression in glioma tissue was related to higher WHO grading (III + IV; OR, 9.900; 95 % CI, 5.943, 16.491; P = 0.000) closely, whereas analysis of three studies of continuous data type indicated that there were no statistical associations (standard mean difference, -1.894; 95 % CI, -4.081, 0.293; P = 0.090). In accordance with funnel plot, Egger test, and Begg test, there was no publication bias. Considering that the continuous data make up only a small proportion of the overall analysis, we believe that our study indicates that CD147 overexpression is potentially related to higher WHO grade. Certainly, more data compiled based on evidence-based medicine are required to further support this conclusion.

Prevention of the Posttraumatic Fibrotic Response in Joints

DTIC Science & Technology

2015-10-01

surgical procedures and subsequent collection of tissues have been developed and are currently used on a regular basis. Major Task 4: Evaluating the...needed to evaluate the utility of the inhibitory antibody to reduce the flexion contracture of injured knee joints. The employed techniques include...second surgery to remove a pin, and it did not change by the end of the 32nd week 1. Major Task 5: Task 4. Data analysis and statistical evaluation

Chemokine-like factor-like MARVEL transmembrane domain-containing 3 expression is associated with a favorable prognosis in esophageal squamous cell carcinoma.

PubMed

Han, Tianci; Shu, Tianci; Dong, Siyuan; Li, Peiwen; Li, Weinan; Liu, Dali; Qi, Ruiqun; Zhang, Shuguang; Zhang, Lin

2017-05-01

Decreased expression of human chemokine-like factor-like MARVEL transmembrane domain-containing 3 (CMTM3) has been identified in a number of human tumors and tumor cell lines, including gastric and testicular cancer, and PC3, CAL27 and Tca-83 cell lines. However, the association between CMTM3 expression and the clinicopathological features and prognosis of esophageal squamous cell carcinoma (ESCC) patients remains unclear. The aim of the present study was to investigate the correlation between CMTM3 expression and clinicopathological parameters and prognosis in ESCC. CMTM3 mRNA and protein expression was analyzed in ESCC and paired non-tumor tissues by quantitative real-time polymerase chain reaction, western blotting and immunohistochemical analysis. The Kaplan-Meier method was used to plot survival curves and the Cox proportional hazards regression model was also used for univariate and multivariate survival analysis. The results revealed that CMTM3 mRNA and protein expression levels were lower in 82.5% (30/40) and 75% (30/40) of ESCC tissues, respectively, when compared with matched non-tumor tissues. Statistical analysis demonstrated that CMTM3 expression was significantly correlated with lymph node metastasis (P=0.002) and clinical stage (P<0.001) in ESCC tissues. Furthermore, the survival time of ESCC patients exhibiting low CMTM3 expression was significantly shorter than that of ESCC patients exhibiting high CMTM3 expression (P=0.01). In addition, Kaplan-Meier survival analysis revealed that the overall survival time of patients exhibiting low CMTM3 expression was significantly decreased compared with patients exhibiting high CMTM3 expression (P=0.010). Cox multivariate analysis indicated that CMTM3 protein expression was an independent prognostic predictor for ESCC after resection. This study indicated that CMTM3 expression is significantly decreased in ESCC tissues and CMTM3 protein expression in resected tumors may present an effective prognostic biomarker.

Dimensional Changes of Fresh Sockets With Reactive Soft Tissue Preservation: A Cone Beam CT Study.

PubMed

Crespi, Roberto; Capparé, Paolo; Crespi, Giovanni; Gastaldi, Giorgio; Gherlone, Enrico Felice

2017-06-01

The aim of this study was to assess dimensional changes of the fresh sockets grafted with collagen sheets and maintenance of reactive soft tissue, using cone beam computed tomography (CBCT). Tooth extractions were performed with maximum preservation of the alveolar housing, reactive soft tissue was left into the sockets and collagen sheets filled bone defects. Cone beam computed tomography were performed before and 3 months after extractions. One hundred forty-five teeth, 60 monoradiculars and 85 molars, were extracted. In total, 269 alveoli were evaluated. In Group A, not statistically significant differences were found between monoradiculars, whereas statistically significant differences (P < 0.05) were found between molars, both for mesial and distal alveoli. In Group B, not statistically significant differences were found between maxillary and mandibular bone changes values (P > 0.05) for all types of teeth. This study reported an atraumatic tooth extraction, reactive soft tissue left in situ, and grafted collagen sponge may be helpful to reduce fresh socket collapse after extraction procedures.

Biocompatibility of Ricinus communis polymer with addition of calcium carbonate compared to titanium. Experimental study in guinea pigs

PubMed Central

Graça, Yorgos Luiz Santos De Salles; Opolski, Ana Cristina; Barboza, Barbara Evelin Gonçalves; Erbano, Bruna Olandoski; Mazzaro, Caroline Cantalejo; Klostermann, Flávia Caroline; Sucharski, Enéas Eduardo; Kubrusly, Luiz Fernando

2014-01-01

Objective The aim of the present investigation was to determine whether the difference in inflammatory tissue reaction between the Riccinus communis (castor) polymer with calcium carbonate and the titanium implant is statistically significant. Methods Thirty-two Cavia porcellus were allocated into four groups of eight animals each. We implanted the two types of materials in the retroperitoneal space of all the animals. They were euthanized at 7, 20, 30 and 40 days after surgery, and an histological study of the samples was conducted. Results All implants showed characteristics of chronic inflammation regardless of the material and timepoint of evaluation. There was no statistically significant difference between Pm+CaCO3 and Ti with regard to the presence of granulation tissue, tissue congestion, histiocytes, lymphocytes, neutrophils, giant cells, and fibrosis (P> 0.05). Conclusion The castor oil polymer plus calcium carbonate implant was not statistically different from the titanium implant regarding inflammatory tissue reaction. PMID:25140479

Changes in ultrasound shear wave elastography properties of normal breast during menstrual cycle.

PubMed

Rzymski, P; Skórzewska, A; Opala, T

2011-01-01

Elastography is a novel technique capable of noninvasively assessing the elastic properties of breast tissue. Because the risk factors for breast cancer include hormonal status and proliferation, the aim of our study was to estimate the intensity of sonoelastographic changes during the menstrual cycle. Eight women aged 20-23 years with regular menstrual cycles underwent B-mode sonography and sonoelastography (ShearWave on Aixplorer, France) on days 3, 10, 17 and 24. Mean values of glandular and fat tissue elasticity did not change statistically significantly during the menstrual cycle as well as glandular to fat tissue ratio. During almost the whole cycle differences between outer and inner quadrants in glandular and fat tissue were statistically significant. The lowest values of elasticity occurred on the 10th day and the highest on the 24th of the menstrual cycle. There were statistically significant differences in elasticity between inner and outer quadrants of both breasts close to day 3 and 17 of the menstrual cycle.

Direct spectrometry: a new alternative for measuring the fluorescence of composite resins and dental tissues.

PubMed

da Silva, Tm; de Oliveira, Hpm; Severino, D; Balducci, I; Huhtala, Mfrl; Gonçalves, Sep

2014-01-01

The aim of this study was to evaluate the fluorescence intensity of different composite resins and compare those values with the fluorescence intensity of dental tissues. Different composite resins were used to make 10 discs (2 mm in depth and 4 mm in diameter) of each brand, divided into groups: 1) Z (Filtek Z350, 3M ESPE), 2) ES (Esthet-X, Dentsply), 3) A (Amelogen Plus, Ultradent), 4) DVS (Durafill-VS, Heraeus Kulzer) with 2 mm composite resin for enamel (A2), 5) OES ([Esthet-X] opaque-OA [1 mm] + enamel-A2 [1 mm]); 6) ODVSI ([Charisma-Opal/Durafill-VSI], opaque-OM (1 mm) + translucent [1mm]), and 7) DVSI ([Durafill- VSI] translucent [2 mm]). Dental tissue specimens were obtained from human anterior teeth cut in a mesiodistal direction to obtain enamel, dentin, and enamel/dentin samples (2 mm). The fluorescence intensity of specimens was directly measured using an optic fiber associated with a spectrometer (Ocean Optics USB 4000) and recorded in graphic form (Origin 8.0 program). Data were submitted to statistical analysis using Dunnet, Tukey, and Kruskall-Wallis tests. Light absorption of the composite resins was obtained in a spectral range from 250 to 450 nm, and that of dental tissues was between 250 and 300 nm. All composite resins were excited at 398 nm and exhibited maximum emissions of around 485 nm. Fluorescence intensity values for all of the resins showed statistically significant differences (measured in arbitrary units [AUs]), with the exception of groups Z and DVS. Group DVSI had the highest fluorescence intensity values (13539 AU), followed by ODVS (10440 AU), DVS (10146 AU), ES (3946 AU), OES (3841 AU), A (3540 AU), and Z (1146 AU). The fluorescence intensity values for the composite resins differed statistically from those of dental tissues (E=1380 AU; D=6262 AU; E/D=3251 AU). The opacity interfered with fluorescence intensity, and group Z demonstrated fluorescence intensity values closest to that of tooth enamel. It is concluded that the fluorescence intensity values were significantly different among the composite resins and compared with dental tissues. The direct spectrofluorimetric method represents a tool for evaluating the fluorescence of composite resins.

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.

PubMed

Merelli, Ivan; Caprera, Andrea; Stella, Alessandra; Del Corvo, Marcello; Milanesi, Luciano; Lazzari, Barbara

2009-10-15

The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can be inspected according to biologically relevant criteria. EST data can be browsed using different dedicated web resources, which allow to investigate library specific gene expression levels and to make comparisons among libraries, highlighting significant differences in gene expression. Nonetheless, no tool is available to examine distributions of quantitative EST collections in Gene Ontology (GO) categories, nor to retrieve information concerning library-dependent EST involvement in metabolic pathways. In this work we present the Human EST Ontology Explorer (HEOE) http://www.itb.cnr.it/ptp/human_est_explorer, a web facility for comparison of expression levels among libraries from several healthy and diseased tissues. The HEOE provides library-dependent statistics on the distribution of sequences in the GO Direct Acyclic Graph (DAG) that can be browsed at each GO hierarchical level. The tool is based on large-scale BLAST annotation of EST sequences. Due to the huge number of input sequences, this BLAST analysis was performed with the aid of grid computing technology, which is particularly suitable to address data parallel task. Relying on the achieved annotation, library-specific distributions of ESTs in the GO Graph were inferred. A pathway-based search interface was also implemented, for a quick evaluation of the representation of libraries in metabolic pathways. EST processing steps were integrated in a semi-automatic procedure that relies on Perl scripts and stores results in a MySQL database. A PHP-based web interface offers the possibility to simultaneously visualize, retrieve and compare data from the different libraries. Statistically significant differences in GO categories among user selected libraries can also be computed. The HEOE provides an alternative and complementary way to inspect EST expression levels with respect to approaches currently offered by other resources. Furthermore, BLAST computation on the whole human EST dataset was a suitable test of grid scalability in the context of large-scale bioinformatics analysis. The HEOE currently comprises sequence analysis from 70 non-normalized libraries, representing a comprehensive overview on healthy and unhealthy tissues. As the analysis procedure can be easily applied to other libraries, the number of represented tissues is intended to increase.

Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images.

PubMed

Nandy, Kaustav; Gudla, Prabhakar R; Amundsen, Ryan; Meaburn, Karen J; Misteli, Tom; Lockett, Stephen J

2012-09-01

Analysis of preferential localization of certain genes within the cell nuclei is emerging as a new technique for the diagnosis of breast cancer. Quantitation requires accurate segmentation of 100-200 cell nuclei in each tissue section to draw a statistically significant result. Thus, for large-scale analysis, manual processing is too time consuming and subjective. Fortuitously, acquired images generally contain many more nuclei than are needed for analysis. Therefore, we developed an integrated workflow that selects, following automatic segmentation, a subpopulation of accurately delineated nuclei for positioning of fluorescence in situ hybridization-labeled genes of interest. Segmentation was performed by a multistage watershed-based algorithm and screening by an artificial neural network-based pattern recognition engine. The performance of the workflow was quantified in terms of the fraction of automatically selected nuclei that were visually confirmed as well segmented and by the boundary accuracy of the well-segmented nuclei relative to a 2D dynamic programming-based reference segmentation method. Application of the method was demonstrated for discriminating normal and cancerous breast tissue sections based on the differential positioning of the HES5 gene. Automatic results agreed with manual analysis in 11 out of 14 cancers, all four normal cases, and all five noncancerous breast disease cases, thus showing the accuracy and robustness of the proposed approach. Published 2012 Wiley Periodicals, Inc.

Automated Tissue Classification Framework for Reproducible Chronic Wound Assessment

PubMed Central

Mukherjee, Rashmi; Manohar, Dhiraj Dhane; Das, Dev Kumar; Achar, Arun; Mitra, Analava; Chakraborty, Chandan

2014-01-01

The aim of this paper was to develop a computer assisted tissue classification (granulation, necrotic, and slough) scheme for chronic wound (CW) evaluation using medical image processing and statistical machine learning techniques. The red-green-blue (RGB) wound images grabbed by normal digital camera were first transformed into HSI (hue, saturation, and intensity) color space and subsequently the “S” component of HSI color channels was selected as it provided higher contrast. Wound areas from 6 different types of CW were segmented from whole images using fuzzy divergence based thresholding by minimizing edge ambiguity. A set of color and textural features describing granulation, necrotic, and slough tissues in the segmented wound area were extracted using various mathematical techniques. Finally, statistical learning algorithms, namely, Bayesian classification and support vector machine (SVM), were trained and tested for wound tissue classification in different CW images. The performance of the wound area segmentation protocol was further validated by ground truth images labeled by clinical experts. It was observed that SVM with 3rd order polynomial kernel provided the highest accuracies, that is, 86.94%, 90.47%, and 75.53%, for classifying granulation, slough, and necrotic tissues, respectively. The proposed automated tissue classification technique achieved the highest overall accuracy, that is, 87.61%, with highest kappa statistic value (0.793). PMID:25114925

A standardised protocol for texture feature analysis of endoscopic images in gynaecological cancer.

PubMed

Neofytou, Marios S; Tanos, Vasilis; Pattichis, Marios S; Pattichis, Constantinos S; Kyriacou, Efthyvoulos C; Koutsouris, Dimitris D

2007-11-29

In the development of tissue classification methods, classifiers rely on significant differences between texture features extracted from normal and abnormal regions. Yet, significant differences can arise due to variations in the image acquisition method. For endoscopic imaging of the endometrium, we propose a standardized image acquisition protocol to eliminate significant statistical differences due to variations in: (i) the distance from the tissue (panoramic vs close up), (ii) difference in viewing angles and (iii) color correction. We investigate texture feature variability for a variety of targets encountered in clinical endoscopy. All images were captured at clinically optimum illumination and focus using 720 x 576 pixels and 24 bits color for: (i) a variety of testing targets from a color palette with a known color distribution, (ii) different viewing angles, (iv) two different distances from a calf endometrial and from a chicken cavity. Also, human images from the endometrium were captured and analysed. For texture feature analysis, three different sets were considered: (i) Statistical Features (SF), (ii) Spatial Gray Level Dependence Matrices (SGLDM), and (iii) Gray Level Difference Statistics (GLDS). All images were gamma corrected and the extracted texture feature values were compared against the texture feature values extracted from the uncorrected images. Statistical tests were applied to compare images from different viewing conditions so as to determine any significant differences. For the proposed acquisition procedure, results indicate that there is no significant difference in texture features between the panoramic and close up views and between angles. For a calibrated target image, gamma correction provided an acquired image that was a significantly better approximation to the original target image. In turn, this implies that the texture features extracted from the corrected images provided for better approximations to the original images. Within the proposed protocol, for human ROIs, we have found that there is a large number of texture features that showed significant differences between normal and abnormal endometrium. This study provides a standardized protocol for avoiding any significant texture feature differences that may arise due to variability in the acquisition procedure or the lack of color correction. After applying the protocol, we have found that significant differences in texture features will only be due to the fact that the features were extracted from different types of tissue (normal vs abnormal).

High Rab27A expression indicates favorable prognosis in CRC.

PubMed

Shi, Chuanbing; Yang, Xiaojun; Ni, Yijiang; Hou, Ning; Xu, Li; Zhan, Feng; Zhu, Huijun; Xiong, Lin; Chen, Pingsheng

2015-06-13

Rab27A is a peculiar member in Rab family and has been suggested to play essential roles in the development of human cancers. However, the association between Rab27A expression and clinicopathological characteristics of colorectal cancer (CRC) has not been elucidated yet. One-step quantitative real-time polymerase chain reaction (qPCR) test with 18 fresh-frozen CRC samples and immunohistochemistry (IHC) analysis in 112 CRC cases were executed to evaluate the relationship between Rab27A expression and the clinicopathological features of CRC. Cox regression and Kaplan-Meier survival analyses were performed to identify the prognostic factors for 112 CRC patients. The results specified that the expression levels of Rab27A mRNA and protein were significantly higher in CRC tissues than that in matched non-cancerous tissues, in both qPCR test (p = 0.029) and IHC analysis (p = 0.020). The IHC data indicated that the Rab27A protein expression in CRC was statistically correlated with lymph node metastasis (p = 0.022) and TNM stage (p = 0.026). Cox multi-factor analysis and Kaplan-Meier method suggested Rab27A protein expression (p = 0.012) and tumor differentiation (p = 0.004) were significantly associated with the overall survival of CRC patients. The data indicated the differentiate expression of Rab27A in CRC tissues and matched non-cancerous tissues. Rab27A may be used as a valuable prognostic biomarker for CRC patients.

Chemometric evaluation of concentrations of trace elements in intervertebral disc tissue in patient with degenerative disc disease.

PubMed

Kubaszewski, Łukasz; Zioła-Frankowska, Anetta; Gasik, Zuzanna; Frankowski, Marcin; Dąbrowski, Mikołaj; Molisak, Bartłomiej; Kaczmarczyk, Jacek; Gasik, Robert

2017-12-23

The work is designed to uncover the pattern of mutual relation among trace elements and epidemiological data in the degenerated intervertebral disk tissue in humans. Hitherto the reason of the degenerative process is not fully understood. Trace elements are the basic components of the biological compound related both its metabolism as well as environmental exposure. The relation pattern among elements occurs gives new perspective in solving the cause of the disease. We have analysed trace elements content in the 30 intervertebral disc from 22 patients with degenerative disc disease. The concentrations of Al, Cu, Cd, Mo, Ni and Pb were determined with Atomic Absorption Spectrometry. To analyse the multidimentional relation between trace element concentration and epidemiological data the chemometric analysis was applied. The similarity have been shown in occurrence of following pairs: Cd-Mo as well as Mg-Zn. The second pair was correlated with Pb concentration. Pb levels are observed to be competitive to Cu concentration. Cd concentration was related to Zn and Mg deficiency. No single but rather cluster of epidemiological data show observable influence on the TE tissue variance. Zn and Cu was related to the male sex. Operation with orthopedic implants were related to combined Al, Mo and Zn concentration. This is the first chemometric analysis of trace elements in disk tissue. It shows multidimentional relations that are missed by the classical statistic. The analysis shows significant relation. The nature of the relations is the basis for further metabolic and environmental research.

System of polarization correlometry of polycrystalline layers of urine in the differentiation stage of diabetes

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Pashkovskaya, N. V.; Marchuk, Y. F.; Dubolazov, O. V.; Savich, V. O.

2015-08-01

The work consists of investigation results of diagnostic efficiency of a new azimuthally stable Muellermatrix method of analysis of laser autofluorescence coordinate distributions of biological liquid layers. A new model of generalized optical anisotropy of biological tissues protein networks is proposed in order to define the processes of laser autofluorescence. The influence of complex mechanisms of both phase anisotropy (linear birefringence and optical activity) and linear (circular) dichroism is taken into account. The interconnections between the azimuthally stable Mueller-matrix elements characterizing laser autofluorescence and different mechanisms of optical anisotropy are determined. The statistic analysis of coordinate distributions of such Mueller-matrix rotation invariants is proposed. Thereupon the quantitative criteria (statistic moments of the 1st to the 4th order) of differentiation of human urine polycrystalline layers for the sake of diagnosing and differentiating cholelithiasis with underlying chronic cholecystitis (group 1) and diabetes mellitus of degree II (group 2) are estimated.

Methods and means of Fourier-Stokes polarimetry and the spatial-frequency filtering of phase anisotropy manifestations in endometriosis diagnostics

NASA Astrophysics Data System (ADS)

Ushenko, A. G.; Dubolazov, O. V.; Ushenko, Vladimir A.; Ushenko, Yu. A.; Sakhnovskiy, M. Yu.; Prydiy, O. G.; Lakusta, I. I.; Novakovskaya, O. Yu.; Melenko, S. R.

2016-12-01

This research presents investigation results of diagnostic efficiency of a new azimuthally stable Mueller-matrix method of laser autofluorescence coordinate distributions analysis of dried polycrystalline films of uterine cavity peritoneal fluid. A new model of generalized optical anisotropy of biological tissues protein networks is proposed in order to define the processes of laser autofluorescence. The influence of complex mechanisms of both phase anisotropy (linear birefringence and optical activity) and linear (circular) dichroism is taken into account. The interconnections between the azimuthally stable Mueller-matrix elements characterizing laser autofluorescence and different mechanisms of optical anisotropy are determined. The statistic analysis of coordinate distributions of such Mueller-matrix rotation invariants is proposed. Thereupon the quantitative criteria (statistic moments of the 1st to the 4th order) of differentiation of dried polycrystalline films of peritoneal fluid - group 1 (healthy donors) and group 2 (uterus endometriosis patients) are estimated.

Validation of a Radiography-Based Quantification Designed to Longitudinally Monitor Soft Tissue Calcification in Skeletal Muscle.

PubMed

Moore, Stephanie N; Hawley, Gregory D; Smith, Emily N; Mignemi, Nicholas A; Ihejirika, Rivka C; Yuasa, Masato; Cates, Justin M M; Liu, Xulei; Schoenecker, Jonathan G

2016-01-01

Soft tissue calcification, including both dystrophic calcification and heterotopic ossification, may occur following injury. These lesions have variable fates as they are either resorbed or persist. Persistent soft tissue calcification may result in chronic inflammation and/or loss of function of that soft tissue. The molecular mechanisms that result in the development and maturation of calcifications are uncertain. As a result, directed therapies that prevent or resorb soft tissue calcifications remain largely unsuccessful. Animal models of post-traumatic soft tissue calcification that allow for cost-effective, serial analysis of an individual animal over time are necessary to derive and test novel therapies. We have determined that a cardiotoxin-induced injury of the muscles in the posterior compartment of the lower extremity represents a useful model in which soft tissue calcification develops remote from adjacent bones, thereby allowing for serial analysis by plain radiography. The purpose of the study was to design and validate a method for quantifying soft tissue calcifications in mice longitudinally using plain radiographic techniques and an ordinal scoring system. Muscle injury was induced by injecting cardiotoxin into the posterior compartment of the lower extremity in mice susceptible to developing soft tissue calcification. Seven days following injury, radiographs were obtained under anesthesia. Multiple researchers applied methods designed to standardize post-image processing of digital radiographs (N = 4) and quantify soft tissue calcification (N = 6) in these images using an ordinal scoring system. Inter- and intra-observer agreement for both post-image processing and the scoring system used was assessed using weighted kappa statistics. Soft tissue calcification quantifications by the ordinal scale were compared to mineral volume measurements (threshold 450.7mgHA/cm3) determined by μCT. Finally, sample-size calculations necessary to discriminate between a 25%, 50%, 75%, and 100% difference in STiCSS score 7 days following burn/CTX induced muscle injury were determined. Precision analysis demonstrated substantial to good agreement for both post-image processing (κ = 0.73 to 0.90) and scoring (κ = 0.88 to 0.93), with low inter- and intra-observer variability. Additionally, there was a strong correlation in quantification of soft tissue calcification between the ordinal system and by mineral volume quantification by μCT (Spearman r = 0.83 to 0.89). The ordinal scoring system reliably quantified soft tissue calcification in a burn/CTX-induced soft tissue calcification model compared to non-injured controls (Mann-Whitney rank test: P = 0.0002, ***). Sample size calculations revealed that 6 mice per group would be required to detect a 50% difference in STiCSS score with a power of 0.8. Finally, the STiCSS was demonstrated to reliably quantify soft tissue calcification [dystrophic calcification and heterotopic ossification] by radiographic analysis, independent of the histopathological state of the mineralization. Radiographic analysis can discriminate muscle injury-induced soft tissue calcification from adjacent bone and follow its clinical course over time without requiring the sacrifice of the animal. While the STiCSS cannot identify the specific type of soft tissue calcification present, it is still a useful and valid method by which to quantify the degree of soft tissue calcification. This methodology allows for longitudinal measurements of soft tissue calcification in a single animal, which is relatively less expensive, less time-consuming, and exposes the animal to less radiation than in vivo μCT. Therefore, this high-throughput, longitudinal analytic method for quantifying soft tissue calcification is a viable alternative for the study of soft tissue calcification.

Validation of a Radiography-Based Quantification Designed to Longitudinally Monitor Soft Tissue Calcification in Skeletal Muscle

PubMed Central

Moore, Stephanie N.; Hawley, Gregory D.; Smith, Emily N.; Mignemi, Nicholas A.; Ihejirika, Rivka C.; Yuasa, Masato; Cates, Justin M. M.; Liu, Xulei; Schoenecker, Jonathan G.

2016-01-01

Introduction Soft tissue calcification, including both dystrophic calcification and heterotopic ossification, may occur following injury. These lesions have variable fates as they are either resorbed or persist. Persistent soft tissue calcification may result in chronic inflammation and/or loss of function of that soft tissue. The molecular mechanisms that result in the development and maturation of calcifications are uncertain. As a result, directed therapies that prevent or resorb soft tissue calcifications remain largely unsuccessful. Animal models of post-traumatic soft tissue calcification that allow for cost-effective, serial analysis of an individual animal over time are necessary to derive and test novel therapies. We have determined that a cardiotoxin-induced injury of the muscles in the posterior compartment of the lower extremity represents a useful model in which soft tissue calcification develops remote from adjacent bones, thereby allowing for serial analysis by plain radiography. The purpose of the study was to design and validate a method for quantifying soft tissue calcifications in mice longitudinally using plain radiographic techniques and an ordinal scoring system. Methods Muscle injury was induced by injecting cardiotoxin into the posterior compartment of the lower extremity in mice susceptible to developing soft tissue calcification. Seven days following injury, radiographs were obtained under anesthesia. Multiple researchers applied methods designed to standardize post-image processing of digital radiographs (N = 4) and quantify soft tissue calcification (N = 6) in these images using an ordinal scoring system. Inter- and intra-observer agreement for both post-image processing and the scoring system used was assessed using weighted kappa statistics. Soft tissue calcification quantifications by the ordinal scale were compared to mineral volume measurements (threshold 450.7mgHA/cm3) determined by μCT. Finally, sample-size calculations necessary to discriminate between a 25%, 50%, 75%, and 100% difference in STiCSS score 7 days following burn/CTX induced muscle injury were determined. Results Precision analysis demonstrated substantial to good agreement for both post-image processing (κ = 0.73 to 0.90) and scoring (κ = 0.88 to 0.93), with low inter- and intra-observer variability. Additionally, there was a strong correlation in quantification of soft tissue calcification between the ordinal system and by mineral volume quantification by μCT (Spearman r = 0.83 to 0.89). The ordinal scoring system reliably quantified soft tissue calcification in a burn/CTX-induced soft tissue calcification model compared to non-injured controls (Mann-Whitney rank test: P = 0.0002, ***). Sample size calculations revealed that 6 mice per group would be required to detect a 50% difference in STiCSS score with a power of 0.8. Finally, the STiCSS was demonstrated to reliably quantify soft tissue calcification [dystrophic calcification and heterotopic ossification] by radiographic analysis, independent of the histopathological state of the mineralization. Conclusions Radiographic analysis can discriminate muscle injury-induced soft tissue calcification from adjacent bone and follow its clinical course over time without requiring the sacrifice of the animal. While the STiCSS cannot identify the specific type of soft tissue calcification present, it is still a useful and valid method by which to quantify the degree of soft tissue calcification. This methodology allows for longitudinal measurements of soft tissue calcification in a single animal, which is relatively less expensive, less time-consuming, and exposes the animal to less radiation than in vivo μCT. Therefore, this high-throughput, longitudinal analytic method for quantifying soft tissue calcification is a viable alternative for the study of soft tissue calcification. PMID:27438007

Connective tissue grafts for thickening peri-implant tissues at implant placement. One-year results from an explanatory split-mouth randomised controlled clinical trial.

PubMed

Wiesner, Günter; Esposito, Marco; Worthington, Helen; Schlee, Markus

2010-01-01

Nothing to declare. To evaluate whether connective tissue grafts performed at implant placement could be effective in augmenting peri-implant soft tissues. Ten partially edentulous patients requiring at least one single implant in the premolar or molar areas of both sides of the mandible were randomised to have one side augmented at implant placement with a connective soft tissue graft harvested from the palate or no augmentation. After 3 months of submerged healing, abutments were placed and within 1 month definitive crowns were permanently cemented. Outcome measures were implant success, any complications, peri-implant marginal bone level changes, patient satisfaction and preference, thickness of the soft tissues and aesthetics (pink aesthetic score) evaluated by an independent and blinded assessor 1 year after loading. One year after loading, no patients dropped out, no implants failed and no complications occurred. Both groups lost statistically significant amounts of peri-implant bone 1 year after loading (0.8 mm in the grafted group and 0.6 mm in the non-grafted group), but there was no statistically significant difference between groups. Soft tissues at augmented sites were 1.3 mm thicker (P < 0.001) and had a significantly better pink aesthetic score (P < 0.001). Patients were highly satisfied (no statistically significant differences between treatments) though they preferred the aesthetics of the augmented sites (P = 0.031). However, five patients would not undergo the grafting procedure again and two were uncertain. Connective tissue grafts are effective in increasing soft tissue thickness, thus improving aesthetics. Longer follow-ups are needed to evaluate the stability of peri-implant tissues over time.

Prevalence of Soft Tissue Calcifications in CBCT Images of Mandibular Region.

PubMed

Khojastepour, Leila; Haghnegahdar, Abdolaziz; Sayar, Hamed

2017-06-01

Most of the soft tissue calcifications within the head and neck region might not be accompanied by clinical symptoms but may indicate some pathological conditions. The aim of this research was to determine the prevalence of soft tissue calcifications in cone beam computed tomography (CBCT) images of mandibular region. In this cross sectional study the CBCT images of 602 patients including 294 men and 308 women with mean age 41.38±15.18 years were evaluated regarding the presence, anatomical location; type (single or multiple) and size of soft tissue calcification in mandibular region. All CBCT images were acquired by NewTom VGi scanner. Odds ratio and chi-square tests were used for data analysis and p < 0.05 was considered to be statistically significant. 156 out of 602 patients had at least one soft tissue calcification in their mandibular region (25.9%. of studied population with mean age 51.7±18.03 years). Men showed significantly higher rate of soft tissue calcification than women (30.3% vs. 21.8%). Soft tissue calcification was predominantly seen at posterior region of the mandible (88%) and most of them were single (60.7%). The prevalence of soft tissue calcification increased with age. Most of the detected soft tissue calcifications were smaller than 3mm (90%). Soft tissue calcifications in mandibular area were a relatively common finding especially in posterior region and more likely to happen in men and in older age group.

C. trachomatis in female reproductive tract infections and RFLP-based genotyping: a 16-year study from a tertiary care hospital.

PubMed

Gita, Satpathy; Suneeta, Mittal; Anjana, Sharma; Niranjan, Nayak; Sujata, Mohanty; Pandey, R M

2011-01-01

Presence of Chlamydia trachomatis in endocervix was determined in 2466 women attending a tertiary care hospital in New Delhi, India over a period of 16 years, using a monoclonal-based direct immunofluorescence assay, tissue culture isolation, and a conventional PCR assay. Chlamydia antigen could be detected in 391 out of 2466 (15.85%) of patients studied; in 27.27% women with PID, 16.74% women with cervicitis, 16.03% women with infertility, and 12.06% women with adverse pregnancy outcomes, respectively. There was a statistically significant decreasing trend in Chlamydia antigen positivity between the years 1994-1999 and 2000-2004; the apparent decline in antigen positivity between the years 2000-2004 and 2005-2010 was not statistically significant. Antigen detection assay detected equal number of positives as the PCR assay; tissue culture isolation demonstrated lower positivity. In a few representative specimens from cervicitis patients, genotyping was done using RFLP pattern analysis of C. trachomatis MOMP gene amplified by PCR assay, all of these belonged to Chlamydia trachomatis serovar E.

C. trachomatis in Female Reproductive Tract Infections and RFLP-Based Genotyping: A 16-Year Study from a Tertiary Care Hospital

PubMed Central

Gita, Satpathy; Suneeta, Mittal; Anjana, Sharma; Niranjan, Nayak; Sujata, Mohanty; Pandey, R. M.

2011-01-01

Presence of Chlamydia trachomatis in endocervix was determined in 2466 women attending a tertiary care hospital in New Delhi, India over a period of 16 years, using a monoclonal-based direct immunofluorescence assay, tissue culture isolation, and a conventional PCR assay. Chlamydia antigen could be detected in 391 out of 2466 (15.85%) of patients studied; in 27.27% women with PID, 16.74% women with cervicitis, 16.03% women with infertility, and 12.06% women with adverse pregnancy outcomes, respectively. There was a statistically significant decreasing trend in Chlamydia antigen positivity between the years 1994–1999 and 2000–2004; the apparent decline in antigen positivity between the years 2000–2004 and 2005–2010 was not statistically significant. Antigen detection assay detected equal number of positives as the PCR assay; tissue culture isolation demonstrated lower positivity. In a few representative specimens from cervicitis patients, genotyping was done using RFLP pattern analysis of C. trachomatis MOMP gene amplified by PCR assay, all of these belonged to Chlamydia trachomatis serovar E. PMID:21747643

Bi-PROF

PubMed Central

Gries, Jasmin; Schumacher, Dirk; Arand, Julia; Lutsik, Pavlo; Markelova, Maria Rivera; Fichtner, Iduna; Walter, Jörn; Sers, Christine; Tierling, Sascha

2013-01-01

The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 102-104 sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer. PMID:23803588

An exploratory thermographic investigation of the effects of connective tissue massage on autonomic function.

PubMed

Holey, Liz A; Dixon, John; Selfe, James

2011-09-01

The purpose of this study was to measure effects of connective tissue massage (CTM) on the autonomic nervous system using thermography and physiological measurements. A repeated-measures design was used. The setting was a university laboratory. Skin temperature at the site of massage, blood pressure, heart rate, and dorsal foot temperature were measured in 8 healthy participants before CTM, immediately after, and at 15-minute intervals for 1 hour. The effect of CTM on skin temperature was statistically significant, P = .011. Post hoc pairwise comparisons revealed that the 15-, 30-, 45-, and 60-minute data all differed significantly from the pre-CTM data (all P < .05) and also from the immediately post-CTM data (all P < .05). For diastolic blood pressure, the main analysis of variance showed a statistical significance at P = .062. For other variables, there was no evidence for an effect. Evidence was seen of some effects of CTM on autonomic function. This is information that will increase our knowledge of how CTM affects the autonomic nervous system. Copyright © 2011 National University of Health Sciences. Published by Mosby, Inc. All rights reserved.

Association of Glycemic Status with Bone Turnover Markers in Type 2 Diabetes Mellitus.

PubMed

Kulkarni, Sweta Vilas; Meenatchi, Suruthi; Reeta, R; Ramesh, Ramasamy; Srinivasan, A R; Lenin, C

2017-01-01

Type 2 diabetes mellitus has profound implications on the skeleton. Even though bone mineral density is increased in type 2 diabetes mellitus patients, they are more prone for fractures. The weakening of bone tissue in type 2 diabetes mellitus can be due to uncontrolled blood sugar levels leading to high levels of bone turnover markers in blood. The aim of this study is to find the association between glycemic status and bone turnover markers in type 2 diabetes mellitus. This case-control study was carried out in a tertiary health care hospital. Fifty clinically diagnosed type 2 diabetes mellitus patients in the age group between 30 and 50 years were included as cases. Fifty age- and gender-matched healthy nondiabetics were included as controls. Patients with complications and chronic illness were excluded from the study. Depending on glycated hemoglobin (HbA1c) levels, patients were grouped into uncontrolled (HbA1c >7%, n = 36) and controlled (HbA1c <7%, n = 14) diabetics. Based on duration of diabetes, patients were grouped into newly diagnosed, 1-2 years, 3-5 years, and >5 years. Serum osteocalcin (OC), bone alkaline phosphatase (BAP), acid phosphatase (ACP), and HbA1c levels were estimated. OC/BAP and OC/ACP ratio was calculated. Student's t -test, analysis of variance, and Chi-square tests were used for analysis. Receiver operating characteristic (ROC) curve analysis was done for OC/BAP and OC/ACP ratios. Serum OC, HbA1c, and OC/BAP ratio were increased in cases when compared to controls and were statistically significant ( P < 0.001). OC/ACP ratio was decreased in type 2 diabetes mellitus and was statistically significant ( P = 0.01). In patients with >5-year duration of diabetes, HbA1c level was high and was statistically significant ( P < 0.042). BAP levels were high in uncontrolled diabetics but statistically not significant. ROC curve showed OC/BAP ratio better marker than OC/ACP ratio. Uncontrolled type 2 diabetes mellitus affects bone tissue resulting in variations in bone turnover markers. Bone turnover markers are better in predicting recent changes in bone morphology and are cost effective.

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

Visual characterization of histologic specimens is known to suffer from intra- and inter-observer variability. To help address this, we developed an automated framework for characterizing digitized histology specimens based on a novel application of color histogram and color texture analysis. We perform a preliminary evaluation of this framework using a set of 73 trichrome-stained, digitized slides of normal breast tissue which were visually assessed by an expert pathologist in terms of the percentage of collagenous stroma, stromal collagen density, duct-lobular unit density and the presence of elastosis. For each slide, our algorithm automatically segments the tissue region based on the lightness channel in CIELAB colorspace. Within each tissue region, a color histogram feature vector is extracted using a common color palette for trichrome images generated with a previously described method. Then, using a whole-slide, lattice-based methodology, color texture maps are generated using a set of color co-occurrence matrix statistics: contrast, correlation, energy and homogeneity. The extracted features sets are compared to the visually assessed tissue characteristics. Overall, the extracted texture features have high correlations to both the percentage of collagenous stroma (r=0.95, p<0.001) and duct-lobular unit density (r=0.71, p<0.001) seen in the tissue samples, and several individual features were associated with either collagen density and/or the presence of elastosis (p<=0.05). This suggests that the proposed framework has promise as a means to quantitatively extract descriptors reflecting tissue-level characteristics and thus could be useful in detecting and characterizing histological processes in digitized histology specimens.

Study of the tactile perception of bathroom tissues: Comparison between the sensory evaluation by a handfeel panel and a tribo-acoustic artificial finger.

PubMed

Thieulin, C; Pailler-Mattei, C; Vargiolu, R; Lancelot, S; Zahouani, H

2017-02-01

Tactile perception is one of the sensorial modes most stimulated by our daily environment. In particular, perceived softness is an important parameter for judging the sensory quality of surfaces and fabrics. Unfortunately, its assessment greatly depends on the tactile sense of each person, which in turn depends on many factors. Currently, the predominant method for evaluating the tactile perception of fabrics is the human handfeel panel. This qualitative approach does not permit the quantitative measure of touch feel perception. In this study, we present a new artificial finger device to investigate the tactile sensing of ten bathroom tissues. It enables simultaneously measuring the friction and vibrations caused when sliding an artificial finger on the surface of the tissue. The comparison between the results obtained with the artificial finger and the tactile perception evaluated using a handfeel panel showed that the artificial finger is able to separate the two parts of the tactile perception of bathroom tissues: softness and surface texture (velvetiness). The statistical analysis suggests that there is a good correlation between the vibrations measured with the artificial finger and the softness evaluated by the panel. It then shows that the friction measured by the artificial finger is related to the surface texture of a bathroom tissue. The ability of the artificial finger to mimic human touch is demonstrated. Finally, a Principal Component Analysis orders the signatures of the tactile perception of the bathroom tissues in four different groups. Copyright © 2016. Published by Elsevier B.V.

Tissue distribution of perfluoroalkyl acids and health status in wild Mozambique tilapia (Oreochromis mossambicus) from Loskop Dam, Mpumalanga, South Africa.

PubMed

Bangma, Jacqueline T; Reiner, Jessica L; Botha, Hannes; Cantu, Theresa M; Gouws, Marco A; Guillette, Matthew P; Koelmel, Jeremy P; Luus-Powell, Wilmien J; Myburgh, Jan; Rynders, Olivia; Sara, Joseph R; Smit, Willem J; Bowden, John A

2017-11-01

This study examined concentrations of 15 perfluoroalkyl acids (PFAAs) in tissues from male Mozambique tilapia (Oreochromis mossambicus) collected at Loskop Dam, Mpumalanga, South Africa in 2014 and 2016. Nine of the 15 PFAAs were detected frequently and were included in statistical analysis and included two of the most commonly known PFAAs, perfluorooctanesulfonic acid (PFOS) (median, 41.6ng/g) and perfluorooctanoic acid (PFOA) (median, 0.0825ng/g). Of the tissues measured, plasma (2016 and 2014 median, 22.2ng/g) contained the highest PFAA burden followed by (in descending order): liver (median, 11.6ng/g), kidney (median, 9.04ng/g), spleen (median, 5.92ng/g), adipose (median, 2.54ng/g), and muscle (median, 1.11ng/g). Loskop Dam tilapia have been affected by an inflammatory disease of the adipose tissue known as pansteatitis, so this study also aimed to investigate relationships between PFAA tissue concentrations and incidence of pansteatitis or fish health status. Results revealed that healthy tilapia exhibited an overall higher (p-value<0.05) PFAA burden than pansteatitis-affected tilapia across all tissues. Further analysis showed that organs previously noted in the literature to contain the highest PFAA concentrations, such as kidney, liver, and plasma, were the organs driving the difference in PFAA burden between the two tilapia groups. Care must be taken in the interpretations we draw from not only the results of our study, but also other PFAA measurements made on populations (human and wildlife alike) under differing health status. Copyright © 2017. Published by Elsevier B.V.

Computed Tomographic Evaluation of Posttreatment Soft-Tissue Changes by Using a Lymphedema Scoring System in Patients with Oral Cancer.

PubMed

Akashi, Masaya; Teraoka, Shun; Kakei, Yasumasa; Kusumoto, Junya; Hasegawa, Takumi; Minamikawa, Tsutomu; Hashikawa, Kazunobu; Komori, Takahide

2018-04-01

This study aimed to evaluate posttreatment soft-tissue changes in patients with oral cancer with computed tomography (CT). To accomplish that purpose, a scoring system was established, referring to the criteria of lower leg lymphedema (LE). One hundred and six necks in 95 patients who underwent oral oncologic surgery with neck dissection (ND) were analyzed retrospectively using routine follow-up CT images. A two-point scoring system to evaluate soft-tissue changes (so-called "LE score") was established as follows: Necks with a "honeycombing" appearance were assigned 1 point. Necks with "taller than wide" fat lobules were assigned 1 point. Necks with neither appearance were assigned 0 points. Comparisons between patients with LE score ≥1 and LE score = 0 at 6 months postoperatively were performed using the Fisher exact test for discrete variables and the Mann-Whitney U test for continuous variables. Univariate predictors associated with posttreatment changes (i.e., LE score ≥1 at 6 months postoperatively) were entered into a multivariate logistic regression analysis. Values of p < 0.05 were considered to indicate statistical significance. The occurrence of the posttreatment soft-tissue changes was 32%. Multivariate logistic regression analysis showed that postoperative radiation therapy (RT) and bilateral ND were potential risk factors of posttreatment soft-tissue changes on CT images. Sequential evaluation of "honeycombing" and the "taller than wide" appearances on routine follow-up CT revealed the persistence of posttreatment soft-tissue changes in patients who underwent oral cancer treatment, and those potential risk factors were postoperative RT and bilateral ND.

Aronia melanocarpa Treatment and Antioxidant Status in Selected Tissues in Wistar Rats

PubMed Central

Krośniak, Mirosław; Sanocka, Ilona; Bartoń, Henryk; Hebda, Tomasz; Francik, Sławomir

2014-01-01

Aronia juice is considered to be a source of compounds with high antioxidative potential. We conducted a study on the impact of compounds in the Aronia juice on oxidative stress in plasma and brain tissues. The influence of Aronia juice on oxidative stress parameters was tested with the use of a model with a high content of fructose and nonsaturated fats. Therefore, the activity of enzymatic (catalase, CAT, and paraoxonase, PON) and nonenzymatic (thiol groups, SH, and protein carbonyl groups, PCG) oxidative stress markers, which indicate changes in the carbohydrate and protein profiles, was marked in brain tissue homogenates. Adding Aronia caused statistically significant increase in the CAT activity in plasma in all tested diets, while the PON activity showed a statistically significant increase only in case of high fat diet. In animals fed with Aronia juice supplemented with carbohydrates or fat, statistically significant increase in the PON activity and the decrease in the CAT activity in brain tissue were observed. In case of the high fat diet, an increase in the number of SH groups and a decrease in the number of PCG groups in brain tissue were observed. PMID:25057488

Aronia melanocarpa treatment and antioxidant status in selected tissues in Wistar rats.

PubMed

Francik, Renata; Krośniak, Mirosław; Sanocka, Ilona; Bartoń, Henryk; Hebda, Tomasz; Francik, Sławomir

2014-01-01

Aronia juice is considered to be a source of compounds with high antioxidative potential. We conducted a study on the impact of compounds in the Aronia juice on oxidative stress in plasma and brain tissues. The influence of Aronia juice on oxidative stress parameters was tested with the use of a model with a high content of fructose and nonsaturated fats. Therefore, the activity of enzymatic (catalase, CAT, and paraoxonase, PON) and nonenzymatic (thiol groups, SH, and protein carbonyl groups, PCG) oxidative stress markers, which indicate changes in the carbohydrate and protein profiles, was marked in brain tissue homogenates. Adding Aronia caused statistically significant increase in the CAT activity in plasma in all tested diets, while the PON activity showed a statistically significant increase only in case of high fat diet. In animals fed with Aronia juice supplemented with carbohydrates or fat, statistically significant increase in the PON activity and the decrease in the CAT activity in brain tissue were observed. In case of the high fat diet, an increase in the number of SH groups and a decrease in the number of PCG groups in brain tissue were observed.

Optimization image of magnetic resonance imaging (MRI) T2 fast spin echo (FSE) with variation echo train length (ETL) on the rupture tendon achilles case

NASA Astrophysics Data System (ADS)

Muzamil, Akhmad; Haries Firmansyah, Achmad

2017-05-01

The research was done the optimization image of Magnetic Resonance Imaging (MRI) T2 Fast Spin Echo (FSE) with variation Echo Train Length (ETL) on the Rupture Tendon Achilles case. This study aims to find the variations Echo Train Length (ETL) from the results of ankle’s MRI image and find out how the value of Echo Train Length (ETL) works on the MRI ankle to produce optimal image. In this research, the used ETL variations were 12 and 20 with the interval 2 on weighting T2 FSE sagittal. The study obtained the influence of Echo Train Length (ETL) on the quality of ankle MRI image sagittal using T2 FSE weighting and analyzed in 25 images of five patients. The data analysis has done quantitatively with the Region of Interest (ROI) directly on computer MRI image planes which conducted statistical tests Signal to Noise Ratio (SNR) and Contras to Noise Ratio (CNR). The Signal to Noise Ratio (SNR) was the highest finding on fat tissue, while the Contras to Noise Ratio (CNR) on the Tendon-Fat tissue with ETL 12 found in two patients. The statistics test showed the significant SNR value of the 0.007 (p<0.05) of Tendon tissue, 0.364 (p>0.05) of the Fat, 0.912 (p>0.05) of the Fibula, and 0.436 (p>0.05) of the Heel Bone. For the contrast to noise ratio (CNR) of the Tendon-FAT tissue was about 0.041 (p>0.05). The results of the study showed that ETL variation with T2 FSE sagittal weighting had difference at Tendon tissue and Tendon-Fat tissue for MRI imaging quality. SNR and CNR were an important aspect on imaging optimization process to give the diagnose information.

Analysis methodology and development of a statistical tool for biodistribution data from internal contamination with actinides.

PubMed

Lamart, Stephanie; Griffiths, Nina M; Tchitchek, Nicolas; Angulo, Jaime F; Van der Meeren, Anne

2017-03-01

The aim of this work was to develop a computational tool that integrates several statistical analysis features for biodistribution data from internal contamination experiments. These data represent actinide levels in biological compartments as a function of time and are derived from activity measurements in tissues and excreta. These experiments aim at assessing the influence of different contamination conditions (e.g. intake route or radioelement) on the biological behavior of the contaminant. The ever increasing number of datasets and diversity of experimental conditions make the handling and analysis of biodistribution data difficult. This work sought to facilitate the statistical analysis of a large number of datasets and the comparison of results from diverse experimental conditions. Functional modules were developed using the open-source programming language R to facilitate specific operations: descriptive statistics, visual comparison, curve fitting, and implementation of biokinetic models. In addition, the structure of the datasets was harmonized using the same table format. Analysis outputs can be written in text files and updated data can be written in the consistent table format. Hence, a data repository is built progressively, which is essential for the optimal use of animal data. Graphical representations can be automatically generated and saved as image files. The resulting computational tool was applied using data derived from wound contamination experiments conducted under different conditions. In facilitating biodistribution data handling and statistical analyses, this computational tool ensures faster analyses and a better reproducibility compared with the use of multiple office software applications. Furthermore, re-analysis of archival data and comparison of data from different sources is made much easier. Hence this tool will help to understand better the influence of contamination characteristics on actinide biokinetics. Our approach can aid the optimization of treatment protocols and therefore contribute to the improvement of the medical response after internal contamination with actinides.

Metabolomic Markers of Altered Nucleotide Metabolism in Early Stage Adenocarcinoma

PubMed Central

Wikoff, William R.; Grapov, Dmitry; Fahrmann, Johannes F.; DeFelice, Brian; Rom, William; Pass, Harvey; Kim, Kyoungmi; Nguyen, UyenThao; Taylor, Sandra L.; Kelly, Karen; Fiehn, Oliver; Miyamoto, Suzanne

2015-01-01

Adenocarcinoma, a type of non-small-cell lung cancer (NSCLC), is the most frequently diagnosed lung cancer and the leading cause of lung cancer mortality in the United States. It is well documented that biochemical changes occur early in the transition from normal to cancer cells, but the extent to which these alterations affect tumorigenesis in adenocarcinoma remains largely unknown. Herein we describe the application of mass spectrometry and multivariate statistical analysis in one of the largest biomarker research studies to date aimed at distinguishing metabolic differences between malignant and non-malignant lung tissue. Gas chromatography time-of-flight mass spectrometry was used to measure 462 metabolites in 39 malignant and non-malignant lung tissue pairs from current or former smokers with early stage (Stage IA–IB) adenocarcinoma. Statistical mixed effects models, orthogonal partial least squares discriminant analysis and network integration, were used to identify key cancer-associated metabolic perturbations in adenocarcinoma compared to non-malignant tissue. Cancer-associated biochemical alterations were characterized by: 1) decreased glucose levels, consistent with the Warburg effect, 2) changes in cellular redox status highlighted by elevations in cysteine and antioxidants, alpha- and gamma-tocopherol, 3) elevations in nucleotide metabolites 5,6-dihydrouracil and xanthine suggestive of increased dihydropyrimidine dehydrogenase and xanthine oxidoreductase activity, 4) increased 5'-deoxy-5'-methylthioadenosine levels indicative of reduced purine salvage and increased de novo purine synthesis and 5) coordinated elevations in glutamate and UDP-N-acetylglucosamine suggesting increased protein glycosylation. The present study revealed distinct metabolic perturbations associated with early stage lung adenocarcinoma which may provide candidate molecular targets for personalizing therapeutic interventions and treatment efficacy monitoring. PMID:25657018

Interval between surgery and radiotherapy: effect on local control of soft tissue sarcoma.

PubMed

Ballo, Matthew T; Zagars, Gunar K; Cormier, Janice N; Hunt, Kelly K; Feig, Barry W; Patel, Shreyaskumar R; Pisters, Peter W T

2004-04-01

To evaluate the clinical significance of the interval between surgery and postoperative radiotherapy (RT) for patients with soft tissue sarcoma. The records of 799 patients who underwent postoperative RT for soft tissue sarcoma between 1960 and 2000 were retrospectively reviewed. Univariate and multivariate analyses were used to evaluate the potential impact of the timing of postoperative RT on the rate of local control (LC). The actuarial overall LC rate was 79% at 10 years and 78% at 15 years. Univariate analysis indicated that the factors associated with an inferior 10-year LC rate were positive resection margins (p <0.0001); treatment for recurrent disease (p <0.0001); primary location in the head and neck or deep trunk (p <0.0001); age >64 years (p <0.0001); histopathologic subtype of malignant fibrous histiocytoma, neurogenic sarcoma, or epithelioid sarcoma (p = 0.01); tumor size >10 cm (p = 0.02); postoperative radiation dose <64 Gy (p = 0.03); and high histologic grade (p = 0.05). On multivariate analysis, all these factors remained statistically significant, except for high histologic grade and large size. A delay between surgery and the start of RT of >30 days was associated with a decreased 10-year LC rate, but this association was not statistically significant (76% vs. 83%, p = 0.07). The potential association between RT delay and inferior LC could be explained by an imbalance in the distribution of other prognostic factors. The interval between surgery and RT did not significantly impact the 10-year LC rate. These findings indicate that an RT delay should not be viewed as an independent adverse factor for LC and that treatment intensification may not be necessary for patients in whom a treatment delay has already occurred.

Aberrant Expression of Calretinin, D2-40 and Mesothelin in Mucinous and Non-Mucinous Colorectal Carcinomas and Relation to Clinicopathological Features and Prognosis.

PubMed

Foda, Abd AlRahman Mohammad; El-Hawary, Amira Kamal; Hamed, Hazem

2016-10-01

CRC is a heterogeneous disease in terms of morphology, invasive behavior, metastatic capacity, and clinical outcome. Recently, many so-called mesothelial markers, including calretinin, D2-40, WT1, thrombomodulin, mesothelin, and others, have been certified. The aim of this study was to assess the immunohistochemical expression of calretinin and other mesothelial markers (D2-40 and mesothelin) in colorectal mucinous adenocarcinoma (MA) and non mucinous adenocarcinoma (NMA) specimens and relation to clinicopathological features and prognosis using manual tissue microarray technique. We studied tumor tissue specimens from 150 patients with colorectal MA and NMA who underwent radical surgery from January 2007 to January 2012. High-density manual tissue microarrays were constructed using a modified mechanical pencil tip technique, and paraffin sections were submitted for immunohistochemistry using Calretinin, D2-40 and mesothelin expressions. We found that NMA showed significantly more calretinin and D2-40 expression than MA In contrast, no statistically significant difference between NMA and MA was detected in mesothelin expression. There were no statistically significant relations between any of the clinicopathological or histological parameters and any of the three markers. In a univariate analysis, neither calretinin nor D2-40 expressions showed any significant relations to DFS or OS. However, mesothelin luminal expression was significantly associated with worse DFS. Multivariate Cox regression analysis proved that luminal mesothelin expression was an independent negative prognostic factor in NMA. In conclusion, Calretinin, D2-40 and mesothelin are aberrantly expressed in a proportion of CRC cases with more expression in NMA than MA. Aberrant expression of these mesothelial markers was not associated with clinicopathological or histological features of CRCs. Only mesothelin expression appears to be a strong predictor of adverse prognosis.

VEGF: A critical driver for angiogenesis and subsequent tumor growth: An IHC study

PubMed Central

Kapoor, Prakhar; Deshmukh, RS

2012-01-01

Background: Tumors require blood supply for their growth and dissemination. It is a well accepted paradigm that tumors recruit new blood vessels from the existing circulation (angiogenesis) and this participates in tumor invasion and metastasis. Studies in the literature provide evidence for expression of Vascular Endothelial Growth Factor (VEGF) by the tumor for neo-angiogenesis, which is not only required for the tumor growth but also its metastasis. Based on the literary evidences we carried out an Immuno-Histochemical (IHC) study for VEGF in Oral Squamous Cell Carcinoma (OSCC) tissues to provide a strong link between the factor and oral cancer. Aim: To analyze the expression of VEGF in OSCC tissues of different histological grades, clinical sizes and lymph node status and to use this as an indicator for disease progression by helping in delineating a risk population, that may benefit from an attractive adjuvant therapeutic strategy for OSCC. Settings and Design: Studies published from 1990 till 2010 have only seen the association of VEGF with tumor angiogenesis and its possible role in metastasis. This is the first study that takes into account the clinical status of the lymph nodes and VEGF expressivity in a sample size of 30 cases. Materials and Methods: 30 oral squamous cell carcinoma tissue slides were stained using Hematoxylin and Eosin stain (to confirm the diagnosis) and immunohistochemically using VEGF antibody. IHC stained slides were thereafter evaluated for the positivity and intensity. Statistical Analysis: The result was subjected to statistical analysis using Chi-square test Results and Conclusion: VEGF positivity was seen in approximately. 90% of cases which was independent of histological grade of OSCC. However the intensity increased with the clinical size of cancer and from palpable lymph node to a tender and hard lymph node. PMID:23248460

Azimuthally invariant Mueller-matrix mapping of optically anisotropic layers of biological networks of blood plasma in the diagnosis of liver disease

NASA Astrophysics Data System (ADS)

Ushenko, A. G.; Dubolazov, A. V.; Ushenko, V. A.; Ushenko, Yu. A.; Sakhnovskiy, M. Y.; Pavlyukovich, O.; Pavlyukovich, N.; Novakovskaya, O.; Gorsky, M. P.

2016-09-01

The model of Mueller-matrix description of mechanisms of optical anisotropy that typical for polycrystalline layers of the histological sections of biological tissues and fluids - optical activity, birefringence, as well as linear and circular dichroism - is suggested. Within the statistical analysis distributions quantities of linear and circular birefringence and dichroism the objective criteria of differentiation of myocardium histological sections (determining the cause of death); films of blood plasma (liver pathology); peritoneal fluid (endometriosis of tissues of women reproductive sphere); urine (kidney disease) were determined. From the point of view of probative medicine the operational characteristics (sensitivity, specificity and accuracy) of the method of Mueller-matrix reconstruction of optical anisotropy parameters were found.

Characterization of Cement Particles Found in Peri-implantitis-Affected Human Biopsy Specimens.

PubMed

Burbano, Maria; Wilson, Thomas G; Valderrama, Pilar; Blansett, Jonathan; Wadhwani, Chandur P K; Choudhary, Pankaj K; Rodriguez, Lucas C; Rodrigues, Danieli C

2015-01-01

Peri-implantitis is a disease characterized by soft tissue inflammation and continued loss of supporting bone, which can result in implant failure. Peri-implantitis is a multifactorial disease, and one of its triggering factors may be the presence of excess cement in the soft tissues surrounding an implant. This descriptive study evaluated the composition of foreign particles from 36 human biopsy specimens with 19 specimens selected for analysis. The biopsy specimens were obtained from soft tissues affected by peri-implantitis around cement-retained implant crowns and compared with the elemental composition of commercial luting cement. Nineteen biopsy specimens were chosen for the comparison, and five test cements (TempBond, Telio, Premier Implant Cement, Intermediate Restorative Material, and Relyx) were analyzed using scanning electron microscopy equipped with energy dispersive x-ray spectroscopy. This enabled the identification of the chemical composition of foreign particles embedded in the tissue specimens and the composition of the five cements. Statistical analysis was conducted using classification trees to pair the particles present in each specimen with the known cements. The particles in each biopsy specimen could be associated with one of the commercial cements with a level of probability ranging between .79 and 1. TempBond particles were found in one biopsy specimen, Telio particles in seven, Premier Implant Cement particles in four, Relyx particles in four, and Intermediate Restorative Material particles in three. Particles found in human soft tissue biopsy specimens around implants affected by peri-implant disease were associated with five commercially available dental cements.

Impact of metals on histopathology and expression of HSP 70 in different tissues of Milk fish (Chanos chanos) of Kaattuppalli Island, South East Coast, India.

PubMed

Rajeshkumar, Sivakumar; Munuswamy, Natesan

2011-04-01

Histological and Immunohistochemical studies were carried out to document the possible impact of heavy metal contamination in different tissues of Chanos chanos. Heavy metals such as Cu, Pb, Zn, Cd, Mn and Fe were predominant in water, sediment and biota of Kaattuppalli Island and varied significantly between two different sites. Histological changes such as swelling of muscle fiber and break down of muscle bundles were noted in the muscle. Similarly gill filament cell proliferation, increase in intercellular spaces and primary and secondary lamellar epithelium were evident in gills. The hepatocytes showed damage of central vein and rupture of irregular hepatic plate with more number of vacuoles in the fish collected from polluted site compared to that from the less polluted site. The impact of pollution was also assessed in different tissues by immunohistochemistry using primary antibody (mouse monoclonal HSP70 antibody 1:2000) and secondary antibody (HRP conjugated antibody) for expression of stress protein. Immunostaining analysis showed expression of HSP70 with high intensity in the tissues of fish collected from polluted site compared to less polluted sites. Further, HSP70 positive cells were analyzed from six locations per fish tissue section. One-way analysis of variance (ANOVA) followed by least significant difference (LSD) was used to check if the expression was significant. Results indicate that the values are statistically significant at the two different sampling sites (P<0.05). Copyright © 2011 Elsevier Ltd. All rights reserved.

Drying method has no substantial effect on δ(15)N or δ(13)C values of muscle tissue from teleost fishes.

PubMed

Bessey, Cindy; Vanderklift, Mathew A

2014-02-15

Stable isotope analysis (SIA) is a powerful tool in many fields of research that enables quantitative comparisons among studies, if similar methods have been used. The goal of this study was to determine if three different drying methods commonly used to prepare samples for SIA yielded different δ(15)N and δ(13)C values. Muscle subsamples from 10 individuals each of three teleost species were dried using three methods: (i) oven, (ii) food dehydrator, and (iii) freeze-dryer. All subsamples were analysed for δ(15)N and δ(13)C values, and nitrogen and carbon content, using a continuous flow system consisting of a Delta V Plus mass spectrometer and a Flush 1112 elemental analyser via a Conflo IV universal interface. The δ(13)C values were normalized to constant lipid content using the equations proposed by McConnaughey and McRoy. Although statistically significant, the differences in δ(15)N values between the drying methods were small (mean differences ≤0.21‰). The differences in δ(13)C values between the drying methods were not statistically significant, and normalising the δ(13)C values to constant lipid content reduced the mean differences for all treatments to ≤0.65‰. A statistically significant difference of ~2% in C content existed between tissues dried in a food dehydrator and those dried in a freeze-dryer for two fish species. There was no significant effect of fish size on the differences between methods. No substantial effect of drying method was found on the δ(15)N or δ(13)C values of teleost muscle tissue. Copyright © 2013 John Wiley & Sons, Ltd.

Which one is more effective for the treatment of rat sepsis model: thalidomide or etanercept?

PubMed

Ilhan, N; Susam, S; Gul, H F; Bardas, R; Ilhan, N

2017-01-01

We aimed to investigate the protective effect of selected treatment agents on liver injury in lipopolysaccharide (LPS)-induced rat sepsis model. The sepsis includes complex inflammatory responses between a microbial pathogen and the host immune system, and leads to organ failure and also death. This study was performed with 29 male Wistar Albino rats. Rats were divided randomly into five groups: Sham group, LPS-treated sepsis group, LPS+thalidomide treated group, LPS+etanercept treated group and LPS+thalidomide+etanercept treated group, respectively. Liver tissue tumor necrosis factor α (TNF-α), interleukin 1β (IL-1β) and interleukin 6 (IL-6) levels were determined by enzyme-linked immuno-sorbent assay (ELISA) method. The expression of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) was performed using western blot analysis. The levels of tissue TNF-α, IL-1β and IL-6 were found statistically significantly higher in sepsis group than in the sham group. TNF-α levels were found statistically significantly decreased in LPS+etanercept and LPS+thalidomide+etanercept treated groups when compared with LPS group (p < 0.05). For IL-1β and IL-6 levels a statistically significant decline was observed in the LPS+thalidomide and LPS+etanercept treated groups compared to the LPS group (p < 0.05). Expression of NF-κB protein in liver tissue was significantly elevated in the LPS group compared to sham group (p < 0.001). In treatment groups, a marked decrease was observed in NF-κB protein expression. The results of this investigation suggested that etanercept and thalidomide administration may have a beneficial effect on LPS-induced sepsis. So, the present study may have significant clinical relevance, but clinical trials are needed to confirm these results (Tab. 1, Fig. 1, Ref. 36).

A comparative study to evaluate liquid dish washing soap as an alternative to xylene and alcohol in deparaffinization and hematoxylin and eosin staining.

PubMed

Pandey, Pinki; Dixit, Alok; Tanwar, Aparna; Sharma, Anuradha; Mittal, Sanjeev

2014-07-01

Our study presents a new deparaffinizing and hematoxylin and eosin (H and E) staining method that involves the use of easily available, nontoxic and eco-friendly liquid diluted dish washing soap (DWS) by completely eliminating expensive and hazardous xylene and alcohol from deparaffinizing and rehydration prior to staining, staining and from dehydration prior to mounting. The aim was to evaluate and compare the quality of liquid DWS treated xylene and alcohol free (XAF) sections with that of the conventional H and E sections. A total of 100 paraffin embedded tissue blocks from different tissues were included. From each tissue block, one section was stained with conventional H and E (normal sections) and the other with XAF H and E (soapy sections) staining method. Slides were scored using five parameters: Nuclear, cytoplasmic, clarity, uniformity, and crispness of staining. Z-test was used for statistical analysis. Soapy sections scored better for cytoplasmic (90%) and crisp staining (95%) with a statistically significant difference. Whereas for uniformity of staining, normal sections (88%) scored over soapy sections (72%) (Z = 2.82, P < 0.05). For nuclear (90%) and clarity of staining (90%) total scored favored soapy sections, but the difference was not statistically significant. About 84% normal sections stained adequately for diagnosis when compared with 86% in soapy sections (Z = 0.396, P > 0.05). Liquid DWS is a safe and efficient alternative to xylene and alcohol in deparaffinization and routine H and E staining procedure. We are documenting this project that can be used as a model for other histology laboratories.

A comparative study to evaluate liquid dish washing soap as an alternative to xylene and alcohol in deparaffinization and hematoxylin and eosin staining

PubMed Central

Pandey, Pinki; Dixit, Alok; Tanwar, Aparna; Sharma, Anuradha; Mittal, Sanjeev

2014-01-01

Introduction: Our study presents a new deparaffinizing and hematoxylin and eosin (H and E) staining method that involves the use of easily available, nontoxic and eco-friendly liquid diluted dish washing soap (DWS) by completely eliminating expensive and hazardous xylene and alcohol from deparaffinizing and rehydration prior to staining, staining and from dehydration prior to mounting. The aim was to evaluate and compare the quality of liquid DWS treated xylene and alcohol free (XAF) sections with that of the conventional H and E sections. Materials and Methods: A total of 100 paraffin embedded tissue blocks from different tissues were included. From each tissue block, one section was stained with conventional H and E (normal sections) and the other with XAF H and E (soapy sections) staining method. Slides were scored using five parameters: Nuclear, cytoplasmic, clarity, uniformity, and crispness of staining. Z-test was used for statistical analysis. Results: Soapy sections scored better for cytoplasmic (90%) and crisp staining (95%) with a statistically significant difference. Whereas for uniformity of staining, normal sections (88%) scored over soapy sections (72%) (Z = 2.82, P < 0.05). For nuclear (90%) and clarity of staining (90%) total scored favored soapy sections, but the difference was not statistically significant. About 84% normal sections stained adequately for diagnosis when compared with 86% in soapy sections (Z = 0.396, P > 0.05). Conclusion: Liquid DWS is a safe and efficient alternative to xylene and alcohol in deparaffinization and routine H and E staining procedure. We are documenting this project that can be used as a model for other histology laboratories. PMID:25328332

Quantification and localization of mast cells in periapical lesions.

PubMed

Mahita, V N; Manjunatha, B S; Shah, R; Astekar, M; Purohit, S; Kovvuru, S

2015-01-01

Periapical lesions occur in response to chronic irritation in periapical tissue, generally resulting from an infected root canal. Specific etiological agents of induction, participating cell population and growth factors associated with maintenance and resolution of periapical lesions are incompletely understood. Among the cells found in periapical lesions, mast cells have been implicated in the inflammatory mechanism. Quantifications and the possible role played by mast cells in the periapical granuloma and radicular cyst. Hence, this study is to emphasize the presence (localization) and quantification of mast cells in periapical granuloma and radicular cyst. A total of 30 cases and out of which 15 of periapical granuloma and 15 radicular cyst, each along with the case details from the previously diagnosed cases in the department of oral pathology were selected for the study. The gender distribution showed male 8 (53.3%) and females 7 (46.7%) in periapical granuloma cases and male 10 (66.7%) and females 5 (33.3%) in radicular cyst cases. The statistical analysis used was unpaired t-test. Mean mast cell count in periapical granuloma subepithelial and deeper connective tissue, was 12.40 (0.99%) and 7.13 (0.83%), respectively. The mean mast cell counts in subepithelial and deeper connective tissue of radicular cyst were 17.64 (1.59%) and 12.06 (1.33%) respectively, which was statistically significant. No statistical significant difference was noted among males and females. Mast cells were more in number in radicular cyst. Based on the concept that mast cells play a critical role in the induction of inflammation, it is logical to use therapeutic agents to alter mast cell function and secretion, to thwart inflammation at its earliest phases. These findings may suggest the possible role of mast cells in the pathogenesis of periapical lesions.

Intraoperative Nerve Blocks Fail to Improve Quality of Recovery after Tissue Expander Breast Reconstruction: A Prospective, Double-Blinded, Randomized, Placebo-Controlled Clinical Trial.

PubMed

Lanier, Steven T; Lewis, Kevin C; Kendall, Mark C; Vieira, Brittany L; De Oliveira, Gildasio; Nader, Anthony; Kim, John Y S; Alghoul, Mohammed

2018-03-01

The authors' study represents the first level I evidence to assess whether intraoperative nerve blocks improve the quality of recovery from immediate tissue expander/implant breast reconstruction. A prospective, randomized, double-blinded, placebo-controlled clinical trial was conducted in which patients undergoing immediate tissue expander/implant breast reconstruction were randomized to either (1) intraoperative intercostal and pectoral nerve blocks with 0.25% bupivacaine with 1:200,000 epinephrine and 4 mg of dexamethasone or (2) sham nerve blocks with normal saline. The 40-item Quality of Recovery score, pain score, and opioid use in the postoperative period were compared statistically between groups. Power analysis ensured 80 percent power to detect a 10-point (clinically significant) difference in the 40-item Quality of Recovery score. Forty-seven patients were enrolled. Age, body mass index, laterality, mastectomy type, and lymph node dissection were similar between groups. There were no statistical differences in quality of recovery, pain burden as measured by visual analogue scale, opioid consumption, antiemetic use, or length of hospital stay between groups at 24 hours after surgery. Mean global 40-item Quality of Recovery scores were 169 (range, 155 to 182) for the treatment arm and 165 (range, 143 to 179) for the placebo arm (p = 0.36), indicating a high quality of recovery in both groups. Although intraoperative nerve blocks can be a safe adjunct to a comprehensive postsurgical recovery regimen, the authors' results indicate no effect on overall quality of recovery from tissue expander/implant breast reconstruction. Therapeutic, I.

Comparative Evaluation of Platelet-Rich Fibrin Biomaterial and Open Flap Debridement in the Treatment of Two and Three Wall Intrabony Defects

PubMed Central

Ajwani, Himanshu; Shetty, Sharath; Gopalakrishnan, Dharmarajan; Kathariya, Rahul; Kulloli, Anita; Dolas, R S; Pradeep, A R

2015-01-01

Background: Platelet-rich concentrates are the most widely used regenerative biomaterials. Stimulation and acceleration of soft and hard tissue healing are due to local and continuous delivery of growth factors and proteins, mimicking the needs of the physiological wound healing and reparative tissue processes. This article aims to evaluate the clinical efficacy of open flap debridement (OFD) with or without platelet-rich fibrin (PRF) in the treatment of intrabony defects. Materials and Methods: Twenty subjects with forty intrabony defects were treated with either autologous PRF with open-flap debridement (test, n = 20) or open-flap debridement alone (control, n = 20). Soft tissue parameters included: Plaque index, sulcus bleeding index, probing depth, relative attachment level and gingival marginal level (GML). The hard tissue parameters included-distances from: Cement enamel junction to the base of the defect (CEJ-BOD): Alveolar crest to the base of the defect (AC-BOD): And CEJ to AC. The parameters were recorded at baseline and at 9 months postoperatively calculated using standardized radiographs by image-analysis software. Results: Statistically significant (0.005*) intragroup improvements were seen with all the hard and soft parameters in both test and control groups, except for GML. Statistically significant improvements were seen with the mean defect fill (CEJ-BOD and AC-BOD) (P = 0.003*) when intergroup comparisons were made. Conclusions: Adjunctive use of PRF with OFD significantly improves defect fill when compared to OFD alone. PRF has consistently been showing regenerative potential; it is simple, easy and inexpensive biomaterial compared with bone grafts. PMID:25954068

An allogenic cell-based implant for meniscal lesions.

PubMed

Weinand, Christian; Peretti, Giuseppe M; Adams, Samuel B; Bonassar, Lawrence J; Randolph, Mark A; Gill, Thomas J

2006-11-01

Meniscal tears in the avascular zones do not heal. Although tissue-engineering approaches using cells seeded onto scaffolds could expand the indication for meniscal repair, harvesting autologous cells could cause additional trauma to the patient. Allogenic cells, however, could provide an unlimited amount of cells. Allogenic cells from 2 anatomical sources can repair lesions in the avascular region of the meniscus. Controlled laboratory study. Both autologous and allogenic chondrocytes were seeded onto a Vicryl mesh scaffold and sutured into a bucket-handle lesion created in the medial menisci of 17 swine. Controls consisted of 3 swine knees treated with unseeded implants and controls from a previous experiment in which 4 swine were treated with suture only and 4 with no treatment. Menisci were harvested after 12 weeks and evaluated histologically for new tissue and percentage of interface healing surface; they were also evaluated statistically. The lesions were closed in 15 of 17 menisci. None of the control samples demonstrated healing. Histologic analysis of sequential cuts through the lesion showed formation of new scar-like tissue in all experimental samples. One of 8 menisci was completely healed in the allogenic group and 2 of 9 in the autologous group; the remaining samples were partially healed in both groups. No statistically significant differences in the percentage of healing were observed between the autologous and allogenic cell-based implants. Use of autologous and allogenic chondrocytes delivered via a biodegradable mesh enhanced healing of avascular meniscal lesions. This study demonstrates the potential of a tissue-engineered cellular repair of the meniscus using autologous and allogenic chondrocytes.

B7-H1 expression is associated with expansion of regulatory T cells in colorectal carcinoma

PubMed Central

Hua, Dong; Sun, Jing; Mao, Yong; Chen, Lu-Jun; Wu, Yu-Yu; Zhang, Xue-Guang

2012-01-01

AIM: To investigate the expression of B7-H1 in human colorectal carcinoma (CRC) to define its regulating effects on T cells in tumor microenvironment. METHODS: One hundred and two paraffin blocks and 33 fresh samples of CRC tissues were subject to this study. Immunohistochemistry was performed for B7-H1 and CD3 staining in CRC tissues. Ficoll-Hypaque density gradient centrifugation was used to isolate peripheral blood mononuclear cells of fresh CRC tissues; flow cytometry and immunofluorescence staining were used for detection of regulatory T cells. Data was analyzed with statistical software. RESULTS: Costimulatory molecule B7-H1 was found strongly expressed in CRC tissues, localized in tumor cell membrane and cytoplasm, while weak or none expression of B7-H1 was detected in pared normal colorectal tissues. Meanwhile, CD3 positive T cells were found congregated in CRC tumor nest and stroma. Statistic analysis showed that B7-H1 expression level was negatively correlated to the total T cell density in tumor nest (P < 0.0001) and tumor stroma (P = 0.0200) of 102 cases of CRC tissues. Among the total T cells, a variable amount of regulatory T cells with a clear Foxp3+ (forkhead box P3) staining could be detected in CRC tissues and patients’ blood. Interestingly, in the 33 samples (15 cases of B7-H1high CRC tissues and 18 cases of B7-H1low CRC tissues) of freshly isolated mononuclear cells from CRC tissues, the percentages of CD4+Foxp3+ and CD8+Foxp3+ regulatory T cells were found remarkably higher in B7-H1high CRC tissues than in B7-H1low CRC tissues (P = 0.0024, P = 0.0182), indicating that B7-H1 expression was involved in proliferation of regulatory T cell. No significant difference was found in CRC peripheral blood (P = 0.0863, P = 0.0678). PD-1 is the specific ligand for B7-H1 pathway transferring inhibitory signal to T cell, which is expressed by activated T cell. Our further analysis of PD-1 expression on T cells in CRC tissues showed that conventional T cells (CD4+Foxp3-/CD8+Foxp3-), which was thought to contribute to the anti-tumor immune response, highly expressed PD-1; while regulatory T cells (CD4+Foxp3+/CD8+Foxp3-) almost failed to express PD-1. The average percentage of PD-1 expression on regulatory T cells was significantly higher than the percentage of PD-1 on conventional T cells (CD4+Foxp3- T cell, P < 0.0001; CD8+Foxp3- T cell, P < 0.0001). The diverse expression of PD-1 might lead to different fate of T cell subsets in B7-H1 over-expression CRC tumor microenvironment. CONCLUSION: B7-H1 expression in tumor cells can inhibit the conventional T cell proliferation in tumor microenvironment through the PD-1 expression on conventional T cells. PMID:22408358

Atrial Electrogram Fractionation Distribution before and after Pulmonary Vein Isolation in Human Persistent Atrial Fibrillation-A Retrospective Multivariate Statistical Analysis.

PubMed

Almeida, Tiago P; Chu, Gavin S; Li, Xin; Dastagir, Nawshin; Tuan, Jiun H; Stafford, Peter J; Schlindwein, Fernando S; Ng, G André

2017-01-01

Purpose: Complex fractionated atrial electrograms (CFAE)-guided ablation after pulmonary vein isolation (PVI) has been used for persistent atrial fibrillation (persAF) therapy. This strategy has shown suboptimal outcomes due to, among other factors, undetected changes in the atrial tissue following PVI. In the present work, we investigate CFAE distribution before and after PVI in patients with persAF using a multivariate statistical model. Methods: 207 pairs of atrial electrograms (AEGs) were collected before and after PVI respectively, from corresponding LA regions in 18 persAF patients. Twelve attributes were measured from the AEGs, before and after PVI. Statistical models based on multivariate analysis of variance (MANOVA) and linear discriminant analysis (LDA) have been used to characterize the atrial regions and AEGs. Results: PVI significantly reduced CFAEs in the LA (70 vs. 40%; P < 0.0001). Four types of LA regions were identified, based on the AEGs characteristics: (i) fractionated before PVI that remained fractionated after PVI (31% of the collected points); (ii) fractionated that converted to normal (39%); (iii) normal prior to PVI that became fractionated (9%) and; (iv) normal that remained normal (21%). Individually, the attributes failed to distinguish these LA regions, but multivariate statistical models were effective in their discrimination ( P < 0.0001). Conclusion: Our results have unveiled that there are LA regions resistant to PVI, while others are affected by it. Although, traditional methods were unable to identify these different regions, the proposed multivariate statistical model discriminated LA regions resistant to PVI from those affected by it without prior ablation information.

Impact of timing on soft tissue augmentation during implant treatment: A systematic review and meta-analysis.

PubMed

Lin, Cho-Ying; Chen, Zhaozhao; Pan, Whei-Lin; Wang, Hom-Lay

2018-05-01

To achieve a predictable esthetic and functional outcome, soft tissue augmentation has become popular in implant treatment. The aim of this systematic review and meta-analysis was to assess the influence of different timing for soft tissue augmentation during implant treatment on soft tissue conditions and its stability. Electronic and manual searches for articles written in English up to September 2017 were performed by two independent reviewers. Human clinical studies with the purpose of evaluating outcomes (at least 3-month follow-up) of autogenous soft tissue graft for augmentation during implant treatment, either simultaneous or after implant placement (staged), were included. Cumulative changes of keratinized tissue width (KTW), soft tissue thickness (STT), and mid-buccal mucosal recession (MR) data were analyzed with a random-effects model to compare the postoperative outcomes. Twenty-nine human studies (eight randomized clinical trials, six cohort studies, and 15 case series) that met the inclusion criteria were included. For the overall data, the weighted mean STT gain (1 year after surgery) was 1.03 mm (95% CI: 0.78-1.29 mm), among which the simultaneous group was 1.12 mm (95% CI: 0.75-1.49 mm) and staged group (3-6 months after implant placement) was 0.95 mm (95% CI: 0.58-1.31 mm). There was no statistically significant difference in KTW and MR between 3 months and more than 3 months after surgery. This review revealed that the stability of soft tissue, in terms of KTW and mid-buccal MR, can be obtained 3 months after surgery. There is no difference between simultaneous and staged soft tissue augmentation during implant treatment, and both procedures significantly enhance KTW and STT. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Comparative assessment of Graves' disease and main extrathyroidal manifestation, Graves' ophthalmopathy, by non-targeted metabolite profiling of blood and orbital tissue.

PubMed

Ji, Dong Yoon; Park, Se Hee; Park, Soo Jin; Kim, Kyoung Heon; Ku, Cheol Ryong; Shin, Dong Yeob; Yoon, Jin Sook; Lee, Do Yup; Lee, Eun Jig

2018-06-18

Graves' disease (GD) is an autoimmune disorder that causes the overproduction of thyroid hormones and consequent cascade of systemic metabolism dysfunction. Moreover, Graves' ophthalmopathy (GO) is the main extrathyroidal manifestation of Graves' disease (GD). The goal of the study was to identify metabolic signatures in association with diagnostic biomarkers of GD without GO and GO, respectively. Ninety metabolites were profiled and analyzed based on a non-targeted primary metabolite profiling from plasma samples of 21 GD patients without GO, 26 subjects with GO, and 32 healthy subjects. Multivariate statistics showed a clear discrimination between healthy controls and disease group (R2Y = 0.518, Q2 = 0.478) and suggested a biomarker panel consisting of 10 metabolites. Among them, most of metabolites showed the positive association with the levels of thyrotropin receptor antibodies. With combination of proline and 1,5-anhydroglucitol, which were identified as GO-specific modulators, the re-constructed biomarker model greatly improved the statistical power and also facilitated simultaneous discrimination among healthy control, GO, and GD without GO groups (AUC = 0.845-0.935). Finally, the comparative analysis of tissue metabolite profiles from GO patients proposed putative metabolic linkage between orbital adipose/connective tissues and the biofluidic consequences, in which fumarate, proline, phenylalanine, and glycerol were coordinately altered with the blood metabolites.

Comparison of two modalities: a novel technique, 'chromohysteroscopy', and blind endometrial sampling for the evaluation of abnormal uterine bleeding.

PubMed

Alay, Asli; Usta, Taner A; Ozay, Pinar; Karadugan, Ozgur; Ates, Ugur

2014-05-01

The objective of this study was to compare classical blind endometrial tissue sampling with hysteroscopic biopsy sampling following methylene blue dyeing in premenopausal and postmenopausal patients with abnormal uterine bleeding. A prospective case-control study was carried out in the Office Hysteroscopy Unit. Fifty-four patients with complaints of abnormal uterine bleeding were evaluated. Data of 38 patients were included in the statistical analysis. Three groups were compared by examining samples obtained through hysteroscopic biopsy before and after methylene blue dyeing, and classical blind endometrial tissue sampling. First, uterine cavity was evaluated with office hysteroscopy. Methylene blue dye was administered through the hysteroscopic inlet. Tissue samples were obtained from stained and non-stained areas. Blind endometrial sampling was performed in the same patients immediately after the hysteroscopy procedure. The results of hysteroscopic biopsy from methylene blue stained and non-stained areas and blind biopsy were compared. No statistically significant differences were determined in the comparison of biopsy samples obtained from methylene-blue stained, non-stained areas and blind biopsy (P > 0.05). We suggest that chromohysteroscopy is not superior to endometrial sampling in cases of abnormal uterine bleeding. Further studies with greater sample sizes should be performed to assess the validity of routine use of endometrial dyeing. © 2014 The Authors. Journal of Obstetrics and Gynaecology Research © 2014 Japan Society of Obstetrics and Gynecology.

NMR-based metabolomics approach to study the toxicity of lambda-cyhalothrin to goldfish (Carassius auratus).

PubMed

Li, Minghui; Wang, Junsong; Lu, Zhaoguang; Wei, Dandan; Yang, Minghua; Kong, Lingyi

2014-01-01

In this study, a (1)H nuclear magnetic resonance (NMR) based metabolomics approach was applied to investigate the toxicity of lambda-cyhalothrin (LCT) in goldfish (Carassius auratus). LCT showed tissue-specific damage to gill, heart, liver and kidney tissues of goldfish. NMR profiling combined with statistical methods such as orthogonal partial least squares discriminant analysis (OPLS-DA) and two-dimensional statistical total correlation spectroscopy (2D-STOCSY) was developed to discern metabolite changes occurring after one week LCT exposure in brain, heart and kidney tissues of goldfish. LCT exposure influenced levels of many metabolites (e.g., leucine, isoleucine and valine in brain and kidney; lactate in brain, heart and kidney; alanine in brain and kidney; choline in brain, heart and kidney; taurine in brain, heart and kidney; N-acetylaspartate in brain; myo-inositol in brain; phosphocreatine in brain and heart; 2-oxoglutarate in brain; cis-aconitate in brain, and etc.), and broke the balance of neurotransmitters and osmoregulators, evoked oxidative stress, disturbed metabolisms of energy and amino acids. The implication of glutamate-glutamine-gamma-aminobutyric axis in LCT induced toxicity was demonstrated for the first time. Our findings demonstrated the applicability and potential of metabolomics approach for the elucidation of toxicological effects of pesticides and the underlying mechanisms, and the discovery of biomarkers for pesticide pollution in aquatic environment. Copyright © 2013 Elsevier B.V. All rights reserved.

NGF protects corneal, retinal, and cutaneous tissues/cells from phototoxic effect of UV exposure.

PubMed

Rocco, Maria Luisa; Balzamino, Bijorn Omar; Aloe, Luigi; Micera, Alessandra

2018-04-01

Based on evidence that nerve growth factor (NGF) exerts healing action on damaged corneal, retinal, and cutaneous tissues, the present study sought to assess whether topical NGF application can prevent and/or protect epithelial cells from deleterious effects of ultraviolet (UV) radiation. Eyes from 40 young-adult Sprague Dawley rats and cutaneous tissues from 36 adult nude mice were exposed to UVA/B lamp for 60 min, either alone or in the presence of murine NGF. Corneal, retinal, and cutaneous tissues were sampled/processed for morphological, immunohistochemical, and biomolecular analysis, and results were compared statistically. UV exposure affected both biochemical and molecular expression of NGF and trkA NGFR in corneal, retinal, and cutaneous tissues while UV exposure coupled to NGF treatment enhanced NGF and trkA NGFR expression as well as reduced cell death. Overall, the findings of this in vivo/ex vivo study show the NGF ability to reduce the potential UV damage. Although the mechanism underneath this effect needs further investigation, these observations prospect the development of a pharmacological NGF-based therapy devoted to maintain cell function when exposed to phototoxic UV radiation.

Practical protocols for fast histopathology by Fourier transform infrared spectroscopic imaging

NASA Astrophysics Data System (ADS)

Keith, Frances N.; Reddy, Rohith K.; Bhargava, Rohit

2008-02-01

Fourier transform infrared (FT-IR) spectroscopic imaging is an emerging technique that combines the molecular selectivity of spectroscopy with the spatial specificity of optical microscopy. We demonstrate a new concept in obtaining high fidelity data using commercial array detectors coupled to a microscope and Michelson interferometer. Next, we apply the developed technique to rapidly provide automated histopathologic information for breast cancer. Traditionally, disease diagnoses are based on optical examinations of stained tissue and involve a skilled recognition of morphological patterns of specific cell types (histopathology). Consequently, histopathologic determinations are a time consuming, subjective process with innate intra- and inter-operator variability. Utilizing endogenous molecular contrast inherent in vibrational spectra, specially designed tissue microarrays and pattern recognition of specific biochemical features, we report an integrated algorithm for automated classifications. The developed protocol is objective, statistically significant and, being compatible with current tissue processing procedures, holds potential for routine clinical diagnoses. We first demonstrate that the classification of tissue type (histology) can be accomplished in a manner that is robust and rigorous. Since data quality and classifier performance are linked, we quantify the relationship through our analysis model. Last, we demonstrate the application of the minimum noise fraction (MNF) transform to improve tissue segmentation.

Dual-modal cancer detection based on optical pH sensing and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Kim, Soogeun; Lee, Seung Ho; Min, Sun Young; Byun, Kyung Min; Lee, Soo Yeol

2017-10-01

A dual-modal approach using Raman spectroscopy and optical pH sensing was investigated to discriminate between normal and cancerous tissues. Raman spectroscopy has demonstrated the potential for in vivo cancer detection. However, Raman spectroscopy has suffered from strong fluorescence background of biological samples and subtle spectral differences between normal and disease tissues. To overcome those issues, pH sensing is adopted to Raman spectroscopy as a dual-modal approach. Based on the fact that the pH level in cancerous tissues is lower than that in normal tissues due to insufficient vasculature formation, the dual-modal approach combining the chemical information of Raman spectrum and the metabolic information of pH level can improve the specificity of cancer diagnosis. From human breast tissue samples, Raman spectra and pH levels are measured using fiber-optic-based Raman and pH probes, respectively. The pH sensing is based on the dependence of pH level on optical transmission spectrum. Multivariate statistical analysis is performed to evaluate the classification capability of the dual-modal method. The analytical results show that the dual-modal method based on Raman spectroscopy and optical pH sensing can improve the performance of cancer classification.

Automated palpation for breast tissue discrimination based on viscoelastic biomechanical properties.

PubMed

Tsukune, Mariko; Kobayashi, Yo; Miyashita, Tomoyuki; Fujie, G Masakatsu

2015-05-01

Accurate, noninvasive methods are sought for breast tumor detection and diagnosis. In particular, a need for noninvasive techniques that measure both the nonlinear elastic and viscoelastic properties of breast tissue has been identified. For diagnostic purposes, it is important to select a nonlinear viscoelastic model with a small number of parameters that highly correlate with histological structure. However, the combination of conventional viscoelastic models with nonlinear elastic models requires a large number of parameters. A nonlinear viscoelastic model of breast tissue based on a simple equation with few parameters was developed and tested. The nonlinear viscoelastic properties of soft tissues in porcine breast were measured experimentally using fresh ex vivo samples. Robotic palpation was used for measurements employed in a finite element model. These measurements were used to calculate nonlinear viscoelastic parameters for fat, fibroglandular breast parenchyma and muscle. The ability of these parameters to distinguish the tissue types was evaluated in a two-step statistical analysis that included Holm's pairwise [Formula: see text] test. The discrimination error rate of a set of parameters was evaluated by the Mahalanobis distance. Ex vivo testing in porcine breast revealed significant differences in the nonlinear viscoelastic parameters among combinations of three tissue types. The discrimination error rate was low among all tested combinations of three tissue types. Although tissue discrimination was not achieved using only a single nonlinear viscoelastic parameter, a set of four nonlinear viscoelastic parameters were able to reliably and accurately discriminate fat, breast fibroglandular tissue and muscle.

A Comparative Study on the Role of Xpert MTB/RIF in Testing Different Types of Spinal Tuberculosis Tissue Specimens.

PubMed

Tang, Liang; Feng, Shiqing; Gao, Ruixiao; Han, Chenfu; Sun, Xiaochen; Bao, Yucheng; Zhang, Wenlong

2017-12-01

The aim of the present study was to compare the efficacy of the commercial Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) test for evaluating different types of spinal tuberculosis (TB) tissue specimens. Pus, granulation tissue, and caseous necrotic tissue specimens from 223 patients who were diagnosed with spinal TB and who underwent curettage were collected for bacterial culture and the Xpert MTB/RIF assay to calculate the positive rate. Bacterial culture and phenotypic drug sensitivity testing (pDST) were adopted as the gold standards to calculate the sensitivity and specificity of the Xpert bacterial detection and drug resistance (DR) test. The positive rate (68.61% ± 7.35%) from the Xpert MTB/RIF assays of spinal TB patients' tissue specimens was higher compared with bacterial culture (44.39% ± 6.51%, Z = 5.1642, p < 0.01), and the positive rates from Xpert MTB/RIF assays on the three types of specimens were all higher than those of bacterial culture, with statistically significant results for pus and granulation tissue specimens. The positive rates for pus using the two bacteriological tests were higher than those for granulation tissue but were not statistically significant. However, the positive rates obtained from granulation tissue were statistically significantly higher than those obtained from caseous necrotic tissue. With bacterial culture and pDST as the gold standards, the sensitivity of Xpert MTB/RIF assays for MTB was 96.97%, while the sensitivity and specificity of the DR test also remained relatively high. For efficient and accurate diagnosis of spinal TB and DR and timely provision of effective treatment, multiple specimens, especially the pus of spinal TB patients, should be collected for Xpert MTB/RIF assays.

Integrative Genome Comparison of Primary and Metastatic Melanomas

PubMed Central

Feng, Bin; Nazarian, Rosalynn M.; Bosenberg, Marcus; Wu, Min; Scott, Kenneth L.; Kwong, Lawrence N.; Xiao, Yonghong; Cordon-Cardo, Carlos; Granter, Scott R.; Ramaswamy, Sridhar; Golub, Todd; Duncan, Lyn M.; Wagner, Stephan N.; Brennan, Cameron; Chin, Lynda

2010-01-01

A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of effective therapeutics and prognostic diagnostics for melanoma patients. In this study, we conducted global genomic characterization of primary and metastatic melanomas to examine the genomic landscape associated with metastatic progression. In addition to uncovering three genomic subclasses of metastastic melanomas, we delineated 39 focal and recurrent regions of amplification and deletions, many of which encompassed resident genes that have not been implicated in cancer or metastasis. To identify progression-associated metastasis gene candidates, we applied a statistical approach, Integrative Genome Comparison (IGC), to define 32 genomic regions of interest that were significantly altered in metastatic relative to primary melanomas, encompassing 30 resident genes with statistically significant expression deregulation. Functional assays on a subset of these candidates, including MET, ASPM, AKAP9, IMP3, PRKCA, RPA3, and SCAP2, validated their pro-invasion activities in human melanoma cells. Validity of the IGC approach was further reinforced by tissue microarray analysis of Survivin showing significant increased protein expression in thick versus thin primary cutaneous melanomas, and a progression correlation with lymph node metastases. Together, these functional validation results and correlative analysis of human tissues support the thesis that integrated genomic and pathological analyses of staged melanomas provide a productive entry point for discovery of melanoma metastases genes. PMID:20520718

Bayesian approach to estimate AUC, partition coefficient and drug targeting index for studies with serial sacrifice design.

PubMed

Wang, Tianli; Baron, Kyle; Zhong, Wei; Brundage, Richard; Elmquist, William

2014-03-01

The current study presents a Bayesian approach to non-compartmental analysis (NCA), which provides the accurate and precise estimate of AUC 0 (∞) and any AUC 0 (∞) -based NCA parameter or derivation. In order to assess the performance of the proposed method, 1,000 simulated datasets were generated in different scenarios. A Bayesian method was used to estimate the tissue and plasma AUC 0 (∞) s and the tissue-to-plasma AUC 0 (∞) ratio. The posterior medians and the coverage of 95% credible intervals for the true parameter values were examined. The method was applied to laboratory data from a mice brain distribution study with serial sacrifice design for illustration. Bayesian NCA approach is accurate and precise in point estimation of the AUC 0 (∞) and the partition coefficient under a serial sacrifice design. It also provides a consistently good variance estimate, even considering the variability of the data and the physiological structure of the pharmacokinetic model. The application in the case study obtained a physiologically reasonable posterior distribution of AUC, with a posterior median close to the value estimated by classic Bailer-type methods. This Bayesian NCA approach for sparse data analysis provides statistical inference on the variability of AUC 0 (∞) -based parameters such as partition coefficient and drug targeting index, so that the comparison of these parameters following destructive sampling becomes statistically feasible.

Can macrocirculation changes predict nonhealing diabetic foot ulcers?

PubMed

Lee, Ye-Na; Kim, Hyon-Surk; Kang, Jeong-A; Han, Seung-Kyu

2014-01-01

Transcutaneous partial oxygen tension (TcpO2) is considered the gold standard for assessment of tissue oxygenation, which is an essential factor for wound healing. The purpose of this study was to evaluate the association between macrocirculation and TcpO2 in persons with diabetes mellitus. Ninety-eight patients with diabetic foot ulcers participated in the study (61 men and 37 women). The subjects had a mean age of 66.6 years (range, 30-83 years) and were treated at the Diabetic Wound Center of Korea University Guro Hospital, Seoul, Republic of Korea. Macrocirculation was evaluated using 2 techniques: computed tomographic angiography and Doppler ultrasound. Macrocirculation scores were based on the patency of the two tibial arteries in 98 patients. Computed tomographic angiography and Doppler ultrasound scores (0-4 points) were given according to intraluminal filling defects and arterial pulse waveform of each vessel, respectively. Tissue oxygenation was measured by TcpO2. Macrocirculation scores were statistically analyzed as a function of the TcpO2. Statistical analysis revealed no significant linear trend between the macrocirculation status and TcpO2. Biavariate analysis using the Fisher exact test, Mantel-Haenszel tests, and McNemar-Bowker tests also found no significant relationship between macrocirculation and TcpO2. Computed tomographic angiography and Doppler ultrasound are not sufficiently reliable substitutes for TcpO2 measurements in regard to determining the optimal treatment for diabetic patients.

Computer-aided Prognosis of Neuroblastoma on Whole-slide Images: Classification of Stromal Development

PubMed Central

Sertel, O.; Kong, J.; Shimada, H.; Catalyurek, U.V.; Saltz, J.H.; Gurcan, M.N.

2009-01-01

We are developing a computer-aided prognosis system for neuroblastoma (NB), a cancer of the nervous system and one of the most malignant tumors affecting children. Histopathological examination is an important stage for further treatment planning in routine clinical diagnosis of NB. According to the International Neuroblastoma Pathology Classification (the Shimada system), NB patients are classified into favorable and unfavorable histology based on the tissue morphology. In this study, we propose an image analysis system that operates on digitized H&E stained whole-slide NB tissue samples and classifies each slide as either stroma-rich or stroma-poor based on the degree of Schwannian stromal development. Our statistical framework performs the classification based on texture features extracted using co-occurrence statistics and local binary patterns. Due to the high resolution of digitized whole-slide images, we propose a multi-resolution approach that mimics the evaluation of a pathologist such that the image analysis starts from the lowest resolution and switches to higher resolutions when necessary. We employ an offine feature selection step, which determines the most discriminative features at each resolution level during the training step. A modified k-nearest neighbor classifier is used to determine the confidence level of the classification to make the decision at a particular resolution level. The proposed approach was independently tested on 43 whole-slide samples and provided an overall classification accuracy of 88.4%. PMID:20161324

Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples.

PubMed

Zhao, Qi; Liu, Yuanning; Zhang, Ning; Hu, Menghan; Zhang, Hao; Joshi, Trupti; Xu, Dong

2018-01-01

In recent years, an increasing number of studies have reported the presence of plant miRNAs in human samples, which resulted in a hypothesis asserting the existence of plant-derived exogenous microRNA (xenomiR). However, this hypothesis is not widely accepted in the scientific community due to possible sample contamination and the small sample size with lack of rigorous statistical analysis. This study provides a systematic statistical test that can validate (or invalidate) the plant-derived xenomiR hypothesis by analyzing 388 small RNA sequencing data from human samples in 11 types of body fluids/tissues. A total of 166 types of plant miRNAs were found in at least one human sample, of which 14 plant miRNAs represented more than 80% of the total plant miRNAs abundance in human samples. Plant miRNA profiles were characterized to be tissue-specific in different human samples. Meanwhile, the plant miRNAs identified from microbiome have an insignificant abundance compared to those from humans, while plant miRNA profiles in human samples were significantly different from those in plants, suggesting that sample contamination is an unlikely reason for all the plant miRNAs detected in human samples. This study also provides a set of testable synthetic miRNAs with isotopes that can be detected in situ after being fed to animals.

Bladder cancer diagnosis during cystoscopy using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Grimbergen, M. C. M.; van Swol, C. F. P.; Draga, R. O. P.; van Diest, P.; Verdaasdonk, R. M.; Stone, N.; Bosch, J. H. L. R.

2009-02-01

Raman spectroscopy is an optical technique that can be used to obtain specific molecular information of biological tissues. It has been used successfully to differentiate normal and pre-malignant tissue in many organs. The goal of this study is to determine the possibility to distinguish normal tissue from bladder cancer using this system. The endoscopic Raman system consists of a 6 Fr endoscopic probe connected to a 785nm diode laser and a spectral recording system. A total of 107 tissue samples were obtained from 54 patients with known bladder cancer during transurethral tumor resection. Immediately after surgical removal the samples were placed under the Raman probe and spectra were collected and stored for further analysis. The collected spectra were analyzed using multivariate statistical methods. In total 2949 Raman spectra were recorded ex vivo from cold cup biopsy samples with 2 seconds integration time. A multivariate algorithm allowed differentiation of normal and malignant tissue with a sensitivity and specificity of 78,5% and 78,9% respectively. The results show the possibility of discerning normal from malignant bladder tissue by means of Raman spectroscopy using a small fiber based system. Despite the low number of samples the results indicate that it might be possible to use this technique to grade identified bladder wall lesions during endoscopy.

MUC4: a novel prognostic factor of oral squamous cell carcinoma.

PubMed

Hamada, Tomofumi; Wakamatsu, Tsunenobu; Miyahara, Mayumi; Nagata, Satoshi; Nomura, Masahiro; Kamikawa, Yoshiaki; Yamada, Norishige; Batra, Surinder K; Yonezawa, Suguru; Sugihara, Kazumasa

2012-04-15

MUC4 mucin is now known to be expressed in various normal and cancer tissues. We have previously reported that MUC4 expression is a novel prognostic factor in several malignant tumors; however, it has not been investigated in oral squamous cell carcinoma (OSCC). The aim of our study is to evaluate the prognostic significance of MUC4 expression in OSCC. We examined the expression profile of MUC4 in OSCC tissues from 150 patients using immunohistochemistry. Its prognostic significance in OSCC was statistically analyzed. MUC4 was expressed in 61 of the 150 patients with OSCC. MUC4 expression was significantly correlated with higher T classification (p = 0.0004), positive nodal metastasis (p = 0.049), advanced tumor stage (p = 0.002), diffuse invasion of cancer cells (p = 0.004) and patient's death (p = 0.004) in OSCC. Multivariate analysis showed that MUC4 expression (p = 0.011), tumor location (p = 0.032) and diffuse invasion (p = 0.009) were statistically significant risk factors. Backward stepwise multivariate analysis demonstrated MUC4 expression (p = 0.0015) and diffuse invasion (p = 0.018) to be statistically significant independent risk factors of poor survival in OSCC. The disease-free and overall survival of patients with MUC4 expression was significantly worse than those without MUC4 expression (p < 0.0001 and p = 0.0001). In addition, the MUC4 expression was a significant risk factor for local recurrence and subsequent nodal metastasis in OSCC (p = 0.017 and p = 0.0001). We first report MUC4 overexpression is an independent factor for poor prognosis of patients with OSCC; therefore, patients with OSCC showing positive MUC4 expression should be followed up carefully. Copyright © 2011 UICC.

Diet and liver apoptosis in rats: a particular metabolic pathway.

PubMed

Monteiro, Maria Emilia Lopes; Xavier, Analucia Rampazzo; Azeredo, Vilma Blondet

2017-03-30

Various studies have indicated an association between modifi cation in dietary macronutrient composition and liver apoptosis. To explain how changes in metabolic pathways associated with a high-protein, high-fat, and low-carbohydrate diet causes liver apoptosis. Two groups of rats were compared. An experimental diet group (n = 8) using a high-protein (59.46%), high-fat (31.77%), and low-carbohydrate (8.77%) diet versus a control one (n = 9) with American Institute of Nutrition (AIN)-93-M diet. Animals were sacrificed after eight weeks, the adipose tissue weighed, the liver removed for flow cytometry analysis, and blood collected to measure glucose, insulin, glucagon, IL-6, TNF, triglycerides, malondialdehyde, and β-hydroxybutyrate. Statistical analysis was carried out using the unpaired and parametric Student's t-test and Pearson's correlation coeffi ents. Significance was set at p < 0.05. Animals from the experimental group presented less adipose tissue than dose of the control group. Percentage of nonviable hepatocytes in the experimental group was 2.18 times larger than the control group (p = 0.001). No statistically significant differences were found in capillary glucose, insulin, glucagon, IL-6, or TNF-α between two groups. Plasmatic β-hydroxybutyrate and malondialdehyde of the experimental group expressed higher levels and triglycerides lower levels compared with the control group. The results show a positive and significant correlation between the percentage of nonviable hepatocytes and malondialdehyde levels (p = 0.0217) and a statistically significant negative correlation with triglycerides levels (p = 0.006). Results suggest that plasmatic malondialdehyde and triglyceride levels are probably good predictors of liver damage associated with an experimental low-carbohydrate diet in rats.

Development and application of Fourier-transform infrared chemical imaging of tumour in human tissue.

PubMed

Petter, C H; Heigl, N; Rainer, M; Bakry, R; Pallua, J; Bonn, G K; Huck, C W

2009-01-01

Fourier-transform infrared (FT-IR) based mapping and imaging is a fast emerging technology which is being increasingly applied to investigate tissues in the high-throughput mode. The high resolution close to the cellular level, the possibility to determine the bio-distribution of molecules of interest (proteins, peptides, lipids, carbohydrates) without any pre-treatment and the offer to yield molecular structure information have brought evidence that this technique allows to gain new insights in cancer pathology. Thus, several individual mainly protein and peptide cancer markers ("biomarkers") can be identified from FT-IR tissue images, enabling accurate discrimination between healthy and tumour areas. Optimal data acquisition (spatial resolution, spectral resolution, signal to noise ratio), classification, and validation are necessary to establish practical protocols that can be translated to the qualitative and quantitative clinical routine analysis. Thereby, the development of modern fast infrared imaging systems has strongly supported its acceptance in clinical histopathology. In this review, the necessity of analysis based on global cancer statistics, instrumental setups and developments, experimental state of the art are summarised and applications to investigate different kinds of cancer (e.g., prostate, breast, cervical, colon, oral cavity) are shown and discussed in detail.

Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures.

PubMed

Knight, V Bleu; Serrano, Elba E

2017-01-01

Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of neural tissue organization with engineered scaffolds. In this study, we used high throughput transcriptomic and imaging methods to determine the impact of a hydrogel, PuraMatrix™, on human glial cells in vitro . Parallel studies were undertaken with cells grown in a monolayer environment on tissue culture polystyrene. When the Normal Human Astrocyte (NHA) cell line is grown in a hydrogel matrix environment, the glial cells adopt a structural organization that resembles that of neuronal-glial cocultures, where neurons form clusters that are distinct from the surrounding glia. Statistical analysis of next generation RNA sequencing data uncovered a set of genes that are differentially expressed in the monolayer and matrix hydrogel environments. Functional analysis demonstrated that hydrogel-upregulated genes can be grouped into three broad categories: neuronal differentiation and/or neural plasticity, response to neural insult, and sensory perception. Our results demonstrate that hydrogel biomaterials have the potential to transform human glial cell identity, and may have applications in the repair of damaged brain tissue.

Cervical soft tissue imaging using a mobile CBCT scanner with a flat panel detector in comparison with corresponding CT and MRI data sets.

PubMed

Heiland, Max; Pohlenz, Philipp; Blessmann, Marco; Habermann, Christian R; Oesterhelweg, Lars; Begemann, Philipp C; Schmidgunst, Christian; Blake, Felix A S; Püschel, Klaus; Schmelzle, Rainer; Schulze, Dirk

2007-12-01

The aim of this study was to evaluate soft tissue image quality of a mobile cone-beam computed tomography (CBCT) scanner with an integrated flat-panel detector. Eight fresh human cadavers were used in this study. For evaluation of soft tissue visualization, CBCT data sets and corresponding computed tomography (CT) and magnetic resonance imaging (MRI) data sets were acquired. Evaluation was performed with the help of 10 defined cervical anatomical structures. The statistical analysis of the scoring results of 3 examiners revealed the CBCT images to be of inferior quality regarding the visualization of most of the predefined structures. Visualization without a significant difference was found regarding the demarcation of the vertebral bodies and the pyramidal cartilages, the arteriosclerosis of the carotids (compared with CT), and the laryngeal skeleton (compared with MRI). Regarding arteriosclerosis of the carotids compared with MRI, CBCT proved to be superior. The integration of a flat-panel detector improves soft tissue visualization using a mobile CBCT scanner.

Ancestry and BMI Influences on Facial Soft Tissue Depths for A Cohort of Chinese and Caucasoid Women in Dunedin, New Zealand.

PubMed

Baillie, Louisa J; Mirijali, Seyed Ali; Niven, Brian E; Blyth, Phil; Dias, George J

2015-09-01

This study measured and assessed facial soft tissue depths (FSTDs) in adult female Chinese and New Zealand (NZ) Europeans (Caucasoids). Ultrasound was used to obtain depths at nine landmarks on 108 healthy subjects (51 Chinese, 57 NZ European), erect positioned, of same age group (18-29 years). Height and weight were also recorded. Statistical analysis focused on comparison of tissue depth between the two ancestry groups and the influence of Body Mass Index (BMI) (kg/m2). Results showed mean depth differences at Supra M2 and Infra M2 landmarks significantly greater for Chinese than Caucasoid women for all three BMI Classes (BMI<20, 20≤BMI<25, 25≤BMI<30), even BMI<20. For both groups BMI positively correlated with FSTD values at all landmarks except Labrale superius. This study enabled ancestry and BMI influence on FSTDs to be observed and compared for two distinct groups. Results add to knowledge about facial tissue depth variation. © 2015 American Academy of Forensic Sciences.

Application of a novel sorting system for equine mesenchymal stem cells (MSCs)

PubMed Central

Radtke, Catherine L.; Nino-Fong, Rodolfo; Esparza Gonzalez, Blanca P.; McDuffee, Laurie A.

2014-01-01

The objective of this study was to validate non-equilibrium gravitational field-flow fractionation (GrFFF), an immunotag-less method of sorting mesenchymal stem cells (MSCs) into subpopulations, for use with MSCs derived from equine muscle tissue, periosteal tissue, bone marrow, and adipose tissue. Cells were collected from 6 young, adult horses, postmortem. Cells were isolated from left semitendinosus muscle tissue, periosteal tissue from the distomedial aspect of the right tibia, bone marrow aspirates from the fourth and fifth sternebrae, and left supragluteal subcutaneous adipose tissue. Aliquots of 800 × 103 MSCs from each tissue source were separated and injected into a ribbon-like capillary device by continuous flow (GrFFF proprietary system). Cells were sorted into 6 fractions and absorbencies [optical density (OD)] were read. Six fractions from each of the 6 aliquots were then combined to provide pooled fractions that had adequate cell numbers to seed at equal concentrations into assays. Equine muscle tissue-derived, periosteal tissue-derived, bone marrow-derived, and adipose tissue-derived mesenchymal stem cells were consistently sorted into 6 fractions that remained viable for use in further assays. Fraction 1 had more cuboidal morphology in culture when compared to the other fractions. Statistical analysis of the fraction absorbencies (OD) revealed a P-value of < 0.05 when fractions 2 and 3 were compared to fractions 1, 4, 5, and 6. It was concluded that non-equilibrium GrFFF is a valid method for sorting equine muscle tissue-derived, periosteal tissue-derived, bone marrow-derived, and adipose tissue-derived mesenchymal stem cells into subpopulations that remain viable, thus securing its potential for use in equine stem cell applications and veterinary medicine. PMID:25355998

Optical characterization of pancreatic normal and tumor tissues with double integrating sphere system

NASA Astrophysics Data System (ADS)

Kiris, Tugba; Akbulut, Saadet; Kiris, Aysenur; Gucin, Zuhal; Karatepe, Oguzhan; Bölükbasi Ates, Gamze; Tabakoǧlu, Haşim Özgür

2015-03-01

In order to develop minimally invasive, fast and precise diagnostic and therapeutic methods in medicine by using optical methods, first step is to examine how the light propagates, scatters and transmitted through medium. So as to find out appropriate wavelengths, it is required to correctly determine the optical properties of tissues. The aim of this study is to measure the optical properties of both cancerous and normal ex-vivo pancreatic tissues. Results will be compared to detect how cancerous and normal tissues respond to different wavelengths. Double-integrating-sphere system and computational technique inverse adding doubling method (IAD) were used in the study. Absorption and reduced scattering coefficients of normal and cancerous pancreatic tissues have been measured within the range of 500-650 nm. Statistical significant differences between cancerous and normal tissues have been obtained at 550 nm and 630 nm for absorption coefficients. On the other hand; there were no statistical difference found for scattering coefficients at any wavelength.

Interactive classification and content-based retrieval of tissue images

NASA Astrophysics Data System (ADS)

Aksoy, Selim; Marchisio, Giovanni B.; Tusk, Carsten; Koperski, Krzysztof

2002-11-01

We describe a system for interactive classification and retrieval of microscopic tissue images. Our system models tissues in pixel, region and image levels. Pixel level features are generated using unsupervised clustering of color and texture values. Region level features include shape information and statistics of pixel level feature values. Image level features include statistics and spatial relationships of regions. To reduce the gap between low-level features and high-level expert knowledge, we define the concept of prototype regions. The system learns the prototype regions in an image collection using model-based clustering and density estimation. Different tissue types are modeled using spatial relationships of these regions. Spatial relationships are represented by fuzzy membership functions. The system automatically selects significant relationships from training data and builds models which can also be updated using user relevance feedback. A Bayesian framework is used to classify tissues based on these models. Preliminary experiments show that the spatial relationship models we developed provide a flexible and powerful framework for classification and retrieval of tissue images.

Diagnostic potential of real-time elastography (RTE) and shear wave elastography (SWE) to differentiate benign and malignant thyroid nodules: A systematic review and meta-analysis.

PubMed

Hu, Xiangdong; Liu, Yujiang; Qian, Linxue

2017-10-01

Real-time elastography (RTE) and shear wave elastography (SWE) are noninvasive and easily available imaging techniques that measure the tissue strain, and it has been reported that the sensitivity and the specificity of elastography were better in differentiating between benign and malignant thyroid nodules than conventional technologies. Relevant articles were searched in multiple databases; the comparison of elasticity index (EI) was conducted with the Review Manager 5.0. Forest plots of the sensitivity and specificity and SROC curve of RTE and SWE were performed with STATA 10.0 software. In addition, sensitivity analysis and bias analysis of the studies were conducted to examine the quality of articles; and to estimate possible publication bias, funnel plot was used and the Egger test was conducted. Finally 22 articles which eventually satisfied the inclusion criteria were included in this study. After eliminating the inefficient, benign and malignant nodules were 2106 and 613, respectively. The meta-analysis suggested that the difference of EI between benign and malignant nodules was statistically significant (SMD = 2.11, 95% CI [1.67, 2.55], P < .00001). The overall sensitivities of RTE and SWE were roughly comparable, whereas the difference of specificities between these 2 methods was statistically significant. In addition, statistically significant difference of AUC between RTE and SWE was observed between RTE and SWE (P < .01). The specificity of RTE was statistically higher than that of SWE; which suggests that compared with SWE, RTE may be more accurate on differentiating benign and malignant thyroid nodules.

The Raman spectrum character of skin tumor induced by UVB

NASA Astrophysics Data System (ADS)

Wu, Shulian; Hu, Liangjun; Wang, Yunxia; Li, Yongzeng

2016-03-01

In our study, the skin canceration processes induced by UVB were analyzed from the perspective of tissue spectrum. A home-made Raman spectral system with a millimeter order excitation laser spot size combined with a multivariate statistical analysis for monitoring the skin changed irradiated by UVB was studied and the discrimination were evaluated. Raman scattering signals of the SCC and normal skin were acquired. Spectral differences in Raman spectra were revealed. Linear discriminant analysis (LDA) based on principal component analysis (PCA) were employed to generate diagnostic algorithms for the classification of skin SCC and normal. The results indicated that Raman spectroscopy combined with PCA-LDA demonstrated good potential for improving the diagnosis of skin cancers.

Prognostic significance of MCM 2 and Ki-67 in neuroblastic tumors in children.

PubMed

Lewandowska, Magdalena; Taran, Katarzyna; Sitkiewicz, Anna; Andrzejewska, Ewa

2015-12-02

Neuroblastic tumors can be characterized by three features: spontaneous regression, maturation and aggressive proliferation. The most common and routinely used method of assessing tumor cell proliferation is to determine the Ki-67 index in the tumor tissue. Despite numerous studies, neuroblastoma biology is not fully understood, which makes treatment results unsatisfactory. MCM 2 is a potential prognostic factor in the neuroblastoma group. The study is based on retrospective analysis of 35 patients treated for neuroblastic tumors in the Department of Pediatric Surgery and Oncology of the Medical University of Lodz, during the period 2001-2011. The material comprised tissues of 16 tumors excised during the operation and 19 biopsy specimens. Immunohistochemical examinations were performed with immunoperoxidase using mouse monoclonal anti-MCM 2 and anti-Ki-67 antibodies. We observed that MCM 2 expression ranged from 2% to 98% and the Ki-67 index ranged from 0 to 95%. There was a statistically significant correlation between expression of MCM 2 and the value of the Ki-67 index and a correlation close to statistical significance between expression of MCM 2 and unfavorable histopathology. There was no statistical relationship between expression of MCM 2 and age over 1 year and N-myc amplification. The presented research shows that MCM 2 may have prognostic significance in neuroblastic pediatric tumors and as a potential prognostic factor could be the starting point of new individualized therapy.

Bioacumulation of trace elements in hepatic and renal tissues of the white mullet Mugil curema Valenciennes, 1836 (Actinopterygii, Mugilidae) in two coastal systems in southeastern Brazil

NASA Astrophysics Data System (ADS)

Fernandez, W. S.; Dias, J. F.; Boufleur, L. A.; Amaral, L.; Yoneama, M. L.; Dias, J. F.

2014-01-01

The aim of this study is to investigate the presence and the concentration of trace elements in hepatic and renal tissues of white mullet (Mugil curema) by Particle-induced X-ray emission (PIXE). Fish specimens were collected in two coastal areas of São Paulo state-Brazil: the Santos estuary (from March 2009 to February 2010) and the Cananéia-Iguape coastal estuarine system (from May 2008 to April 2009). For the elemental analysis, n = 470 sample tissues (liver and kidney) were pooled according to location and type of organ. Trace elements such as Fe, Cu, Zn and Br were observed in both tissues of M. curema with concentrations ranging from 800 μg g-1 for Fe to 7 μg g-1 for Cu. The concentrations of Cu and Zn showed statistical significant differences among the tissues of M. curema (p < 0.05). Relatively higher concentrations of Cu and Zn were observed in the liver tissue. There was no significantly difference in the elemental concentrations between the two studied areas. The Cu levels in liver tissues of M. curema were found to be above the maximum limits for consumption, according to the United States Environmental Protection Agency (EPA) and Brazilian National Health Surveillance Agency (ANVISA).

Elephantiasis nostras verrucosa: an institutional analysis of 21 cases.

PubMed

Dean, Steven M; Zirwas, Matthew J; Horst, Anthony Vander

2011-06-01

Previous reports regarding elephantiasis nostras verrucosa (ENV) have been typically limited to 3 or fewer patients. We sought to statistically ascertain what demographic features and clinical variables are associated with ENV. A retrospective chart review of 21 patients with ENV from 2006 to 2008 was performed and statistically analyzed. All 21 patients were obese (morbid obesity in 91%) with a mean body mass index of 55.8. The average maximal calf circumference was 63.7 cm. Concurrent chronic venous insufficiency was identified in 15 patients (71%). ENV was predominantly bilateral (86%) and typically involved the calves (81%). Proximal cutaneous involvement (thighs 19%/abdomen 9.5%) was less common. Eighteen (86%) related a history of lower extremity cellulitis/lymphangitis and/or manifested soft-tissue infection upon presentation. Multisegmental ENV was statistically more likely in setting of a higher body mass index (P = .02), larger calf circumference (P = .01), multiple lymphedema risk factors (P = .05), ulcerations (P < .001), and nodules (P < .001). Calf circumference was significantly and proportionally linked to developing lower extremity ulcerations (P = .02). Ulcerations and nodules were significantly prone to occur concomitantly (P = .05). Nodules appeared more likely to exist in the presence of a higher body mass index (P = .06) and multiple lymphedema risk factors (P = .06). The statistical conclusions were potentially inhibited by the relatively small cohort. The study was retrospective. Our data confirm the association among obesity, soft-tissue infection, and ENV. Chronic venous insufficiency may be an underappreciated risk factor in the genesis of ENV. Copyright © 2010 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

Acellular dermal matrix for mucogingival surgery: a meta-analysis.

PubMed

Gapski, Ricardo; Parks, Christopher Allen; Wang, Hom-Lay

2005-11-01

Many clinical studies revealed the effectiveness of acellular dermal matrix (ADM) in the treatment of mucogingival defects. The purpose of this meta-analysis was to compare the efficacy of ADM-based root coverage (RC) and ADM-based increase in keratinized tissues to other commonly used mucogingival surgeries. Meta-analysis was limited to randomized clinical trials (RCT). Articles from January 1, 1990 to October 2004 related to ADM were searched utilizing the MEDLINE database from the National Library of Medicine, the Cochrane Oral Health Group Specialized Trials Registry, and through hand searches of reviews and recent journals. Relevant studies were identified, ranked independently, and mean data from each were weighted accordingly. Selected outcomes were analyzed using a meta-analysis software program. The significant estimates of the treatment effects from different trials were assessed by means of Cochrane's test of heterogeneity. 1) Few RCT studies were found to compile the data. In summary, selection identified eight RCT that met the inclusion criteria. There were four studies comparing ADM versus a connective tissue graft for root coverage procedures, two studies comparing ADM versus coronally advanced flap (CAF) for root coverage procedures, and two studies comparing ADM to free gingival graft in augmentation of keratinized tissue. 2) There were no statistically significant differences between groups for any of the outcomes measured (recession coverage, keratinized tissue formation, probing depths, and clinical attachment levels). 3) The majority of the analyses demonstrated moderate to high levels of heterogeneity. 4) Considering the heterogeneity values found among the studies, certain trends could be found: a) three out of four studies favored the ADM-RC group for recession coverage; b) a connective tissue graft tended to increase keratinized tissue compared to ADM (0.52-mm difference; P = 0.11); c) there were trends of increased clinical attachment gains comparing ADM to CAF procedures (0.56-mm difference; P = 0.16). Differences in study design and lack of data precluded an adequate and complete pooling of data for a more comprehensive analysis. Therefore, considering the trends presented in this study, there is a need for further randomized clinical studies of ADM procedures in comparison to common mucogingival surgical procedures to confirm our findings. It is difficult to draw anything other than tentative conclusions from this meta-analysis of ADM for mucogingival surgery, primarily because of the weakness in the design and reporting of existing trials.

AN INVERSE MODELING APPROACH FOR STRESS ESTIMATION IN MITRAL VALVE ANTERIOR LEAFLET VALVULOPLASTY FOR IN-VIVO VALVULAR BIOMATERIAL ASSESSMENT

PubMed Central

Lee, Chung-Hao; Amini, Rouzbeh; Gorman, Robert C.; Gorman, Joseph H.; Sacks, Michael S.

2013-01-01

Estimation of regional tissue stresses in the functioning heart valve remains an important goal in our understanding of normal valve function and in developing novel engineered tissue strategies for valvular repair and replacement. Methods to accurately estimate regional tissue stresses are thus needed for this purpose, and in particular to develop accurate, statistically informed means to validate computational models of valve function. Moreover, there exists no currently accepted method to evaluate engineered heart valve tissues and replacement heart valve biomaterials undergoing valvular stresses in blood contact. While we have utilized mitral valve anterior leaflet valvuloplasty as an experimental approach to address this limitation, robust computational techniques to estimate implant stresses are required. In the present study, we developed a novel numerical analysis approach for estimation of the in-vivo stresses of the central region of the mitral valve anterior leaflet (MVAL) delimited by a sonocrystal transducer array. The in-vivo material properties of the MVAL were simulated using an inverse FE modeling approach based on three pseudo-hyperelastic constitutive models: the neo-Hookean, exponential-type isotropic, and full collagen-fiber mapped transversely isotropic models. A series of numerical replications with varying structural configurations were developed by incorporating measured statistical variations in MVAL local preferred fiber directions and fiber splay. These model replications were then used to investigate how known variations in the valve tissue microstructure influence the estimated ROI stresses and its variation at each time point during a cardiac cycle. Simulations were also able to include estimates of the variation in tissue stresses for an individual specimen dataset over the cardiac cycle. Of the three material models, the transversely anisotropic model produced the most accurate results, with ROI averaged stresses at the fully-loaded state of 432.6±46.5 kPa and 241.4±40.5 kPa in the radial and circumferential directions, respectively. We conclude that the present approach can provide robust instantaneous mean and variation estimates of tissue stresses of the central regions of the MVAL. PMID:24275434

Further Development of a Tissue Engineered Muscle Repair Construct In Vitro for Enhanced Functional Recovery Following Implantation In Vivo in a Murine Model of Volumetric Muscle Loss Injury

DTIC Science & Technology

2012-01-01

ence ( LSD ) correction. Statistical significance was set at an aɘ.05. Statistical analyses were performed using SPSS 18.0. Results BAM...Tissue Eng Part A 16, 1395, 2010. 15. Page, R.L., Malcuit, C., Vilner, L., Vojtic, I., Shaw , S., Hed- blom, E., Hu, J., Pins, G.D., Rolle, M.W., and

Prevalence of Soft Tissue Calcifications in CBCT Images of Mandibular Region

PubMed Central

Khojastepour, Leila; Haghnegahdar, Abdolaziz; Sayar, Hamed

2017-01-01

Statement of the Problem: Most of the soft tissue calcifications within the head and neck region might not be accompanied by clinical symptoms but may indicate some pathological conditions. Purpose: The aim of this research was to determine the prevalence of soft tissue calcifications in cone beam computed tomography (CBCT) images of mandibular region. Materials and Method: In this cross sectional study the CBCT images of 602 patients including 294 men and 308 women with mean age 41.38±15.18 years were evaluated regarding the presence, anatomical location; type (single or multiple) and size of soft tissue calcification in mandibular region. All CBCT images were acquired by NewTom VGi scanner. Odds ratio and chi-square tests were used for data analysis and p< 0.05 was considered to be statistically significant. Results: 156 out of 602 patients had at least one soft tissue calcification in their mandibular region (25.9%. of studied population with mean age 51.7±18.03 years). Men showed significantly higher rate of soft tissue calcification than women (30.3% vs. 21.8%). Soft tissue calcification was predominantly seen at posterior region of the mandible (88%) and most of them were single (60.7%). The prevalence of soft tissue calcification increased with age. Most of the detected soft tissue calcifications were smaller than 3mm (90%). Conclusion: Soft tissue calcifications in mandibular area were a relatively common finding especially in posterior region and more likely to happen in men and in older age group. PMID:28620632

Effects of large pressure amplitude low frequency noise in the parotid gland perivasculo-ductal connective tissue.

PubMed

Oliveira, Pedro; Brito, José; Mendes, João; da Fonseca, Jorge; Águas, Artur; Martins dos Santos, José

2013-01-01

In tissues and organs exposed to large pressure amplitude low frequency noise fibrosis occurs in the absence of inflammatory signs, which is thought to be a protective response. In the parotid gland the perivasculo-ductal connective tissue surrounds arteries, veins and the ductal tree. Perivasculo-ductal connective tissue is believed to function as a mechanical stabilizer of the glandular tissue. In order to quantify the proliferation of perivasculo-ductal connective tissue in large pressure amplitude low frequency noise-exposed rats we used sixty Wistar rats which were equally divided into 6 groups. One group kept in silence, and the remaining five exposed to continuous large pressure amplitude low frequency noise: g1-168h (1 week); g2-504h (3 weeks); g3-840h (5 weeks); g4-1512h (9 weeks); and g5-2184h (13 weeks). After exposure, parotid glands were removed and the perivasculo-ductal connective tissue area was measured in all groups. We applied ANOVA statistical analysis, using SPSS 13.0. The global trend is an increase in the average perivasculo-ductal connective tissue areas, that develops linearly and significantly with large pressure amplitude low frequency noise exposure time (p < 0.001). It has been suggested that the biological response to large pressure amplitude low frequency noise exposure is associated with the need to maintain structural integrity. The structural reinforcement would be achieved by increased perivasculo-ductal connective tissue. Hence, these results show that in response to large pressure amplitude low frequency noise exposure, rat parotid glands increase their perivasculo-ductal connective tissue.

Laser scanning cytometry as a tool for biomarker validation

NASA Astrophysics Data System (ADS)

Mittag, Anja; Füldner, Christiane; Lehmann, Jörg; Tarnok, Attila

2013-03-01

Biomarkers are essential for diagnosis, prognosis, and therapy. As diverse is the range of diseases the broad is the range of biomarkers and the material used for analysis. Whereas body fluids can be relatively easily obtained and analyzed, the investigation of tissue is in most cases more complicated. The same applies for the screening and the evaluation of new biomarkers and the estimation of the binding of biomarkers found in animal models which need to be transferred into applications in humans. The latter in particular is difficult if it recognizes proteins or cells in tissue. A better way to find suitable cellular biomarkers for immunoscintigraphy or PET analyses may be therefore the in situ analysis of the cells in the respective tissue. In this study we present a method for biomarker validation using Laser Scanning Cytometry which allows the emulation of future in vivo analysis. The biomarker validation is exemplarily shown for rheumatoid arthritis (RA) on synovial membrane. Cryosections were scanned and analyzed by phantom contouring. Adequate statistical methods allowed the identification of suitable markers and combinations. The fluorescence analysis of the phantoms allowed the discrimination between synovial membrane of RA patients and non-RA control sections by using median fluorescence intensity and the "affected area". As intensity and area are relevant parameters of in vivo imaging (e.g. PET scan) too, the presented method allows emulation of a probable outcome of in vivo imaging, i.e. the binding of the target protein and hence, the validation of the potential of the respective biomarker.

Deregulation of obesity-relevant genes is associated with progression in BMI and the amount of adipose tissue in pigs.

PubMed

Mentzel, Caroline M Junker; Cardoso, Tainã Figueiredo; Pipper, Christian Bressen; Jacobsen, Mette Juul; Jørgensen, Claus Bøttcher; Cirera, Susanna; Fredholm, Merete

2018-02-01

The aim of this study was to elucidate the relative impact of three phenotypes often used to characterize obesity on perturbation of molecular pathways involved in obesity. The three obesity-related phenotypes are (1) body mass index (BMI), (2) amount of subcutaneous adipose tissue (SATa), and (3) amount of retroperitoneal adipose tissue (RPATa). Although it is generally accepted that increasing amount of RPATa is 'unhealthy', a direct comparison of the relative impact of the three obesity-related phenotypes on gene expression has, to our knowledge, not been performed previously. We have used multiple linear models to analyze altered gene expression of selected obesity-related genes in tissues collected from 19 female pigs phenotypically characterized with respect to the obesity-related phenotypes. Gene expression was assessed by high-throughput qPCR in RNA from liver, skeletal muscle and abdominal adipose tissue. The stringent statistical approach used in the study has increased the power of the analysis compared to the classical approach of analysis in divergent groups of individuals. Our approach led to the identification of key components of cellular pathways that are modulated in the three tissues in association with changes in the three obesity-relevant phenotypes (BMI, SATa and RPATa). The deregulated pathways are involved in biosynthesis and transcript regulation in adipocytes, in lipid transport, lipolysis and metabolism, and in inflammatory responses. Deregulation seemed more comprehensive in liver (23 genes) compared to abdominal adipose tissue (10 genes) and muscle (3 genes). Notably, the study supports the notion that excess amount of intra-abdominal adipose tissue is associated with a greater metabolic disease risk. Our results provide molecular support for this notion by demonstrating that increasing amount of RPATa has a higher impact on perturbation of cellular pathways influencing obesity and obesity-related metabolic traits compared to increase in BMI and amount of SATa.

Correspondence of DNA Methylation Between Blood and Brain Tissue and Its Application to Schizophrenia Research.

PubMed

Walton, Esther; Hass, Johanna; Liu, Jingyu; Roffman, Joshua L; Bernardoni, Fabio; Roessner, Veit; Kirsch, Matthias; Schackert, Gabriele; Calhoun, Vince; Ehrlich, Stefan

2016-03-01

Given the difficulty of procuring human brain tissue, a key question in molecular psychiatry concerns the extent to which epigenetic signatures measured in more accessible tissues such as blood can serve as a surrogate marker for the brain. Here, we aimed (1) to investigate the blood-brain correspondence of DNA methylation using a within-subject design and (2) to identify changes in DNA methylation of brain-related biological pathways in schizophrenia.We obtained paired blood and temporal lobe biopsy samples simultaneously from 12 epilepsy patients during neurosurgical treatment. Using the Infinium 450K methylation array we calculated similarity of blood and brain DNA methylation for each individual separately. We applied our findings by performing gene set enrichment analyses (GSEA) of peripheral blood DNA methylation data (Infinium 27K) of 111 schizophrenia patients and 122 healthy controls and included only Cytosine-phosphate-Guanine (CpG) sites that were significantly correlated across tissues.Only 7.9% of CpG sites showed a statistically significant, large correlation between blood and brain tissue, a proportion that although small was significantly greater than predicted by chance. GSEA analysis of schizophrenia data revealed altered methylation profiles in pathways related to precursor metabolites and signaling peptides.Our findings indicate that most DNA methylation markers in peripheral blood do not reliably predict brain DNA methylation status. However, a subset of peripheral data may proxy methylation status of brain tissue. Restricting the analysis to these markers can identify meaningful epigenetic differences in schizophrenia and potentially other brain disorders. © The Author 2015. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

[Elevated expression of CLOCK is associated with poor prognosis in hepatocellular carcinoma].

PubMed

Li, Bo; Yang, Xiliang; Li, Jiaqi; Yang, Yi; Yan, Zhaoyong; Zhang, Hongxin; Mu, Jiao

2018-02-01

Objective To evaluate the expression of circadian locomotor output cycles kaput (CLOCK) and its effects on cell growth in hepatocellular carcinoma (HCC). Methods The expression of CLOCK in 158 pairs of human HCC tissues and matched noncancerous samples was detected by immunohistochemical (IHC) staining. The expression of CLOCK in HCC patients was also verified using the data from GEO and TCGA (a total of 356 cases). The relationship between CLOCK expression and clinicopathological features of HCC patients was analyzed by single factor statistical analysis. Kaplan-Meier survival curves of HCC patients were drawn to study the relationship between the expression level of CLOCK and the survival state. The effect of CLOCK on the growth of HepG2 cells was detected by MTS assay. Results The expression of CLOCK in HCC tissues was significantly higher than that in the adjacent tissues, and the up-regulation of CLOCK expression in HCC tissue was also confirmed in the public data of HCC (356 cases). HCC patients were divided into low CLOCK expression group and high CLOCK expression group. Univariate analysis showed that the expression of CLOCK was related to tumor size, TNM stage, and portal vein invasion in HCC patients. HCC patients with low CLOCK expression had longer overall survival time and relapse-free survival time than those with high CLOCK expression. The proliferation of cells significantly decreased after the expression of CLOCK was knocked down in HepG2 cells. Conclusion The expression of CLOCK in HCC tissues was much higher than that in normal liver tissues, and the high expression of CLOCK indicated the poor prognosis. The knockdown of CLOCK in HCC cells could inhibit the proliferation of HepG2 cells.

Short Term Culture of Vitrified Human Ovarian Cortical Tissue to Assess the Cryopreservation Outcome: Molecular and Morphological Analysis.

PubMed

Ramezani, Mehdi; Salehnia, Mojdeh; Jafarabadi, Mina

2017-01-01

The aim of the present study was to evaluate the effectiveness of human ovarian vitrification protocol followed with in vitro culture at the morphological and molecular levels. Ovarian tissues were obtained from 10 normal transsexual women and cut into small pieces and were divided into non-vitrified and vitrified groups and some of the tissues fragments in both groups were randomly cultured for two weeks. The morphological study using hematoxylin and eosin and Masson's trichrome staining was done. The analysis of mean follicular density, 17-β estradiol (E2) and anti mullerian hormone (AMH), and real-time RT-PCR was down for the evaluation of expression of genes related to folliculogenesis. Data were compared by paired-samples and independent-samples T test. Values of p<0.05 were considered statistically significant. The proportion of normal follicles did not show significant difference between vitrified and non-vitrified groups before and after culture but these rates and the mean follicle density significantly decreased in both cultured tissues (p<0.05). The expression of genes was similar in vitrified and non-vitrified groups but in cultured tissues the expression of GDF9 and FSHR genes increased and the expression of FIGLA and KIT-L genes decreased (p<0.05). An increase in E2 and AMH concentration was observed after 14 days of culture in both groups. In conclusion, the present study indicated that the follicular development and gene expression in vitrified ovarian tissue was not altered before and after in vitro culture, thus this method could be useful for fertility preservation; however, additional studies are needed to improve the culture condition.

Insulin Response Genes in Different Stages of Periodontal Disease

PubMed Central

Yu, N.; Barros, S.P.; Zhang, S.; Moss, K.L.; Phillips, S.T.; Offenbacher, S.

2015-01-01

Bacterial infections are known to alter glucose metabolism within tissues via mechanisms of inflammation. We conducted this study to examine whether insulin response genes are differentially expressed in gingival tissues, comparing samples from experimental gingivitis and periodontitis subjects to those from healthy individuals. Total RNA was extracted from gingival biopsies from 26 participants: 8 periodontally healthy, 9 experimental gingivitis, and 9 periodontitis subjects. Gene expression patterns were evaluated with a polymerase chain reaction array panel to examine 84 candidate genes involved with glucose metabolism, insulin resistance, and obesity. Array data were evaluated with a t test adjusted by the false discover rate (P < 0.05), and ingenuity pathway analysis was performed for statistical testing of pathways. Although tissue samples were not sufficient to enable protein quantification, we confirmed the upregulation of the key gene using lipopolysaccharide-stimulated primary gingival epithelial cells by Western blot. The mRNA expression patterns of genes that are associated with insulin response and glucose metabolism are markedly different in experimental gingivitis subjects compared with healthy controls. Thirty-two genes are upregulated significantly by at least 2-fold, adjusted for false discover rate (P < 0.05). Periodontitis subjects show similar but attenuated changes in gene expression patterns, and no genes meet the significance criteria. Ingenuity pathway analysis demonstrates significant activation of the carbohydrate metabolism network in experimental gingivitis but not in periodontitis. G6PD protein increases in response to lipopolysaccharide stimulation in primary gingival epithelial cells, which is in the same direction as upregulated mRNA in tissues. Acute gingival inflammation may be associated with tissue metabolism changes, but these changes are not evident in chronic periodontitis. This study suggests that acute gingival inflammation may induce localized changes that modify tissue insulin/glucose metabolism. PMID:25924856

Decreased expression of 14-3-3 σ, an early event of malignant transformation of respiratory epithelium, also facilitates progression of squamous cell lung cancer

PubMed Central

Sun, Nan; Wu, Yongkai; Huang, Bo; Liu, Qian; Dong, Yinan; Ding, Jianqiao; Liu, Yongyu

2015-01-01

Background It has been shown that 14-3-3 σ serves as a tumor suppressor gene, and is downregulated in various tumor tissues. However, the role of 14-3-3 σ during the initiation and progression of lung squamous cell carcinoma (SqCC) is not well understood. Methods The expression status of 14-3-3 σ in archival tissue samples from 40 lung SqCC patients (36 with normal bronchia, 19 squamous metaplasia, and 17 dysplasia/carcinoma in situ, in their tissue samples) was examined by immunohistochemical analysis. The proliferation rate and tumor formation ability of the H520 cell transfected with 14-3-3 σ was tested with methyl thiazolyl tetrazolium assay and nude mice subcutaneous injection, respectively. Results In the normal bronchial epithelia, 14-3-3 σ was highly expressed, whereas it was significantly decreased in precancerous and cancerous tissues. Compared with matched invasive cancer tissues, the expression level of 14-3-3 σ in squamous metaplasia was significantly higher (P = 0.049), while that in dysplasia/carcinoma in situ showed no significant changes (P = 0.135). Statistical analysis showed that the expression level of 14-3-3 σ in tumor tissue was associated with the differentiation grade of the tumor (P = 0.001) and the prognosis of the patient (P = 0.003). The overexpression of 14-3-3 σ significantly suppressed the proliferation of H520 cells in vitro and in vivo. Conclusion The inactivation of 14-3-3 σ may be a very early event in tumorigenesis and could facilitate the initiation and progression of lung SqCC in a sustainable way. PMID:26557909

Computer-aided, multi-modal, and compression diffuse optical studies of breast tissue

NASA Astrophysics Data System (ADS)

Busch, David Richard, Jr.

Diffuse Optical Tomography and Spectroscopy permit measurement of important physiological parameters non-invasively through ˜10 cm of tissue. I have applied these techniques in measurements of human breast and breast cancer. My thesis integrates three loosely connected themes in this context: multi-modal breast cancer imaging, automated data analysis of breast cancer images, and microvascular hemodynamics of breast under compression. As per the first theme, I describe construction, testing, and the initial clinical usage of two generations of imaging systems for simultaneous diffuse optical and magnetic resonance imaging. The second project develops a statistical analysis of optical breast data from many spatial locations in a population of cancers to derive a novel optical signature of malignancy; I then apply this data-derived signature for localization of cancer in additional subjects. Finally, I construct and deploy diffuse optical instrumentation to measure blood content and blood flow during breast compression; besides optics, this research has implications for any method employing breast compression, e.g., mammography.

Colorimeter and scanning electron microscopy analysis of teeth submitted to internal bleaching.

PubMed

Martin-Biedma, Benjamin; Gonzalez-Gonzalez, Teresa; Lopes, Manuela; Lopes, Luis; Vilar, Rui; Bahillo, José; Varela-Patiño, Purificación

2010-02-01

This in vitro study compared the tooth color and the ultrastructure of internal dental tissues before and after internal bleaching. Sodium perborate was placed in the pulp chamber of endodontically treated molars and sealed with intermediate restorative material. The test samples were stored in a physiologic solution, and the bleaching agent was replaced every 7 days. A control group was used. After 1 month, the colors of the test and control samples were measured with a colorimeter, and the internal surfaces were observed under field emission scanning electron microscopy (FESEM). Statistically significant differences were found between the test and control sample colors. The FESEM ultrastructure analysis of the internal enamel and dentin surfaces did not show any changes after the internal bleaching. The results of the present study show that sodium perborate is effective in bleaching nonvital teeth and does not produce ultrastructural changes in the dental tissues. Copyright 2010 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Complex degree of mutual anisotropy in diagnostics of biological tissues physiological changes

NASA Astrophysics Data System (ADS)

Ushenko, Yu. A.; Dubolazov, O. V.; Karachevtcev, A. O.; Zabolotna, N. I.

2011-05-01

To characterize the degree of consistency of parameters of the optically uniaxial birefringent protein nets of blood plasma a new parameter - complex degree of mutual anisotropy is suggested. The technique of polarization measuring the coordinate distributions of the complex degree of mutual anisotropy of blood plasma is developed. It is shown that statistic approach to the analysis of complex degree of mutual anisotropy distributions of blood plasma is effective in the diagnosis and differentiation of acute inflammation - acute and gangrenous appendicitis.

Complex degree of mutual anisotropy in diagnostics of biological tissues physiological changes

NASA Astrophysics Data System (ADS)

Ushenko, Yu. A.; Dubolazov, A. V.; Karachevtcev, A. O.; Zabolotna, N. I.

2011-09-01

To characterize the degree of consistency of parameters of the optically uniaxial birefringent protein nets of blood plasma a new parameter - complex degree of mutual anisotropy is suggested. The technique of polarization measuring the coordinate distributions of the complex degree of mutual anisotropy of blood plasma is developed. It is shown that statistic approach to the analysis of complex degree of mutual anisotropy distributions of blood plasma is effective in the diagnosis and differentiation of acute inflammation - acute and gangrenous appendicitis.

Developing a Zebrafish Model of NF1 for Structure-Function Analysis and Identification of Modifier Genes

DTIC Science & Technology

2010-04-01

equipped with a spinning-disc confocal system ( Yokogawa ) was used. The statistical significance of changes to OPC cell numbers and migration upon nf1...that they are expressed in overlapping tissues. We examined the expression of both genes by whole mount in situ hybridization between the 4- cell stage...sorted cells confirmed expression, particularly in the vascular endothelium (Figure 4E-G), while RNA from 1- cell embryos indicate that both genes are

A compound scattering pdf for the ultrasonic echo envelope and its relationship to K and Nakagami distributions.

PubMed

Shankar, P Mohana

2003-03-01

A compound probability density function (pdf) is presented to describe the envelope of the backscattered echo from tissue. This pdf allows local and global variation in scattering cross sections in tissue. The ultrasonic backscattering cross sections are assumed to be gamma distributed. The gamma distribution also is used to model the randomness in the average cross sections. This gamma-gamma model results in the compound scattering pdf for the envelope. The relationship of this compound pdf to the Rayleigh, K, and Nakagami distributions is explored through an analysis of the signal-to-noise ratio of the envelopes and random number simulations. The three parameter compound pdf appears to be flexible enough to represent envelope statistics giving rise to Rayleigh, K, and Nakagami distributions.

Comparative evaluation of guided tissue regeneration with use of collagen-based barrier freeze-dried dura mater allograft for mandibular class 2 furcation defects (a comparative controlled clinical study).

PubMed

Patel, Sandeep; Kubavat, Ajay; Ruparelia, Brijesh; Agarwal, Arvind; Panda, Anup

2012-01-01

The aim of periodontal surgery is complete regeneration. The present study was designed to evaluate and compare clinically soft tissue changes in form of probing pocket depth, gingival shrinkage, attachment level and hard tissue changes in form of horizontal and vertical bone level using resorbable membranes. Twelve subjects with bilateral class 2 furcation defects were selected. After initial phase one treatment, open debridement was performed in control site while freezedried dura mater allograft was used in experimental site. Soft and hard tissue parameters were registered intrasurgically. Nine months reentry ensured better understanding and evaluation of the final outcome of the study. Guided tissue regeneration is a predictable treatment modality for class 2 furcation defect. There was statistically significant reduction in pocket depth as compared to control (p < 0.01). There is statistically significant increase in periodontal attachment level within control and experimental sites showed better results (p < 0.01). For hard tissue parameter, significant defect fill resulted in experimental group, while in control group, less significant defect fill was found in horizontal direction and nonsignificant defect fill was found in vertical direction. The results showed statistically significant improvement in soft and hard tissue parameters and less gingival shrinkage in experimental sites compared to control site. The use of FDDMA in furcation defects helps us to achieve predictable results. This cross-linked collagen membrane has better handling properties and ease of procurement as well as economic viability making it a logical material to be used in regenerative surgeries.

Regenerate Healing Outcomes in Unilateral Mandibular Distraction Osteogenesis Using Quantitative Histomorphometry

PubMed Central

Schwarz, Daniel A.; Arman, Krikor G.; Kakwan, Mehreen S.; Jamali, Ameen M.; Elmeligy, Ayman A.; Buchman, Steven R.

2015-01-01

Background The authors’ goal was to ascertain regenerate bone-healing metrics using quantitative histomorphometry at a single consolidation period. Methods Rats underwent either mandibular distraction osteogenesis (n=7) or partially reduced fractures (n=7); their contralateral mandibles were used as controls (n=11). External fixators were secured and unilateral osteotomies performed, followed by either mandibular distraction osteogenesis (4 days’ latency, then 0.3 mm every 12 hours for 8 days; 5.1 mm) or partially reduced fractures (fixed immediately postoperatively; 2.1 mm); both groups underwent 4 weeks of consolidation. After tissue processing, bone volume/tissue volume ratio, osteoid volume/tissue volume ratio, and osteocyte count per high-power field were analyzed by means of quantitative histomorphometry. Results Contralateral mandibles had statistically greater bone volume/tissue volume ratio and osteocyte count per high-power field compared with both mandibular distraction osteogenesis and partially reduced fractures by almost 50 percent, whereas osteoid volume/tissue volume ratio was statistically greater in both mandibular distraction osteogenesis specimens and partially reduced fractures compared with contralateral mandibles. No statistical difference in bone volume/tissue volume ratio, osteoid volume/tissue volume ratio, or osteocyte count per high-power field was found between mandibular distraction osteogenesis specimens and partially reduced fractures. Conclusions The authors’ findings demonstrate significantly decreased bone quantity and maturity in mandibular distraction osteogenesis specimens and partially reduced fractures compared with contralateral mandibles using the clinically analogous protocols. If these results are extrapolated clinically, treatment strategies may require modification to ensure reliable, predictable, and improved outcomes. PMID:20463629

BanTeC: a software tool for management of corneal transplantation.

PubMed

López-Alvarez, P; Caballero, F; Trias, J; Cortés, U; López-Navidad, A

2005-11-01

Until recently, all cornea information at our tissue bank was managed manually, no specific database or computer tool had been implemented to provide electronic versions of documents and medical reports. The main objective of the BanTeC project was therefore to create a computerized system to integrate and classify all the information and documents used in the center in order to facilitate management of retrieved, transplanted corneal tissues. We used the Windows platform to develop the project. Microsoft Access and Microsoft Jet Engine were used at the database level and Data Access Objects was the chosen data access technology. In short, the BanTeC software seeks to computerize the tissue bank. All the initial stages of the development have now been completed, from specification of needs, program design and implementation of the software components, to the total integration of the final result in the real production environment. BanTeC will allow the generation of statistical reports for analysis to improve our performance.

Optical biopsy using fluorescence spectroscopy for prostate cancer diagnosis

NASA Astrophysics Data System (ADS)

Wu, Binlin; Gao, Xin; Smith, Jason; Bailin, Jacob

2017-02-01

Native fluorescence spectra are acquired from fresh normal and cancerous human prostate tissues. The fluorescence data are analyzed using a multivariate analysis algorithm such as non-negative matrix factorization. The nonnegative spectral components are retrieved and attributed to the native fluorophores such as collagen, reduced nicotinamide adenine dinucleotide (NADH), and flavin adenine dinucleotide (FAD) in tissue. The retrieved weights of the components, e.g. NADH and FAD are used to estimate the relative concentrations of the native fluorophores and the redox ratio. A machine learning algorithm such as support vector machine (SVM) is used for classification to distinguish normal and cancerous tissue samples based on either the relative concentrations of NADH and FAD or the redox ratio alone. The classification performance is shown based on statistical measures such as sensitivity, specificity, and accuracy, along with the area under receiver operating characteristic (ROC) curve. A cross validation method such as leave-one-out is used to evaluate the predictive performance of the SVM classifier to avoid bias due to overfitting.

Canary TMA — EDRN Public Portal

Cancer.gov

This protocol describes a multi-center, retrospective, case-cohort tissue microarray (TMA) study to evaluate tissue biomarkers for their ability to predict recurrent prostate cancer at the time of radical prostatectomy (RP). Candidate biomarkers will be assessed by performing tissue localization studies on TMAs containing recurrent prostate cancer and non-recurrent prostate cancer. De-identified data will be transferred to a central repository for statistical analysis. Participating institutions will use a variation of case-cohort sampling to randomly select a subset of patients from a retrospectively constructed RP cohort and/or perform selected assays on the cohort. The study endpoint is time to recurrence; of primary interest is five year recurrence free survival. Recurrent prostate cancer is defined by 1) a single serum prostate-specific antigen (PSA) level greater than 0.2 ng/mL after RP and/or 2) receipt of salvage or secondary therapy after RP and/or 3) clinical or radiological evidence of metastatic disease. Non-recurrent prostate cancer is defined as disease with no evidence of recurrence.

Assessing risk factors for periodontitis using regression

NASA Astrophysics Data System (ADS)

Lobo Pereira, J. A.; Ferreira, Maria Cristina; Oliveira, Teresa

2013-10-01

Multivariate statistical analysis is indispensable to assess the associations and interactions between different factors and the risk of periodontitis. Among others, regression analysis is a statistical technique widely used in healthcare to investigate and model the relationship between variables. In our work we study the impact of socio-demographic, medical and behavioral factors on periodontal health. Using regression, linear and logistic models, we can assess the relevance, as risk factors for periodontitis disease, of the following independent variables (IVs): Age, Gender, Diabetic Status, Education, Smoking status and Plaque Index. The multiple linear regression analysis model was built to evaluate the influence of IVs on mean Attachment Loss (AL). Thus, the regression coefficients along with respective p-values will be obtained as well as the respective p-values from the significance tests. The classification of a case (individual) adopted in the logistic model was the extent of the destruction of periodontal tissues defined by an Attachment Loss greater than or equal to 4 mm in 25% (AL≥4mm/≥25%) of sites surveyed. The association measures include the Odds Ratios together with the correspondent 95% confidence intervals.

Evaluation of centrifuged bone marrow on bone regeneration around implants in rabbit tibia.

PubMed

Betoni, Walter; Queiroz, Thallita P; Luvizuto, Eloá R; Valentini-Neto, Rodolpho; Garcia-Júnior, Idelmo R; Bernabé, Pedro F E

2012-12-01

To evaluate the bone regeneration of cervical defects produced around titanium implants filled with blood clot and filled with centrifuged bone marrow (CBM) by means of histomorphometric analysis. Twelve rabbits received 2 titanium implants in each right tibia, with the upper cortical prepared with a 5-mm drill and the lower cortex with a 3-mm-diameter drill. Euthanasia was performed to allow analysis at 7, 21, and 60 days after operation. The samples were embedded in light curing resin, cut and stained with alizarin red and Stevenel blue for a histomorphometric analysis of the bone-to-implant contact (BIC) and the bone area around implant (BA). The values obtained were statistically analyzed using the nonparametric Kruskal-Wallis test (P = 0.05). At 60 days postoperation, the groups had their cervical defects completely filled by neoformed bone tissue. There was no statistically significant difference between the groups regarding BIC and BA during the analyzed periods. There was no difference in the bone repair of periimplant cervical defects with or without the use of CBM.

Human brain cancer studied by resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zhou, Yan; Liu, Cheng-Hui; Sun, Yi; Pu, Yang; Boydston-White, Susie; Liu, Yulong; Alfano, Robert R.

2012-11-01

The resonance Raman (RR) spectra of six types of human brain tissues are examined using a confocal micro-Raman system with 532-nm excitation in vitro. Forty-three RR spectra from seven subjects are investigated. The spectral peaks from malignant meningioma, stage III (cancer), benign meningioma (benign), normal meningeal tissues (normal), glioblastoma multiforme grade IV (cancer), acoustic neuroma (benign), and pituitary adenoma (benign) are analyzed. Using a 532-nm excitation, the resonance-enhanced peak at 1548 cm-1 (amide II) is observed in all of the tissue specimens, but is not observed in the spectra collected using the nonresonance Raman system. An increase in the intensity ratio of 1587 to 1605 cm-1 is observed in the RR spectra collected from meningeal cancer tissue as compared with the spectra collected from the benign and normal meningeal tissue. The peak around 1732 cm-1 attributed to fatty acids (lipids) are diminished in the spectra collected from the meningeal cancer tumors as compared with the spectra from normal and benign tissues. The characteristic band of spectral peaks observed between 2800 and 3100 cm-1 are attributed to the vibrations of methyl (-CH3) and methylene (-CH2-) groups. The ratio of the intensities of the spectral peaks of 2935 to 2880 cm-1 from the meningeal cancer tissues is found to be lower in comparison with that of the spectral peaks from normal, and benign tissues, which may be used as a distinct marker for distinguishing cancerous tissues from normal meningeal tissues. The statistical methods of principal component analysis and the support vector machine are used to analyze the RR spectral data collected from meningeal tissues, yielding a diagnostic sensitivity of 90.9% and specificity of 100% when two principal components are used.

Geometrical features assessment of liver's tumor with application of artificial neural network evolved by imperialist competitive algorithm.

PubMed

Keshavarz, M; Mojra, A

2015-05-01

Geometrical features of a cancerous tumor embedded in biological soft tissue, including tumor size and depth, are a necessity in the follow-up procedure and making suitable therapeutic decisions. In this paper, a new socio-politically motivated global search strategy which is called imperialist competitive algorithm (ICA) is implemented to train a feed forward neural network (FFNN) to estimate the tumor's geometrical characteristics (FFNNICA). First, a viscoelastic model of liver tissue is constructed by using a series of in vitro uniaxial and relaxation test data. Then, 163 samples of the tissue including a tumor with different depths and diameters are generated by making use of PYTHON programming to link the ABAQUS and MATLAB together. Next, the samples are divided into 123 samples as training dataset and 40 samples as testing dataset. Training inputs of the network are mechanical parameters extracted from palpation of the tissue through a developing noninvasive technology called artificial tactile sensing (ATS). Last, to evaluate the FFNNICA performance, outputs of the network including tumor's depth and diameter are compared with desired values for both training and testing datasets. Deviations of the outputs from desired values are calculated by a regression analysis. Statistical analysis is also performed by measuring Root Mean Square Error (RMSE) and Efficiency (E). RMSE in diameter and depth estimations are 0.50 mm and 1.49, respectively, for the testing dataset. Results affirm that the proposed optimization algorithm for training neural network can be useful to characterize soft tissue tumors accurately by employing an artificial palpation approach. Copyright © 2015 John Wiley & Sons, Ltd.

The Effect of Phosphatidylcholine and Deoxycholate Compound Injections to the Localized Adipose Tissue: An Experimental Study with a Murine Model

PubMed Central

Noh, Yongjoon

2012-01-01

Background Phosphatidylcholine (PPC) and deoxycholate (DCA) compound has been recently used for the purpose of partial lipolysis and is valued for its efficacy and lower invasiveness compared to liposuction and dermolipectomy used previously. In this article, the authors discuss the efficacy of the PPC dissolved in DCA via an experimental rat study model, along with suggesting a useful animal experimental model for the study of adipose tissue and lipolysis. Methods Bilateral inguinal fat pads of an experimental rat were elevated with the deep inferior epigastric vessel as the sole vascular pedicle. Normal saline was injected on one side as a control group and a PPC and DCA compound was injected on the other side. After 4 days, the rats were euthanized for microscopic tissue examination. The pathology was scored by a semiquantitative system in 4 categories: normal fat amount, fat necrosis, inflammatory activity, and stage of fibrosis. A Wilcoxon signed-rank test powered by SPSS packet program was used for statistical analysis and to determine significance. Results Microscopic examination was performed on the obtained samples, and the experimental data of all four categories showed significant histologic differences compared to the control group. All of the data also showed statistical significance by the Wilcoxon signedrank test (P<0.01). Conclusions In the inguinal fat pad rat model, the control group and the experimental group had a differed significantly in the amount of normal fat tissue, inflammation, necrosis, and fibrosis. We recommend the rat inguinal fat pad model used in this study, as it is likely to be useful in related research. PMID:23094238

pH influences the biocompatibility of methylene blue solutions.

PubMed

Gusman, David Jonathan Rodrigues; Cintra, Luciano Tavares Angelo; Novaes, Vivian Cristina Noronha; Matheus, Henrique Rinaldi; de Araujo, Nathália Januario; de Almeida, Juliano Milanezi

2018-01-01

The aim of this study was to investigate the biocompatibility of methylene blue at different pH levels through the method of implantation in subcutaneous tissue. Eighty-four sterilized polyethylene tubes were allocated in the subcutaneous tissue of 28 rats, each one receiving four tubes, set into four groups: group tube (G-T)-empty tube, fibrin group (G-F)-tube filled with fibrin sponge, group methylene blue pH 7 (G-MB/pH 7)-tube filled with fibrin sponge soaked by methylene blue (100 μg/ml) at pH 7.0, and group methylene blue pH 1 (G-MB/pH 1)-tube filled with fibrin sponge and soaked by methylene blue (100 μg/ml) at pH 1.0. After 7, 15, and 30 days, seven animals from each group were euthanized, and the tubes involved by the surrounding tissue were removed and fixed with 4% buffered formaldehyde solution. The collected pieces were processed and histological sections (4 μm) were stained with hematoxylin and eosin and analyzed by light microscopy. Scores were assigned to analysis of histopathologic parameters. The results were statistically analyzed by the Kruskal-Wallis test (p ≤ 0.05). At 7 and 30 days, the G-MB/pH 1 group showed no significant difference in the G-T control group, while G-MB/pH 7 had a significant increase on tissue reaction, also when compared to G-T. At 15 days, there was no statistical difference between the groups. Within the limits of this study, it is concluded that methylene blue at pH 1.0 provides better biocompatibility than at pH 7.0.

A non-invasive method to produce pressure ulcers of varying severity in a spinal cord-injured rat model.

PubMed

Ahmed, A K; Goodwin, C R; Sarabia-Estrada, R; Lay, F; Ansari, A M; Steenbergen, C; Pang, C; Cohen, R; Born, L J; Matsangos, A E; Ng, C; Marti, G P; Abu-Bonsrah, N; Phillips, N A; Suk, I; Sciubba, D M; Harmon, J W

2016-12-01

Experimental study. The objective of this study was to establish a non-invasive model to produce pressure ulcers of varying severity in animals with spinal cord injury (SCI). The study was conducted at the Johns Hopkins Hospital in Baltimore, Maryland, USA. A mid-thoracic (T7-T9) left hemisection was performed on Sprague-Dawley rats. At 7 days post SCI, rats received varying degrees of pressure on the left posterior thigh region. Laser Doppler Flowmetry was used to record blood flow. Animals were killed 12 days after SCI. A cardiac puncture was performed for blood chemistry, and full-thickness tissue was harvested for histology. Doppler blood flow after SCI prior to pressure application was 237.808±16.175 PFUs at day 7. Following pressure application, there was a statistically significant decrease in blood flow in all pressure-applied groups in comparison with controls with a mean perfusion of 118.361±18.223 (P<0.001). White blood cell counts and creatine kinase for each group were statistically significant from the control group (P=0.0107 and P=0.0028, respectively). We have created a novel animal model of pressure ulcer formation in the setting of a SCI. Histological analysis revealed different stages of injury corresponding to the amount of pressure the animals were exposed to with decreased blood flow immediately after the insult along with a subsequent marked increase in blood flow the next day, conducive to an ischemia-reperfusion injury (IRI) and a possible inflammatory response following tissue injury. Following ischemia and hypoxia secondary to microcirculation impairment, free radicals generate lipid peroxidation, leading to ischemic tissue damage. Future studies should be aimed at measuring free radicals during this period of increased blood flow, following tissue ischemia.

Is the nonlipomatous component of dedifferentiated liposarcoma always soft tissue on CT? Analysis of CT densities and correlation with rate of growth in 60 patients.

PubMed

Tirumani, Sree Harsha; Wagner, Andrew J; Tirumani, Harika; Shinagare, Atul B; Jagannathan, Jyothi P; Hornick, Jason L; George, Suzanne; Ramaiya, Nikhil H

2015-06-01

To define the various CT densities of nonlipomatous component of dedifferentiated liposarcoma (DDLPS) and to determine if the rate of growth varies with density. This study identified 60 patients with DDPLS (38 men, 22 women; mean age at diagnosis 59 years, range, 35-82 years) who had one or more resections. CT scan immediately before the surgical resection (presurgery) and up to a maximum of one year before the surgery (baseline) was reviewed by two radiologists to note the density of the nonlipomatous elements and rate of growth during that period. Clinical and histopathological data were extracted from electronic medical records. Rate of growth of various densities was compared using Kruskal-Wallis test. Three distinct densities of the nonlipomatous component were noted: soft tissue density (SD), fluid density (FD), and mixed density (MD). Of 109 lesions on the presurgery scan (SD = 78; MD = 22; FD = 9), scans at baseline were available for 72/109 lesions (SD = 49; MD = 14; FD = 9). Median growth rate/month without treatment, with chemotherapy, and with radiotherapy were 40%, 24%, and 62%, respectively, for SD lesions and 28%, 61%, and 52% for MD lesions. For FD lesions, it was 72% and 35%, respectively, without treatment and with chemotherapy. There was no statistical difference in the rate of growth of various densities. Density changed over time in 8/72 (11%) lesions, including 2/49 SD lesions (to MD), 1/14 MD lesions (to SD), and 5/9 FD lesions (to SD). DDLPS has three distinct CT densities of which soft tissue density is the most common. Despite not being statistically significant, fluid density lesions had rapid growth rate and often converted to soft tissue density in our study.

An in vitro evaluation of the degree of pulp tissue dissolution through different root canal irrigation protocols.

PubMed

Amato, Massimo; Pantaleo, Giuseppe; Abtellatif, Dina; Blasi, Andrea; Gagliani, Massimo; Iandolo, Alfredo

2018-01-01

The aim of this study is to evaluate in vitro , using artificial lateral canals, the rate of dissolution of the pulp tissue through different protocols of canal irrigation. One hundred artificial canals provided with lateral canals have been used. Each lateral canal was filled with pulp tissue and calibrated to 0.002 mg. All canals were irrigated using five different protocols. Five groups have been used for the experiment: Group A, distilled water (control); Group B, preheated NaOCl; Group C, NaOCl heated inside the canal; Group D, NaOCl ultrasonically activated; and Group E, NaOCl heated inside the canal with ultrasonic activation. All samples were weighed through professional microbalance in three different phases: before insertion of the pulp tissue into the lateral canal, after insertion of the pulp tissue and, finally, after different protocols of irrigation. A statistical analysis with Kruskal-Wallis test and Mann-Whitney test was performed. The partial dissolution of the pulp tissue inside the artificial lateral canal occurs only using the protocol with NaOCl heated inside the canal with ultrasonic activation. Other irrigation protocols are not able to dissolve the pulp tissue. The main objective of endodontic therapy is the removal of damaged tissues and bacteria. Modern literature highlights that it is impossible to remove all the pulp tissues and bacteria from the whole endodontic space. Hence, to achieve excellence and get positive results in the short and long term, it is necessary to use techniques and technologies that may increase the degree of root canal detersion.

Exploring the mechanical behavior of degrading swine neural tissue at low strain rates via the fractional Zener constitutive model.

PubMed

Bentil, Sarah A; Dupaix, Rebecca B

2014-02-01

The ability of the fractional Zener constitutive model to predict the behavior of postmortem swine brain tissue was examined in this work. Understanding tissue behavior attributed to degradation is invaluable in many fields such as the forensic sciences or cases where only cadaveric tissue is available. To understand how material properties change with postmortem age, the fractional Zener model was considered as it includes parameters to describe brain stiffness and also the parameter α, which quantifies the viscoelasticity of a material. The relationship between the viscoelasticity described by α and tissue degradation was examined by fitting the model to data collected in a previous study (Bentil, 2013). This previous study subjected swine neural tissue to in vitro unconfined compression tests using four postmortem age groups (<6h, 24h, 3 days, and 1 week). All samples were compressed to a strain level of 10% using two compressive rates: 1mm/min and 5mm/min. Statistical analysis was used as a tool to study the influence of the fractional Zener constants on factors such as tissue degradation and compressive rate. Application of the fractional Zener constitutive model to the experimental data showed that swine neural tissue becomes less stiff with increased postmortem age. The fractional Zener model was also able to capture the nonlinear viscoelastic features of the brain tissue at low strain rates. The results showed that the parameter α was better correlated with compressive rate than with postmortem age. © 2013 Published by Elsevier Ltd.

B7-H1 expression is associated with expansion of regulatory T cells in colorectal carcinoma.

PubMed

Hua, Dong; Sun, Jing; Mao, Yong; Chen, Lu-Jun; Wu, Yu-Yu; Zhang, Xue-Guang

2012-03-07

To investigate the expression of B7-H1 in human colorectal carcinoma (CRC) to define its regulating effects on T cells in tumor microenvironment. One hundred and two paraffin blocks and 33 fresh samples of CRC tissues were subject to this study. Immunohistochemistry was performed for B7-H1 and CD3 staining in CRC tissues. Ficoll-Hypaque density gradient centrifugation was used to isolate peripheral blood mononuclear cells of fresh CRC tissues; flow cytometry and immunofluorescence staining were used for detection of regulatory T cells. Data was analyzed with statistical software. Costimulatory molecule B7-H1 was found strongly expressed in CRC tissues, localized in tumor cell membrane and cytoplasm, while weak or none expression of B7-H1 was detected in pared normal colorectal tissues. Meanwhile, CD3 positive T cells were found congregated in CRC tumor nest and stroma. Statistic analysis showed that B7-H1 expression level was negatively correlated to the total T cell density in tumor nest (P < 0.0001) and tumor stroma (P = 0.0200) of 102 cases of CRC tissues. Among the total T cells, a variable amount of regulatory T cells with a clear Foxp3⁺ (forkhead box P3) staining could be detected in CRC tissues and patients' blood. Interestingly, in the 33 samples (15 cases of B7-H1(high) CRC tissues and 18 cases of B7-H1(low) CRC tissues) of freshly isolated mononuclear cells from CRC tissues, the percentages of CD4⁺Foxp3⁺ and CD8⁺Foxp3⁺ regulatory T cells were found remarkably higher in B7-H1(high) CRC tissues than in B7-H1(low) CRC tissues (P = 0.0024, P = 0.0182), indicating that B7-H1 expression was involved in proliferation of regulatory T cell. No significant difference was found in CRC peripheral blood (P = 0.0863, P = 0.0678). PD-1 is the specific ligand for B7-H1 pathway transferring inhibitory signal to T cell, which is expressed by activated T cell. Our further analysis of PD-1 expression on T cells in CRC tissues showed that conventional T cells (CD4⁺Foxp3⁻/CD8⁺Foxp3⁻), which was thought to contribute to the anti-tumor immune response, highly expressed PD-1; while regulatory T cells (CD4⁺Foxp3⁺/CD8⁺Foxp3⁻) almost failed to express PD-1. The average percentage of PD-1 expression on regulatory T cells was significantly higher than the percentage of PD-1 on conventional T cells (CD4⁺Foxp3⁻ T cell, P < 0.0001; CD8⁺Foxp3⁻ T cell, P < 0.0001). The diverse expression of PD-1 might lead to different fate of T cell subsets in B7-H1 over-expression CRC tumor microenvironment. B7-H1 expression in tumor cells can inhibit the conventional T cell proliferation in tumor microenvironment through the PD-1 expression on conventional T cells.

Optical redox ratio using endogenous fluorescence to assess the metabolic changes associated with treatment response of bioconjugated gold nanoparticles in streptozotocin-induced diabetic rats

NASA Astrophysics Data System (ADS)

Adavallan, K.; Gurushankar, K.; Nazeer, Shaiju S.; Gohulkumar, M.; Jayasree, Ramapurath S.; Krishnakumar, N.

2017-06-01

Fluorescence spectroscopic techniques have the potential to assess the metabolic changes during disease development and evaluation of treatment response in a non-invasive and label-free manner. The present study aims to evaluate the effect of mulberry-mediated gold nanoparticles (MAuNPs) in comparison with mulberry leaf extract alone (MLE) for monitoring endogenous fluorophores and to quantify the metabolic changes associated with mitochondrial redox states during streptozotocin-induced diabetic liver tissues using fluorescence spectroscopy. Two mitochondrial metabolic coenzymes, reduced nicotinamide dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD) are autofluorescent and are important optical biomarkers to estimate the redox state of a cell. Significant differences in the autofluorescence spectral signatures between the control and the experimental diabetic animals have been noticed under the excitation wavelength at 320 nm with emission ranging from 350-550 nm. A direct correlation between the progression of diabetes and the levels of collagen and optical redox ratio was observed. The results revealed that a significant increase in the emission of collagen in diabetic liver tissues as compared with the control liver tissues. Moreover, there was a significant decrease in the optical redox ratio (FAD/(FAD  +  NADH)) observed in diabetic control liver tissues, which indicates an increased oxidative stress compared to the liver tissues of control rats. Further, the extent of increased oxidative stress was confirmed by the reduced levels of reduced glutathione (GSH) in diabetic liver tissues. On a comparative basis, treatment with MAuNPs was found to be more effective than MLE for reducing the progression of diabetes and improving the optical redox ratio to a near normal range in streptozotocin-induced diabetic liver tissues. Furthermore, principal component analysis followed by linear discriminant analysis (PC-LDA) has been used to classify the autofluorescence emission spectra from the control and the experimental group of diabetic rats. The results of this study raise the important possibility that fluorescence spectroscopy in conjunction with multivariate statistical analysis has tremendous potential for monitoring or potentially predicting responses to therapy.

The Statistical Value of Raw Fluorescence Signal in Luminex xMAP Based Multiplex Immunoassays

PubMed Central

Breen, Edmond J.; Tan, Woei; Khan, Alamgir

2016-01-01

Tissue samples (plasma, saliva, serum or urine) from 169 patients classified as either normal or having one of seven possible diseases are analysed across three 96-well plates for the presences of 37 analytes using cytokine inflammation multiplexed immunoassay panels. Censoring for concentration data caused problems for analysis of the low abundant analytes. Using fluorescence analysis over concentration based analysis allowed analysis of these low abundant analytes. Mixed-effects analysis on the resulting fluorescence and concentration responses reveals a combination of censoring and mapping the fluorescence responses to concentration values, through a 5PL curve, changed observed analyte concentrations. Simulation verifies this, by showing a dependence on the mean florescence response and its distribution on the observed analyte concentration levels. Differences from normality, in the fluorescence responses, can lead to differences in concentration estimates and unreliable probabilities for treatment effects. It is seen that when fluorescence responses are normally distributed, probabilities of treatment effects for fluorescence based t-tests has greater statistical power than the same probabilities from concentration based t-tests. We add evidence that the fluorescence response, unlike concentration values, doesn’t require censoring and we show with respect to differential analysis on the fluorescence responses that background correction is not required. PMID:27243383

Amelogenin in odontogenic cysts and tumors: An immunohistochemical study

PubMed Central

Anigol, Praveen; Kamath, Venkatesh V.; Satelur, Krishnanand; Anand, Nagaraja; Yerlagudda, Komali

2014-01-01

Background: Amelogenins are the major enamel proteins that play a major role in the biomineralization and structural organization of enamel. Aberrations of enamel-related proteins are thought to be involved in oncogenesis of odontogenic epithelium. The expression of amelogenin is possibly an indicator of differentiation of epithelial cells in the odontogenic lesions. Aims and Objectives: The present study aimed to observe the expression of amelogenin immunohistochemically in various odontogenic lesions. Materials and Methods: Paraffin sections of 40 odontogenic lesions were stained immunohistochemically with amelogenin antibodies. The positivity, pattern and intensity of expression of the amelogenin antibody were assessed, graded and statistically compared between groups of odontogenic cysts and tumors. Results: Almost all the odontogenic lesions expressed amelogenin in the epithelial component with the exception of an ameloblastic carcinoma. Differing grades of intensity and pattern were seen between the cysts and tumors. Intensity of expression was uniformly prominent in all odontogenic lesions with hard tissue formation. Statistical analysis however did not indicate significant differences between the two groups. Conclusion: The expression of amelogenin antibody is ubiquitous in odontogenic tissues and can be used as a definitive marker for identification of odontogenic epithelium. PMID:25937729

Responses of Cell Renewal Systems to Long-term Low-Level Radiation Exposure: A Feasibility Study Applying Advanced Molecular Biology Techniques on Available Histological and Cytological Material of Exposed Animals and Men

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

Fliedner Theodor M.; Feinendegen Ludwig E.; Meineke Viktor

2005-02-28

First results of this feasibility study showed that evaluation of the stored material of the chronically irradiated dogs with modern molecular biological techniques proved to be successful and extremely promising. Therefore an in deep analysis of at least part of the huge amount of remaining material is of outmost interest. The methods applied in this feasibility study were pathological evaluation with different staining methods, protein analysis by means of immunohistochemistry, strand break analysis with the TdT-assay, DNA- and RNA-analysis as well as genomic examination by gene array. Overall more than 50% of the investigated material could be used. In particularmore » the results of an increased stimulation of the immune system within the dogs of the 3mSv group as both compared to the control and higher dose groups gives implications for the in depth study of the cellular events occurring in context with low dose radiation. Based on the findings of this study a further evaluation and statistically analysis of more material can help to identify promising biomarkers for low dose radiation. A systematic evaluation of a correlation of dose rates and strand breaks within the dog tissue might moreover help to explain mechanisms of tolerance to IR. One central problem is that most sequences for dog specific primers are not known yet. The discovery of the dog genome is still under progress. In this study the isolation of RNA within the dog tissue was successful. But up to now there are no gene arrays or gene chips commercially available, tested and adapted for canine tissue. The uncritical use of untested genomic test systems for canine tissue seems to be ineffective at the moment, time consuming and ineffective. Next steps in the investigation of genomic changes after IR within the stored dog tissue should be limited to quantitative RT-PCR of tested primer sequences for the dog. A collaboration with institutions working in the field of the discovery of the dog genome could have synergistic effects.« less

The effect of autologous fibrin tissue adhesive on postoperative cerebrospinal fluid leak in spinal cord surgery: a randomized controlled trial.

PubMed

Nakamura, Hiroshi; Matsuyama, Yukihiro; Yoshihara, Hisatake; Sakai, Yoshihito; Katayama, Yoshito; Nakashima, Shojiro; Takamatsu, Jyunki; Ishiguro, Naoki

2005-07-01

A prospective randomized study evaluating the efficacy of autologous fibrin tissue adhesive for decreasing postoperative cerebrospinal fluid (CSF) leak in spinal cord surgery. To compare postoperative CSF leak in 3 groups (i.e., autologous fibrin tissue adhesive used, commercial fibrin glue used, and no fibrin tissue adhesive used) of patients undergoing spinal surgery who needed dural incision. Spinal cord operations, particularly when dural incision is inevitable, sometimes involve postoperative CSF leak. Because CSF leak is a serious complication, countermeasure is necessary to prevent it after dural suture. Commercial fibrin tissue adhesive was formerly used. Because the possibility of prion infection was widely noticed, commercial fibrin tissue adhesive containing animal components has been used less often. In 13 of 39 cases in which dural incision would be made, 400 mL whole blood was drawn, and autologous fibrin tissue adhesive was made of plasma. Cases were divided into 3 groups: (1) dural closure alone, (2) use of autologous fibrin tissue adhesive after dural closure, and (3) use of commercial fibrin tissue adhesive after dural closure. The primary outcome measure was determined as postoperative (3 days) volume of drainage fluid, and results were analyzed using the analysis of variance. The secondary outcome measure was general blood test, coagulation assay, and plasma fibrinogen, and these were analyzed also using the analysis of variance. There was a significant difference in the primary outcome between the autologous and control groups. No complications such as infection or continuous CSF leak were observed in any case. The mean volume of drainage fluid was 586.2 mL in the group with autologous fibrin tissue adhesive and 1026.1 mL in the group without fibrin tissue adhesive. The volume of drainage fluid was significantly lower in the former group than that in the latter group. There was no statistical difference between the volumes of the group with autologous adhesive and with commercial adhesive (639.2 mL). We used autologous fibrin tissue adhesive as a new sealant after dural closure instead of commercial fibrin tissue adhesive. No definitive CSF leak was observed, and the volume of drainage fluid was significantly lower in the group with autologous fibrin tissue adhesive than that in the group without fibrin tissue adhesive. The use of autologous fibrin tissue adhesive was superior to that of commercial fibrin tissue adhesive in cost.

Review of Quantitative Ultrasound: Envelope Statistics and Backscatter Coefficient Imaging and Contributions to Diagnostic Ultrasound.

PubMed

Oelze, Michael L; Mamou, Jonathan

2016-02-01

Conventional medical imaging technologies, including ultrasound, have continued to improve over the years. For example, in oncology, medical imaging is characterized by high sensitivity, i.e., the ability to detect anomalous tissue features, but the ability to classify these tissue features from images often lacks specificity. As a result, a large number of biopsies of tissues with suspicious image findings are performed each year with a vast majority of these biopsies resulting in a negative finding. To improve specificity of cancer imaging, quantitative imaging techniques can play an important role. Conventional ultrasound B-mode imaging is mainly qualitative in nature. However, quantitative ultrasound (QUS) imaging can provide specific numbers related to tissue features that can increase the specificity of image findings leading to improvements in diagnostic ultrasound. QUS imaging can encompass a wide variety of techniques including spectral-based parameterization, elastography, shear wave imaging, flow estimation, and envelope statistics. Currently, spectral-based parameterization and envelope statistics are not available on most conventional clinical ultrasound machines. However, in recent years, QUS techniques involving spectral-based parameterization and envelope statistics have demonstrated success in many applications, providing additional diagnostic capabilities. Spectral-based techniques include the estimation of the backscatter coefficient (BSC), estimation of attenuation, and estimation of scatterer properties such as the correlation length associated with an effective scatterer diameter (ESD) and the effective acoustic concentration (EAC) of scatterers. Envelope statistics include the estimation of the number density of scatterers and quantification of coherent to incoherent signals produced from the tissue. Challenges for clinical application include correctly accounting for attenuation effects and transmission losses and implementation of QUS on clinical devices. Successful clinical and preclinical applications demonstrating the ability of QUS to improve medical diagnostics include characterization of the myocardium during the cardiac cycle, cancer detection, classification of solid tumors and lymph nodes, detection and quantification of fatty liver disease, and monitoring and assessment of therapy.

Review of quantitative ultrasound: envelope statistics and backscatter coefficient imaging and contributions to diagnostic ultrasound

PubMed Central

Oelze, Michael L.; Mamou, Jonathan

2017-01-01

Conventional medical imaging technologies, including ultrasound, have continued to improve over the years. For example, in oncology, medical imaging is characterized by high sensitivity, i.e., the ability to detect anomalous tissue features, but the ability to classify these tissue features from images often lacks specificity. As a result, a large number of biopsies of tissues with suspicious image findings are performed each year with a vast majority of these biopsies resulting in a negative finding. To improve specificity of cancer imaging, quantitative imaging techniques can play an important role. Conventional ultrasound B-mode imaging is mainly qualitative in nature. However, quantitative ultrasound (QUS) imaging can provide specific numbers related to tissue features that can increase the specificity of image findings leading to improvements in diagnostic ultrasound. QUS imaging techniques can encompass a wide variety of techniques including spectral-based parameterization, elastography, shear wave imaging, flow estimation and envelope statistics. Currently, spectral-based parameterization and envelope statistics are not available on most conventional clinical ultrasound machines. However, in recent years QUS techniques involving spectral-based parameterization and envelope statistics have demonstrated success in many applications, providing additional diagnostic capabilities. Spectral-based techniques include the estimation of the backscatter coefficient, estimation of attenuation, and estimation of scatterer properties such as the correlation length associated with an effective scatterer diameter and the effective acoustic concentration of scatterers. Envelope statistics include the estimation of the number density of scatterers and quantification of coherent to incoherent signals produced from the tissue. Challenges for clinical application include correctly accounting for attenuation effects and transmission losses and implementation of QUS on clinical devices. Successful clinical and pre-clinical applications demonstrating the ability of QUS to improve medical diagnostics include characterization of the myocardium during the cardiac cycle, cancer detection, classification of solid tumors and lymph nodes, detection and quantification of fatty liver disease, and monitoring and assessment of therapy. PMID:26761606

Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (danio rerio)

PubMed Central

2012-01-01

Background Development and application of transcriptomics-based gene classifiers for ecotoxicological applications lag far behind those of biomedical sciences. Many such classifiers discovered thus far lack vigorous statistical and experimental validations. A combination of genetic algorithm/support vector machines and genetic algorithm/K nearest neighbors was used in this study to search for classifiers of endocrine-disrupting chemicals (EDCs) in zebrafish. Searches were conducted on both tissue-specific and tissue-combined datasets, either across the entire transcriptome or within individual transcription factor (TF) networks previously linked to EDC effects. Candidate classifiers were evaluated by gene set enrichment analysis (GSEA) on both the original training data and a dedicated validation dataset. Results Multi-tissue dataset yielded no classifiers. Among the 19 chemical-tissue conditions evaluated, the transcriptome-wide searches yielded classifiers for six of them, each having approximately 20 to 30 gene features unique to a condition. Searches within individual TF networks produced classifiers for 15 chemical-tissue conditions, each containing 100 or fewer top-ranked gene features pooled from those of multiple TF networks and also unique to each condition. For the training dataset, 10 out of 11 classifiers successfully identified the gene expression profiles (GEPs) of their targeted chemical-tissue conditions by GSEA. For the validation dataset, classifiers for prochloraz-ovary and flutamide-ovary also correctly identified the GEPs of corresponding conditions while no classifier could predict the GEP from prochloraz-brain. Conclusions The discrepancies in the performance of these classifiers were attributed in part to varying data complexity among the conditions, as measured to some degree by Fisher’s discriminant ratio statistic. This variation in data complexity could likely be compensated by adjusting sample size for individual chemical-tissue conditions, thus suggesting a need for a preliminary survey of transcriptomic responses before launching a full scale classifier discovery effort. Classifier discovery based on individual TF networks could yield more mechanistically-oriented biomarkers. GSEA proved to be a flexible and effective tool for application of gene classifiers but a similar and more refined algorithm, connectivity mapping, should also be explored. The distribution characteristics of classifiers across tissues, chemicals, and TF networks suggested a differential biological impact among the EDCs on zebrafish transcriptome involving some basic cellular functions. PMID:22849515

Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images.

PubMed

Nguyen, Luong; Tosun, Akif Burak; Fine, Jeffrey L; Lee, Adrian V; Taylor, D Lansing; Chennubhotla, S Chakra

2017-07-01

Segmenting a broad class of histological structures in transmitted light and/or fluorescence-based images is a prerequisite for determining the pathological basis of cancer, elucidating spatial interactions between histological structures in tumor microenvironments (e.g., tumor infiltrating lymphocytes), facilitating precision medicine studies with deep molecular profiling, and providing an exploratory tool for pathologists. This paper focuses on segmenting histological structures in hematoxylin- and eosin-stained images of breast tissues, e.g., invasive carcinoma, carcinoma in situ, atypical and normal ducts, adipose tissue, and lymphocytes. We propose two graph-theoretic segmentation methods based on local spatial color and nuclei neighborhood statistics. For benchmarking, we curated a data set of 232 high-power field breast tissue images together with expertly annotated ground truth. To accurately model the preference for histological structures (ducts, vessels, tumor nets, adipose, etc.) over the remaining connective tissue and non-tissue areas in ground truth annotations, we propose a new region-based score for evaluating segmentation algorithms. We demonstrate the improvement of our proposed methods over the state-of-the-art algorithms in both region- and boundary-based performance measures.

Quantitative assessment of effect of preanalytic cold ischemic time on protein expression in breast cancer tissues.

PubMed

Neumeister, Veronique M; Anagnostou, Valsamo; Siddiqui, Summar; England, Allison Michal; Zarrella, Elizabeth R; Vassilakopoulou, Maria; Parisi, Fabio; Kluger, Yuval; Hicks, David G; Rimm, David L

2012-12-05

Companion diagnostic tests can depend on accurate measurement of protein expression in tissues. Preanalytic variables, especially cold ischemic time (time from tissue removal to fixation in formalin) can affect the measurement and may cause false-negative results. We examined 23 proteins, including four commonly used breast cancer biomarker proteins, to quantify their sensitivity to cold ischemia in breast cancer tissues. A series of 93 breast cancer specimens with known time-to-fixation represented in a tissue microarray and a second series of 25 matched pairs of core needle biopsies and breast cancer resections were used to evaluate changes in antigenicity as a function of cold ischemic time. Estrogen receptor (ER), progesterone receptor (PgR), HER2 or Ki67, and 19 other antigens were tested. Each antigen was measured using the AQUA method of quantitative immunofluorescence on at least one series. All statistical tests were two-sided. We found no evidence for loss of antigenicity with time-to-fixation for ER, PgR, HER2, or Ki67 in a 4-hour time window. However, with a bootstrapping analysis, we observed a trend toward loss for ER and PgR, a statistically significant loss of antigenicity for phosphorylated tyrosine (P = .0048), and trends toward loss for other proteins. There was evidence of increased antigenicity in acetylated lysine, AKAP13 (P = .009), and HIF1A (P = .046), which are proteins known to be expressed in conditions of hypoxia. The loss of antigenicity for phosphorylated tyrosine and increase in expression of AKAP13, and HIF1A were confirmed in the biopsy/resection series. Key breast cancer biomarkers show no evidence of loss of antigenicity, although this dataset assesses the relatively short time beyond the 1-hour limit in recent guidelines. Other proteins show changes in antigenicity in both directions. Future studies that extend the time range and normalize for heterogeneity will provide more comprehensive information on preanalytic variation due to cold ischemic time.

A statistical motion model based on biomechanical simulations for data fusion during image-guided prostate interventions.

PubMed

Hu, Yipeng; Morgan, Dominic; Ahmed, Hashim Uddin; Pendsé, Doug; Sahu, Mahua; Allen, Clare; Emberton, Mark; Hawkes, David; Barratt, Dean

2008-01-01

A method is described for generating a patient-specific, statistical motion model (SMM) of the prostate gland. Finite element analysis (FEA) is used to simulate the motion of the gland using an ultrasound-based 3D FE model over a range of plausible boundary conditions and soft-tissue properties. By applying principal component analysis to the displacements of the FE mesh node points inside the gland, the simulated deformations are then used as training data to construct the SMM. The SMM is used to both predict the displacement field over the whole gland and constrain a deformable surface registration algorithm, given only a small number of target points on the surface of the deformed gland. Using 3D transrectal ultrasound images of the prostates of five patients, acquired before and after imposing a physical deformation, to evaluate the accuracy of predicted landmark displacements, the mean target registration error was found to be less than 1.9 mm.

Assessment of the mechanics of a tissue-engineered rat trachea in an image-processing environment.

PubMed

Silva, Thiago Henrique Gomes da; Pazetti, Rogerio; Aoki, Fabio Gava; Cardoso, Paulo Francisco Guerreiro; Valenga, Marcelo Henrique; Deffune, Elenice; Evaristo, Thaiane; Pêgo-Fernandes, Paulo Manuel; Moriya, Henrique Takachi

2014-07-01

Despite the recent success regarding the transplantation of tissue-engineered airways, the mechanical properties of these grafts are not well understood. Mechanical assessment of a tissue-engineered airway graft before implantation may be used in the future as a predictor of function. The aim of this preliminary work was to develop a noninvasive image-processing environment for the assessment of airway mechanics. Decellularized, recellularized and normal tracheas (groups DECEL, RECEL, and CONTROL, respectively) immersed in Krebs-Henseleit solution were ventilated by a small-animal ventilator connected to a Fleisch pneumotachograph and two pressure transducers (differential and gauge). A camera connected to a stereomicroscope captured images of the pulsation of the trachea before instillation of saline solution and after instillation of Krebs-Henseleit solution, followed by instillation with Krebs-Henseleit with methacholine 0.1 M (protocols A, K and KMCh, respectively). The data were post-processed with computer software and statistical comparisons between groups and protocols were performed. There were statistically significant variations in the image measurements of the medial region of the trachea between the groups (two-way analysis of variance [ANOVA], p<0.01) and of the proximal region between the groups and protocols (two-way ANOVA, p<0.01). The technique developed in this study is an innovative method for performing a mechanical assessment of engineered tracheal grafts that will enable evaluation of the viscoelastic properties of neo-tracheas prior to transplantation.

Segmentation of bone and soft tissue regions in digital radiographic images of extremities

NASA Astrophysics Data System (ADS)

Pakin, S. Kubilay; Gaborski, Roger S.; Barski, Lori L.; Foos, David H.; Parker, Kevin J.

2001-07-01

This paper presents an algorithm for segmentation of computed radiography (CR) images of extremities into bone and soft tissue regions. The algorithm is a region-based one in which the regions are constructed using a growing procedure with two different statistical tests. Following the growing process, tissue classification procedure is employed. The purpose of the classification is to label each region as either bone or soft tissue. This binary classification goal is achieved by using a voting procedure that consists of clustering of regions in each neighborhood system into two classes. The voting procedure provides a crucial compromise between local and global analysis of the image, which is necessary due to strong exposure variations seen on the imaging plate. Also, the existence of regions whose size is large enough such that exposure variations can be observed through them makes it necessary to use overlapping blocks during the classification. After the classification step, resulting bone and soft tissue regions are refined by fitting a 2nd order surface to each tissue, and reevaluating the label of each region according to the distance between the region and surfaces. The performance of the algorithm is tested on a variety of extremity images using manually segmented images as gold standard. The experiments showed that our algorithm provided a bone boundary with an average area overlap of 90% compared to the gold standard.

Porites white patch syndrome: associated viruses and disease physiology

NASA Astrophysics Data System (ADS)

Lawrence, S. A.; Davy, J. E.; Wilson, W. H.; Hoegh-Guldberg, O.; Davy, S. K.

2015-03-01

In recent decades, coral reefs worldwide have undergone significant changes in response to various environmental and anthropogenic impacts. Among the numerous causes of reef degradation, coral disease is one factor that is to a large extent still poorly understood. Here, we characterize the physiology of white patch syndrome (WPS), a disease affecting poritid corals on the Great Barrier Reef. WPS manifests as small, generally discrete patches of tissue discolouration. Physiological analysis revealed that chlorophyll a content was significantly lower in lesions than in healthy tissues, while host protein content remained constant, suggesting that host tissue is not affected by WPS. This was confirmed by transmission electron microscope (TEM) examination, which showed intact host tissue within lesions. TEM also revealed that Symbiodinium cells are lost from the host gastrodermis with no apparent harm caused to the surrounding host tissue. Also present in the electron micrographs were numerous virus-like particles (VLPs), in both coral and Symbiodinium cells. Small (<50 nm diameter) icosahedral VLPs were significantly more abundant in coral tissue taken from diseased colonies, and there was an apparent, but not statistically significant, increase in abundance of filamentous VLPs in Symbiodinium cells from diseased colonies. There was no apparent increase in prokaryotic or eukaryotic microbial abundance in diseased colonies. Taken together, these results suggest that viruses infecting the coral and/or its resident Symbiodinium cells may be the causative agents of WPS.

Elastin density: Link between histological and biomechanical properties of vaginal tissue in women with pelvic organ prolapse?

PubMed

de Landsheere, Laurent; Brieu, Mathias; Blacher, Silvia; Munaut, Carine; Nusgens, Betty; Rubod, Chrystèle; Noel, Agnès; Foidart, Jean-Michel; Nisolle, Michelle; Cosson, Michel

2016-04-01

The aim of the study was to correlate histological and biomechanical characteristics of the vaginal wall in women with pelvic organ prolapse (POP). Tissue samples were collected from the anterior [point Ba; POP Questionnaire (POP-Q)] and/or posterior (point Bp; POP-Q) vaginal wall of 15 women who underwent vaginal surgery for POP. Both histological and biomechanical assessments were performed from the same tissue samples in 14 of 15 patients. For histological assessment, the density of collagen and elastin fibers was determined by combining high-resolution virtual imaging and computer-assisted digital image analysis. For biomechanical testing, uniaxial tension tests were performed to evaluate vaginal tissue stiffness at low (C0) and high (C1) deformation rates. Biomechanical testing highlights the hyperelastic behavior of the vaginal wall. At low strains (C0), vaginal tissue appeared stiffer when elastin density was low. We found a statistically significant inverse relationship between C0 and the elastin/collagen ratio (p = 0.048) in the lamina propria. However, at large strain levels (C1), no clear relationship was observed between elastin density or elastin/collagen ratio and stiffness, likely reflecting the large dispersion of the mechanical behavior of the tissue samples. Histological and biomechanical properties of the vaginal wall vary from patient to patient. This study suggests that elastin density deserves consideration as a relevant factor of vaginal stiffness in women with POP.

Expression of osteoprotegerin, RNAK and RANKL genes in femoral head avascular necrosis and related signaling pathway.

PubMed

Miao, Qingtang; Hao, Sibin; Li, Hongmei; Sun, Fang; Wang, Xueling

2015-01-01

Femoral head avascular necrosis (AVN) causes the damage of hip joint and related dysfunctions, thus consisting of a clinical challenge. Osteoprotegerin (OPG), receptor activator of nuclear factor κB (RANK) and its ligand (RANKL) all regulate the formation of bones via gene transcriptional regulation for the balance between osteoblasts and osteoclasts. This study thus investigated the expressional profiles of OPG, RANK and RANKL genes in AVN patients, and explored related molecular mediating pathways. Real-time qPCR was used to measure the gene expression of OPG, RANK and RANKL genes in AVN femoral head tissue samples from 42 patients, along with normal tissues. Western blotting analysis was performed to quantify protein levels of OPG and RANKL. There was a trend but not statistically significant elevation of mRNA levels of OPG in femoral head AVN tissues compared to normal tissues (P>0.05). The expression of RNAK and RNAKL, however, was significantly elevated in necrotic tissues (P<0.05). No significant difference in protein levels of OPG or RANKL between groups. The expression of OPG, RANK and RANKL genes exert a crucial role in the progression of AVN, suggesting their roles in mediating bone homeostasis and potential effects on bone destruction.

GPX4 and GPX7 Over-Expression in Human Hepatocellular Carcinoma Tissues

PubMed Central

Guerriero, E.; Capone, F.; Accardo, M.; Sorice, A.; Costantini, M.; Colonna, G.; Castello, G.

2015-01-01

Hepatocellular carcinoma (HCC) is the most common type of liver cancer and is still one of the most fatal cancers. Hence, it needs to identify always new putative markers to improve its diagnosis and prognosis. The selenium is an essential trace mineral implicated as a key factor in the early stage of cancer and exerts its biological function through the selenoproteins. In the last years our group has been studying the involvement of some selenoproteins in HCC. However, no many data are reported in literature about the correlation between HCC and the glutathione peroxidases (GPXs), both selenium and non selenium-containing GPXs. In this paper we have evaluated the GPX4 and GPX7 expression in some paraffin-embedded tissues from liver biopsy of patients with hepatitis C virus (HCV)-related cirrhosis and HCC by immunohistochemistry and RT-qPCR analysis. Our results evidenced that i) GPX4 and GPX7 had a statistically significant over-expression in HCC tissues compared to cirrhotic counterparts used as non tumor tissues, and ii) their expression was higher in grade III HCC tissues with respect to grade I-II samples. Therefore, we propose to use GPX4 and GPX7 as possible markers for improving HCC diagnosis/prognosis. PMID:26708178

Dual-modal cancer detection based on optical pH sensing and Raman spectroscopy.

PubMed

Kim, Soogeun; Lee, Seung Ho; Min, Sun Young; Byun, Kyung Min; Lee, Soo Yeol

2017-10-01

A dual-modal approach using Raman spectroscopy and optical pH sensing was investigated to discriminate between normal and cancerous tissues. Raman spectroscopy has demonstrated the potential for in vivo cancer detection. However, Raman spectroscopy has suffered from strong fluorescence background of biological samples and subtle spectral differences between normal and disease tissues. To overcome those issues, pH sensing is adopted to Raman spectroscopy as a dual-modal approach. Based on the fact that the pH level in cancerous tissues is lower than that in normal tissues due to insufficient vasculature formation, the dual-modal approach combining the chemical information of Raman spectrum and the metabolic information of pH level can improve the specificity of cancer diagnosis. From human breast tissue samples, Raman spectra and pH levels are measured using fiber-optic-based Raman and pH probes, respectively. The pH sensing is based on the dependence of pH level on optical transmission spectrum. Multivariate statistical analysis is performed to evaluate the classification capability of the dual-modal method. The analytical results show that the dual-modal method based on Raman spectroscopy and optical pH sensing can improve the performance of cancer classification. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils

PubMed Central

Gueriau, Pierre; Mocuta, Cristian; Dutheil, Didier B.; Cohen, Serge X.; Thiaudière, Dominique; Charbonnier, Sylvain; Clément, Gaël; Bertrand, Loïc

2014-01-01

The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies. PMID:24489809

Trace elemental imaging of rare earth elements discriminates tissues at microscale in flat fossils.

PubMed

Gueriau, Pierre; Mocuta, Cristian; Dutheil, Didier B; Cohen, Serge X; Thiaudière, Dominique; Charbonnier, Sylvain; Clément, Gaël; Bertrand, Loïc

2014-01-01

The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies.

RAMAN spectroscopy imaging improves the diagnosis of papillary thyroid carcinoma

NASA Astrophysics Data System (ADS)

Rau, Julietta V.; Graziani, Valerio; Fosca, Marco; Taffon, Chiara; Rocchia, Massimiliano; Crucitti, Pierfilippo; Pozzilli, Paolo; Onetti Muda, Andrea; Caricato, Marco; Crescenzi, Anna

2016-10-01

Recent investigations strongly suggest that Raman spectroscopy (RS) can be used as a clinical tool in cancer diagnosis to improve diagnostic accuracy. In this study, we evaluated the efficiency of Raman imaging microscopy to discriminate between healthy and neoplastic thyroid tissue, by analyzing main variants of Papillary Thyroid Carcinoma (PTC), the most common type of thyroid cancer. We performed Raman imaging of large tissue areas (from 100 × 100 μm2 up to 1 × 1 mm2), collecting 38 maps containing about 9000 Raman spectra. Multivariate statistical methods, including Linear Discriminant Analysis (LDA), were applied to translate Raman spectra differences between healthy and PTC tissues into diagnostically useful information for a reliable tissue classification. Our study is the first demonstration of specific biochemical features of the PTC profile, characterized by significant presence of carotenoids with respect to the healthy tissue. Moreover, this is the first evidence of Raman spectra differentiation between classical and follicular variant of PTC, discriminated by LDA with high efficiency. The combined histological and Raman microscopy analyses allow clear-cut integration of morphological and biochemical observations, with dramatic improvement of efficiency and reliability in the differential diagnosis of neoplastic thyroid nodules, paving the way to integrative findings for tumorigenesis and novel therapeutic strategies.

Infrared thermal measurements of laser soft tissue ablation as a function of air/water coolant for Nd:YAG and diode lasers

NASA Astrophysics Data System (ADS)

Gekelman, Diana; Yamamoto, Andrew; Oto, Marvin G.; White, Joel M.

2003-06-01

The purpose of this investigation was to measure the maximum temperature at the Nd:YAG and Diode lasers fiberoptic tips as a function of air/water coolant, during soft tissue ablation in pig jaws. A pulsed Nd:YAG laser (1064nm) and a Diode laser (800-830 nm) were used varying parameters of power, conditioning or not of the fiber tip, under 4 settings of air/water coolant. The maximum temperature at the fiber tip was measured using an infra-red camera and the interaction of the fiber with the porcine soft tissue was evaluated. A two-factor ANOVA was used for statistical analysis (p<=0.05). Nd:YAG laser interaction with soft tissues produced temperatures levels directly proportional to power increase, but the conditioning of the fiber tip did not influence the temperature rise. On the other hand, conditioning of the fiber tip did influence the temperature rise for Diode laser. The addition of air/water coolant, for both lasers, did not promote temperature rise consistent with cutting and coagulation of porcine soft tissue. Laser parameters affect the fiberoptic surface temperature, and the addition of air/water coolant significantly lowered surface temperature on the fiberoptic tip for all lasers and parameters tested.

Mesenchymal stem cells promote hard-tissue repair after direct pulp capping.

PubMed

Obeid, Maram; Saber, Shehab El Din Mohamed; Ismael, Alaa El Din; Hassanien, Ehab

2013-05-01

The aim of this study was to investigate the potential of autologous mesenchymal bone marrow stem cells (BMSCs) to promote hard-tissue formation after direct pulp capping procedures. Bone marrow was aspirated from the iliac crest of healthy dogs of nonspecific race. Mononuclear cells were obtained using the Histopaque (Sigma-Aldrich, St Louis, MO) protocol and cultured for 21 days. Direct pulp capping procedures were performed in posterior teeth, and then mineral trioxide aggregate (MTA), hydroxyapatite/tricalcium phosphate, or BMSCs were used as direct pulp capping agents. After 3 months, animals were sacrificed, and jaw segments were processed for radiographic examination using cone-beam computed tomography scanning and histologic examination to assess the formation of a hard-tissue barrier according to a scoring system. The longitudinal and cross-sectional radiophotographs and histologic sections confirmed the formation of an evident calcific barrier after direct pulp capping with MTA and BMSCs. Statistical analysis of the scores given for radiographic and histologic calcific bridge formation showed that both MTA and BMSCs had a comparable tendency to produce a hard-tissue barrier that was significantly higher than hydroxyapatite tricalcium phosphate (P < .05). Autologous mesenchymal BMSCs were able to promote hard-tissue formation after direct pulp capping procedures. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

[Efficacy of fibrin tissue adhesive in the attachment of autogenous conjuntival graft on primary pterygium surgery].

PubMed

Rubin, Michel Risnic; Dantas, Paulo Elias C; Nishiwaki-Dantas, M Cristina; Felberg, Sergio

2011-01-01

To compare the efficacy of conjunctival autograft surgery with the attachment to the scleral bed using fibrin tissue adhesive or mononylon 10-0 suture after resection of primary pterygium. A comparative, prospective and randomized clinical trial was performed in 47 eyes of 47 patients with primary medial located pterygium. Group 1 (adhesive) was composed by 21 patients that underwent conjunctival autograft closure with fibrin tissue adhesive (Quixil™) and Group 2 (suture) was composed by 26 patients that underwent pterygium surgery with mononylon 10-0 (Ethicon(®)) suture (suture group) after pterygium excision. All surgeries were performed by the same surgeon. Patients were assessed on the preoperative period and on the 1(st), 14(th) and 21(st) postoperative days. They were followed-up with a questionnaire of ocular discomfort and by the surgical time spent, ocular hyperemia, complications and recurrence signals, being the recurrence also evaluated at the 6th postoperative month. Data were submitted to statistical analysis. A value of p<0.005 was considered statistically significant. The average surgical time was 19.05 ± 6.12 minutes in group 1 (glue) and 48.15 ± 7.13 minutes in the group 2 (suture) (p<0.001). The ocular discomfort scale analysis showed a lower score in the 1(st) (p<0.005), 7(th) (p<0.001) and 21(th) (p<0.001) postoperative days in group 1. Ocular hyperemia was less intense in all periods of this study in group 1 (p<0.001). Complications were one in each group and both were managed with clinical treatment until the 21(th) postoperative day. There was one recurrence in group 1 and two in group 2 until the 6(th) postoperative month. In the surgical management of primary pterygium, fibrin tissue adhesive attached the conjunctival autograft, decreased the surgical time and diminished the conjunctival hyperemia and ocular discomfort with similar recurrences on the postoperative period, compared to fixation with mononylon 10.0 suture, proving to be an excellent option for conjunctival autograft attachment in primary pterygium surgery.

Brain tissues volume measurements from 2D MRI using parametric approach

NASA Astrophysics Data System (ADS)

L'vov, A. A.; Toropova, O. A.; Litovka, Yu. V.

2018-04-01

The purpose of the paper is to propose a fully automated method of volume assessment of structures within human brain. Our statistical approach uses maximum interdependency principle for decision making process of measurements consistency and unequal observations. Detecting outliers performed using maximum normalized residual test. We propose a statistical model which utilizes knowledge of tissues distribution in human brain and applies partial data restoration for precision improvement. The approach proposes completed computationally efficient and independent from segmentation algorithm used in the application.

MRMC analysis of agreement studies

NASA Astrophysics Data System (ADS)

Gallas, Brandon D.; Anam, Amrita; Chen, Weijie; Wunderlich, Adam; Zhang, Zhiwei

2016-03-01

The purpose of this work is to present and evaluate methods based on U-statistics to compare intra- or inter-reader agreement across different imaging modalities. We apply these methods to multi-reader multi-case (MRMC) studies. We measure reader-averaged agreement and estimate its variance accounting for the variability from readers and cases (an MRMC analysis). In our application, pathologists (readers) evaluate patient tissue mounted on glass slides (cases) in two ways. They evaluate the slides on a microscope (reference modality) and they evaluate digital scans of the slides on a computer display (new modality). In the current work, we consider concordance as the agreement measure, but many of the concepts outlined here apply to other agreement measures. Concordance is the probability that two readers rank two cases in the same order. Concordance can be estimated with a U-statistic and thus it has some nice properties: it is unbiased, asymptotically normal, and its variance is given by an explicit formula. Another property of a U-statistic is that it is symmetric in its inputs; it doesn't matter which reader is listed first or which case is listed first, the result is the same. Using this property and a few tricks while building the U-statistic kernel for concordance, we get a mathematically tractable problem and efficient software. Simulations show that our variance and covariance estimates are unbiased.

Needle-less local anesthesia: clinical evaluation of the effectiveness of the jet anesthesia Injex in local anesthesia in dentistry.

PubMed

Dabarakis, Nikolaos N; Alexander, Veis; Tsirlis, Anastasios T; Parissis, Nikolaos A; Nikolaos, Maroufidis

2007-01-01

To clinically evaluate the jet injection Injex (Rösch AG Medizintechnik) using 2 different anesthetic solutions, and to compare the jet injection and the standard needle injection techniques. Of the 32 patients in the study, 10 received mepivacaine 3% anesthetic solution by means of the jet injection technique, while the remaining 22 patients received lidocaine 2% with epinephrine 1:80,000 by the same method. The 14 patients in whom pulp anesthesia was achieved were selected for an additional evaluation of the pulp reaction using standard needle injection anesthesia. The differences between the 2 compounds with Injex were statistically evaluated by means of independent-samples t test analysis. The differences between subgroups receiving both jet injection and needle injection anesthesia were evaluated by means of paired t test analysis. The administration of mepivacaine 3% using Injex did not achieve pulp anesthesia in any of the 10 patients, although the soft tissue anesthesia was successful. The administration of lidocaine with epinephrine using Injex resulted in pulp anesthesia in only 14 patients; soft tissue anesthesia was observed in all patients of this group. There was no statistically significant difference between Injex and the needle injection technique in onset of anesthesia. However, the duration of anesthesia was significantly longer for the needle infiltration group than for the Injex injection group. The anesthetic solution should be combined with a vasoconstriction agent when the Injex technique is implemented.

A bioreactor test system to mimic the biological and mechanical environment of oral soft tissues and to evaluate substitutes for connective tissue grafts.

PubMed

Mathes, Stephanie H; Wohlwend, Lorenz; Uebersax, Lorenz; von Mentlen, Roger; Thoma, Daniel S; Jung, Ronald E; Görlach, Christoph; Graf-Hausner, Ursula

2010-12-15

Gingival cells of the oral connective tissue are exposed to complex mechanical forces during mastication, speech, tooth movement and orthodontic treatments. Especially during wound healing following surgical procedures, internal and external forces may occur, creating pressure upon the newly formed tissue. This clinical situation has to be considered when developing biomaterials to augment soft tissue in the oral cavity. In order to pre-evaluate a collagen sponge intended to serve as a substitute for autogenous connective tissue grafts (CTGs), a dynamic bioreactor system was developed. Pressure and shear forces can be applied in this bioreactor in addition to a constant medium perfusion to cell-material constructs. Three-dimensional volume changes and stiffness of the matrices were analyzed. In addition, cell responses such as cell vitality and extracellular matrix (ECM) production were investigated. The number of metabolic active cells constantly increased under fully dynamic culture conditions. The sponges remained elastic even after mechanical forces were applied for 14 days. Analysis of collagen type I and fibronectin revealed a statistically significant accumulation of these ECM molecules (P < 0.05-0.001) when compared to static cultures. An increased expression of tenascin-c, indicating tissue remodeling processes, was observed under dynamic conditions only. The results indicate that the tested in vitro cell culture system was able to mimic both the biological and mechanical environments of the clinical situation in a healing wound. © 2010 Wiley Periodicals, Inc.

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance

PubMed Central

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-01-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC. PMID:29113241

Expression of the cytoskeleton regulatory protein Mena in human gastric carcinoma and its prognostic significance.

PubMed

Xu, Lihua; Tan, Huo; Liu, Ruiming; Huang, Qungai; Zhang, Nana; Li, Xi; Wang, Jiani

2017-11-01

The cytoskeleton regulatory protein Mena is reportedly overexpressed in breast cancer; however, data regarding its expression level and clinical significance in gastric carcinoma (GC) is limited. The aim of the present study was to investigate Mena expression levels and prognostic significance in GC. Mena mRNA expression level was determined by reverse transcription-quantitative polymerase chain reaction in 10 paired GC and adjacent normal tissues. The Mena protein expression level was analyzed in paraffin-embedded GC samples and adjacent normal tissues by immunohistochemistry. Statistical analyses were also performed to evaluate the clinicopathological significance of Mena. The results revealed that the mRNA expression level of Mena was significantly higher in G Ct issues compared with in adjacent normal tissues from10 paired samples. In the paraffin-embedded tissue samples, the protein expression level of Mena was higher in G Ct issues compared with in adjacent normal tissues. Compared with adjacent normal tissues, Mena overexpression was observed in 52.83% (56/106) of patients. The overexpression of Mena was significantly associated with the T stage (P=0.033), tumor-node-metastasis (TNM) stage (P<0.001) and decreased overall survival (P<0.001). Based on a multivariate analysis, Mena expression level was an independent prognostic factor for overall survival time. In conclusion, Mena wasoverexpressed in G C tissues and significantly associated with the T stage, TNM stage and overall survival time. Mena may therefore be suitable as a prognostic indicator for patients with GC.

In vitro 3D regeneration-like growth of human patient brain tissue.

PubMed

Tang-Schomer, M D; Wu, W B; Kaplan, D L; Bookland, M J

2018-05-01

In vitro culture of primary neurons is widely adapted with embryonic but not mature brain tissue. Here, we extended a previously developed bioengineered three-dimensional (3D) embryonic brain tissue model to resected normal patient brain tissue in an attempt to regenerate human neurons in vitro. Single cells and small sized (diameter < 100 μm) spheroids from dissociated brain tissue were seeded into 3D silk fibroin-based scaffolds, with or without collagen or Matrigel, and compared with two-dimensional cultures and scaffold-free suspension cultures. Changes of cell phenotypes (neuronal, astroglial, neural progenitor, and neuroepithelial) were quantified with flow cytometry and analyzed with a new method of statistical analysis specifically designed for percentage comparison. Compared with a complete lack of viable cells in conventional neuronal cell culture condition, supplements of vascular endothelial growth factor-containing pro-endothelial cell condition led to regenerative growth of neurons and astroglial cells from "normal" human brain tissue of epilepsy surgical patients. This process involved delayed expansion of Nestin+ neural progenitor cells, emergence of TUJ1+ immature neurons, and Vimentin+ neuroepithelium-like cell sheet formation in prolonged cultures (14 weeks). Micro-tissue spheroids, but not single cells, supported the brain tissue growth, suggesting importance of preserving native cell-cell interactions. The presence of 3D scaffold, but not hydrogel, allowed for Vimentin+ cell expansion, indicating a different growth mechanism than pluripotent cell-based brain organoid formation. The slow and delayed process implied an origin of quiescent neural precursors in the neocortex tissue. Further optimization of the 3D tissue model with primary human brain cells could provide personalized brain disease models. Copyright © 2018 John Wiley & Sons, Ltd.

Refrigeration and freezing of porcine tissue does not affect the retardation of fragment simulating projectiles.

PubMed

Breeze, J; Carr, D J; Mabbott, A; Beckett, S; Clasper, J C

2015-05-01

Explosively propelled fragments are the most common cause of injury to UK service personnel in modern conflicts. Numerical injury models to simulate such injuries utilise algorithms based upon gelatin and animal tissue testing but data is limited on many fragment simulating projectiles and these simulants cannot represent human anatomy. Testing with post mortem specimens may overcome this limitation but no information exists about how post mortem tissue changes and storage conditions in humans or animals may affect projectile penetration. Two chisel nosed cylinders (0.49 g and 1.10 g) and a 0.51 g (5 mm) sphere were fired into three groups of porcine tissue (fresh, refrigerated and frozen then refrigerated) and compared to 20% gelatin. Depth of projectile penetration was ascertained with the assistance of computed tomography and kinetic energy absorption by tissues measured using Doppler radar and high speed photography. No difference in depth of penetration was found between porcine tissue stored in the different manners compared with 20% gelatin by impact velocities less than 100 m/s. Insufficient numbers of projectiles were retained in tissue at higher velocities for statistical analysis to be undertaken. Energy absorbed per millimetre of tissue ranged between 0.42 and 0.98 J/mm for different porcine tissue despite differing storage. This pilot study would suggest that the effect of refrigerating or freezing porcine tissue followed by thawing has no effect on its ability to retard these projectiles. Further research is required to ascertain if these results occur at greater velocities and for other types of projectile. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

In vitro fabrication of a tissue engineered human cardiovascular patch for future use in cardiovascular surgery.

PubMed

Yang, Chao; Sodian, Ralf; Fu, Ping; Lüders, Cora; Lemke, Thees; Du, Jing; Hübler, Michael; Weng, Yuguo; Meyer, Rudolf; Hetzer, Roland

2006-01-01

One approach to tissue engineering has been the development of in vitro conditions for the fabrication of functional cardiovascular structures intended for implantation. In this experiment, we developed a pulsatile flow system that provides biochemical and biomechanical signals in order to regulate autologous, human patch-tissue development in vitro. We constructed a biodegradable patch scaffold from porous poly-4-hydroxy-butyrate (P4HB; pore size 80 to 150 microm). The scaffold was seeded with pediatric aortic cells. The cell-seeded patch constructs were placed in a self-developed bioreactor for 7 days to observe potential tissue formation under dynamic cell culture conditions. As a control, cell-seeded scaffolds were not conditioned in the bioreactor system. After maturation in vitro, the analysis of the tissue engineered constructs included biochemical, biomechanical, morphologic, and immunohistochemical examination. Macroscopically, all tissue engineered constructs were covered by cells. After conditioning in the bioreactor, the cells were mostly viable, had grown into the pores, and had formed tissue on the patch construct. Electron microscopy showed confluent smooth surfaces. Additionally, we demonstrated the capacity to generate collagen and elastin under in vitro pulsatile flow conditions in biochemical examination. Biomechanical testing showed mechanical properties of the tissue engineered human patch tissue without any statistical differences in strength or resistance to stretch between the static controls and the conditioned patches. Immunohistochemical examination stained positive for alpha smooth muscle actin, collagen type I, and fibronectin. There was minor tissue formation in the nonconditioned control samples. Porous P4HB may be used to fabricate a biodegradable patch scaffold. Human vascular cells attached themselves to the polymeric scaffold, and extracellular matrix formation was induced under controlled biomechanical and biodynamic stimuli in a self-developed pulsatile bioreactor system.

Improved Rubin-Bodner Model for the Prediction of Soft Tissue Deformations

PubMed Central

Zhang, Guangming; Xia, James J.; Liebschner, Michael; Zhang, Xiaoyan; Kim, Daeseung; Zhou, Xiaobo

2016-01-01

In craniomaxillofacial (CMF) surgery, a reliable way of simulating the soft tissue deformation resulted from skeletal reconstruction is vitally important for preventing the risks of facial distortion postoperatively. However, it is difficult to simulate the soft tissue behaviors affected by different types of CMF surgery. This study presents an integrated bio-mechanical and statistical learning model to improve accuracy and reliability of predictions on soft facial tissue behavior. The Rubin-Bodner (RB) model is initially used to describe the biomechanical behavior of the soft facial tissue. Subsequently, a finite element model (FEM) computers the stress of each node in soft facial tissue mesh data resulted from bone displacement. Next, the Generalized Regression Neural Network (GRNN) method is implemented to obtain the relationship between the facial soft tissue deformation and the stress distribution corresponding to different CMF surgical types and to improve evaluation of elastic parameters included in the RB model. Therefore, the soft facial tissue deformation can be predicted by biomechanical properties and statistical model. Leave-one-out cross-validation is used on eleven patients. As a result, the average prediction error of our model (0.7035mm) is lower than those resulting from other approaches. It also demonstrates that the more accurate bio-mechanical information the model has, the better prediction performance it could achieve. PMID:27717593

Human papillomavirus infection and the malignant transformation of sinonasal inverted papilloma: A meta-analysis.

PubMed

Zhao, Ren-Wu; Guo, Zhi-Qiang; Zhang, Ru-Xin

2016-06-01

A growing number of molecular epidemiological studies have been conducted to evaluate the association between human papillomavirus (HPV) infection and the malignancy of sinonasal inverted papilloma (SNIP). However, the results remain inconclusive. Here, a meta-analysis was conducted to quantitatively assess this association. Case-control studies investigating SNIP tissues for presence of HPV DNA were identified. The odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by the Mantel-Haenszel method. An assessment of publication bias and sensitivity analysis were also performed. We calculated a pooled OR of 2.16 (95% CI=1.46-3.21, P<0.001) without statistically significant heterogeneity or publication bias. Stratification by HPV type showed a stronger association for patients with high-risk HPV (hrHPV) types, HPV-16, HPV-18, and HPV-16/18 infection (OR=8.8 [95% CI: 4.73-16.38], 8.04 [95% CI: 3.34-19.39], 18.57 [95% CI: 4.56-75.70], and 26.24 [4.35-158.47], respectively). When only using PCR studies, pooled ORs for patients with hrHPV, HPV-16, and HPV18 infection still reached statistical significance. However, Egger's test reflected significant publication bias in the HPV-16 sub-analysis (P=0.06), and the adjusted OR was no longer statistically significant (OR=1.65, 95%CI: 0.58-4.63). These results suggest that HPV infection, especially hrHPV (HPV-18), is significantly associated with malignant SNIP. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of Plasma Rich in Growth Factors and Platelet-Rich Fibrin on Proliferation and Viability of Human Gingival Fibroblasts

PubMed Central

Vahabi, Surena; Vaziri, Shahram; Torshabi, Maryam

2015-01-01

Objectives: Platelet preparations are commonly used to enhance bone and soft tissue regeneration. Considering the existing controversies on the efficacy of platelet products for tissue regeneration, more in vitro studies are required. The aim of the present study was to compare the in vitro effects of plasma rich in growth factors (PRGF) and platelet-rich fibrin (PRF) on proliferation and viability of human gingival fibroblasts (HGFs). Materials and Methods: Anitua’s PRGF and Choukran’s PRF were prepared according to the standard protocols. After culture periods of 24, 48 and 72 hours, proliferation of HGFs was evaluated by the methyl thiazol tetrazolium assay. Statistical analysis was performed using one-way ANOVA followed by Tukey-Kramer’s multiple comparisons and P-values<0.05 were considered statistically significant. Results: PRGF treatment induced statistically significant (P<0.001) proliferation of HGF cells compared to the negative control (100% viability) at 24, 48 and 72 hours in values of 123%±2.25%, 102%±2.8% and 101%±3.92%, respectively. The PRF membrane treatment of HGF cells had a statistically significant effect on cell proliferation (21%±1.73%, P<0.001) at 24 hours compared to the negative control. However, at 48 and 72 hours after treatment, PRF had a negative effect on HGF cell proliferation and caused 38% and 60% decrease in viability and proliferation compared to the negative control, respectively. The HGF cell proliferation was significantly higher in PRGF than in PRF group (P< 0.001). Conclusion: This study demonstrated that PRGF had a strong stimulatory effect on HGF cell viability and proliferation compared to PRF. PMID:26877740

Role of Arrival Time Difference Between Lesions and Lung Tissue on Contrast-Enhanced Sonography in the Differential Diagnosis of Subpleural Pulmonary Lesions.

PubMed

Bai, Jing; Yang, Wei; Wang, Song; Guan, Rui-Hong; Zhang, Hui; Fu, Jing-Jing; Wu, Wei; Yan, Kun

2016-07-01

The purpose of this study was to explore the diagnostic value of the arrival time difference between lesions and surrounding lung tissue on contrast-enhanced sonography of subpleural pulmonary lesions. A total of 110 patients with subpleural pulmonary lesions who underwent both conventional and contrast-enhanced sonography and had a definite diagnosis were enrolled. After contrast agent injection, the arrival times in the lesion, lung, and chest wall were recorded. The arrival time differences between various tissues were also calculated. Statistical analysis showed a significant difference in the lesion arrival time, the arrival time difference between the lesion and lung, and the arrival time difference between the chest wall and lesion (all P < .001) for benign and malignant lesions. Receiver operating characteristic curve analysis revealed that the optimal diagnostic criterion was the arrival time difference between the lesion and lung, and that the best cutoff point was 2.5 seconds (later arrival signified malignancy). This new diagnostic criterion showed superior diagnostic accuracy (97.1%) compared to conventional diagnostic criteria. The individualized diagnostic method based on an arrival time comparison using contrast-enhanced sonography had high diagnostic accuracy (97.1%) with good feasibility and could provide useful diagnostic information for subpleural pulmonary lesions.

Bone tissue reactions to biomimetic ion-substituted apatite surfaces on titanium implants.

PubMed

Ballo, Ahmed M; Xia, Wei; Palmquist, Anders; Lindahl, Carl; Emanuelsson, Lena; Lausmaa, Jukka; Engqvist, Håkan; Thomsen, Peter

2012-07-07

The aim of this study was to evaluate the bone tissue response to strontium- and silicon-substituted apatite (Sr-HA and Si-HA) modified titanium (Ti) implants. Sr-HA, Si-HA and HA were grown on thermally oxidized Ti implants by a biomimetic process. Oxidized implants were used as controls. Surface properties, i.e. chemical composition, surface thickness, morphology/pore characteristics, crystal structure and roughness, were characterized with various analytical techniques. The implants were inserted in rat tibiae and block biopsies were prepared for histology, histomorphometry and scanning electron microscopy analysis. Histologically, new bone formed on all implant surfaces. The bone was deposited directly onto the Sr-HA and Si-HA implants without any intervening soft tissue. The statistical analysis showed significant higher amount of bone-implant contact (BIC) for the Si-doped HA modification (P = 0.030), whereas significant higher bone area (BA) for the Sr-doped HA modification (P = 0.034), when compared with the non-doped HA modification. The differences were most pronounced at the early time point. The healing time had a significant impact for both BA and BIC (P < 0.001). The present results show that biomimetically prepared Si-HA and Sr-HA on Ti implants provided bioactivity and promoted early bone formation.

LIBS analysis of artificial calcified tissues matrices.

PubMed

Kasem, M A; Gonzalez, J J; Russo, R E; Harith, M A

2013-04-15

In most laser-based analytical methods, the reproducibility of quantitative measurements strongly depends on maintaining uniform and stable experimental conditions. For LIBS analysis this means that for accurate estimation of elemental concentration, using the calibration curves obtained from reference samples, the plasma parameters have to be kept as constant as possible. In addition, calcified tissues such as bone are normally less "tough" in their texture than many samples, especially metals. Thus, the ablation process could change the sample morphological features rapidly, and result in poor reproducibility statistics. In the present work, three artificial reference sample sets have been fabricated. These samples represent three different calcium based matrices, CaCO3 matrix, bone ash matrix and Ca hydroxyapatite matrix. A comparative study of UV (266 nm) and IR (1064 nm) LIBS for these three sets of samples has been performed under similar experimental conditions for the two systems (laser energy, spot size, repetition rate, irradiance, etc.) to examine the wavelength effect. The analytical results demonstrated that UV-LIBS has improved reproducibility, precision, stable plasma conditions, better linear fitting, and the reduction of matrix effects. Bone ash could be used as a suitable standard reference material for calcified tissue calibration using LIBS with a 266 nm excitation wavelength. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.

PubMed

Li, Ming; Gray, William; Zhang, Haixia; Chung, Christine H; Billheimer, Dean; Yarbrough, Wendell G; Liebler, Daniel C; Shyr, Yu; Slebos, Robbert J C

2010-08-06

Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. Thus, shotgun proteomics data pose challenges in comparing proteomes from different biological states. We developed an analysis strategy using quasi-likelihood Generalized Linear Modeling (GLM), included in a graphical interface software package (QuasiTel) that reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. This approach was compared to four other statistical analysis strategies: Student t test, Wilcoxon rank test, Fisher's Exact test, and Poisson-based GLM. We analyzed the performance of these tests to identify differences in protein levels based on spectral counts in a shotgun data set in which equimolar amounts of 48 human proteins were spiked at different levels into whole yeast lysates. Both GLM approaches and the Fisher Exact test performed adequately, each with their unique limitations. We subsequently compared the proteomes of normal tonsil epithelium and HNSCC using this approach and identified 86 proteins with differential spectral counts between normal tonsil epithelium and HNSCC. We selected 18 proteins from this comparison for verification of protein levels between the individual normal and tumor tissues using liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM-MS). This analysis confirmed the magnitude and direction of the protein expression differences in all 6 proteins for which reliable data could be obtained. Our analysis demonstrates that shotgun proteomic data sets from different tissue phenotypes are sufficiently rich in quantitative information and that statistically significant differences in proteins spectral counts reflect the underlying biology of the samples.

Texture analysis of tissues in Gleason grading of prostate cancer

NASA Astrophysics Data System (ADS)

Alexandratou, Eleni; Yova, Dido; Gorpas, Dimitris; Maragos, Petros; Agrogiannis, George; Kavantzas, Nikolaos

2008-02-01

Prostate cancer is a common malignancy among maturing men and the second leading cause of cancer death in USA. Histopathological grading of prostate cancer is based on tissue structural abnormalities. Gleason grading system is the gold standard and is based on the organization features of prostatic glands. Although Gleason score has contributed on cancer prognosis and on treatment planning, its accuracy is about 58%, with this percentage to be lower in GG2, GG3 and GG5 grading. On the other hand it is strongly affected by "inter- and intra observer variations", making the whole process very subjective. Therefore, there is need for the development of grading tools based on imaging and computer vision techniques for a more accurate prostate cancer prognosis. The aim of this paper is the development of a novel method for objective grading of biopsy specimen in order to support histopathological prognosis of the tumor. This new method is based on texture analysis techniques, and particularly on Gray Level Co-occurrence Matrix (GLCM) that estimates image properties related to second order statistics. Histopathological images of prostate cancer, from Gleason grade2 to Gleason grade 5, were acquired and subjected to image texture analysis. Thirteen texture characteristics were calculated from this matrix as they were proposed by Haralick. Using stepwise variable selection, a subset of four characteristics were selected and used for the description and classification of each image field. The selected characteristics profile was used for grading the specimen with the multiparameter statistical method of multiple logistic discrimination analysis. The subset of these characteristics provided 87% correct grading of the specimens. The addition of any of the remaining characteristics did not improve significantly the diagnostic ability of the method. This study demonstrated that texture analysis techniques could provide valuable grading decision support to the pathologists, concerning prostate cancer prognosis.

Comparative Shotgun Proteomics Using Spectral Count Data and Quasi-Likelihood Modeling

PubMed Central

2010-01-01

Shotgun proteomics provides the most powerful analytical platform for global inventory of complex proteomes using liquid chromatography−tandem mass spectrometry (LC−MS/MS) and allows a global analysis of protein changes. Nevertheless, sampling of complex proteomes by current shotgun proteomics platforms is incomplete, and this contributes to variability in assessment of peptide and protein inventories by spectral counting approaches. Thus, shotgun proteomics data pose challenges in comparing proteomes from different biological states. We developed an analysis strategy using quasi-likelihood Generalized Linear Modeling (GLM), included in a graphical interface software package (QuasiTel) that reads standard output from protein assemblies created by IDPicker, an HTML-based user interface to query shotgun proteomic data sets. This approach was compared to four other statistical analysis strategies: Student t test, Wilcoxon rank test, Fisher’s Exact test, and Poisson-based GLM. We analyzed the performance of these tests to identify differences in protein levels based on spectral counts in a shotgun data set in which equimolar amounts of 48 human proteins were spiked at different levels into whole yeast lysates. Both GLM approaches and the Fisher Exact test performed adequately, each with their unique limitations. We subsequently compared the proteomes of normal tonsil epithelium and HNSCC using this approach and identified 86 proteins with differential spectral counts between normal tonsil epithelium and HNSCC. We selected 18 proteins from this comparison for verification of protein levels between the individual normal and tumor tissues using liquid chromatography−multiple reaction monitoring mass spectrometry (LC−MRM-MS). This analysis confirmed the magnitude and direction of the protein expression differences in all 6 proteins for which reliable data could be obtained. Our analysis demonstrates that shotgun proteomic data sets from different tissue phenotypes are sufficiently rich in quantitative information and that statistically significant differences in proteins spectral counts reflect the underlying biology of the samples. PMID:20586475

Study protocol for the PHANTOM study: prehospital assessment of noninvasive tissue oximetry monitoring.

PubMed

Weatherall, Andrew; Garner, Alan; Lovell, Nigel; Redmond, Stephen; Lee, Anna; Skowno, Justin; Egan, Jonathan

2014-10-03

Traumatic brain injury is a major cause of mortality and morbidity worldwide. It can be worsened by secondary injury particularly with hypoxia or hypotension. Current prehospital guidelines emphasise regular measurement of peripheral oxygen saturation and blood pressure but there is no monitor in use to provide direct information relating to blood flow or oxygen delivery to the brain tissue. This prospective cohort study will assess the utility of near-infrared spectroscopy monitoring in prehospital medicine in demonstrating injury, pathophysiology and associations with long-term functional outcomes. A prospective cohort study will be conducted in prehospital services where physician/paramedic teams respond rapidly to patients suffering significant traumatic injuries. A study observer accompanying the clinical team will apply non-invasive near-infrared spectroscopy tissue oximetry using a Nonin EQUANOX 7610 Regional Oximetry monitor (TM Nonin Medical, Inc.). This will be applied to patients with traumatic injuries less than 30 minutes old requiring transport. Measurements will be taken at two sites on the forehead and one on the forearm. Clinical teams will be blinded to all monitoring values. Near-infrared spectroscopy tissue oximetry parameters of oxyhaemoglobin%, deoxyhaemoglobin%, total tissue haemoglobin index and regional oxygen saturation will be recorded. Separate statistical analysis relating to time spent with cerebral regional oxygen saturation values < 45% and time series analysis will be performed to demonstrate associations with acute phase outcomes including injuries seen on cerebral imaging, and long-term functional outcomes measured by Glasgow Outcome Score and Extended Glasgow Outcome Score will then be undertaken. This prospective cohort study will demonstrate associations evident from the earliest stages of prehospital treatment between near-infrared spectroscopy tissue oximetry values and both acute and long-term outcomes of patients suffering traumatic injuries. This may provide the basis for future interventional studies utilising near-infrared spectroscopy tissue oximetry to guide prehospital trauma care. This trial is registered with the Australian and New Zealand Clinical Trials Registry. The registration number is ACTRN12611001124921 .

Royal jelly and bee pollen decrease bone loss due to osteoporosis in an oophorectomized rat model.

PubMed

Kafadar, Ibrahim Halil; Güney, Ahmet; Türk, Cemil Yildirim; Oner, Mithat; Silici, Sibel

2012-01-01

In this study, we aimed to investigate whether royal jelly and bee pollen reduce the bone loss due to osteoporosis in oophorectomized rat model. Thirty-two female Sprague-Dawley mature rats at six-month-old, weighing 180-260 g were used in the study. The rats were divided into four groups: Sham-operation group, only oophorectomy group, oophorectomy in combination with royal jelly group, and oophorectomy and bee pollen group. The rats were sacrified within 12 weeks following surgery. Bone mineral density (BMD) was measured and blood samples were collected for biochemical analysis before sacrification. Following sacrification, uterine weights were measured and tissue samples were taken to determine bone calcium and phosphate level with imaging through scanning electron microscope. The uterine weights of the rats were found higher in Sham-operation group than the other groups. The difference among the groups was statistically significant (p=0.001). Total body BMD results were similar in all groups and there was not statistically significant difference (p=0.19). The lumbar spine and proximal femur BMD results were statistically significantly higher in the royal jelly and bee pollen groups, compared to only oophorectomy group (p=0.001). Bone tissue calcium and phosphate levels were higher in royal jelly and bee pollen groups. Royal jelly and bee pollen decrease the bone loss due to osteoporosis in oophorectomized rat model. These results may contribute to the clinical practice.

CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation

PubMed Central

Wilke, Marko; Altaye, Mekibib; Holland, Scott K.

2017-01-01

Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating “unusual” populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php. PMID:28275348

CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation.

PubMed

Wilke, Marko; Altaye, Mekibib; Holland, Scott K

2017-01-01

Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating "unusual" populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php.

Prospective multi-centre Voxel Based Morphometry study employing scanner specific segmentations: Procedure development using CaliBrain structural MRI data

PubMed Central

2009-01-01

Background Structural Magnetic Resonance Imaging (sMRI) of the brain is employed in the assessment of a wide range of neuropsychiatric disorders. In order to improve statistical power in such studies it is desirable to pool scanning resources from multiple centres. The CaliBrain project was designed to provide for an assessment of scanner differences at three centres in Scotland, and to assess the practicality of pooling scans from multiple-centres. Methods We scanned healthy subjects twice on each of the 3 scanners in the CaliBrain project with T1-weighted sequences. The tissue classifier supplied within the Statistical Parametric Mapping (SPM5) application was used to map the grey and white tissue for each scan. We were thus able to assess within scanner variability and between scanner differences. We have sought to correct for between scanner differences by adjusting the probability mappings of tissue occupancy (tissue priors) used in SPM5 for tissue classification. The adjustment procedure resulted in separate sets of tissue priors being developed for each scanner and we refer to these as scanner specific priors. Results Voxel Based Morphometry (VBM) analyses and metric tests indicated that the use of scanner specific priors reduced tissue classification differences between scanners. However, the metric results also demonstrated that the between scanner differences were not reduced to the level of within scanner variability, the ideal for scanner harmonisation. Conclusion Our results indicate the development of scanner specific priors for SPM can assist in pooling of scan resources from different research centres. This can facilitate improvements in the statistical power of quantitative brain imaging studies. PMID:19445668

Histological evaluations and inflammatory responses of different dental implant abutment materials: A human histology pilot study.

PubMed

Sampatanukul, Teeratida; Serichetaphongse, Pravej; Pimkhaokham, Atiphan

2018-04-01

Improvements of soft tissue to the abutment surface results in more stable peri-implant conditions, however, few human histological studies have compared soft tissue responses around different abutment materials. To describe the peri-implant tissue around 3 abutment materials; titanium, zirconia, and gold alloy, over an 8-week healing period. Fifteen edentulous sites were treated with implants. Eight weeks later, peri-implant tissue was harvested and processed using a nonseparation resin embedded technique. The tissue attachment characteristics were assessed at clinical stages using the gingival index (GI) score, surgical stage (surgical score), and histological stage (histological attachment percentage). Additionally, the inflammatory responses were evaluated using inflammatory extent and inflammatory cellularity grades. Nonparametrical statistics were used to describe the GI and surgical scores, and analytical statistics were used to analyze the histological attachment percentages as well as the inflammatory extent and cellularity grades amongst the 3 groups. There were no statistically significant differences among the groups for GI score (P = .071) and surgical score (P = .262). Titanium and zirconia exhibited nearly similar mean histological attachment percentages while gold alloy had a significantly lower percentage (P = .004). For the inflammatory extent and cellularity grades, the odds of being one grade higher for gold alloy abutment was 5.18 and 17.8 times that of titanium abutment, respectively. However, for the zirconia abutment, the odds were 0.87 and 7.5 times higher than the titanium group. The tissue around the gold alloy abutments resulted in worse attachment conditions compared with the titanium and zirconia abutments. Inflammation tended to be higher in the tissue around the gold alloy abutments than the titanium and zirconia abutments. © 2017 Wiley Periodicals, Inc.

Evaluating the efficiency of environmental monitoring programs

USGS Publications Warehouse

Levine, Carrie R.; Yanai, Ruth D.; Lampman, Gregory G.; Burns, Douglas A.; Driscoll, Charles T.; Lawrence, Gregory B.; Lynch, Jason; Schoch, Nina

2014-01-01

Statistical uncertainty analyses can be used to improve the efficiency of environmental monitoring, allowing sampling designs to maximize information gained relative to resources required for data collection and analysis. In this paper, we illustrate four methods of data analysis appropriate to four types of environmental monitoring designs. To analyze a long-term record from a single site, we applied a general linear model to weekly stream chemistry data at Biscuit Brook, NY, to simulate the effects of reducing sampling effort and to evaluate statistical confidence in the detection of change over time. To illustrate a detectable difference analysis, we analyzed a one-time survey of mercury concentrations in loon tissues in lakes in the Adirondack Park, NY, demonstrating the effects of sampling intensity on statistical power and the selection of a resampling interval. To illustrate a bootstrapping method, we analyzed the plot-level sampling intensity of forest inventory at the Hubbard Brook Experimental Forest, NH, to quantify the sampling regime needed to achieve a desired confidence interval. Finally, to analyze time-series data from multiple sites, we assessed the number of lakes and the number of samples per year needed to monitor change over time in Adirondack lake chemistry using a repeated-measures mixed-effects model. Evaluations of time series and synoptic long-term monitoring data can help determine whether sampling should be re-allocated in space or time to optimize the use of financial and human resources.

Multimodal fiber-probe spectroscopy for the diagnostics and classification of bladder tumors

NASA Astrophysics Data System (ADS)

Anand, Suresh; Cicchi, Riccardo; Fantechi, Riccardo; Gacci, Mauro; Nesi, Gabriella; Carini, Marco; Pavone, Francesco S.

2017-02-01

The gold standard for the detection of bladder cancer is white light cystoscopy, followed by an invasive biopsy and pathological examination. Tissue pathology is time consuming and often prone to sampling errors. Recently, optical spectroscopy techniques have evolved as promising techniques for the detection of neoplasia. The specific goal of this study is to evaluate the application of combined auto-fluorescence (excited using 378 nm and 445 nm wavelengths) and diffuse reflectance spectroscopy to discriminate normal bladder tissue from tumor at different grades. The fluorescence spectrum at both excitation wavelengths showed an increased spectral intensity in tumors with respect to normal tissues. Reflectance data indicated an increased reflectance in the wavelength range 610 nm - 700 nm for different grades of tumors, compared to normal tissues. The spectral data were further analyzed using principal component analysis for evaluating the sensitivity and specificity for diagnosing tumor. The spectral differences observed between various grades of tumors provides a strong genesis for the future evaluation on a larger patient population to achieve statistical significance. This study indicates that a combined spectroscopic strategy, incorporating fluorescence and reflectance spectroscopy, could improve the capability for diagnosing bladder tumor as well as for differentiating tumors in different grades.

[Clinical-morphological and histometric characteristics of soft tissue wounds in maxilla-facial region of patients in different terms after trauma].

PubMed

Fedorina, T A; Braĭlovskaia, T V

2009-01-01

504 patients with open traumas of face soft tissues which were given primary surgical wounds treatment with reconstructive operations in maxilla-facial surgical clinics of Samara State Medical University in 2005-2008 also received detailed description. The results of statistical analysis of patients' surgical treatment for the previous 5 year period were listed. It was noted that in the majority of cases (75,5%) patients turned to stomatological aid in first hours or first day and night after receiving the injury, more often there were isolated soft tissue injuries (73,3%), tear-contused and cut wounds put together 80,5%. Morphological and histometric studies of operational-biopsy material let determine the character of changes of leucocyte infiltration and of epithelium - stromal interrelation in different zones of wound edges in patients incoming in different terms after trauma. Objective criteria of tissue excision volumes were received in the process of surgical wound treatment. During last 3 years esthetic results of patient treatment with maxilla-facial traumas improved, the postoperative complications frequency was reduced by 8,1% if compared with the previous 5-year period.

Clinicopathological significance of SLP-2 overexpression in human gallbladder cancer.

PubMed

Wang, Wei-Xin; Lin, Qing-Feng; Shen, Dong; Liu, Shao-Ping; Mao, Wei-Dong; Ma, Gui; Qi, Wei-Dong

2014-01-01

Several studies have indicated that overexpression of stomatin-like protein 2 (SLP-2) has been identified in several types of cancer. However, its role and clinical relevance in gallbladder cancer (GBC) is unknown. The purpose of this study was to reveal the prognostic significance of SLP-2 in GBC. The SLP-2 expression was examined at mRNA and protein levels by real-time quantitative polymerase chain reaction (qRT-PCR), and immunohistochemistry in GBC tissues and adjacent noncancerous tissues. Statistical analyses were applied to test the associations between SLP-2 expression, clinicopathologic factors, and prognosis. Immunohistochemistry and qRT-PCR showed that the protein and mRNA expression levels of SLP-2 were both significantly higher in GBC tissues than in adjacent noncancerous tissues. In addition, immunohistochemistry analysis showed that SLP-2 expression was significantly correlated with histological grade (P <0.001), pathologic T stage (P = 0.019), clinical stage (P = 0.001), and lymph node metastasis (P = 0.026). The Kaplan-Meier survival curves indicated that patients with high expression of SLP-2 had shorter overall survival than those with low expression (P <0.001). Meanwhile, the Cox multivariate analysis indicated that high expressions of SLP-2 were an independent prognostic factor for patients with GBC. These data showed that SLP-2 may play an important role in human GBC tumorigenesis, and SLP-2 might serve as a novel prognostic marker in human GBC.

Fluorescence lifetime imaging of endogenous molecules in live mouse cancer models (Conference Presentation)

NASA Astrophysics Data System (ADS)

Svindrych, Zdenek; Wang, Tianxiong; Hu, Song; Periasamy, Ammasi

2017-02-01

NADH and FAD are important endogenous fluorescent coenzymes participating in key enzymatic reactions of cellular metabolism. While fluorescence intensities of NADH and FAD have been used to determine the redox state of cells and tissues, this simple approach breaks down in the case of deep-tissue intravital imaging due to depth- and wavelength-dependent light absorption and scattering. To circumvent this limitation, our research focuses on fluorescence lifetimes of two-photon excited NADH and FAD emission to study the metabolic state of live tissues. In our custom-built scanning microscope we combine tunable femtosecond Ti:sapphire laser (operating at 740 nm for NADH excitation and 890 nm for FAD excitation), two GaAsP hybrid detectors for registering individual fluorescence photons and two Becker and Hickl time correlator boards for high precision lifetime measurements. Together with our rigorous FLIM analysis approach (including image segmentation, multi-exponential decay fitting and detailed statistical analysis) we are able to detect metabolic changes in cancer xenografts (human pancreatic cancer MPanc96 cells injected subcutaneously into the ear of an immunodeficient nude mouse), relative to surrounding healthy tissue. Advantageously, with the same instrumentation we can also take high-resolution and high-contrast images of second harmonic signal (SHG) originating from collagen fibers of both the healthy skin and the growing tumor. The combination of metabolic measurements (NADH and FAD lifetime) and morphological information (collagen SHG) allows us to follow the tumor growth in live mouse model and the changes in tumor microenvironment.

Statistical model of laminar structure for atlas-based segmentation of the fetal brain from in utero MR images

NASA Astrophysics Data System (ADS)

Habas, Piotr A.; Kim, Kio; Chandramohan, Dharshan; Rousseau, Francois; Glenn, Orit A.; Studholme, Colin

2009-02-01

Recent advances in MR and image analysis allow for reconstruction of high-resolution 3D images from clinical in utero scans of the human fetal brain. Automated segmentation of tissue types from MR images (MRI) is a key step in the quantitative analysis of brain development. Conventional atlas-based methods for adult brain segmentation are limited in their ability to accurately delineate complex structures of developing tissues from fetal MRI. In this paper, we formulate a novel geometric representation of the fetal brain aimed at capturing the laminar structure of developing anatomy. The proposed model uses a depth-based encoding of tissue occurrence within the fetal brain and provides an additional anatomical constraint in a form of a laminar prior that can be incorporated into conventional atlas-based EM segmentation. Validation experiments are performed using clinical in utero scans of 5 fetal subjects at gestational ages ranging from 20.5 to 22.5 weeks. Experimental results are evaluated against reference manual segmentations and quantified in terms of Dice similarity coefficient (DSC). The study demonstrates that the use of laminar depth-encoded tissue priors improves both the overall accuracy and precision of fetal brain segmentation. Particular refinement is observed in regions of the parietal and occipital lobes where the DSC index is improved from 0.81 to 0.82 for cortical grey matter, from 0.71 to 0.73 for the germinal matrix, and from 0.81 to 0.87 for white matter.

The overexpression of Rabl3 is associated with pathogenesis and clinicopathologic variables in hepatocellular carcinoma.

PubMed

Pan, Yuhang; Liu, Zhiyong; Feng, Zhiying; Hui, Dayang; Huang, Xiangqi; Tong, Dayue; Jin, Yi

2017-04-01

Overexpression of Rabl3 is associated with some malignancies. However, their relationship with hepatocellular carcinoma remains unclear. In this study, the expression of Rabl3 in hepatocellular carcinoma cell lines, and four pairs of matched hepatocellular carcinoma tissues and their adjacent normal hepatic tissues were detected by quantitative reverse transcription polymerase chain reaction and western blot. In addition, the protein expression of Rabl3 was examined in 162 cases of hepatocellular carcinoma by immunohistochemistry. Rabl3 in hepatocellular carcinoma cell lines was elevated at both messenger RNA and protein levels, and the Rabl3 protein was significantly upregulated by upto 3.3-fold in hepatocellular carcinoma compared with the paired normal hepatic tissues. Immunohistochemical analysis revealed that overexpressions of Rabl3 were 80.2% in hepatocellular carcinoma. Rabl3 is expressed at significantly higher rates in hepatocellular carcinoma compared with adjacent normal hepatic tissue (p < 0.01). Statistical analysis suggested the upregulation of Rabl3 was significantly associated with lymph node metastasis, tumor thrombus of the portal vein, and advanced clinical stage (p < 0.05). Furthermore, we found that overexpression of Rabl3 in hepatocellular carcinoma cells could significantly enhance cell proliferation and growth ability. Conversely, silencing Rabl3 by small hairpin RNA interference caused an inhibition of cell proliferation and growth. Our studies suggest that the Rabl3 is a valuable marker of hepatocellular carcinoma progression and that the overexpression of Rabl3 plays an important role in the development and pathogenesis of hepatocellular carcinoma.

In vitro chronic hepatic disease characterization with a multiparametric ultrasonic approach.

PubMed

Meziri, M; Pereira, W C A; Abdelwahab, A; Degott, C; Laugier, P

2005-03-01

Although, high resolution, real-time ultrasonic (US) imaging is routinely available, image interpretation is based on grey-level and texture and quantitative evaluation is limited. Other potentially useful diagnostic information from US echoes may include modifications in tissue acoustic parameters (speed, attenuation and backscattering) resulting from disease development. Changes in acoustical parameters can be detected using time-of-flight and spectral analysis techniques. The objective of this study is to explore the potential of three parameters together (attenuation coefficient, US speed and integrated backscatter coefficient-IBC) to discriminate healthy and fibrosis subgroups in liver tissue. Echoes from 21 fresh in vitro samples of human liver and from a plane reflector were obtained using a 20-MHz central frequency transducer (6-30 MHz bandpass). The scan plane was parallel to the reflector placed beneath the liver. A 30 x 20 matrix of A-scans was obtained, with a 200-microm step. The samples were classified according to the Metavir scale in five different degrees of fibrosis. US speed, attenuation and IBC were estimated from standard methods described in the literature. Statistical tests were applied to the results of each parameter individually and indicated that it was not possible to identify all the fibrosis groups. Then a discriminant analysis was performed for the three parameters together resulting in a reasonable separation of fibrotic groups. Although the number of tissue samples is limited, this study opens the possibility of enhancing the discriminant capability of ultrasonic parameters of liver tissue disease when they are combined together.

Diagnostic potential of real-time elastography (RTE) and shear wave elastography (SWE) to differentiate benign and malignant thyroid nodules

PubMed Central

Hu, Xiangdong; Liu, Yujiang; Qian, Linxue

2017-01-01

Abstract Background: Real-time elastography (RTE) and shear wave elastography (SWE) are noninvasive and easily available imaging techniques that measure the tissue strain, and it has been reported that the sensitivity and the specificity of elastography were better in differentiating between benign and malignant thyroid nodules than conventional technologies. Methods: Relevant articles were searched in multiple databases; the comparison of elasticity index (EI) was conducted with the Review Manager 5.0. Forest plots of the sensitivity and specificity and SROC curve of RTE and SWE were performed with STATA 10.0 software. In addition, sensitivity analysis and bias analysis of the studies were conducted to examine the quality of articles; and to estimate possible publication bias, funnel plot was used and the Egger test was conducted. Results: Finally 22 articles which eventually satisfied the inclusion criteria were included in this study. After eliminating the inefficient, benign and malignant nodules were 2106 and 613, respectively. The meta-analysis suggested that the difference of EI between benign and malignant nodules was statistically significant (SMD = 2.11, 95% CI [1.67, 2.55], P < .00001). The overall sensitivities of RTE and SWE were roughly comparable, whereas the difference of specificities between these 2 methods was statistically significant. In addition, statistically significant difference of AUC between RTE and SWE was observed between RTE and SWE (P < .01). Conclusion: The specificity of RTE was statistically higher than that of SWE; which suggests that compared with SWE, RTE may be more accurate on differentiating benign and malignant thyroid nodules. PMID:29068996

Quantitative comparison of tympanic membrane displacements using two optical methods to recover the optical phase

NASA Astrophysics Data System (ADS)

Santiago-Lona, Cynthia V.; Hernández-Montes, María del Socorro; Mendoza-Santoyo, Fernando; Esquivel-Tejeda, Jesús

2018-02-01

The study and quantification of the tympanic membrane (TM) displacements add important information to advance the knowledge about the hearing process. A comparative statistical analysis between two commonly used demodulation methods employed to recover the optical phase in digital holographic interferometry, namely the fast Fourier transform and phase-shifting interferometry, is presented as applied to study thin tissues such as the TM. The resulting experimental TM surface displacement data are used to contrast both methods through the analysis of variance and F tests. Data are gathered when the TMs are excited with continuous sound stimuli at levels 86, 89 and 93 dB SPL for the frequencies of 800, 1300 and 2500 Hz under the same experimental conditions. The statistical analysis shows repeatability in z-direction displacements with a standard deviation of 0.086, 0.098 and 0.080 μm using the Fourier method, and 0.080, 0.104 and 0.055 μm with the phase-shifting method at a 95% confidence level for all frequencies. The precision and accuracy are evaluated by means of the coefficient of variation; the results with the Fourier method are 0.06143, 0.06125, 0.06154 and 0.06154, 0.06118, 0.06111 with phase-shifting. The relative error between both methods is 7.143, 6.250 and 30.769%. On comparing the measured displacements, the results indicate that there is no statistically significant difference between both methods for frequencies at 800 and 1300 Hz; however, errors and other statistics increase at 2500 Hz.

Naturally acquired bovine besnoitiosis: Differential distribution of parasites in the skin of chronically infected cattle.

PubMed

Schares, G; Langenmayer, M C; Majzoub-Altweck, M; Scharr, J C; Gentile, A; Maksimov, A; Schares, S; Conraths, F J; Gollnick, N S

2016-01-30

Bovine besnoitiosis is caused by Besnoitia besnoiti, an apicomplexan parasite closely related to Toxoplasma gondii and Neospora caninum. In the acute stage of besnoitiosis, cattle suffer from pyrexia, swollen lymph nodes, anorexia and subcutaneous edema. In the chronic stage, tissue cysts are formed in a variety of tissues including the skin. Knowledge about the distribution of tissue cysts of different parts of the skin of infected animals is scarce. Four chronically infected cattle were euthanized and skin samples were taken from a total of 77 standardized cutaneous locations per animal. Portions of the dermis were taken, from which DNA was extracted and examined by real-time PCR. Cycle of transition (Ct) values reflecting the amount of parasite DNA in the samples were determined. For statistical analysis, samples were attributed to 11 larger skin regions ('OuterHindlegDistal', 'Rump, ForelegMiddle', 'NoseFrontEars', 'CheekEye', 'SideLowerPart', 'ForelegDistal', 'SideUpperPart', 'LegsInner', 'VentralHeadNeck', 'DorsalNeckWithersBackTail'). While all samples revealed a positive result in three female cattle, only 63.6% (49/77) of the samples of a bull showed positive results. For statistical analysis, a Ct value of 45 was assumed for samples with a negative result. The dams showed median Ct values of 16.1, 17.5 and 19.4, while in skin samples of the bull a median Ct value of 37.6 was observed. To determine the differences in DNA concentrations between different locations of the skin of the animals, a relative Ct (relCt) was determined by subtracting for each animal indv the MedianCtindv from each sample Ct. Analyses of the relCt values showed that the highest relative parasite DNA concentrations were observed in the categories 'OuterHindlegDistal', 'Rump', 'ForelegMiddle' and 'NoseFrontEars'. The relCt values in these categories differed statistically significantly from those determined for the categories 'VentralHeadNeck' and 'DorsalNeckWithersBackTail'. The analysis showed clear differences in the distribution and the detectability of parasite DNA in the skin of cattle infected with B. besnoiti. In all four animals, samples from the 'Rump' region (Regio fermoris) showed high parasite DNA concentrations. Because this region is also easily accessible for veterinarians, this skin location appears to be optimal for taking skin biopsies for detection or isolation of B. besnoiti. Copyright © 2015 Elsevier B.V. All rights reserved.

[Prolyl hydroxylase activity in liver specimens in chronic liver diseases (author's transl)].

PubMed

Langness, U; Clausnitzer, H; Verspohl, M; Grasedyck, K

1978-08-25

100 patients were laparoscopied, liver tissue specimens taken from atypically altered areas. Prolyl hydroxylase was determined in the specimen, in parallel tissue was examined by light microscope. 8 groups of patients could be differentiated: Patients 1. with active, 2, with inactive cirrhosis, 3. with fatty infiltrations, 4. with fatty infiltration and mesenchymal reaction, 5. with aggressive, 6. with persistent, 7. with reactive hepatitis, 8. patients without histological changes. In the case of connective tissue increase in the liver prolyl hydroxylase activities were statistically significant above normal. In addition, there was a statistically significant difference between the enzyme activities of each group. A correlation could be found between prolyl hydroxylase activity and morphologically estimated connective tissue formation, but not the serum enzyme activities usually determined in liver diseases. Therefore, could be concluded that prolyl hydroxylase activity is an index of actual collagen biosynthesis in chronic liver diseases.

Data-adaptive test statistics for microarray data.

PubMed

Mukherjee, Sach; Roberts, Stephen J; van der Laan, Mark J

2005-09-01

An important task in microarray data analysis is the selection of genes that are differentially expressed between different tissue samples, such as healthy and diseased. However, microarray data contain an enormous number of dimensions (genes) and very few samples (arrays), a mismatch which poses fundamental statistical problems for the selection process that have defied easy resolution. In this paper, we present a novel approach to the selection of differentially expressed genes in which test statistics are learned from data using a simple notion of reproducibility in selection results as the learning criterion. Reproducibility, as we define it, can be computed without any knowledge of the 'ground-truth', but takes advantage of certain properties of microarray data to provide an asymptotically valid guide to expected loss under the true data-generating distribution. We are therefore able to indirectly minimize expected loss, and obtain results substantially more robust than conventional methods. We apply our method to simulated and oligonucleotide array data. By request to the corresponding author.

Wavelet methodology to improve single unit isolation in primary motor cortex cells

PubMed Central

Ortiz-Rosario, Alexis; Adeli, Hojjat; Buford, John A.

2016-01-01

The proper isolation of action potentials recorded extracellularly from neural tissue is an active area of research in the fields of neuroscience and biomedical signal processing. This paper presents an isolation methodology for neural recordings using the wavelet transform (WT), a statistical thresholding scheme, and the principal component analysis (PCA) algorithm. The effectiveness of five different mother wavelets was investigated: biorthogonal, Daubachies, discrete Meyer, symmetric, and Coifman; along with three different wavelet coefficient thresholding schemes: fixed form threshold, Stein’s unbiased estimate of risk, and minimax; and two different thresholding rules: soft and hard thresholding. The signal quality was evaluated using three different statistical measures: mean-squared error, root-mean squared, and signal to noise ratio. The clustering quality was evaluated using two different statistical measures: isolation distance, and L-ratio. This research shows that the selection of the mother wavelet has a strong influence on the clustering and isolation of single unit neural activity, with the Daubachies 4 wavelet and minimax thresholding scheme performing the best. PMID:25794461

Clinical and biometrical evaluation of socket preservation using demineralized freeze-dried bone allograft with and without the palatal connective tissue as a biologic membrane.

PubMed

Moghaddas, Hamid; Amjadi, Mohammad Reza; Naghsh, Narges

2012-11-01

Alveolar ridge preservation following tooth extraction has the ability to maintain the ridge dimensions and allow the implant placement in an ideal position fulfilling both functional and aesthetic results. The aim of this study was to evaluate the efficacy of the palatal connective tissue as a biological membrane for socket preservation with demineralized freeze-dried bone allograft (DFDBA). Twelve extraction sites were treated with DFDBA with (case group) and without (control group) using autogenous palatal connective tissue membrane before placement of implants. Alveolar width and height, amount of keratinized tissue, and gingival level were measured at pre-determined points using a surgical stent at two times, the time of socket preservation surgery. In both groups a decrease in all socket dimensions was found. The average decrease in socket width, height, keratinized tissue, and gingival level in case group was 1.16, 0.72, 3.58, and 1.27 mm, and in control group was 2.08, 0.86, 4.52, and 1.58 mm respectively. Statistical analysis showed that decrease in socket width (P = 0.012), keratinized tissue (P ≤ 0.001), and gingival level (P = 0.031) in case group was significantly lower than that of the control group. Results showed no meaningful difference in socket height changes when compared with case and control groups (P = 0.148). Under the limits of this study, connective tissue membrane could preserve socket width, amount of keratinized tissue, and the gingival level more effectively than DFDBA alone.

Accurate tissue characterization in low-dose CT imaging with pure iterative reconstruction.

PubMed

Murphy, Kevin P; McLaughlin, Patrick D; Twomey, Maria; Chan, Vincent E; Moloney, Fiachra; Fung, Adrian J; Chan, Faimee E; Kao, Tafline; O'Neill, Siobhan B; Watson, Benjamin; O'Connor, Owen J; Maher, Michael M

2017-04-01

We assess the ability of low-dose hybrid iterative reconstruction (IR) and 'pure' model-based IR (MBIR) images to maintain accurate Hounsfield unit (HU)-determined tissue characterization. Standard-protocol (SP) and low-dose modified-protocol (MP) CTs were contemporaneously acquired in 34 Crohn's disease patients referred for CT. SP image reconstruction was via the manufacturer's recommendations (60% FBP, filtered back projection; 40% ASiR, Adaptive Statistical iterative Reconstruction; SP-ASiR40). MP data sets underwent four reconstructions (100% FBP; 40% ASiR; 70% ASiR; MBIR). Three observers measured tissue volumes using HU thresholds for fat, soft tissue and bone/contrast on each data set. Analysis was via SPSS. Inter-observer agreement was strong for 1530 datapoints (rs > 0.9). MP-MBIR tissue volume measurement was superior to other MP reconstructions and closely correlated with the reference SP-ASiR40 images for all tissue types. MP-MBIR superiority was most marked for fat volume calculation - close SP-ASiR40 and MP-MBIR Bland-Altman plot correlation was seen with the lowest average difference (336 cm 3 ) when compared with other MP reconstructions. Hounsfield unit-determined tissue volume calculations from MP-MBIR images resulted in values comparable to SP-ASiR40 calculations and values that are superior to MP-ASiR images. Accuracy of estimation of volume of tissues (e.g. fat) using segmentation software on low-dose CT images appears optimal when reconstructed with pure IR. © 2016 The Royal Australian and New Zealand College of Radiologists.