Tissue microarrays and quantitative tissue-based image analysis as a tool for oncology biomarker and diagnostic development.

PubMed

Dolled-Filhart, Marisa P; Gustavson, Mark D

2012-11-01

Translational oncology has been improved by using tissue microarrays (TMAs), which facilitate biomarker analysis of large cohorts on a single slide. This has allowed for rapid analysis and validation of potential biomarkers for prognostic and predictive value, as well as for evaluation of biomarker prevalence. Coupled with quantitative analysis of immunohistochemical (IHC) staining, objective and standardized biomarker data from tumor samples can further advance companion diagnostic approaches for the identification of drug-responsive or resistant patient subpopulations. This review covers the advantages, disadvantages and applications of TMAs for biomarker research. Research literature and reviews of TMAs and quantitative image analysis methodology have been surveyed for this review (with an AQUA® analysis focus). Applications such as multi-marker diagnostic development and pathway-based biomarker subpopulation analyses are described. Tissue microarrays are a useful tool for biomarker analyses including prevalence surveys, disease progression assessment and addressing potential prognostic or predictive value. By combining quantitative image analysis with TMAs, analyses will be more objective and reproducible, allowing for more robust IHC-based diagnostic test development. Quantitative multi-biomarker IHC diagnostic tests that can predict drug response will allow for greater success of clinical trials for targeted therapies and provide more personalized clinical decision making.

Developing High-Frequency Quantitative Ultrasound Techniques to Characterize Three-Dimensional Engineered Tissues

NASA Astrophysics Data System (ADS)

Mercado, Karla Patricia E.

Tissue engineering holds great promise for the repair or replacement of native tissues and organs. Further advancements in the fabrication of functional engineered tissues are partly dependent on developing new and improved technologies to monitor the properties of engineered tissues volumetrically, quantitatively, noninvasively, and nondestructively over time. Currently, engineered tissues are evaluated during fabrication using histology, biochemical assays, and direct mechanical tests. However, these techniques destroy tissue samples and, therefore, lack the capability for real-time, longitudinal monitoring. The research reported in this thesis developed nondestructive, noninvasive approaches to characterize the structural, biological, and mechanical properties of 3-D engineered tissues using high-frequency quantitative ultrasound and elastography technologies. A quantitative ultrasound technique, using a system-independent parameter known as the integrated backscatter coefficient (IBC), was employed to visualize and quantify structural properties of engineered tissues. Specifically, the IBC was demonstrated to estimate cell concentration and quantitatively detect differences in the microstructure of 3-D collagen hydrogels. Additionally, the feasibility of an ultrasound elastography technique called Single Tracking Location Acoustic Radiation Force Impulse (STL-ARFI) imaging was demonstrated for estimating the shear moduli of 3-D engineered tissues. High-frequency ultrasound techniques can be easily integrated into sterile environments necessary for tissue engineering. Furthermore, these high-frequency quantitative ultrasound techniques can enable noninvasive, volumetric characterization of the structural, biological, and mechanical properties of engineered tissues during fabrication and post-implantation.

Quantitatively differentiating microstructural variations of skeletal muscle tissues by multispectral Mueller matrix imaging

NASA Astrophysics Data System (ADS)

Dong, Yang; He, Honghui; He, Chao; Ma, Hui

2016-10-01

Polarized light is sensitive to the microstructures of biological tissues and can be used to detect physiological changes. Meanwhile, spectral features of the scattered light can also provide abundant microstructural information of tissues. In this paper, we take the backscattering polarization Mueller matrix images of bovine skeletal muscle tissues during the 24-hour experimental time, and analyze their multispectral behavior using quantitative Mueller matrix parameters. In the processes of rigor mortis and proteolysis of muscle samples, multispectral frequency distribution histograms (FDHs) of the Mueller matrix elements can reveal rich qualitative structural information. In addition, we analyze the temporal variations of the sample using the multispectral Mueller matrix transformation (MMT) parameters. The experimental results indicate that the different stages of rigor mortis and proteolysis for bovine skeletal muscle samples can be judged by these MMT parameters. The results presented in this work show that combining with the multispectral technique, the FDHs and MMT parameters can characterize the microstructural variation features of skeletal muscle tissues. The techniques have the potential to be used as tools for quantitative assessment of meat qualities in food industry.

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

Quantitative polarized Raman spectroscopy in highly turbid bone tissue

NASA Astrophysics Data System (ADS)

Raghavan, Mekhala; Sahar, Nadder D.; Wilson, Robert H.; Mycek, Mary-Ann; Pleshko, Nancy; Kohn, David H.; Morris, Michael D.

2010-05-01

Polarized Raman spectroscopy allows measurement of molecular orientation and composition and is widely used in the study of polymer systems. Here, we extend the technique to the extraction of quantitative orientation information from bone tissue, which is optically thick and highly turbid. We discuss multiple scattering effects in tissue and show that repeated measurements using a series of objectives of differing numerical apertures can be employed to assess the contributions of sample turbidity and depth of field on polarized Raman measurements. A high numerical aperture objective minimizes the systematic errors introduced by multiple scattering. We test and validate the use of polarized Raman spectroscopy using wild-type and genetically modified (oim/oim model of osteogenesis imperfecta) murine bones. Mineral orientation distribution functions show that mineral crystallites are not as well aligned (p<0.05) in oim/oim bones (28+/-3 deg) compared to wild-type bones (22+/-3 deg), in agreement with small-angle X-ray scattering results. In wild-type mice, backbone carbonyl orientation is 76+/-2 deg and in oim/oim mice, it is 72+/-4 deg (p>0.05). We provide evidence that simultaneous quantitative measurements of mineral and collagen orientations on intact bone specimens are possible using polarized Raman spectroscopy.

Quantitative polarized Raman spectroscopy in highly turbid bone tissue.

PubMed

Raghavan, Mekhala; Sahar, Nadder D; Wilson, Robert H; Mycek, Mary-Ann; Pleshko, Nancy; Kohn, David H; Morris, Michael D

2010-01-01

Polarized Raman spectroscopy allows measurement of molecular orientation and composition and is widely used in the study of polymer systems. Here, we extend the technique to the extraction of quantitative orientation information from bone tissue, which is optically thick and highly turbid. We discuss multiple scattering effects in tissue and show that repeated measurements using a series of objectives of differing numerical apertures can be employed to assess the contributions of sample turbidity and depth of field on polarized Raman measurements. A high numerical aperture objective minimizes the systematic errors introduced by multiple scattering. We test and validate the use of polarized Raman spectroscopy using wild-type and genetically modified (oim/oim model of osteogenesis imperfecta) murine bones. Mineral orientation distribution functions show that mineral crystallites are not as well aligned (p<0.05) in oim/oim bones (28+/-3 deg) compared to wild-type bones (22+/-3 deg), in agreement with small-angle X-ray scattering results. In wild-type mice, backbone carbonyl orientation is 76+/-2 deg and in oim/oim mice, it is 72+/-4 deg (p>0.05). We provide evidence that simultaneous quantitative measurements of mineral and collagen orientations on intact bone specimens are possible using polarized Raman spectroscopy.

Unified quantitative characterization of epithelial tissue development

PubMed Central

Guirao, Boris; Rigaud, Stéphane U; Bosveld, Floris; Bailles, Anaïs; López-Gay, Jesús; Ishihara, Shuji; Sugimura, Kaoru

2015-01-01

Understanding the mechanisms regulating development requires a quantitative characterization of cell divisions, rearrangements, cell size and shape changes, and apoptoses. We developed a multiscale formalism that relates the characterizations of each cell process to tissue growth and morphogenesis. Having validated the formalism on computer simulations, we quantified separately all morphogenetic events in the Drosophila dorsal thorax and wing pupal epithelia to obtain comprehensive statistical maps linking cell and tissue scale dynamics. While globally cell shape changes, rearrangements and divisions all significantly participate in tissue morphogenesis, locally, their relative participations display major variations in space and time. By blocking division we analyzed the impact of division on rearrangements, cell shape changes and tissue morphogenesis. Finally, by combining the formalism with mechanical stress measurement, we evidenced unexpected interplays between patterns of tissue elongation, cell division and stress. Our formalism provides a novel and rigorous approach to uncover mechanisms governing tissue development. DOI: http://dx.doi.org/10.7554/eLife.08519.001 PMID:26653285

Correlations between quantitative fat–water magnetic resonance imaging and computed tomography in human subcutaneous white adipose tissue

PubMed Central

Gifford, Aliya; Walker, Ronald C.; Towse, Theodore F.; Brian Welch, E.

2015-01-01

Abstract. Beyond estimation of depot volumes, quantitative analysis of adipose tissue properties could improve understanding of how adipose tissue correlates with metabolic risk factors. We investigated whether the fat signal fraction (FSF) derived from quantitative fat–water magnetic resonance imaging (MRI) scans at 3.0 T correlates to CT Hounsfield units (HU) of the same tissue. These measures were acquired in the subcutaneous white adipose tissue (WAT) at the umbilical level of 21 healthy adult subjects. A moderate correlation exists between MRI- and CT-derived WAT values for all subjects, R2=0.54, p<0.0001, with a slope of −2.6, (95% CI [−3.3,−1.8]), indicating that a decrease of 1 HU equals a mean increase of 0.38% FSF. We demonstrate that FSF estimates obtained using quantitative fat–water MRI techniques correlate with CT HU values in subcutaneous WAT, and therefore, MRI-based FSF could be used as an alternative to CT HU for assessing metabolic risk factors. PMID:26702407

Real-Time Assessment of Mechanical Tissue Trauma in Surgery.

PubMed

Chandler, James H; Mushtaq, Faisal; Moxley-Wyles, Benjamin; West, Nicholas P; Taylor, Gregory W; Culmer, Peter R

2017-10-01

This work presents a method to assess and prevent tissue trauma in real-time during surgery. Tissue trauma occurs routinely during laparoscopic surgery with potentially severe consequences. As such, it is crucial that a surgeon is able to regulate the pressure exerted by surgical instruments. We propose a novel method to assess the onset of tissue trauma by considering the mechanical response of tissue as it is loaded in real-time. We conducted a parametric study using a lab-based grasping model and differing load conditions. Mechanical stress-time data were analyzed to characterize the tissue response to grasps. Qualitative and quantitative histological analyses were performed to inspect damage characteristics of the tissue under different load conditions. These were correlated against the mechanical measures to identify the nature of trauma onset with respect to our predictive metric. Results showed increasing tissue trauma with load and a strong correlation with the mechanical response of the tissue. Load rate and load history also showed a clear effect on tissue response. The proposed method for trauma assessment was effective in identifying damage. The metric can be normalized with respect to loading rate and history, making it feasible in the unconstrained environment of intraoperative surgery. This work demonstrates that tissue trauma can be predicted using mechanical measures in real-time. Applying this technique to laparoscopic tools has the potential to reduce unnecessary tissue trauma and its associated complications by indicating through user feedback or actively regulating the mechanical impact of surgical instruments.

Quantitative Assessment of Effect of Preanalytic Cold Ischemic Time on Protein Expression in Breast Cancer Tissues

PubMed Central

2012-01-01

Background 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. Methods 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. Results 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. Conclusions 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

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

Inter- and intra-observer agreement of BI-RADS-based subjective visual estimation of amount of fibroglandular breast tissue with magnetic resonance imaging: comparison to automated quantitative assessment.

PubMed

Wengert, G J; Helbich, T H; Woitek, R; Kapetas, P; Clauser, P; Baltzer, P A; Vogl, W-D; Weber, M; Meyer-Baese, A; Pinker, Katja

2016-11-01

To evaluate the inter-/intra-observer agreement of BI-RADS-based subjective visual estimation of the amount of fibroglandular tissue (FGT) with magnetic resonance imaging (MRI), and to investigate whether FGT assessment benefits from an automated, observer-independent, quantitative MRI measurement by comparing both approaches. Eighty women with no imaging abnormalities (BI-RADS 1 and 2) were included in this institutional review board (IRB)-approved prospective study. All women underwent un-enhanced breast MRI. Four radiologists independently assessed FGT with MRI by subjective visual estimation according to BI-RADS. Automated observer-independent quantitative measurement of FGT with MRI was performed using a previously described measurement system. Inter-/intra-observer agreements of qualitative and quantitative FGT measurements were assessed using Cohen's kappa (k). Inexperienced readers achieved moderate inter-/intra-observer agreement and experienced readers a substantial inter- and perfect intra-observer agreement for subjective visual estimation of FGT. Practice and experience reduced observer-dependency. Automated observer-independent quantitative measurement of FGT was successfully performed and revealed only fair to moderate agreement (k = 0.209-0.497) with subjective visual estimations of FGT. Subjective visual estimation of FGT with MRI shows moderate intra-/inter-observer agreement, which can be improved by practice and experience. Automated observer-independent quantitative measurements of FGT are necessary to allow a standardized risk evaluation. • Subjective FGT estimation with MRI shows moderate intra-/inter-observer agreement in inexperienced readers. • Inter-observer agreement can be improved by practice and experience. • Automated observer-independent quantitative measurements can provide reliable and standardized assessment of FGT with MRI.

Quantitative fiber-optic Raman spectroscopy for tissue Raman measurements

NASA Astrophysics Data System (ADS)

Duraipandian, Shiyamala; Bergholt, Mads; Zheng, Wei; Huang, Zhiwei

2014-03-01

Molecular profiling of tissue using near-infrared (NIR) Raman spectroscopy has shown great promise for in vivo detection and prognostication of cancer. The Raman spectra measured from the tissue generally contain fundamental information about the absolute biomolecular concentrations in tissue and its changes associated with disease transformation. However, producing analogues tissue Raman spectra present a great technical challenge. In this preliminary study, we propose a method to ensure the reproducible tissue Raman measurements and validated with the in vivo Raman spectra (n=150) of inner lip acquired using different laser powers (i.e., 30 and 60 mW). A rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe was utilized for tissue Raman measurements. The investigational results showed that the variations between the spectra measured with different laser powers are almost negligible, facilitating the quantitative analysis of tissue Raman measurements in vivo.

Optical spectroscopy for quantitative sensing in human pancreatic tissues

NASA Astrophysics Data System (ADS)

Wilson, Robert H.; Chandra, Malavika; Lloyd, William; Chen, Leng-Chun; Scheiman, James; Simeone, Diane; McKenna, Barbara; Mycek, Mary-Ann

2011-07-01

Pancreatic adenocarcinoma has a five-year survival rate of only 6%, largely because current diagnostic methods cannot reliably detect the disease in its early stages. Reflectance and fluorescence spectroscopies have the potential to provide quantitative, minimally-invasive means of distinguishing pancreatic adenocarcinoma from normal pancreatic tissue and chronic pancreatitis. The first collection of wavelength-resolved reflectance and fluorescence spectra and time-resolved fluorescence decay curves from human pancreatic tissues was acquired with clinically-compatible instrumentation. Mathematical models of reflectance and fluorescence extracted parameters related to tissue morphology and biochemistry that were statistically significant for distinguishing between pancreatic tissue types. These results suggest that optical spectroscopy has the potential to detect pancreatic disease in a clinical setting.

A novel semi-quantitative method for measuring tissue bleeding.

PubMed

Vukcevic, G; Volarevic, V; Raicevic, S; Tanaskovic, I; Milicic, B; Vulovic, T; Arsenijevic, S

2014-03-01

In this study, we describe a new semi-quantitative method for measuring the extent of bleeding in pathohistological tissue samples. To test our novel method, we recruited 120 female patients in their first trimester of pregnancy and divided them into three groups of 40. Group I was the control group, in which no dilation was applied. Group II was an experimental group, in which dilation was performed using classical mechanical dilators. Group III was also an experimental group, in which dilation was performed using a hydraulic dilator. Tissue samples were taken from the patients' cervical canals using a Novak's probe via energetic single-step curettage prior to any dilation in Group I and after dilation in Groups II and III. After the tissue samples were prepared, light microscopy was used to obtain microphotographs at 100x magnification. The surfaces affected by bleeding were measured in the microphotographs using the Autodesk AutoCAD 2009 program and its "polylines" function. The lines were used to mark the area around the entire sample (marked A) and to create "polyline" areas around each bleeding area on the sample (marked B). The percentage of the total area affected by bleeding was calculated using the formula: N = Bt x 100 / At where N is the percentage (%) of the tissue sample surface affected by bleeding, At (A total) is the sum of the surfaces of all of the tissue samples and Bt (B total) is the sum of all the surfaces affected by bleeding in all of the tissue samples. This novel semi-quantitative method utilizes the Autodesk AutoCAD 2009 program, which is simple to use and widely available, thereby offering a new, objective and precise approach to estimate the extent of bleeding in tissue samples.

Development of two-photon fluorescence microscopy for quantitative imaging in turbid tissues

NASA Astrophysics Data System (ADS)

Coleno, Mariah Lee

Two-photon laser scanning fluorescence microscopy (TPM) is a high resolution, non-invasive biological imaging technique that can be used to image turbid tissues both in vitro and in vivo at depths of several hundred microns. Although TPM has been widely used to image tissue structures, no one has focused on using TPM to extract quantitative information from turbid tissues at depth. As a result, this thesis addresses the quantitative characterization of two-photon signals in turbid media. Initially, a two-photon microscope system is constructed, and two-photon images that validate system performance are obtained. Then TPM is established as an imaging technique that can be used to validate theoretical observations already listed in the literature. In particular, TPM is found to validate the exponential dependence of the fluorescence intensity decay with depth in turbid tissue model systems. Results from these studies next prompted experimental investigation into whether TPM could be used to determine tissue optical properties. Comparing the exponential dependence of the decay with a Monte Carlo model involving tissue optical properties, TPM is shown to be useful for determining the optical properties (total attenuation coefficient) of thick, turbid tissues on a small spatial scale. Next, a role for TPM for studying and optimizing wound healing is demonstrated. In particular, TPM is used to study the effects of perturbations (growth factors, PDT) on extracellular matrix remodeling in artificially engineered skin tissues. Results from these studies combined with tissue contraction studies are shown to demonstrate ways to modulate tissues to optimize the wound healing immune response and reduce scarring. In the end, TPM is shown to be an extremely important quantitative biological imaging technique that can be used to optimize wound repair.

Assessment of post-implantation integration of engineered tissues using fluorescence lifetime spectroscopy

NASA Astrophysics Data System (ADS)

Elahi, Sakib F.; Lee, Seung Y.; Lloyd, William R.; Chen, Leng-Chun; Kuo, Shiuhyang; Zhou, Ying; Kim, Hyungjin M.; Kennedy, Robert; Marcelo, Cynthia; Feinberg, Stephen E.; Mycek, Mary-Ann

2018-02-01

Clinical translation of engineered tissue constructs requires noninvasive methods to assess construct health and viability after implantation in patients. However, current practices to monitor post-implantation construct integration are either qualitative (visual assessment) or destructive (tissue histology). As label-free fluorescence lifetime sensing can noninvasively characterize pre-implantation construct viability, we employed a handheld fluorescence lifetime spectroscopy probe to quantitatively and noninvasively assess tissue constructs that were implanted in a murine model. We designed the system to be suitable for intravital measurements: portability, localization with precise maneuverability, and rapid data acquisition. Our model tissue constructs were manufactured from primary human cells to simulate patient variability and were stressed to create a range of health states. Secreted amounts of three cytokines that relate to cellular viability were measured in vitro to assess pre-implantation construct health. In vivo optical sensing assessed tissue integration of constructs at one-week and three-weeks post-implantation. At one-week post-implantation, optical parameters correlated with in vitro pre-implantation secretion levels of all three cytokines (p < 0.05). This relationship was no longer seen at three-weeks post-implantation, suggesting comparable tissue integration independent of preimplantation health. Histology confirmed re-epithelialization of these constructs independent of pre-implantation health state, supporting the lack of a correlation. These results suggest that clinical optical diagnostic tools based on label-free fluorescence lifetime sensing of endogenous tissue fluorophores could noninvasively monitor post-implantation integration of engineered tissues.

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

Resected Brain Tissue, Seizure Onset Zone and Quantitative EEG Measures: Towards Prediction of Post-Surgical Seizure Control

PubMed Central

Andrzejak, Ralph G.; Hauf, Martinus; Pollo, Claudio; Müller, Markus; Weisstanner, Christian; Wiest, Roland; Schindler, Kaspar

2015-01-01

Background Epilepsy surgery is a potentially curative treatment option for pharmacoresistent patients. If non-invasive methods alone do not allow to delineate the epileptogenic brain areas the surgical candidates undergo long-term monitoring with intracranial EEG. Visual EEG analysis is then used to identify the seizure onset zone for targeted resection as a standard procedure. Methods Despite of its great potential to assess the epileptogenicty of brain tissue, quantitative EEG analysis has not yet found its way into routine clinical practice. To demonstrate that quantitative EEG may yield clinically highly relevant information we retrospectively investigated how post-operative seizure control is associated with four selected EEG measures evaluated in the resected brain tissue and the seizure onset zone. Importantly, the exact spatial location of the intracranial electrodes was determined by coregistration of pre-operative MRI and post-implantation CT and coregistration with post-resection MRI was used to delineate the extent of tissue resection. Using data-driven thresholding, quantitative EEG results were separated into normally contributing and salient channels. Results In patients with favorable post-surgical seizure control a significantly larger fraction of salient channels in three of the four quantitative EEG measures was resected than in patients with unfavorable outcome in terms of seizure control (median over the whole peri-ictal recordings). The same statistics revealed no association with post-operative seizure control when EEG channels contributing to the seizure onset zone were studied. Conclusions We conclude that quantitative EEG measures provide clinically relevant and objective markers of target tissue, which may be used to optimize epilepsy surgery. The finding that differentiation between favorable and unfavorable outcome was better for the fraction of salient values in the resected brain tissue than in the seizure onset zone is consistent

Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs.

PubMed

Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P; Schrooten, Jan; Geris, Liesbet

2015-01-01

To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial 'design of experiments' approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology.

Assessment of bioburden on human and animal tissues: part 2--results of testing of human tissue and qualification of a composite sample for routine bioburden determination.

PubMed

Kowalski, John B; Merritt, Karen; Gocke, David; Osborne, Joel

2012-08-01

A quantitative method was developed and validated to assess bioburden on tissue from human donors and to compare bioburden determination results to swab culture results from the same donor. An initial study with allograft tissue from 101 donors showed a wide range of bioburden levels; values from no colony-forming units (CFU) detected to >28,000 CFU were observed. Tissues from donors that had swab cultures negative for objectionable microorganisms generally had lower bioburden than tissues from donors where objectionable microorganisms were recovered by swab culturing. In a follow-up study with 1,445 donors, a wide range of bioburden levels was again observed on tissues from donors that were swab culture negative for objectionable microorganisms. Tissues from 885 (61%) of these donors had no recoverable bioburden (<2 CFU). Importantly, tissues from 560 (39%) of the donors had recoverable bioburden which ranged from 1 to >24,000 CFU. Identification of bioburden isolates showed a diversity of genera and species. In compliance with the recent revision of the American Association of Tissue Banks K2.210 Standard, the quantitative bioburden determination method was validated with a composite tissue sample that contains bone and soft tissue sections tested together in one extraction vessel. A recovery efficiency of 68% was validated and the composite sample was shown to be representative of all of the tissues recovered from a donor. The use of the composite sample in conjunction with the quantitative bioburden determination method will facilitate an accurate assessment of the numbers and types of contaminating microorganisms on allografts prior to disinfection/sterilization. This information will ensure that disinfection/sterilization processes are properly validated and the capability of the overall allograft process is understood on a donor by donor basis.

Adipose tissue MRI for quantitative measurement of central obesity.

PubMed

Poonawalla, Aziz H; Sjoberg, Brett P; Rehm, Jennifer L; Hernando, Diego; Hines, Catherine D; Irarrazaval, Pablo; Reeder, Scott B

2013-03-01

To validate adipose tissue magnetic resonance imaging (atMRI) for rapid, quantitative volumetry of visceral adipose tissue (VAT) and total adipose tissue (TAT). Data were acquired on normal adults and clinically overweight girls with Institutional Review Board (IRB) approval/parental consent using sagittal 6-echo 3D-spoiled gradient-echo (SPGR) (26-sec single-breath-hold) at 3T. Fat-fraction images were reconstructed with quantitative corrections, permitting measurement of a physiologically based fat-fraction threshold in normals to identify adipose tissue, for automated measurement of TAT, and semiautomated measurement of VAT. TAT accuracy was validated using oil phantoms and in vivo TAT/VAT measurements validated with manual segmentation. Group comparisons were performed between normals and overweight girls using TAT, VAT, VAT-TAT-ratio (VTR), body-mass-index (BMI), waist circumference, and waist-hip-ratio (WHR). Oil phantom measurements were highly accurate (<3% error). The measured adipose fat-fraction threshold was 96% ± 2%. VAT and TAT correlated strongly with manual segmentation (normals r(2) ≥ 0.96, overweight girls r(2) ≥ 0.99). VAT segmentation required 30 ± 11 minutes/subject (14 ± 5 sec/slice) using atMRI, versus 216 ± 73 minutes/subject (99 ± 31 sec/slice) manually. Group discrimination was significant using WHR (P < 0.001) and VTR (P = 0.004). The atMRI technique permits rapid, accurate measurements of TAT, VAT, and VTR. Copyright © 2012 Wiley Periodicals, Inc.

Translating Periosteum's Regenerative Power: Insights From Quantitative Analysis of Tissue Genesis With a Periosteum Substitute Implant

PubMed Central

Moore, Shannon R.; Heu, Céline; Yu, Nicole Y.C.; Whan, Renee M.; Knothe, Ulf R.; Milz, Stefan

2016-01-01

empirically in surgery to repair tissues as diverse as trachea and bone. In the past 25 years, the number of articles indexed in PubMed for the keywords “periosteum and tissue engineering” and “periosteum and regenerative medicine” has burgeoned. Yet the biggest limitation to the prescriptive use of periosteum is lack of easy access, giving impetus to the development of periosteum substitutes. Recent studies have opened up the possibility to bank periosteal tissues (e.g., from the femoral neck during routine resection for implantation of hip replacements). This study used an interdisciplinary, quantitative approach to assess tissue genesis in modular periosteum substitute implants, with the aim to provide translational strategies for regenerative medicine and tissue engineering. PMID:27465072

Translating Periosteum's Regenerative Power: Insights From Quantitative Analysis of Tissue Genesis With a Periosteum Substitute Implant.

PubMed

Moore, Shannon R; Heu, Céline; Yu, Nicole Y C; Whan, Renee M; Knothe, Ulf R; Milz, Stefan; Knothe Tate, Melissa L

2016-12-01

in surgery to repair tissues as diverse as trachea and bone. In the past 25 years, the number of articles indexed in PubMed for the keywords "periosteum and tissue engineering" and "periosteum and regenerative medicine" has burgeoned. Yet the biggest limitation to the prescriptive use of periosteum is lack of easy access, giving impetus to the development of periosteum substitutes. Recent studies have opened up the possibility to bank periosteal tissues (e.g., from the femoral neck during routine resection for implantation of hip replacements). This study used an interdisciplinary, quantitative approach to assess tissue genesis in modular periosteum substitute implants, with the aim to provide translational strategies for regenerative medicine and tissue engineering. ©AlphaMed Press.

Assessing Quantitative Resistance against Leptosphaeria maculans (Phoma Stem Canker) in Brassica napus (Oilseed Rape) in Young Plants

PubMed Central

Huang, Yong-Ju; Qi, Aiming; King, Graham J.; Fitt, Bruce D. L.

2014-01-01

Quantitative resistance against Leptosphaeria maculans in Brassica napus is difficult to assess in young plants due to the long period of symptomless growth of the pathogen from the appearance of leaf lesions to the appearance of canker symptoms on the stem. By using doubled haploid (DH) lines A30 (susceptible) and C119 (with quantitative resistance), quantitative resistance against L. maculans was assessed in young plants in controlled environments at two stages: stage 1, growth of the pathogen along leaf veins/petioles towards the stem by leaf lamina inoculation; stage 2, growth in stem tissues to produce stem canker symptoms by leaf petiole inoculation. Two types of inoculum (ascospores; conidia) and three assessment methods (extent of visible necrosis; symptomless pathogen growth visualised using the GFP reporter gene; amount of pathogen DNA quantified by PCR) were used. In stage 1 assessments, significant differences were observed between lines A30 and C119 in area of leaf lesions, distance grown along veins/petioles assessed by visible necrosis or by viewing GFP and amount of L. maculans DNA in leaf petioles. In stage 2 assessments, significant differences were observed between lines A30 and C119 in severity of stem canker and amount of L. maculans DNA in stem tissues. GFP-labelled L. maculans spread more quickly from the stem cortex to the stem pith in A30 than in C119. Stem canker symptoms were produced more rapidly by using ascospore inoculum than by using conidial inoculum. These results suggest that quantitative resistance against L. maculans in B. napus can be assessed in young plants in controlled conditions. Development of methods to phenotype quantitative resistance against plant pathogens in young plants in controlled environments will help identification of stable quantitative resistance for control of crop diseases. PMID:24454767

Tissue Quality Assessment Using a Novel Direct Elasticity Assessment Device (The E-Finger): A Cadaveric Study of Prostatectomy Dissection

PubMed Central

Good, Daniel W.; Khan, Ashfaq; Hammer, Steven; Scanlan, Paul; Shu, Wenmiao; Phipps, Simon; Parson, Simon H.; Stewart, Grant D.; Reuben, Robert; McNeill, S. Alan

2014-01-01

Introduction Minimally invasive radical prostatectomy (RP) (robotic and laparoscopic), have brought improvements in the outcomes of RP due to improved views and increased degrees of freedom of surgical devices. Robotic and laparoscopic surgeries do not incorporate haptic feedback, which may result in complications secondary to inadequate tissue dissection (causing positive surgical margins, rhabdosphincter damage, etc). We developed a micro-engineered device (6 mm2 sized) [E-finger]) capable of quantitative elasticity assessment, with amplitude ratio, mean ratio and phase lag representing this. The aim was to assess the utility of the device in differentiating peri-prostatic tissue types in order to guide prostate dissection. Material and Methods Two embalmed and 2 fresh frozen cadavers were used in the study. Baseline elasticity values were assessed in bladder, prostate and rhabdosphincter of pre-dissected embalmed cadavers using the micro-engineered device. A measurement grid was created to span from the bladder, across the prostate and onto the rhabdosphincter of fresh frozen cadavers to enable a systematic quantitative elasticity assessment of the entire area by 2 independent assessors. Tissue was sectioned along each row of elasticity measurement points, and stained with haematoxylin and eosin (H&E). Image analysis was performed with Image Pro Premier to determine the histology at each measurement point. Results Statistically significant differences in elasticity were identified between bladder, prostate and sphincter in both embalmed and fresh frozen cadavers (p = <0.001). Intra-class correlation (ICC) reliability tests showed good reliability (average ICC = 0.851). Sensitivity and specificity for tissue identification was 77% and 70% respectively to a resolution of 6 mm2. Conclusions This cadaveric study has evaluated the ability of our elasticity assessment device to differentiate bladder, prostate and rhabdosphincter to a resolution of 6 mm2. The

Quantitative breast tissue characterization using grating-based x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Willner, M.; Herzen, J.; Grandl, S.; Auweter, S.; Mayr, D.; Hipp, A.; Chabior, M.; Sarapata, A.; Achterhold, K.; Zanette, I.; Weitkamp, T.; Sztrókay, A.; Hellerhoff, K.; Reiser, M.; Pfeiffer, F.

2014-04-01

X-ray phase-contrast imaging has received growing interest in recent years due to its high capability in visualizing soft tissue. Breast imaging became the focus of particular attention as it is considered the most promising candidate for a first clinical application of this contrast modality. In this study, we investigate quantitative breast tissue characterization using grating-based phase-contrast computed tomography (CT) at conventional polychromatic x-ray sources. Different breast specimens have been scanned at a laboratory phase-contrast imaging setup and were correlated to histopathology. Ascertained tumor types include phylloides tumor, fibroadenoma and infiltrating lobular carcinoma. Identified tissue types comprising adipose, fibroglandular and tumor tissue have been analyzed in terms of phase-contrast Hounsfield units and are compared to high-quality, high-resolution data obtained with monochromatic synchrotron radiation, as well as calculated values based on tabulated tissue properties. The results give a good impression of the method’s prospects and limitations for potential tumor detection and the associated demands on such a phase-contrast breast CT system. Furthermore, the evaluated quantitative tissue values serve as a reference for simulations and the design of dedicated phantoms for phase-contrast mammography.

Quantitation of spatially-localized proteins in tissue samples using MALDI-MRM imaging.

PubMed

Clemis, Elizabeth J; Smith, Derek S; Camenzind, Alexander G; Danell, Ryan M; Parker, Carol E; Borchers, Christoph H

2012-04-17

MALDI imaging allows the creation of a "molecular image" of a tissue slice. This image is reconstructed from the ion abundances in spectra obtained while rastering the laser over the tissue. These images can then be correlated with tissue histology to detect potential biomarkers of, for example, aberrant cell types. MALDI, however, is known to have problems with ion suppression, making it difficult to correlate measured ion abundance with concentration. It would be advantageous to have a method which could provide more accurate protein concentration measurements, particularly for screening applications or for precise comparisons between samples. In this paper, we report the development of a novel MALDI imaging method for the localization and accurate quantitation of proteins in tissues. This method involves optimization of in situ tryptic digestion, followed by reproducible and uniform deposition of an isotopically labeled standard peptide from a target protein onto the tissue, using an aerosol-generating device. Data is acquired by MALDI multiple reaction monitoring (MRM) mass spectrometry (MS), and accurate peptide quantitation is determined from the ratio of MRM transitions for the endogenous unlabeled proteolytic peptides to the corresponding transitions from the applied isotopically labeled standard peptides. In a parallel experiment, the quantity of the labeled peptide applied to the tissue was determined using a standard curve generated from MALDI time-of-flight (TOF) MS data. This external calibration curve was then used to determine the quantity of endogenous peptide in a given area. All standard curves generate by this method had coefficients of determination greater than 0.97. These proof-of-concept experiments using MALDI MRM-based imaging show the feasibility for the precise and accurate quantitation of tissue protein concentrations over 2 orders of magnitude, while maintaining the spatial localization information for the proteins.

Application of biospeckles for assessment of structural and cellular changes in muscle tissue

NASA Astrophysics Data System (ADS)

Maksymenko, Oleksandr P.; Muravsky, Leonid I.; Berezyuk, Mykola I.

2015-09-01

A modified spatial-temporal speckle correlation technique for operational assessment of structural changes in muscle tissues after slaughtering is considered. Coefficient of biological activity as a quantitative indicator of structural changes of biochemical processes in biological tissues is proposed. The experimental results have shown that this coefficient properly evaluates the biological activity of pig and chicken muscle tissue samples. Studying the degradation processes in muscle tissue during long-time storage in a refrigerator by measuring the spatial-temporal dynamics of biospeckle patterns is carried out. The reduction of the bioactivity level of refrigerated muscle tissue samples connected with the initiation of muscle fiber cracks and ruptures, reduction of sarcomeres, nuclei deformation, nuclear chromatin diminishing, and destruction of mitochondria is analyzed.

Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

PubMed

Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2013-12-03

We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

Assessment of Renal Hemodynamics and Oxygenation by Simultaneous Magnetic Resonance Imaging (MRI) and Quantitative Invasive Physiological Measurements.

PubMed

Cantow, Kathleen; Arakelyan, Karen; Seeliger, Erdmann; Niendorf, Thoralf; Pohlmann, Andreas

2016-01-01

In vivo assessment of renal perfusion and oxygenation under (patho)physiological conditions by means of noninvasive diagnostic imaging is conceptually appealing. Blood oxygen level-dependent (BOLD) magnetic resonance imaging (MRI) and quantitative parametric mapping of the magnetic resonance (MR) relaxation times T 2* and T 2 are thought to provide surrogates of renal tissue oxygenation. The validity and efficacy of this technique for quantitative characterization of local tissue oxygenation and its changes under different functional conditions have not been systematically examined yet and remain to be established. For this purpose, the development of an integrative multimodality approaches is essential. Here we describe an integrated hybrid approach (MR-PHYSIOL) that combines established quantitative physiological measurements with T 2* (T 2) mapping and MR-based kidney size measurements. Standardized reversible (patho)physiologically relevant interventions, such as brief periods of aortic occlusion, hypoxia, and hyperoxia, are used for detailing the relation between the MR-PHYSIOL parameters, in particular between renal T 2* and tissue oxygenation.

Epithelium percentage estimation facilitates epithelial quantitative protein measurement in tissue specimens.

PubMed

Chen, Jing; Toghi Eshghi, Shadi; Bova, George Steven; Li, Qing Kay; Li, Xingde; Zhang, Hui

2013-12-01

The rapid advancement of high-throughput tools for quantitative measurement of proteins has demonstrated the potential for the identification of proteins associated with cancer. However, the quantitative results on cancer tissue specimens are usually confounded by tissue heterogeneity, e.g. regions with cancer usually have significantly higher epithelium content yet lower stromal content. It is therefore necessary to develop a tool to facilitate the interpretation of the results of protein measurements in tissue specimens. Epithelial cell adhesion molecule (EpCAM) and cathepsin L (CTSL) are two epithelial proteins whose expressions in normal and tumorous prostate tissues were confirmed by measuring staining intensity with immunohistochemical staining (IHC). The expressions of these proteins were measured by ELISA in protein extracts from OCT embedded frozen prostate tissues. To eliminate the influence of tissue heterogeneity on epithelial protein quantification measured by ELISA, a color-based segmentation method was developed in-house for estimation of epithelium content using H&E histology slides from the same prostate tissues and the estimated epithelium percentage was used to normalize the ELISA results. The epithelium contents of the same slides were also estimated by a pathologist and used to normalize the ELISA results. The computer based results were compared with the pathologist's reading. We found that both EpCAM and CTSL levels, measured by ELISA assays itself, were greatly affected by epithelium content in the tissue specimens. Without adjusting for epithelium percentage, both EpCAM and CTSL levels appeared significantly higher in tumor tissues than normal tissues with a p value less than 0.001. However, after normalization by the epithelium percentage, ELISA measurements of both EpCAM and CTSL were in agreement with IHC staining results, showing a significant increase only in EpCAM with no difference in CTSL expression in cancer tissues. These results

Quantitative analysis of the effect of environmental-scanning electron microscopy on collagenous tissues.

PubMed

Lee, Woowon; Toussaint, Kimani C

2018-05-31

Environmental-scanning electron microscopy (ESEM) is routinely applied to various biological samples due to its ability to maintain a wet environment while imaging; moreover, the technique obviates the need for sample coating. However, there is limited research carried out on electron-beam (e-beam) induced tissue damage resulting from using the ESEM. In this paper, we use quantitative second-harmonic generation (SHG) microscopy to examine the effects of e-beam exposure from the ESEM on collagenous tissue samples prepared as either fixed, frozen, wet or dehydrated. Quantitative SHG analysis of tissues, before and after ESEM e-beam exposure in low-vacuum mode, reveals evidence of cross-linking of collagen fibers, however there are no structural differences observed in fixed tissue. Meanwhile wet-mode ESEM appears to radically alter the structure from a regular fibrous arrangement to a more random fiber orientation. We also confirm that ESEM images of collagenous tissues show higher spatial resolution compared to SHG microscopy, but the relative tradeoff with collagen specificity reduces its effectiveness in quantifying collagen fiber organization. Our work provides insight on both the limitations of the ESEM for tissue imaging, and the potential opportunity to use as a complementary technique when imaging fine features in the non-collagenous regions of tissue samples.

Teaching quantitative biology: goals, assessments, and resources

PubMed Central

Aikens, Melissa L.; Dolan, Erin L.

2014-01-01

More than a decade has passed since the publication of BIO2010, calling for an increased emphasis on quantitative skills in the undergraduate biology curriculum. In that time, relatively few papers have been published that describe educational innovations in quantitative biology or provide evidence of their effects on students. Using a “backward design” framework, we lay out quantitative skill and attitude goals, assessment strategies, and teaching resources to help biologists teach more quantitatively. Collaborations between quantitative biologists and education researchers are necessary to develop a broader and more appropriate suite of assessment tools, and to provide much-needed evidence on how particular teaching strategies affect biology students' quantitative skill development and attitudes toward quantitative work. PMID:25368425

Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissues

PubMed Central

Kennedy, Jacob J.; Whiteaker, Jeffrey R.; Schoenherr, Regine M.; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N.; Baird, Geoffrey Stuart; Paulovich, Amanda G.

2016-01-01

Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin embedded (FFPE) tissues. While the feasibility of using targeted, multiple reaction monitoring-mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e. 9 processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R2 = 0.94) and immuno-MRM (R2 = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens. PMID:27462933

Mapping of thermal injury in biologic tissues using quantitative pathologic techniques

NASA Astrophysics Data System (ADS)

Thomsen, Sharon L.

1999-05-01

Qualitative and quantitative pathologic techniques can be used for (1) mapping of thermal injury, (2) comparisons lesion sizes and configurations for different instruments or heating sources and (3) comparisons of treatment effects. Concentric zones of thermal damage form around a single volume heat source. The boundaries between some of these zones are distinct and measurable. Depending on the energy deposition, heating times and tissue type, the zones can include the following beginning at the hotter center and progressing to the cooler periphery: (1) tissue ablation, (2) carbonization, (3) tissue water vaporization, (4) structural protein denaturation (thermal coagulation), (5) vital enzyme protein denaturation, (6) cell membrane disruption, (7) hemorrhage, hemostasis and hyperhemia, (8) tissue necrosis and (9) wound organization and healing.

A method for operative quantitative interpretation of multispectral images of biological tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.

2013-10-01

A method for operative retrieval of spatial distributions of biophysical parameters of a biological tissue by using a multispectral image of it has been developed. The method is based on multiple regressions between linearly independent components of the diffuse reflection spectrum of the tissue and unknown parameters. Possibilities of the method are illustrated by an example of determining biophysical parameters of the skin (concentrations of melanin, hemoglobin and bilirubin, blood oxygenation, and scattering coefficient of the tissue). Examples of quantitative interpretation of the experimental data are presented.

Quantitative real-time optical imaging of the tissue metabolic rate of oxygen consumption

NASA Astrophysics Data System (ADS)

Ghijsen, Michael; Lentsch, Griffin R.; Gioux, Sylvain; Brenner, Matthew; Durkin, Anthony J.; Choi, Bernard; Tromberg, Bruce J.

2018-03-01

The tissue metabolic rate of oxygen consumption (tMRO2) is a clinically relevant marker for a number of pathologies including cancer and arterial occlusive disease. We present and validate a noncontact method for quantitatively mapping tMRO2 over a wide, scalable field of view at 16 frames / s. We achieve this by developing a dual-wavelength, near-infrared coherent spatial frequency-domain imaging (cSFDI) system to calculate tissue optical properties (i.e., absorption, μa, and reduced scattering, μs‧, parameters) as well as the speckle flow index (SFI) at every pixel. Images of tissue oxy- and deoxyhemoglobin concentration ( [ HbO2 ] and [HHb]) are calculated from optical properties and combined with SFI to calculate tMRO2. We validate the system using a series of yeast-hemoglobin tissue-simulating phantoms and conduct in vivo tests in humans using arterial occlusions that demonstrate sensitivity to tissue metabolic oxygen debt and its repayment. Finally, we image the impact of cyanide exposure and toxicity reversal in an in vivo rabbit model showing clear instances of mitochondrial uncoupling and significantly diminished tMRO2. We conclude that dual-wavelength cSFDI provides rapid, quantitative, wide-field mapping of tMRO2 that can reveal unique spatial and temporal dynamics relevant to tissue pathology and viability.

Quantitative Characterization of Tissue Microstructure with Temporal Diffusion Spectroscopy

PubMed Central

Xu, Junzhong; Does, Mark D.; Gore, John C.

2009-01-01

The signals recorded by diffusion-weighted magnetic resonance imaging (DWI) are dependent on the micro-structural properties of biological tissues, so it is possible to obtain quantitative structural information non-invasively from such measurements. Oscillating gradient spin echo (OGSE) methods have the ability to probe the behavior of water diffusion over different time scales and the potential to detect variations in intracellular structure. To assist in the interpretation of OGSE data, analytical expressions have been derived for diffusion-weighted signals with OGSE methods for restricted diffusion in some typical structures, including parallel planes, cylinders and spheres, using the theory of temporal diffusion spectroscopy. These analytical predictions have been confirmed with computer simulations. These expressions suggest how OGSE signals from biological tissues should be analyzed to characterize tissue microstructure, including how to estimate cell nuclear sizes. This approach provides a model to interpret diffusion data obtained from OGSE measurements that can be used for applications such as monitoring tumor response to treatment in vivo. PMID:19616979

A quantitative framework for assessing ecological resilience

EPA Science Inventory

Quantitative approaches to measure and assess resilience are needed to bridge gaps between science, policy, and management. In this paper, we suggest a quantitative framework for assessing ecological resilience. Ecological resilience as an emergent ecosystem phenomenon can be de...

Evaluation of telomere length in human cardiac tissues using cardiac quantitative FISH.

PubMed

Sharifi-Sanjani, Maryam; Meeker, Alan K; Mourkioti, Foteini

2017-09-01

Telomere length has been correlated with various diseases, including cardiovascular disease and cancer. The use of currently available telomere-length measurement techniques is often restricted by the requirement of a large amount of cells (Southern-based techniques) or the lack of information on individual cells or telomeres (PCR-based methods). Although several methods have been used to measure telomere length in tissues as a whole, the assessment of cell-type-specific telomere length provides valuable information on individual cell types. The development of fluorescence in situ hybridization (FISH) technologies enables the quantification of telomeres in individual chromosomes, but the use of these methods is dependent on the availability of isolated cells, which prevents their use with fixed archival samples. Here we describe an optimized quantitative FISH (Q-FISH) protocol for measuring telomere length that bypasses the previous limitations by avoiding contributions from undesired cell types. We have used this protocol on small paraffin-embedded cardiac-tissue samples. This protocol describes step-by-step procedures for tissue preparation, permeabilization, cardiac-tissue pretreatment and hybridization with a Cy3-labeled telomeric repeat complementing (CCCTAA) 3 peptide nucleic acid (PNA) probe coupled with cardiac-specific antibody staining. We also describe how to quantify telomere length by means of the fluorescence intensity and area of each telomere within individual nuclei. This protocol provides comparative cell-type-specific telomere-length measurements in relatively small human cardiac samples and offers an attractive technique to test hypotheses implicating telomere length in various cardiac pathologies. The current protocol (from tissue collection to image procurement) takes ∼28 h along with three overnight incubations. We anticipate that the protocol could be easily adapted for use on different tissue types.

Optical coherence tomography can assess skeletal muscle tissue from mouse models of muscular dystrophy by parametric imaging of the attenuation coefficient

PubMed Central

Klyen, Blake R.; Scolaro, Loretta; Shavlakadze, Tea; Grounds, Miranda D.; Sampson, David D.

2014-01-01

We present the assessment of ex vivo mouse muscle tissue by quantitative parametric imaging of the near-infrared attenuation coefficient µt using optical coherence tomography. The resulting values of the local total attenuation coefficient µt (mean ± standard error) from necrotic lesions in the dystrophic skeletal muscle tissue of mdx mice are higher (9.6 ± 0.3 mm−1) than regions from the same tissue containing only necrotic myofibers (7.0 ± 0.6 mm−1), and significantly higher than values from intact myofibers, whether from an adjacent region of the same sample (4.8 ± 0.3 mm−1) or from healthy tissue of the wild-type C57 mouse (3.9 ± 0.2 mm−1) used as a control. Our results suggest that the attenuation coefficient could be used as a quantitative means to identify necrotic lesions and assess skeletal muscle tissue in mouse models of human Duchenne muscular dystrophy. PMID:24761302

23.4% saline decreases brain tissue volume in severe hepatic encephalopathy as assessed by a quantitative computed tomography marker

PubMed Central

Liotta, Eric M; Lizza, Bryan D; Romanova, Anna L; Guth, James C; Berman, Michael D; Carroll, Timothy J; Francis, Brandon; Ganger, Daniel; Ladner, Daniela P; Maas, Matthew B; Naidech, Andrew M

2016-01-01

Objective Cerebral edema is common in severe hepatic encephalopathy and may be life-threatening. Bolus 23.4% hypertonic saline (HTS) improves surveillance neuromonitoring scores, although its mechanism of action is not clearly established. We investigated the hypothesis that bolus HTS decreases cerebral edema in severe hepatic encephalopathy utilizing a quantitative technique to measure brain and CSF volume changes. Design Retrospective analysis of serial computed tomography (CT) scans and clinical data for a case-control series was performed. Setting Intensive care units of a tertiary care hospital. Patients Patients with severe hepatic encephalopathy treated with 23.4% HTS and control patients who did not receive 23.4% HTS. Methods We used clinically obtained CT scans to measure volumes of the ventricles, intracranial CSF, and brain using a previously validated semi-automated technique (Analyze Direct; Overland Park, KS). Volumes before and after 23.4% HTS were compared with Wilcoxon signed-rank test. Associations between total CSF volume, ventricular volume, serum sodium, and Glasgow Coma Scale Scores were assessed using Spearman correlation. Results Eleven patients with 18 administrations of 23.4% HTS met inclusion criteria. Total CSF (median 47.6 [35.1–69.4] to 61.9 [47.7–87.0] mL, p<0.001) and ventricular volumes (median 8.0 [6.9–9.5] to 9.2 [7.8–11.9] mL, p=0.002) increased and Glasgow Coma Scale Scores improved (median 4 [3–6] to 7 [6–9], p=0.008) after 23.4% HTS. In contrast, total CSF and ventricular volumes decreased in untreated control patients. Serum sodium increase was associated with increase in total CSF volume (r=0.83, p<0.001) and change in total CSF volume was associated with ventricular volume change (r=0.86, p<0.001). Conclusions Total CSF and ventricular volumes increased after 23.4% HTS, consistent with a reduction in brain tissue volume. Total CSF and ventricular volume change may be useful quantitative measures to assess

Accuracy of quantitative visual soil assessment

NASA Astrophysics Data System (ADS)

van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

2016-04-01

Visual soil assessment (VSA) is a method to assess soil quality visually, when standing in the field. VSA is increasingly used by farmers, farm organisations and companies, because it is rapid and cost-effective, and because looking at soil provides understanding about soil functioning. Often VSA is regarded as subjective, so there is a need to verify VSA. Also, many VSAs have not been fine-tuned for contrasting soil types. This could lead to wrong interpretation of soil quality and soil functioning when contrasting sites are compared to each other. We wanted to assess accuracy of VSA, while taking into account soil type. The first objective was to test whether quantitative visual field observations, which form the basis in many VSAs, could be validated with standardized field or laboratory measurements. The second objective was to assess whether quantitative visual field observations are reproducible, when used by observers with contrasting backgrounds. For the validation study, we made quantitative visual observations at 26 cattle farms. Farms were located at sand, clay and peat soils in the North Friesian Woodlands, the Netherlands. Quantitative visual observations evaluated were grass cover, number of biopores, number of roots, soil colour, soil structure, number of earthworms, number of gley mottles and soil compaction. Linear regression analysis showed that four out of eight quantitative visual observations could be well validated with standardized field or laboratory measurements. The following quantitative visual observations correlated well with standardized field or laboratory measurements: grass cover with classified images of surface cover; number of roots with root dry weight; amount of large structure elements with mean weight diameter; and soil colour with soil organic matter content. Correlation coefficients were greater than 0.3, from which half of the correlations were significant. For the reproducibility study, a group of 9 soil scientists and 7

Towards quantitative assessment of calciphylaxis

NASA Astrophysics Data System (ADS)

Deserno, Thomas M.; Sárándi, István.; Jose, Abin; Haak, Daniel; Jonas, Stephan; Specht, Paula; Brandenburg, Vincent

2014-03-01

Calciphylaxis is a rare disease that has devastating conditions associated with high morbidity and mortality. Calciphylaxis is characterized by systemic medial calcification of the arteries yielding necrotic skin ulcerations. In this paper, we aim at supporting the installation of multi-center registries for calciphylaxis, which includes a photographic documentation of skin necrosis. However, photographs acquired in different centers under different conditions using different equipment and photographers cannot be compared quantitatively. For normalization, we use a simple color pad that is placed into the field of view, segmented from the image, and its color fields are analyzed. In total, 24 colors are printed on that scale. A least-squares approach is used to determine the affine color transform. Furthermore, the card allows scale normalization. We provide a case study for qualitative assessment. In addition, the method is evaluated quantitatively using 10 images of two sets of different captures of the same necrosis. The variability of quantitative measurements based on free hand photography is assessed regarding geometric and color distortions before and after our simple calibration procedure. Using automated image processing, the standard deviation of measurements is significantly reduced. The coefficients of variations yield 5-20% and 2-10% for geometry and color, respectively. Hence, quantitative assessment of calciphylaxis becomes practicable and will impact a better understanding of this rare but fatal disease.

Assessment of cancer and virus antigens for cross-reactivity in human tissues.

PubMed

Jaravine, Victor; Raffegerst, Silke; Schendel, Dolores J; Frishman, Dmitrij

2017-01-01

Cross-reactivity (CR) or invocation of autoimmune side effects in various tissues has important safety implications in adoptive immunotherapy directed against selected antigens. The ability to predict CR (on-target and off-target toxicities) may help in the early selection of safer therapeutically relevant target antigens. We developed a methodology for the calculation of quantitative CR for any defined peptide epitope. Using this approach, we performed assessment of 4 groups of 283 currently known human MHC-class-I epitopes including differentiation antigens, overexpressed proteins, cancer-testis antigens and mutations displayed by tumor cells. In addition, 89 epitopes originating from viral sources were investigated. The natural occurrence of these epitopes in human tissues was assessed based on proteomics abundance data, while the probability of their presentation by MHC-class-I molecules was modelled by the method of Keşmir et al. which combines proteasomal cleavage, TAP affinity and MHC-binding predictions. The results of these analyses for many previously defined peptides are presented as CR indices and tissue profiles. The methodology thus allows for quantitative comparisons of epitopes and is suggested to be suited for the assessment of epitopes of candidate antigens in an early stage of development of adoptive immunotherapy. Our method is implemented as a Java program, with curated datasets stored in a MySQL database. It predicts all naturally possible self-antigens for a given sequence of a therapeutic antigen (or epitope) and after filtering for predicted immunogenicity outputs results as an index and profile of CR to the self-antigens in 22 human tissues. The program is implemented as part of the iCrossR webserver, which is publicly available at http://webclu.bio.wzw.tum.de/icrossr/ CONTACT: d.frishman@wzw.tum.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press

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

PubMed Central

Li, Weizhe; Germain, Ronald N.

2017-01-01

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

Quantitative assessment of soft tissue deformation using digital speckle pattern interferometry: studies on phantom breast models.

PubMed

Karuppanan, Udayakumar; Unni, Sujatha Narayanan; Angarai, Ganesan R

2017-01-01

Assessment of mechanical properties of soft matter is a challenging task in a purely noninvasive and noncontact environment. As tissue mechanical properties play a vital role in determining tissue health status, such noninvasive methods offer great potential in framing large-scale medical screening strategies. The digital speckle pattern interferometry (DSPI)-based image capture and analysis system described here is capable of extracting the deformation information from a single acquired fringe pattern. Such a method of analysis would be required in the case of the highly dynamic nature of speckle patterns derived from soft tissues while applying mechanical compression. Soft phantoms mimicking breast tissue optical and mechanical properties were fabricated and tested in the DSPI out of plane configuration set up. Hilbert transform (HT)-based image analysis algorithm was developed to extract the phase and corresponding deformation of the sample from a single acquired fringe pattern. The experimental fringe contours were found to correlate with numerically simulated deformation patterns of the sample using Abaqus finite element analysis software. The extracted deformation from the experimental fringe pattern using the HT-based algorithm is compared with the deformation value obtained using numerical simulation under similar conditions of loading and the results are found to correlate with an average %error of 10. The proposed method is applied on breast phantoms fabricated with included subsurface anomaly mimicking cancerous tissue and the results are analyzed.

Assessment of Intervertebral Disc Degeneration Based on Quantitative MRI Analysis: an in vivo study

PubMed Central

Grunert, Peter; Hudson, Katherine D.; Macielak, Michael R.; Aronowitz, Eric; Borde, Brandon H.; Alimi, Marjan; Njoku, Innocent; Ballon, Douglas; Tsiouris, Apostolos John; Bonassar, Lawrence J.; Härtl, Roger

2015-01-01

Study design Animal experimental study Objective To evaluate a novel quantitative imaging technique for assessing disc degeneration. Summary of Background Data T2-relaxation time (T2-RT) measurements have been used to quantitatively assess disc degeneration. T2 values correlate with the water content of inter vertebral disc tissue and thereby allow for the indirect measurement of nucleus pulposus (NP) hydration. Methods We developed an algorithm to subtract out MRI voxels not representing NP tissue based on T2-RT values. Filtered NP voxels were used to measure nuclear size by their amount and nuclear hydration by their mean T2-RT. This technique was applied to 24 rat-tail intervertebral discs’ (IVDs), which had been punctured with an 18-gauge needle according to different techniques to induce varying degrees of degeneration. NP voxel count and average T2-RT were used as parameters to assess the degeneration process at 1 and 3 months post puncture. NP voxel counts were evaluated against X-ray disc height measurements and qualitative MRI studies based on the Pfirrmann grading system. Tails were collected for histology to correlate NP voxel counts to histological disc degeneration grades and to NP cross-sectional area measurements. Results NP voxel count measurements showed strong correlations to qualitative MRI analyses (R2=0.79, p<0.0001), histological degeneration grades (R2=0.902, p<0.0001) and histological NP cross-sectional area measurements (R2=0.887, p<0.0001). In contrast to NP voxel counts, the mean T2-RT for each punctured group remained constant between months 1 and 3. The mean T2-RTs for the punctured groups did not show a statistically significant difference from those of healthy IVDs (63.55ms ±5.88ms month 1 and 62.61ms ±5.02ms) at either time point. Conclusion The NP voxel count proved to be a valid parameter to quantitatively assess disc degeneration in a needle puncture model. The mean NP T2-RT does not change significantly in needle

Qualitative and quantitative mass spectrometry imaging of drugs and metabolites in tissue at therapeutic levels.

PubMed

Sun, Na; Walch, Axel

2013-08-01

Mass spectrometry imaging (MSI) is a rapidly evolving technology that yields qualitative and quantitative distribution maps of small pharmaceutical-active molecules and their metabolites in tissue sections in situ. The simplicity, high sensitivity and ability to provide comprehensive spatial distribution maps of different classes of biomolecules make MSI a valuable tool to complement histopathology for diagnostics and biomarker discovery. In this review, qualitative and quantitative MSI of drugs and metabolites in tissue at therapeutic levels are discussed and the impact of this technique in drug discovery and clinical research is highlighted.

Quantitative Imaging of Young's Modulus of Soft Tissues from Ultrasound Water Jet Indentation: A Finite Element Study

PubMed Central

Lu, Min-Hua; Mao, Rui; Lu, Yin; Liu, Zheng; Wang, Tian-Fu; Chen, Si-Ping

2012-01-01

Indentation testing is a widely used approach to evaluate mechanical characteristics of soft tissues quantitatively. Young's modulus of soft tissue can be calculated from the force-deformation data with known tissue thickness and Poisson's ratio using Hayes' equation. Our group previously developed a noncontact indentation system using a water jet as a soft indenter as well as the coupling medium for the propagation of high-frequency ultrasound. The novel system has shown its ability to detect the early degeneration of articular cartilage. However, there is still lack of a quantitative method to extract the intrinsic mechanical properties of soft tissue from water jet indentation. The purpose of this study is to investigate the relationship between the loading-unloading curves and the mechanical properties of soft tissues to provide an imaging technique of tissue mechanical properties. A 3D finite element model of water jet indentation was developed with consideration of finite deformation effect. An improved Hayes' equation has been derived by introducing a new scaling factor which is dependent on Poisson's ratios v, aspect ratio a/h (the radius of the indenter/the thickness of the test tissue), and deformation ratio d/h. With this model, the Young's modulus of soft tissue can be quantitatively evaluated and imaged with the error no more than 2%. PMID:22927890

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

PubMed Central

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

2015-01-01

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

Quantitative breast MRI radiomics for cancer risk assessment and the monitoring of high-risk populations

NASA Astrophysics Data System (ADS)

Mendel, Kayla R.; Li, Hui; Giger, Maryellen L.

2016-03-01

Breast density is routinely assessed qualitatively in screening mammography. However, it is challenging to quantitatively determine a 3D density from a 2D image such as a mammogram. Furthermore, dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is used more frequently in the screening of high-risk populations. The purpose of our study is to segment parenchyma and to quantitatively determine volumetric breast density on pre-contrast axial DCE-MRI images (i.e., non-contrast) using a semi-automated quantitative approach. In this study, we retroactively examined 3D DCE-MRI images taken for breast cancer screening of a high-risk population. We analyzed 66 cases with ages between 28 and 76 (mean 48.8, standard deviation 10.8). DCE-MRIs were obtained on a Philips 3.0 T scanner. Our semi-automated DCE-MRI algorithm includes: (a) segmentation of breast tissue from non-breast tissue using fuzzy cmeans clustering (b) separation of dense and fatty tissues using Otsu's method, and (c) calculation of volumetric density as the ratio of dense voxels to total breast voxels. We examined the relationship between pre-contrast DCE-MRI density and clinical BI-RADS density obtained from radiology reports, and obtained a statistically significant correlation [Spearman ρ-value of 0.66 (p < 0.0001)]. Our method within precision medicine may be useful for monitoring high-risk populations.

Application of Real-Time Fluorescent PCR for Quantitative Assessment of Neospora caninum Infections in Organotypic Slice Cultures of Rat Central Nervous System Tissue

PubMed Central

Müller, Norbert; Vonlaufen, Nathalie; Gianinazzi, Christian; Leib, Stephen L.; Hemphill, Andrew

2002-01-01

The previously described Nc5-specific PCR test for the diagnosis of Neospora caninum infections was used to develop a quantitative PCR assay which allows the determination of infection intensities within different experimental and diagnostic sample groups. The quantitative PCR was performed by using a dual fluorescent hybridization probe system and the LightCycler Instrument for online detection of amplified DNA. This assay was successfully applied for demonstrating the parasite proliferation kinetics in organotypic slice cultures of rat brain which were infected in vitro with N. caninum tachyzoites. This PCR-based method of parasite quantitation with organotypic brain tissue samples can be regarded as a novel ex vivo approach for exploring different aspects of cerebral N. caninum infection. PMID:11773124

Quantitative assessment of soft tissue deformation using digital speckle pattern interferometry: studies on phantom breast models

PubMed Central

Karuppanan, Udayakumar; Unni, Sujatha Narayanan; Angarai, Ganesan R.

2017-01-01

Abstract. Assessment of mechanical properties of soft matter is a challenging task in a purely noninvasive and noncontact environment. As tissue mechanical properties play a vital role in determining tissue health status, such noninvasive methods offer great potential in framing large-scale medical screening strategies. The digital speckle pattern interferometry (DSPI)–based image capture and analysis system described here is capable of extracting the deformation information from a single acquired fringe pattern. Such a method of analysis would be required in the case of the highly dynamic nature of speckle patterns derived from soft tissues while applying mechanical compression. Soft phantoms mimicking breast tissue optical and mechanical properties were fabricated and tested in the DSPI out of plane configuration set up. Hilbert transform (HT)-based image analysis algorithm was developed to extract the phase and corresponding deformation of the sample from a single acquired fringe pattern. The experimental fringe contours were found to correlate with numerically simulated deformation patterns of the sample using Abaqus finite element analysis software. The extracted deformation from the experimental fringe pattern using the HT-based algorithm is compared with the deformation value obtained using numerical simulation under similar conditions of loading and the results are found to correlate with an average %error of 10. The proposed method is applied on breast phantoms fabricated with included subsurface anomaly mimicking cancerous tissue and the results are analyzed. PMID:28180134

Devising tissue ingrowth metrics: a contribution to the computational characterization of engineered soft tissue healing.

PubMed

Alves, Antoine; Attik, Nina; Bayon, Yves; Royet, Elodie; Wirth, Carine; Bourges, Xavier; Piat, Alexis; Dolmazon, Gaëlle; Clermont, Gaëlle; Boutrand, Jean-Pierre; Grosgogeat, Brigitte; Gritsch, Kerstin

2018-03-14

The paradigm shift brought about by the expansion of tissue engineering and regenerative medicine away from the use of biomaterials, currently questions the value of histopathologic methods in the evaluation of biological changes. To date, the available tools of evaluation are not fully consistent and satisfactory for these advanced therapies. We have developed a new, simple and inexpensive quantitative digital approach that provides key metrics for structural and compositional characterization of the regenerated tissues. For example, metrics provide the tissue ingrowth rate (TIR) which integrates two separate indicators; the cell ingrowth rate (CIR) and the total collagen content (TCC) as featured in the equation, TIR% = CIR% + TCC%. Moreover a subset of quantitative indicators describing the directional organization of the collagen (relating structure and mechanical function of tissues), the ratio of collagen I to collagen III (remodeling quality) and the optical anisotropy property of the collagen (maturity indicator) was automatically assessed as well. Using an image analyzer, all metrics were extracted from only two serial sections stained with either Feulgen & Rossenbeck (cell specific) or Picrosirius Red F3BA (collagen specific). To validate this new procedure, three-dimensional (3D) scaffolds were intraperitoneally implanted in healthy and in diabetic rats. It was hypothesized that quantitatively, the healing tissue would be significantly delayed and of poor quality in diabetic rats in comparison to healthy rats. In addition, a chemically modified 3D scaffold was similarly implanted in a third group of healthy rats with the assumption that modulation of the ingrown tissue would be quantitatively present in comparison to the 3D scaffold-healthy group. After 21 days of implantation, both hypotheses were verified by use of this novel computerized approach. When the two methods were run in parallel, the quantitative results revealed fine details and

Shear Wave Elastography--A New Quantitative Assessment of Post-Irradiation Neck Fibrosis.

PubMed

Liu, K H; Bhatia, K; Chu, W; He, L T; Leung, S F; Ahuja, A T

2015-08-01

Shear wave elastography (SWE) is a new technique which provides quantitative assessment of soft tissue stiffness. The aim of this study was to assess the reliability of SWE stiffness measurements and its usefulness in evaluating post-irradiation neck fibrosis. 50 subjects (25 patients with previous radiotherapy to the neck and 25 sex and age-matched controls) were recruited for comparison of SWE stiffness measurements (Aixplorer, Supersonic Imagine). 30 subjects (16 healthy individuals and 14 post-irradiated patients) were recruited for a reliability study of SWE stiffness measurements. SWE stiffness measurements of the sternocleidomastoid muscle and the overlying subcutaneous tissues of the neck were made. The cross-sectional area and thickness of the sternocleidomastoid muscle and the overlying subcutaneous tissue thickness of the neck were also measured. The post-irradiation duration of the patients was recorded. The intraclass correlation coefficients for the intraoperator and interoperator reliability of deep and subcutaneous tissue SWE stiffness ranged from 0.90-0.99 and 0.77-0.94, respectively. The SWE stiffness measurements (mean +/- SD) of deep and subcutaneous tissues were significantly higher in the post-irradiated patients (64.6 ± 46.8 kPa and 63.9 ± 53.1 kPa, respectively) than the sex and age-matched controls (19.9 ± 7.8 kPa and 15.3 ± 8.37 respectively) (p < 0.001). The SWE stiffness increased with increasing post-irradiation therapy duration in the Kruskal Wallis test (p < 0.001) and correlated with muscle atrophy and subcutaneous tissue thinning (p < 0.01). SWE is a reliable technique and may potentially be an objective and specific tool in quantifying deep and subcutaneous tissue stiffness, which in turn reflects the severity of neck fibrosis. © Georg Thieme Verlag KG Stuttgart · New York.

Structural and quantitative expression analyses of HERV gene family in human tissues.

PubMed

Ahn, Kung; Kim, Heui-Soo

2009-08-31

Human endogenous retroviruses (HERVs) have been implicated in the pathogenesis of several human diseases as multi-copy members in the human genome. Their gene expression profiling could provide us with important insights into the pathogenic relationship between HERVs and cancer. In this study, we have evaluated the genomic structure and quantitatively determined the expression patterns in the env gene of a variety of HERV family members located on six specific loci by the RetroTector 10 program, as well as real-time RT-PCR amplification. The env gene transcripts evidenced significant differences in the human tumor/normal adjacent tissues (colon, liver, uterus, lung and testis). As compared to the adjacent normal tissues, high levels of expression were noted in testis tumor tissues for HERV-K, in liver and lung tumor tissues for HERV-R, in liver, lung, and testis tumor tissues for HERV-H, and in colon and liver tumor tissues for HERV-P. These data warrant further studies with larger groups of patients to develop biomarkers for specific human cancers.

A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

USGS Publications Warehouse

Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

2017-01-01

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

Quantitative micro-elastography: imaging of tissue elasticity using compression optical coherence elastography

PubMed Central

Kennedy, Kelsey M.; Chin, Lixin; McLaughlin, Robert A.; Latham, Bruce; Saunders, Christobel M.; Sampson, David D.; Kennedy, Brendan F.

2015-01-01

Probing the mechanical properties of tissue on the microscale could aid in the identification of diseased tissues that are inadequately detected using palpation or current clinical imaging modalities, with potential to guide medical procedures such as the excision of breast tumours. Compression optical coherence elastography (OCE) maps tissue strain with microscale spatial resolution and can delineate microstructural features within breast tissues. However, without a measure of the locally applied stress, strain provides only a qualitative indication of mechanical properties. To overcome this limitation, we present quantitative micro-elastography, which combines compression OCE with a compliant stress sensor to image tissue elasticity. The sensor consists of a layer of translucent silicone with well-characterized stress-strain behaviour. The measured strain in the sensor is used to estimate the two-dimensional stress distribution applied to the sample surface. Elasticity is determined by dividing the stress by the strain in the sample. We show that quantification of elasticity can improve the ability of compression OCE to distinguish between tissues, thereby extending the potential for inter-sample comparison and longitudinal studies of tissue elasticity. We validate the technique using tissue-mimicking phantoms and demonstrate the ability to map elasticity of freshly excised malignant and benign human breast tissues. PMID:26503225

Quantitative Microbial Risk Assessment Tutorial - Primer

EPA Science Inventory

This document provides a Quantitative Microbial Risk Assessment (QMRA) primer that organizes QMRA tutorials. The tutorials describe functionality of a QMRA infrastructure, guide the user through software use and assessment options, provide step-by-step instructions for implementi...

Quantitative sonoelastography for the in vivo assessment of skeletal muscle viscoelasticity

NASA Astrophysics Data System (ADS)

Hoyt, Kenneth; Kneezel, Timothy; Castaneda, Benjamin; Parker, Kevin J.

2008-08-01

A novel quantitative sonoelastography technique for assessing the viscoelastic properties of skeletal muscle tissue was developed. Slowly propagating shear wave interference patterns (termed crawling waves) were generated using a two-source configuration vibrating normal to the surface. Theoretical models predict crawling wave displacement fields, which were validated through phantom studies. In experiments, a viscoelastic model was fit to dispersive shear wave speed sonoelastographic data using nonlinear least-squares techniques to determine frequency-independent shear modulus and viscosity estimates. Shear modulus estimates derived using the viscoelastic model were in agreement with that obtained by mechanical testing on phantom samples. Preliminary sonoelastographic data acquired in healthy human skeletal muscles confirm that high-quality quantitative elasticity data can be acquired in vivo. Studies on relaxed muscle indicate discernible differences in both shear modulus and viscosity estimates between different skeletal muscle groups. Investigations into the dynamic viscoelastic properties of (healthy) human skeletal muscles revealed that voluntarily contracted muscles exhibit considerable increases in both shear modulus and viscosity estimates as compared to the relaxed state. Overall, preliminary results are encouraging and quantitative sonoelastography may prove clinically feasible for in vivo characterization of the dynamic viscoelastic properties of human skeletal muscle.

Assessment of biological leaf tissue using biospeckle laser imaging technique

NASA Astrophysics Data System (ADS)

Ansari, M. Z.; Mujeeb, A.; Nirala, A. K.

2018-06-01

We report on the application of an optical imaging technique, the biospeckle laser, as a potential tool to assess biological and medicinal plant leaves. The biospeckle laser technique is a non-invasive and non-destructive optical technique used to investigate biological objects. Just after their removal from plants, the torn leaves were used for biospeckle laser imaging. Quantitative evaluation of the biospeckle data using the inertia moment (IM) of the time history speckle pattern, showed that the IM can be utilized to provide a biospeckle signature to the plant leaves. It showed that leaves from different plants can have their own characteristic IM values. We further investigated the infected regions of the leaves that display a relatively lower biospeckle activity than the healthy tissue. It was easy to discriminate between the infected and healthy regions of the leaf tissue. The biospeckle technique can successfully be implemented as a potential tool for the taxonomy of quality leaves. Furthermore, the technique can help boost the quality of ayurvedic medicines.

Quantitative Susceptibility Mapping after Sports-Related Concussion.

PubMed

Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

2018-06-07

Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of

Mechanical Model Analysis for Quantitative Evaluation of Liver Fibrosis Based on Ultrasound Tissue Elasticity Imaging

NASA Astrophysics Data System (ADS)

Shiina, Tsuyoshi; Maki, Tomonori; Yamakawa, Makoto; Mitake, Tsuyoshi; Kudo, Masatoshi; Fujimoto, Kenji

2012-07-01

Precise evaluation of the stage of chronic hepatitis C with respect to fibrosis has become an important issue to prevent the occurrence of cirrhosis and to initiate appropriate therapeutic intervention such as viral eradication using interferon. Ultrasound tissue elasticity imaging, i.e., elastography can visualize tissue hardness/softness, and its clinical usefulness has been studied to detect and evaluate tumors. We have recently reported that the texture of elasticity image changes as fibrosis progresses. To evaluate fibrosis progression quantitatively on the basis of ultrasound tissue elasticity imaging, we introduced a mechanical model of fibrosis progression and simulated the process by which hepatic fibrosis affects elasticity images and compared the results with those clinical data analysis. As a result, it was confirmed that even in diffuse diseases like chronic hepatitis, the patterns of elasticity images are related to fibrous structural changes caused by hepatic disease and can be used to derive features for quantitative evaluation of fibrosis stage.

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.

Quantitative Volumetric K-Means Cluster Segmentation of Fibroglandular Tissue and Skin in Breast MRI.

PubMed

Niukkanen, Anton; Arponen, Otso; Nykänen, Aki; Masarwah, Amro; Sutela, Anna; Liimatainen, Timo; Vanninen, Ritva; Sudah, Mazen

2017-10-18

Mammographic breast density (MBD) is the most commonly used method to assess the volume of fibroglandular tissue (FGT). However, MRI could provide a clinically feasible and more accurate alternative. There were three aims in this study: (1) to evaluate a clinically feasible method to quantify FGT with MRI, (2) to assess the inter-rater agreement of MRI-based volumetric measurements and (3) to compare them to measurements acquired using digital mammography and 3D tomosynthesis. This retrospective study examined 72 women (mean age 52.4 ± 12.3 years) with 105 disease-free breasts undergoing diagnostic 3.0-T breast MRI and either digital mammography or tomosynthesis. Two observers analyzed MRI images for breast and FGT volumes and FGT-% from T1-weighted images (0.7-, 2.0-, and 4.0-mm-thick slices) using K-means clustering, data from histogram, and active contour algorithms. Reference values were obtained with Quantra software. Inter-rater agreement for MRI measurements made with 2-mm-thick slices was excellent: for FGT-%, r = 0.994 (95% CI 0.990-0.997); for breast volume, r = 0.985 (95% CI 0.934-0.994); and for FGT volume, r = 0.979 (95% CI 0.958-0.989). MRI-based FGT-% correlated strongly with MBD in mammography (r = 0.819-0.904, P < 0.001) and moderately to high with MBD in tomosynthesis (r = 0.630-0.738, P < 0.001). K-means clustering-based assessments of the proportion of the fibroglandular tissue in the breast at MRI are highly reproducible. In the future, quantitative assessment of FGT-% to complement visual estimation of FGT should be performed on a more regular basis as it provides a component which can be incorporated into the individual's breast cancer risk stratification.

Quantitative methods in assessment of neurologic function.

PubMed

Potvin, A R; Tourtellotte, W W; Syndulko, K; Potvin, J

1981-01-01

Traditionally, neurologists have emphasized qualitative techniques for assessing results of clinical trials. However, in recent years qualitative evaluations have been increasingly augmented by quantitative tests for measuring neurologic functions pertaining to mental state, strength, steadiness, reactions, speed, coordination, sensation, fatigue, gait, station, and simulated activities of daily living. Quantitative tests have long been used by psychologists for evaluating asymptomatic function, assessing human information processing, and predicting proficiency in skilled tasks; however, their methodology has never been directly assessed for validity in a clinical environment. In this report, relevant contributions from the literature on asymptomatic human performance and that on clinical quantitative neurologic function are reviewed and assessed. While emphasis is focused on tests appropriate for evaluating clinical neurologic trials, evaluations of tests for reproducibility, reliability, validity, and examiner training procedures, and for effects of motivation, learning, handedness, age, and sex are also reported and interpreted. Examples of statistical strategies for data analysis, scoring systems, data reduction methods, and data display concepts are presented. Although investigative work still remains to be done, it appears that carefully selected and evaluated tests of sensory and motor function should be an essential factor for evaluating clinical trials in an objective manner.

The application of quantitative cytochemistry to the study of diseases of the connective tissues.

PubMed

Henderson, B

1983-01-01

The connective tissues are a complex organisation of tissues, cells and intercellular materials spread throughout the body and are subject to a large number of diseases. Such complexity makes the study of the metabolism of the connective tissues in health and more particularly in disease states difficult if one uses conventional biochemical methodology. Fortunately the techniques of quantitative cytochemistry, as developed in recent years, have made it possible to study the metabolism of even such complex and refractory connective tissues as bone. Using properly validated assays of enzyme activity in unfixed sections from various tissues a number of the diseases of the connective tissues have been studied. For example the synovia from patients with rheumatoid arthritis and related conditions have been studied using these techniques and marked alterations in the metabolism of the synovial lining cell population of this tissue have been demonstrated. These alterations in metabolism are believed to be related to the destruction of cartilage and bone found in such diseases. Investigations of the metabolism of the chondrocytes of articular cartilage in a strain of mice which spontaneously develops osteoarthritis has revealed a lack of certain key enzymes of carbohydrate metabolism in precisely those areas where degradation of the matrix of articular cartilage begins suggesting a causal relationship between these events. These same techniques have been used to study the cellular kinetics and metabolism of the dermis and epidermis in the disfiguring disease, psoriasis. The metabolism of healing bone fractures, the diagnosis and treatment of the mucopolysaccharidoses and the metabolic effects of currently used anti-inflammatory and anti-rheumatic drugs have also been examined. Perhaps the most exciting aspect of these studies has been the development and use of the technique of the cytochemical bioassay (CBA) to study hormonally mediated diseases of the connective tissues

Quantitative assessment of Cerenkov luminescence for radioguided brain tumor resection surgery

NASA Astrophysics Data System (ADS)

Klein, Justin S.; Mitchell, Gregory S.; Cherry, Simon R.

2017-05-01

Cerenkov luminescence imaging (CLI) is a developing imaging modality that detects radiolabeled molecules via visible light emitted during the radioactive decay process. We used a Monte Carlo based computer simulation to quantitatively investigate CLI compared to direct detection of the ionizing radiation itself as an intraoperative imaging tool for assessment of brain tumor margins. Our brain tumor model consisted of a 1 mm spherical tumor remnant embedded up to 5 mm in depth below the surface of normal brain tissue. Tumor to background contrast ranging from 2:1 to 10:1 were considered. We quantified all decay signals (e±, gamma photon, Cerenkov photons) reaching the brain volume surface. CLI proved to be the most sensitive method for detecting the tumor volume in both imaging and non-imaging strategies as assessed by contrast-to-noise ratio and by receiver operating characteristic output of a channelized Hotelling observer.

Expression quantitative trait loci: replication, tissue- and sex-specificity in mice.

PubMed

van Nas, Atila; Ingram-Drake, Leslie; Sinsheimer, Janet S; Wang, Susanna S; Schadt, Eric E; Drake, Thomas; Lusis, Aldons J

2010-07-01

By treating the transcript abundance as a quantitative trait, gene expression can be mapped to local or distant genomic regions relative to the gene encoding the transcript. Local expression quantitative trait loci (eQTL) generally act in cis (that is, control the expression of only the contiguous structural gene), whereas distal eQTL act in trans. Distal eQTL are more difficult to identify with certainty due to the fact that significant thresholds are very high since all regions of the genome must be tested, and confounding factors such as batch effects can produce false positives. Here, we compare findings from two large genetic crosses between mouse strains C3H/HeJ and C57BL/6J to evaluate the reliability of distal eQTL detection, including "hotspots" influencing the expression of multiple genes in trans. We found that >63% of local eQTL and >18% of distal eQTL were replicable at a threshold of LOD > 4.3 between crosses and 76% of local and >24% of distal eQTL at a threshold of LOD > 6. Additionally, at LOD > 4.3 four tissues studied (adipose, brain, liver, and muscle) exhibited >50% preservation of local eQTL and >17% preservation of distal eQTL. We observed replicated distal eQTL hotspots between the crosses on chromosomes 9 and 17. Finally, >69% of local eQTL and >10% of distal eQTL were preserved in most tissues between sexes. We conclude that most local eQTL are highly replicable between mouse crosses, tissues, and sex as compared to distal eQTL, which exhibited modest replicability.

Assessment of tissue polarimetric properties using Stokes polarimetric imaging with circularly polarized illumination.

PubMed

Qi, Ji; He, Honghui; Lin, Jianyu; Dong, Yang; Chen, Dongsheng; Ma, Hui; Elson, Daniel S

2018-04-01

Tissue-depolarization and linear-retardance are the main polarization characteristics of interest for bulk tissue characterization, and are normally interpreted from Mueller polarimetry. Stokes polarimetry can be conducted using simpler instrumentation and in a shorter time. Here, we use Stokes polarimetric imaging with circularly polarized illumination to assess the circular-depolarization and linear-retardance properties of tissue. Results obtained were compared with Mueller polarimetry in transmission and reflection geometry, respectively. It is found that circular-depolarization obtained from these 2 methods is very similar in both geometries, and that linear-retardance is highly quantitatively similar for transmission geometry and qualitatively similar for reflection geometry. The majority of tissue circular-depolarization and linear-retardance image information (represented by local image contrast features) obtained from Mueller polarimetry is well preserved from Stokes polarimetry in both geometries. These findings can be referred to for further understanding tissue Stokes polarimetric data, and for further application of Stokes polarimetry under the circumstances where short acquisition time or low optical system complexity is a priority, such as polarimetric endoscopy and microscopy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitatively characterizing the microstructural features of breast ductal carcinoma tissues in different progression stages by Mueller matrix microscope.

PubMed

Dong, Yang; Qi, Ji; He, Honghui; He, Chao; Liu, Shaoxiong; Wu, Jian; Elson, Daniel S; Ma, Hui

2017-08-01

Polarization imaging has been recognized as a potentially powerful technique for probing the microstructural information and optical properties of complex biological specimens. Recently, we have reported a Mueller matrix microscope by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission-light microscope, and applied it to differentiate human liver and cervical cancerous tissues with fibrosis. In this paper, we apply the Mueller matrix microscope for quantitative detection of human breast ductal carcinoma samples at different stages. The Mueller matrix polar decomposition and transformation parameters of the breast ductal tissues in different regions and at different stages are calculated and analyzed. For more quantitative comparisons, several widely-used image texture feature parameters are also calculated to characterize the difference in the polarimetric images. The experimental results indicate that the Mueller matrix microscope and the polarization parameters can facilitate the quantitative detection of breast ductal carcinoma tissues at different stages.

Multimodal imaging of cutaneous wound tissue

NASA Astrophysics Data System (ADS)

Zhang, Shiwu; Gnyawali, Surya; Huang, Jiwei; Ren, Wenqi; Gordillo, Gayle; Sen, Chandan K.; Xu, Ronald

2015-01-01

Quantitative assessment of wound tissue ischemia, perfusion, and inflammation provides critical information for appropriate detection, staging, and treatment of chronic wounds. However, few methods are available for simultaneous assessment of these tissue parameters in a noninvasive and quantitative fashion. We integrated hyperspectral, laser speckle, and thermographic imaging modalities in a single-experimental setup for multimodal assessment of tissue oxygenation, perfusion, and inflammation characteristics. Algorithms were developed for appropriate coregistration between wound images acquired by different imaging modalities at different times. The multimodal wound imaging system was validated in an occlusion experiment, where oxygenation and perfusion maps of a healthy subject's upper extremity were continuously monitored during a postocclusive reactive hyperemia procedure and compared with standard measurements. The system was also tested in a clinical trial where a wound of three millimeters in diameter was introduced on a healthy subject's lower extremity and the healing process was continuously monitored. Our in vivo experiments demonstrated the clinical feasibility of multimodal cutaneous wound imaging.

Quantitative risk assessment system (QRAS)

NASA Technical Reports Server (NTRS)

Tan, Zhibin (Inventor); Mosleh, Ali (Inventor); Weinstock, Robert M (Inventor); Smidts, Carol S (Inventor); Chang, Yung-Hsien (Inventor); Groen, Francisco J (Inventor); Swaminathan, Sankaran (Inventor)

2001-01-01

A quantitative risk assessment system (QRAS) builds a risk model of a system for which risk of failure is being assessed, then analyzes the risk of the system corresponding to the risk model. The QRAS performs sensitivity analysis of the risk model by altering fundamental components and quantifications built into the risk model, then re-analyzes the risk of the system using the modifications. More particularly, the risk model is built by building a hierarchy, creating a mission timeline, quantifying failure modes, and building/editing event sequence diagrams. Multiplicities, dependencies, and redundancies of the system are included in the risk model. For analysis runs, a fixed baseline is first constructed and stored. This baseline contains the lowest level scenarios, preserved in event tree structure. The analysis runs, at any level of the hierarchy and below, access this baseline for risk quantitative computation as well as ranking of particular risks. A standalone Tool Box capability exists, allowing the user to store application programs within QRAS.

Assessment of and standardization for quantitative nondestructive test

NASA Technical Reports Server (NTRS)

Neuschaefer, R. W.; Beal, J. B.

1972-01-01

Present capabilities and limitations of nondestructive testing (NDT) as applied to aerospace structures during design, development, production, and operational phases are assessed. It will help determine what useful structural quantitative and qualitative data may be provided from raw materials to vehicle refurbishment. This assessment considers metal alloys systems and bonded composites presently applied in active NASA programs or strong contenders for future use. Quantitative and qualitative data has been summarized from recent literature, and in-house information, and presented along with a description of those structures or standards where the information was obtained. Examples, in tabular form, of NDT technique capabilities and limitations have been provided. NDT techniques discussed and assessed were radiography, ultrasonics, penetrants, thermal, acoustic, and electromagnetic. Quantitative data is sparse; therefore, obtaining statistically reliable flaw detection data must be strongly emphasized. The new requirements for reusable space vehicles have resulted in highly efficient design concepts operating in severe environments. This increases the need for quantitative NDT evaluation of selected structural components, the end item structure, and during refurbishment operations.

Development of CD3 cell quantitation algorithms for renal allograft biopsy rejection assessment utilizing open source image analysis software.

PubMed

Moon, Andres; Smith, Geoffrey H; Kong, Jun; Rogers, Thomas E; Ellis, Carla L; Farris, Alton B Brad

2018-02-01

Renal allograft rejection diagnosis depends on assessment of parameters such as interstitial inflammation; however, studies have shown interobserver variability regarding interstitial inflammation assessment. Since automated image analysis quantitation can be reproducible, we devised customized analysis methods for CD3+ T-cell staining density as a measure of rejection severity and compared them with established commercial methods along with visual assessment. Renal biopsy CD3 immunohistochemistry slides (n = 45), including renal allografts with various degrees of acute cellular rejection (ACR) were scanned for whole slide images (WSIs). Inflammation was quantitated in the WSIs using pathologist visual assessment, commercial algorithms (Aperio nuclear algorithm for CD3+ cells/mm 2 and Aperio positive pixel count algorithm), and customized open source algorithms developed in ImageJ with thresholding/positive pixel counting (custom CD3+%) and identification of pixels fulfilling "maxima" criteria for CD3 expression (custom CD3+ cells/mm 2 ). Based on visual inspections of "markup" images, CD3 quantitation algorithms produced adequate accuracy. Additionally, CD3 quantitation algorithms correlated between each other and also with visual assessment in a statistically significant manner (r = 0.44 to 0.94, p = 0.003 to < 0.0001). Methods for assessing inflammation suggested a progression through the tubulointerstitial ACR grades, with statistically different results in borderline versus other ACR types, in all but the custom methods. Assessment of CD3-stained slides using various open source image analysis algorithms presents salient correlations with established methods of CD3 quantitation. These analysis techniques are promising and highly customizable, providing a form of on-slide "flow cytometry" that can facilitate additional diagnostic accuracy in tissue-based assessments.

Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

EPA Science Inventory

The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

Towards automated early cancer detection: Non-invasive, fluorescence-based approaches for quantitative assessment of cells and tissue to identify pre-cancers

NASA Astrophysics Data System (ADS)

Levitt, Jonathan Michael

Cancer is the second leading cause of death globally, second only to heart disease. As in many diseases, patient survival is directly related to how early lesions are detected. Using conventional screening methods, the early changes associated with cancer, which occur on the microscopic scale, can easily go overlooked. Due to the inherent drawbacks of conventional techniques we present non-invasive, optically based methods to acquire high resolution images from live samples and assess cellular function associated with the onset of disease. Specifically, we acquired fluorescence images from NADH and FAD to quantify morphology and metabolic activity. We first conducted studies to monitor monolayers of keratinocytes in response to apoptosis which has been shown to be disrupted during cancer progression. We found that as keratinocytes undergo apoptosis there are populations of mitochondria that exhibit a higher metabolic activity that become progressively confined to a gradually smaller perinuclear region. To further assess the changes associated with early cancer growth we developed automated methods to rapidly quantify fluorescence images and extract morphological and metabolic information from life tissue. In this study, we simultaneously quantified mitochondrial organization, metabolic activity, nuclear size distribution, and the localization of the structural protein keratin, to differentiate between normal and pre-cancerous engineered tissues. We found the degree mitochondrial organization, as determined from the fractal derived Hurst parameter, was well correlated to level of cellular differentiation. We also found that the metabolic activity in the pre-cancerous cells was greater and more consistent throughout tissue depths in comparison to normal tissue. Keratin localization, also quantified from the fluorescence images, we found it to be confined to the uppermost layers of normal tissue while it was more evenly distributed in the precancerous tissues. To

An effective method for the quantitative detection of porcine endogenous retrovirus in pig tissues.

PubMed

Zhang, Peng; Yu, Ping; Wang, Wei; Zhang, Li; Li, Shengfu; Bu, Hong

2010-05-01

Xenotransplantation shows great promise for providing a virtually limitless supply of cells, tissues, and organs for a variety of therapeutical procedures. However, the potential of porcine endogenous retrovirus (PERV) as a human-tropic pathogen, particularly as a public health risk, is a major concern for xenotransplantation. This study focus on the detection of copy number in various tissues and organs in Banna Minipig Inbreed (BMI) from 2006 to 2007 in West China Hospital, Sichuan University. Real-time quantitative polymerase chain reaction (SYBR Green I) was performed in this study. The results showed that the pol gene had the most copy number in tissues compared with gag, envA, and envB. Our experiment will offer a rapid and accurate method for the detection of the copy number in various tissues and was especially suitable for the selection of tissues or organs in future clinical xenotransplantation.

Checklist and Scoring System for the Assessment of Soft Tissue Preservation in CT Examinations of Human Mummies: Application to the Tyrolean Iceman.

PubMed

Panzer, Stephanie; Pernter, Patrizia; Piombino-Mascali, Dario; Jankauskas, Rimantas; Zesch, Stephanie; Rosendahl, Wilfried; Hotz, Gerhard; Zink, Albert R

2017-12-01

Purpose  Soft tissues make a skeleton into a mummy and they allow for a diagnosis beyond osteology. Following the approach of structured reporting in clinical radiology, a recently developed checklist was used to evaluate the soft tissue preservation status of the Tyrolean Iceman using computed tomography (CT). The purpose of this study was to apply the "Checklist and Scoring System for the Assessment of Soft Tissue Preservation in CT Examinations of Human Mummies" to the Tyrolean Iceman, and to compare the Iceman's soft tissue preservation score to the scores calculated for other mummies. Materials and Methods  A whole-body (CT) (SOMATOM Definition Flash, Siemens, Forchheim, Germany) consisting of five scans, performed in January 2013 in the Department of Radiodiagnostics, Central Hospital, Bolzano, was used (slice thickness 0.6 mm; kilovolt ranging from 80 to 140). For standardized evaluation the "CT Checklist and Scoring System for the Assessment of Soft Tissue Preservation in Human Mummies" was used. Results  All checkpoints under category "A. Soft Tissues of Head and Musculoskeletal System" and more than half in category "B. Organs and Organ Systems" were observed. The scoring system accounted for a total score of 153 (out of 200). The comparison of the scores between the Iceman and three mummy collections from Vilnius, Lithuania, and Palermo, Sicily, as well as one Egyptian mummy resulted in overall higher soft tissue preservation scores for the Iceman. Conclusion  Application of the checklist allowed for standardized assessment and documentation of the Iceman's soft tissue preservation status. The scoring system allowed for a quantitative comparison between the Iceman and other mummies. The Iceman showed remarkable soft tissue preservation. Key Points   · The approach of structured reporting can be transferred to paleoradiology.. · The checklist allowed for standardized soft tissue assessment and documentation.. · The scoring system

Three-dimensional histology: tools and application to quantitative assessment of cell-type distribution in rabbit heart

PubMed Central

Burton, Rebecca A.B.; Lee, Peter; Casero, Ramón; Garny, Alan; Siedlecka, Urszula; Schneider, Jürgen E.; Kohl, Peter; Grau, Vicente

2014-01-01

Aims Cardiac histo-anatomical organization is a major determinant of function. Changes in tissue structure are a relevant factor in normal and disease development, and form targets of therapeutic interventions. The purpose of this study was to test tools aimed to allow quantitative assessment of cell-type distribution from large histology and magnetic resonance imaging- (MRI) based datasets. Methods and results Rabbit heart fixation during cardioplegic arrest and MRI were followed by serial sectioning of the whole heart and light-microscopic imaging of trichrome-stained tissue. Segmentation techniques developed specifically for this project were applied to segment myocardial tissue in the MRI and histology datasets. In addition, histology slices were segmented into myocytes, connective tissue, and undefined. A bounding surface, containing the whole heart, was established for both MRI and histology. Volumes contained in the bounding surface (called ‘anatomical volume’), as well as that identified as containing any of the above tissue categories (called ‘morphological volume’), were calculated. The anatomical volume was 7.8 cm3 in MRI, and this reduced to 4.9 cm3 after histological processing, representing an ‘anatomical’ shrinkage by 37.2%. The morphological volume decreased by 48% between MRI and histology, highlighting the presence of additional tissue-level shrinkage (e.g. an increase in interstitial cleft space). The ratio of pixels classified as containing myocytes to pixels identified as non-myocytes was roughly 6:1 (61.6 vs. 9.8%; the remaining fraction of 28.6% was ‘undefined’). Conclusion Qualitative and quantitative differentiation between myocytes and connective tissue, using state-of-the-art high-resolution serial histology techniques, allows identification of cell-type distribution in whole-heart datasets. Comparison with MRI illustrates a pronounced reduction in anatomical and morphological volumes during histology processing. PMID

Physiologic Basis for Understanding Quantitative Dehydration Assessment

DTIC Science & Technology

2012-01-01

Perspective Physiologic basis for understanding quantitative dehydration assessment1–4 Samuel N Cheuvront, Robert W Kenefick, Nisha Charkoudian, and...Michael N Sawka ABSTRACT Dehydration (body water deficit) is a physiologic state that can have profound implications for human health and performance...review the physiologic basis for understanding quantitative dehydration as- sessment. We highlight how phenomenologic interpretations of de- hydration

Checklist and Scoring System for the Assessment of Soft Tissue Preservation in CT Examinations of Human Mummies.

PubMed

Panzer, Stephanie; Mc Coy, Mark R; Hitzl, Wolfgang; Piombino-Mascali, Dario; Jankauskas, Rimantas; Zink, Albert R; Augat, Peter

2015-01-01

The purpose of this study was to develop a checklist for standardized assessment of soft tissue preservation in human mummies based on whole-body computed tomography examinations, and to add a scoring system to facilitate quantitative comparison of mummies. Computed tomography examinations of 23 mummies from the Capuchin Catacombs of Palermo, Sicily (17 adults, 6 children; 17 anthropogenically and 6 naturally mummified) and 7 mummies from the crypt of the Dominican Church of the Holy Spirit of Vilnius, Lithuania (5 adults, 2 children; all naturally mummified) were used to develop the checklist following previously published guidelines. The scoring system was developed by assigning equal scores for checkpoints with equivalent quality. The checklist was evaluated by intra- and inter-observer reliability. The finalized checklist was applied to compare the groups of anthropogenically and naturally mummified bodies. The finalized checklist contains 97 checkpoints and was divided into two main categories, "A. Soft Tissues of Head and Musculoskeletal System" and "B. Organs and Organ Systems", each including various subcategories. The complete checklist had an intra-observer reliability of 98% and an inter-observer reliability of 93%. Statistical comparison revealed significantly higher values in anthropogenically compared to naturally mummified bodies for the total score and for three subcategories. In conclusion, the developed checklist allows for a standardized assessment and documentation of soft tissue preservation in whole-body computed tomography examinations of human mummies. The scoring system facilitates a quantitative comparison of the soft tissue preservation status between single mummies or mummy collections.

European Organisation for Research and Treatment of Cancer (EORTC) Pathobiology Group standard operating procedure for the preparation of human tumour tissue extracts suited for the quantitative analysis of tissue-associated biomarkers.

PubMed

Schmitt, Manfred; Mengele, Karin; Schueren, Elisabeth; Sweep, Fred C G J; Foekens, John A; Brünner, Nils; Laabs, Juliane; Malik, Abha; Harbeck, Nadia

2007-03-01

With the new concept of 'individualized treatment and targeted therapies', tumour tissue-associated biomarkers have been given a new role in selection of cancer patients for treatment and in cancer patient management. Tumour biomarkers can give support to cancer patient stratification and risk assessment, treatment response identification, or to identifying those patients who are expected to respond to certain anticancer drugs. As the field of tumour-associated biomarkers has expanded rapidly over the last years, it has become increasingly apparent that a strong need exists to establish guidelines on how to easily disintegrate the tumour tissue for assessment of the presence of tumour tissue-associated biomarkers. Several mechanical tissue (cell) disruption techniques exist, ranging from bead mill homogenisation and freeze-fracturing through to blade or pestle-type homogenisation, to grinding and ultrasonics. Still, only a few directives have been given on how fresh-frozen tumour tissues should be processed for the extraction and determination of tumour biomarkers. The PathoBiology Group of the European Organisation for Research and Treatment of Cancer therefore has devised a standard operating procedure for the standardised preparation of human tumour tissue extracts which is designed for the quantitative analysis of tumour tissue-associated biomarkers. The easy to follow technical steps involved require 50-300 mg of deep-frozen cancer tissue placed into small size (1.2 ml) cryogenic tubes. These are placed into the shaking flask of a Mikro-Dismembrator S machine (bead mill) to pulverise the tumour tissue in the capped tubes in the deep-frozen state by use of a stainless steel ball, all within 30 s of exposure. RNA is isolated from the pulverised tissue following standard procedures. Proteins are extracted from the still frozen pulverised tissue by addition of Tris-buffered saline to obtain the cytosol fraction of the tumour or by the Tris buffer supplemented with

Hyperspectral Imaging and SPA-LDA Quantitative Analysis for Detection of Colon Cancer Tissue

NASA Astrophysics Data System (ADS)

Yuan, X.; Zhang, D.; Wang, Ch.; Dai, B.; Zhao, M.; Li, B.

2018-05-01

Hyperspectral imaging (HSI) has been demonstrated to provide a rapid, precise, and noninvasive method for cancer detection. However, because HSI contains many data, quantitative analysis is often necessary to distill information useful for distinguishing cancerous from normal tissue. To demonstrate that HSI with our proposed algorithm can make this distinction, we built a Vis-NIR HSI setup and made many spectral images of colon tissues, and then used a successive projection algorithm (SPA) to analyze the hyperspectral image data of the tissues. This was used to build an identification model based on linear discrimination analysis (LDA) using the relative reflectance values of the effective wavelengths. Other tissues were used as a prediction set to verify the reliability of the identification model. The results suggest that Vis-NIR hyperspectral images, together with the spectroscopic classification method, provide a new approach for reliable and safe diagnosis of colon cancer and could lead to advances in cancer diagnosis generally.

Equilibrium ex vivo calibration of homogenized tissue for in vivo SPME quantitation of doxorubicin in lung tissue.

PubMed

Roszkowska, Anna; Tascon, Marcos; Bojko, Barbara; Goryński, Krzysztof; Dos Santos, Pedro Reck; Cypel, Marcelo; Pawliszyn, Janusz

2018-06-01

The fast and sensitive determination of concentrations of anticancer drugs in specific organs can improve the efficacy of chemotherapy and minimize its adverse effects. In this paper, ex vivo solid-phase microextraction (SPME) coupled to LC-MS/MS as a method for rapidly quantitating doxorubicin (DOX) in lung tissue was optimized. Furthermore, the theoretical and practical challenges related to the real-time monitoring of DOX levels in the lung tissue of a living organism (in vivo SPME) are presented. In addition, several parameters for ex vivo/in vivo SPME studies, such as extraction efficiency of autoclaved fibers, intact/homogenized tissue differences, critical tissue amount, and the absence of an internal standard are thoroughly examined. To both accurately quantify DOX in solid tissue and minimize the error related to the lack of an internal standard, a calibration method at equilibrium conditions was chosen. In optimized ex vivo SPME conditions, the targeted compound was extracted by directly introducing a 15 mm (45 µm thickness) mixed-mode fiber into 15 g of homogenized tissue for 20 min, followed by a desorption step in an optimal solvent mixture. The detection limit for DOX was 2.5 µg g -1 of tissue. The optimized ex vivo SPME method was successfully applied for the analysis of DOX in real pig lung biopsies, providing an averaged accuracy and precision of 103.2% and 12.3%, respectively. Additionally, a comparison between SPME and solid-liquid extraction revealed good agreement. The results presented herein demonstrate that the developed SPME method radically simplifies the sample preparation step and eliminates the need for tissue biopsies. These results suggest that SPME can accurately quantify DOX in different tissue compartments and can be potentially useful for monitoring and adjusting drug dosages during chemotherapy in order to achieve effective and safe concentrations of doxorubicin. Copyright © 2018 Elsevier B.V. All rights reserved.

INTRACELLULAR LOCALIZATION AND QUANTITATION OF TRITIATED ANTIGENS IN RETICULOENDOTHELIAL TISSUES OF MICE DURING SECONDARY AND HYPERIMMUNE RESPONSES

PubMed Central

Roberts, Audrey N.; Haurowitz, Felix

1962-01-01

Autoradiography and quantitative radiochemical techniques have been used to determine intracellular localization of tritium and the quantity of tissue-bound tritium, respectively, following injections of H3-aniline azo PGG or H3-arsanilazo PGG to yield hyperimmune or secondary response stimulation in mice. Autoradiography revealed intracytoplasmic localization of grains in macrophages of spleen and lung sections, and in Kupffer cells of liver sections following intravenous and subcutaneous injections of H3-aniline azo PGG. Quantitation of tissue section surface radioactivities in the windowless flow counter and scintillation counter, and of dissolved tissue section activities in the scintillation counter, showed that greatest radioactivity was present in lung tissue, with less in spleen, liver, and mesenteric lymph nodes from these hyperimmunized mice. Autoradiographic studies on tissue sections from mice in secondary response stimulation after subcutaneous foot-pad injections of H3-arsanilazo PGG, showed intracellular and extracellular grains over regional popliteal node sections, with intracytoplasmic grain localization over macrophages and pyroninophilic plasmacytes. Scattered macrophages in spleen and lung sections also contained intracytoplasmic radioactivity. Clusters of antibody-synthesizing cells in the regional lymph nodes were demonstrated with fluorescence microscopy, and these cells were compared to similar cells possessing radioactivity as observed in the section autoradiographs. An occasional Russell body plasma cell containing specific antibody was observed in splenic impressions. Windowless flow counting showed that greatest radioactivity was in regional node sections, with less in spleen and lung, and none in contralateral lymph nodes. A quantitative comparison between windowless flow counting and autoradiography revealed that 20 counts were required to yield one silver grain. PMID:13974279

Quantitative analysis of collagen change between normal and cancerous thyroid tissues based on SHG method

NASA Astrophysics Data System (ADS)

Chen, Xiwen; Huang, Zufang; Xi, Gangqin; Chen, Yongjian; Lin, Duo; Wang, Jing; Li, Zuanfang; Sun, Liqing; Chen, Jianxin; Chen, Rong

2012-03-01

Second-harmonic generation (SHG) is proved to be a high spatial resolution, large penetration depth and non-photobleaching method. In our study, SHG method was used to investigate the normal and cancerous thyroid tissue. For SHG imaging performance, system parameters were adjusted for high-contrast images acquisition. Each x-y image was recorded in pseudo-color, which matches the wavelength range in the visible spectrum. The acquisition time for a 512×512-pixels image was 1.57 sec; each acquired image was averaged four frames to improve the signal-to-noise ratio. Our results indicated that collagen presence as determined by counting the ratio of the SHG pixels over the whole pixels for normal and cancerous thyroid tissues were 0.48+/-0.05, 0.33+/-0.06 respectively. In addition, to quantitatively assess collagen-related changes, we employed GLCM texture analysis to the SHG images. Corresponding results showed that the correlation both fell off with distance in normal and cancerous group. Calculated value of Corr50 (the distance where the correlation crossed 50% of the initial correlation) indicated significant difference. This study demonstrates that SHG method can be used as a complementary tool in thyroid histopathology.

In vivo EPR oximetry using an isotopically-substituted nitroxide: Potential for quantitative measurement of tissue oxygen

PubMed Central

Weaver, John; Burks, Scott R.; Liu, Ke Jian; Kao, Joseph P.Y.; Rosen, Gerald M.

2017-01-01

Variations in brain oxygen (O2) concentration can have profound effects on brain physiology. Thus, the ability to quantitate local O2 concentrations noninvasively in vivo could significantly enhance understanding of several brain pathologies. However, quantitative O2 mapping in the brain has proven difficult. The electron paramagnetic resonance (EPR) spectra of nitroxides are sensitive to molecular O2 and can be used to estimate O2 concentrations in aqueous media. We recently synthesized labile-ester-containing nitroxides, such as 3-acetoxymethoxycarbonyl-2,2,5,5-tetramethyl-1-pyrrolidinyloxyl (nitroxide 4), which accumulate in cerebral tissue after in situ hydrolysis, and thus enable spatial mapping of O2 concentrations in the mouse brain by EPR imaging. In an effort to improve O2 quantitation, we prepared 3-acetoxymethox ycarbonyl-2,2,5,5-tetra(2H3)methyl-1-(3,4,4-2H3,1-15N)pyrrolidinyloxyl (nitroxide 2), which proved to be a more sensitive probe than its normo-isotopic version for quantifying O2 in aqueous solutions of various O2 concentrations. We now demonstrate that this isotopically substituted nitroxide is ~2-fold more sensitive in vivo than the normo-isotopic nitroxide 4. Moreover, in vitro and in vivo EPR spectral-spatial imaging results with nitroxide 2 demonstrate significant improvement in resolution, reconstruction and spectral response to local O2 concentrations in cerebral tissue. Thus, isotopic-substituted nitroxides, such as 2, are excellent sensors for in vivo O2 quantitation in tissues, such as the brain. PMID:27567323

In vivo EPR oximetry using an isotopically-substituted nitroxide: Potential for quantitative measurement of tissue oxygen

NASA Astrophysics Data System (ADS)

Weaver, John; Burks, Scott R.; Liu, Ke Jian; Kao, Joseph P. Y.; Rosen, Gerald M.

2016-10-01

Variations in brain oxygen (O2) concentration can have profound effects on brain physiology. Thus, the ability to quantitate local O2 concentrations noninvasively in vivo could significantly enhance understanding of several brain pathologies. However, quantitative O2 mapping in the brain has proven difficult. The electron paramagnetic resonance (EPR) spectra of nitroxides are sensitive to molecular O2 and can be used to estimate O2 concentrations in aqueous media. We recently synthesized labile-ester-containing nitroxides, such as 3-acetoxymethoxycarbonyl-2,2,5,5-tetramethyl-1-pyrrolidinyloxyl (nitroxide 4), which accumulate in cerebral tissue after in situ hydrolysis, and thus enable spatial mapping of O2 concentrations in the mouse brain by EPR imaging. In an effort to improve O2 quantitation, we prepared 3-acetoxymethoxycarbonyl-2,2,5,5-tetra(2H3)methyl-1-(3,4,4-2H3,1-15N)pyrrolidinyloxyl (nitroxide 2), which proved to be a more sensitive probe than its normo-isotopic version for quantifying O2 in aqueous solutions of various O2 concentrations. We now demonstrate that this isotopically substituted nitroxide is ∼2-fold more sensitive in vivo than the normo-isotopic nitroxide 4. Moreover, in vitro and in vivo EPR spectral-spatial imaging results with nitroxide 2 demonstrate significant improvement in resolution, reconstruction and spectral response to local O2 concentrations in cerebral tissue. Thus, isotopic-substituted nitroxides, such as 2, are excellent sensors for in vivo O2 quantitation in tissues, such as the brain.

Quantitative bioimaging of p-boronophenylalanine in thin liver tissue sections as a tool for treatment planning in boron neutron capture therapy.

PubMed

Reifschneider, Olga; Schütz, Christian L; Brochhausen, Christoph; Hampel, Gabriele; Ross, Tobias; Sperling, Michael; Karst, Uwe

2015-03-01

An analytical method using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was developed and applied to assess enrichment of 10B-containing p-boronophenylalanine-fructose (BPA-f) and its pharmacokinetic distribution in human tissues after application for boron neutron capture therapy (BNCT). High spatial resolution (50 μm) and limits of detection in the low parts-per-billion range were achieved using a Nd:YAG laser of 213 nm wavelength. External calibration by means of 10B-enriched standards based on whole blood proved to yield precise quantification results. Using this calibration method, quantification of 10B in cancerous and healthy tissue was carried out. Additionally, the distribution of 11B was investigated, providing 10B enrichment in the investigated tissues. Quantitative imaging of 10B by means of LA-ICP-MS was demonstrated as a new option to characterise the efficacy of boron compounds for BNCT.

Anatomical and functional assessment of brown adipose tissue by magnetic resonance imaging.

PubMed

Chen, Y Iris; Cypess, Aaron M; Sass, Christina A; Brownell, Anna-Liisa; Jokivarsi, Kimmo T; Kahn, C Ronald; Kwong, Kenneth K

2012-07-01

Brown adipose tissue (BAT) is the primary tissue responsible for nonshivering thermogenesis in mammals. The amount of BAT and its level of activation help regulate the utilization of excessive calories for thermogenesis as opposed to storage in white adipose tissue (WAT) which would lead to weight gain. Over the past several years, BAT activity in vivo has been primarily assessed by positron emission tomography-computed tomography (PET-CT) scan using 2-[18F]-fluoro-2-deoxy-D-glucose (18F-FDG) to measure glucose utilization associated with BAT mitochondrial respiration. In this study, we demonstrate the feasibility of mapping and estimating BAT volume and metabolic function in vivo in rats at a 9.4T magnetic resonance imaging (MRI) scanner using sequences available from clinical MR scanners. Based on the morphological characteristics of BAT, we measured the volume distribution of BAT with MRI sequences that have strong fat-water contrast. We also investigated BAT volume by utilizing spin-echo MRI sequences. The in vivo MRI-estimated BAT volumes were correlated with direct measurement of BAT mass from dissected samples. Using MRI, we also were able to map hemodynamic responses to changes in BAT metabolism induced pharmacologically by β3-adrenergic receptor agonist, CL-316,243 and compare this to BAT activity in response to CL-316,243 assessed by PET 18F-FDG. In conclusion, we demonstrate the feasibility of measuring BAT volume and function in vivo using routine MRI sequences. The MRI measurement of BAT volume is consistent with quantitative measurement of the tissue ex vivo.

ACVP-11: Quantitative Assessment of Lymphoid Tissue Fibrosis in Formalin-Fixed Tissue Specimens | Frederick National Laboratory for Cancer Research

Cancer.gov

The Tissue Analysis Core (TAC) within the AIDS and Cancer Virus Program will process, embed, and perform microtomy on fixed tissue samples presented in ethanol. Collagen I, Collagen III, or Fibronectin immunohistochemistry will be performed, in order

The acellular matrix (ACM) for bladder tissue engineering: A quantitative magnetic resonance imaging study.

PubMed

Cheng, Hai-Ling Margaret; Loai, Yasir; Beaumont, Marine; Farhat, Walid A

2010-08-01

Bladder acellular matrices (ACMs) derived from natural tissue are gaining increasing attention for their role in tissue engineering and regeneration. Unlike conventional scaffolds based on biodegradable polymers or gels, ACMs possess native biomechanical and many acquired biologic properties. Efforts to optimize ACM-based scaffolds are ongoing and would be greatly assisted by a noninvasive means to characterize scaffold properties and monitor interaction with cells. MRI is well suited to this role, but research with MRI for scaffold characterization has been limited. This study presents initial results from quantitative MRI measurements for bladder ACM characterization and investigates the effects of incorporating hyaluronic acid, a natural biomaterial useful in tissue-engineering and regeneration. Measured MR relaxation times (T(1), T(2)) and diffusion coefficient were consistent with increased water uptake and glycosaminoglycan content observed on biochemistry in hyaluronic acid ACMs. Multicomponent MRI provided greater specificity, with diffusion data showing an acellular environment and T(2) components distinguishing the separate effects of increased glycosaminoglycans and hydration. These results suggest that quantitative MRI may provide useful information on matrix composition and structure, which is valuable in guiding further development using bladder ACMs for organ regeneration and in strategies involving the use of hyaluronic acid.

QUANTITATIVE PROCEDURES FOR NEUROTOXICOLOGY RISK ASSESSMENT

EPA Science Inventory

In this project, previously published information on biologically based dose-response model for brain development was used to quantitatively evaluate critical neurodevelopmental processes, and to assess potential chemical impacts on early brain development. This model has been ex...

Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags.

PubMed

Megger, Dominik Andre; Rosowski, Kristin; Ahrens, Maike; Bracht, Thilo; Eisenacher, Martin; Schlaak, Jörg F; Weber, Frank; Hoffmann, Andreas-Claudius; Meyer, Helmut E; Baba, Hideo A; Sitek, Barbara

2017-03-01

Human hepatocellular carcinoma (HCC) is a severe malignant disease, and accurate and reliable diagnostic markers are still needed. This study was aimed for the discovery of novel marker candidates by quantitative proteomics. Proteomic differences between HCC and nontumorous liver tissue were studied by mass spectrometry. Among several significantly upregulated proteins, translocator protein 18 (TSPO) and Ras-related protein Rab-1A (RAB1A) were selected for verification by immunohistochemistry in an independent cohort. For RAB1A, a high accuracy for the discrimination of HCC and nontumorous liver tissue was observed. RAB1A was verified to be a potent biomarker candidate for HCC.

Muscle and Myotendinous Tissue Properties at the Distal Tibia as Assessed by High-Resolution Peripheral Quantitative Computed Tomography.

PubMed

Erlandson, M C; Wong, A K O; Szabo, E; Vilayphiou, N; Zulliger, M A; Adachi, J D; Cheung, A M

High-resolution peripheral quantitative computed tomography (HR-pQCT) quantifies bone microstructure and density at the distal tibia where there is also a sizable amount of myotendinous (muscle and tendon) tissue (M T ); however, there is no method for the quantification of M T . This study aimed (1) to assess the feasibility of using HR-pQCT distal tibia scans to estimate M T properties using a custom algorithm, and (2) to determine the relationship between M T properties at the distal tibia and mid-leg muscle density (MD) obtained from pQCT. Postmenopausal women from the Hamilton cohort of the Canadian Multicenter Osteoporosis Study had a single-slice (2.3 ± 0.5 mm) 66% site pQCT scan measuring muscle cross-sectional area (MCSA) and MD. A standard HR-pQCT scan was acquired at the distal tibia. HR-pQCT-derived M T cross-sectional area (M T CSA) and M T density (M T D) were calculated using a custom algorithm in which thresholds (34.22-194.32 mg HA/cm 3 ) identified muscle seed volumes and were iteratively expanded. Pearson and Bland-Altman plots were used to assess correlations and systematic differences between pQCT- and HR-pQCT-derived muscle properties. Among 45 women (mean age: 74.6 ± 8.5 years, body mass index: 25.9 ± 4.3 kg/m 2 ), M T D was moderately correlated with mid-leg MD across the 2 modalities (r = 0.69-0.70, p < 0.01). Bland-Altman analyses revealed no evidence of directional bias for M T D-MD. HR-pQCT and pQCT measures of M T CSA and MCSA were moderately correlated (r = 0.44, p < 0.01). Bland-Altman plots for M T CSA revealed that larger MCSAs related to larger discrepancy between the distal and the mid-leg locations. This is the first study to assess the ability of HR-pQCT to measure M T size, density, and morphometry. HR-pQCT-derived M T D was moderately correlated with mid-leg MD from pQCT. This relationship suggests that distal M T may share common properties with muscle throughout the length of the leg

Probing myocardium biomechanics using quantitative optical coherence elastography

NASA Astrophysics Data System (ADS)

Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

2015-03-01

We present a quantitative optical coherence elastographic method for noncontact assessment of the myocardium elasticity. The method is based on shear wave imaging optical coherence tomography (SWI-OCT), where a focused air-puff system is used to induce localized tissue deformation through a low-pressure short-duration air stream and a phase-sensitive OCT system is utilized to monitor the propagation of the induced tissue displacement with nanoscale sensitivity. The 1-D scanning of M-mode OCT imaging and the application of optical phase retrieval and mapping techniques enable the reconstruction and visualization of 2-D depth-resolved shear wave propagation in tissue with ultra-high frame rate. The feasibility of this method in quantitative elasticity measurement is demonstrated on tissue-mimicking phantoms with the estimated Young's modulus compared with uniaxial compression tests. We also performed pilot experiments on ex vivo mouse cardiac muscle tissues with normal and genetically altered cardiomyocytes. Our results indicate this noncontact quantitative optical coherence elastographic method can be a useful tool for the cardiac muscle research and studies.

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.

Tissue Characterization with Quantitative High-Resolution Magic Angle Spinning Chemical Exchange Saturation Transfer Z-Spectroscopy.

PubMed

Zhou, Iris Yuwen; Fuss, Taylor L; Igarashi, Takahiro; Jiang, Weiping; Zhou, Xin; Cheng, Leo L; Sun, Phillip Zhe

2016-11-01

Chemical exchange saturation transfer (CEST) provides sensitive magnetic resonance (MR) contrast for probing dilute compounds via exchangeable protons, serving as an emerging molecular imaging methodology. CEST Z-spectrum is often acquired by sweeping radiofrequency saturation around bulk water resonance, offset by offset, to detect CEST effects at characteristic chemical shift offsets, which requires prolonged acquisition time. Herein, combining high-resolution magic angle spinning (HRMAS) with concurrent application of gradient and rf saturation to achieve fast Z-spectral acquisition, we demonstrated the feasibility of fast quantitative HRMAS CEST Z-spectroscopy. The concept was validated with phantoms, which showed excellent agreement with results obtained from conventional HRMAS MR spectroscopy (MRS). We further utilized the HRMAS Z-spectroscopy for fast ex vivo quantification of ischemic injury with rodent brain tissues after ischemic stroke. This method allows rapid and quantitative CEST characterization of biological tissues and shows potential for a host of biomedical applications.

[Assessment Method of Remnant α-1, 3-galactosyle Epitopes in Animal Tissue-derived Biomaterials].

PubMed

Shan, Yongqiang; Xu, Liming; Ke, Linnan; Lu, Yan; Shao, Anliang; Zhang, Na; Zeng, Bixin

2015-06-01

The aim of this study was to establish an assessment method for determining α-Gal (α-1, 3-galactosyle) epitopes contained in animal tissue or animal tissue-derived biological materials with ELISA inhibition assay. Firstly, a 96 well plate was coated with Gal α-1, 3-Gal/bovine serum albumin (BSA) as a solid phase antigen and meanwhile, the anti-α-Gal M86 was used to react with α-Gal antigens which contained in the test materials. Then, the residual antibodies (M86) in the supernatant of M86-Gal reaction mixture were measured using ELISA inhibition assay by the α-Gal coating plate. The inhibition curve of the ELISA inhibition assay, the R2 = 0.999, was well established. Checking using both α-Gal positive materials (rat liver tissues) and α-Gal negative materials (human placenta tissues) showed a good sensitivity and specificity. Based on the presently established method, the α-Gal expression profile of rat tissues, decellular animal tissue-derived biological materials and porcine dermal before and after decellular treatment were determined. The M86 ELISA inhibition assay method, which can quantitatively determine the α-Gal antigens contained in animal tissues or animal tissue-derived biomaterials, was refined. This M86 specific antibody based-ELISA inhibition assay established in the present study has good sensitivity and specificity, and could be a useful method for determining remnant α-1, 3Gal antigens in animal tissue-derived biomaterials.

Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging

NASA Astrophysics Data System (ADS)

Bassan, Paul; Sachdeva, Ashwin; Shanks, Jonathan H.; Brown, Mick D.; Clarke, Noel W.; Gardner, Peter

2014-03-01

Fourier transform infrared (FT-IR) chemical imaging has been demonstrated as a promising technique to complement histopathological assessment of biomedical tissue samples. Current histopathology practice involves preparing thin tissue sections and staining them using hematoxylin and eosin (H&E) after which a histopathologist manually assess the tissue architecture under a visible microscope. Studies have shown that there is disagreement between operators viewing the same tissue suggesting that a complementary technique for verification could improve the robustness of the evaluation, and improve patient care. FT-IR chemical imaging allows the spatial distribution of chemistry to be rapidly imaged at a high (diffraction-limited) spatial resolution where each pixel represents an area of 5.5 × 5.5 μm2 and contains a full infrared spectrum providing a chemical fingerprint which studies have shown contains the diagnostic potential to discriminate between different cell-types, and even the benign or malignant state of prostatic epithelial cells. We report a label-free (i.e. no chemical de-waxing, or staining) method of imaging large pieces of prostate tissue (typically 1 cm × 2 cm) in tens of minutes (at a rate of 0.704 × 0.704 mm2 every 14.5 s) yielding images containing millions of spectra. Due to refractive index matching between sample and surrounding paraffin, minimal signal processing is required to recover spectra with their natural profile as opposed to harsh baseline correction methods, paving the way for future quantitative analysis of biochemical signatures. The quality of the spectral information is demonstrated by building and testing an automated cell-type classifier based upon spectral features.

Assessing laser-tissue damage with bioluminescent imaging

NASA Astrophysics Data System (ADS)

Wilmink, Gerald J.; Opalenik, Susan R.; Beckham, Josh T.; Davidson, Jeffrey M.; Jansen, Eric D.

2006-07-01

Effective medical laser procedures are achieved by selecting laser parameters that minimize undesirable tissue damage. Traditionally, human subjects, animal models, and monolayer cell cultures have been used to study wound healing, tissue damage, and cellular effects of laser radiation. Each of these models has significant limitations, and consequently, a novel skin model is needed. To this end, a highly reproducible human skin model that enables noninvasive and longitudinal studies of gene expression was sought. In this study, we present an organotypic raft model (engineered skin) used in combination with bioluminescent imaging (BLI) techniques. The efficacy of the raft model was validated and characterized by investigating the role of heat shock protein 70 (hsp70) as a sensitive marker of thermal damage. The raft model consists of human cells incorporated into an extracellular matrix. The raft cultures were transfected with an adenovirus containing a murine hsp70 promoter driving transcription of luciferase. The model enables quantitative analysis of spatiotemporal expression of proteins using BLI. Thermal stress was induced on the raft cultures by means of a constant temperature water bath or with a carbon dioxide (CO2) laser (λ=10.6 µm, 0.679 to 2.262 W/cm2, cw, unfocused Gaussian beam, ωL=4.5 mm, 1 min exposure). The bioluminescence was monitored noninvasively with an IVIS 100 Bioluminescent Imaging System. BLI indicated that peak hsp70 expression occurs 4 to 12 h after exposure to thermal stress. A minimum irradiance of 0.679 W/cm2 activated the hsp70 response, and a higher irradiance of 2.262 W/cm2 was associated with a severe reduction in hsp70 response due to tissue ablation. Reverse transcription polymerase chain reaction demonstrated that hsp70 mRNA levels increased with prolonged heating exposures. Enzyme-linked immunosorbent protein assays confirmed that luciferase was an accurate surrogate for hsp70 intracellular protein levels. Hematoxylin and

Physiologic basis for understanding quantitative dehydration assessment.

PubMed

Cheuvront, Samuel N; Kenefick, Robert W; Charkoudian, Nisha; Sawka, Michael N

2013-03-01

Dehydration (body water deficit) is a physiologic state that can have profound implications for human health and performance. Unfortunately, dehydration can be difficult to assess, and there is no single, universal gold standard for decision making. In this article, we review the physiologic basis for understanding quantitative dehydration assessment. We highlight how phenomenologic interpretations of dehydration depend critically on the type (dehydration compared with volume depletion) and magnitude (moderate compared with severe) of dehydration, which in turn influence the osmotic (plasma osmolality) and blood volume-dependent compensatory thresholds for antidiuretic and thirst responses. In particular, we review new findings regarding the biological variation in osmotic responses to dehydration and discuss how this variation can help provide a quantitative and clinically relevant link between the physiology and phenomenology of dehydration. Practical measures with empirical thresholds are provided as a starting point for improving the practice of dehydration assessment.

Quantitation of Indoleacetic Acid Conjugates in Bean Seeds by Direct Tissue Hydrolysis 1

PubMed Central

Bialek, Krystyna; Cohen, Jerry D.

1989-01-01

Gas chromatography-selected ion monitoring-mass spectral analysis using [13C6]indole-3-acetic acid (IAA) as an internal standard provides an effective means for quantitation of IAA liberated during direct strong basic hydrolysis of bean (Phaseolus vulgaris L.) seed powder, provided that extra precautions are undertaken to exclude oxygen from the reaction vial. Direct seed powder hydrolysis revealed that the major portion of amide IAA conjugates in bean seeds are not extractable by aqueous acetone, the solvent used commonly for IAA conjugate extraction from seeds and other plant tissues. Strong basic hydrolysis of plant tissue can be used to provide new information on IAA content. Images Figure 1 PMID:16666783

Quantitative Evaluation of Atherosclerotic Plaque Using Ultrasound Tissue Characterization.

NASA Astrophysics Data System (ADS)

Yigiter, Ersin

comparing averaged power spectra in small time windows at different depths for a series of A-lines. Comparisons between consequent averaged spectra at different depths provided the magnitude and frequency dependence of attenuation. Non-invasive characterization of the physical state of the tissue with quantitative ultrasound holds great promise for the extension of the diagnostic power of conventional B-mode imaging.

Design of 3-D adipospheres for quantitative metabolic study

PubMed Central

Akama, Takeshi; Leung, Brendan M.; Labuz, Joseph M.; Takayama, Shuichi; Chun, Tae-Hwa

2017-01-01

Quantitative assessment of adipose mitochondrial activity is critical for better understanding of adipose tissue function in obesity and diabetes. While the two-dimensional (2-D) tissue culture method has been sufficient to discover key molecules that regulate adipocyte differentiation and function, the method is insufficient to determine the role of extracellular matrix (ECM) molecules and their modifiers, such as matrix metalloproteinases (MMPs), in regulating adipocyte function in three-dimensional (3-D) in vivo-like microenvironments. By using a 3-D hanging drop tissue culture system, we are able to produce scalable 3-D adipospheres that are suitable for quantitative mitochondrial study in 3-D microenvironment. PMID:28244051

Quantitative segmentation of fluorescence microscopy images of heterogeneous tissue: Approach for tuning algorithm parameters

NASA Astrophysics Data System (ADS)

Mueller, Jenna L.; Harmany, Zachary T.; Mito, Jeffrey K.; Kennedy, Stephanie A.; Kim, Yongbaek; Dodd, Leslie; Geradts, Joseph; Kirsch, David G.; Willett, Rebecca M.; Brown, J. Quincy; Ramanujam, Nimmi

2013-02-01

The combination of fluorescent contrast agents with microscopy is a powerful technique to obtain real time images of tissue histology without the need for fixing, sectioning, and staining. The potential of this technology lies in the identification of robust methods for image segmentation and quantitation, particularly in heterogeneous tissues. Our solution is to apply sparse decomposition (SD) to monochrome images of fluorescently-stained microanatomy to segment and quantify distinct tissue types. The clinical utility of our approach is demonstrated by imaging excised margins in a cohort of mice after surgical resection of a sarcoma. Representative images of excised margins were used to optimize the formulation of SD and tune parameters associated with the algorithm. Our results demonstrate that SD is a robust solution that can advance vital fluorescence microscopy as a clinically significant technology.

Quantitative fluorescence and elastic scattering tissue polarimetry using an Eigenvalue calibrated spectroscopic Mueller matrix system.

PubMed

Soni, Jalpa; Purwar, Harsh; Lakhotia, Harshit; Chandel, Shubham; Banerjee, Chitram; Kumar, Uday; Ghosh, Nirmalya

2013-07-01

A novel spectroscopic Mueller matrix system has been developed and explored for both fluorescence and elastic scattering polarimetric measurements from biological tissues. The 4 × 4 Mueller matrix measurement strategy is based on sixteen spectrally resolved (λ = 400 - 800 nm) measurements performed by sequentially generating and analyzing four elliptical polarization states. Eigenvalue calibration of the system ensured high accuracy of Mueller matrix measurement over a broad wavelength range, either for forward or backscattering geometry. The system was explored for quantitative fluorescence and elastic scattering spectroscopic polarimetric studies on normal and precancerous tissue sections from human uterine cervix. The fluorescence spectroscopic Mueller matrices yielded an interesting diattenuation parameter, exhibiting differences between normal and precancerous tissues.

Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics Using MicroPestle-Assisted Pressure-Cycling Technology.

PubMed

Shao, Shiying; Guo, Tiannan; Gross, Vera; Lazarev, Alexander; Koh, Ching Chiek; Gillessen, Silke; Joerger, Markus; Jochum, Wolfram; Aebersold, Ruedi

2016-06-03

The reproducible and efficient extraction of proteins from biopsy samples for quantitative analysis is a critical step in biomarker and translational research. Recently, we described a method consisting of pressure-cycling technology (PCT) and sequential windowed acquisition of all theoretical fragment ions-mass spectrometry (SWATH-MS) for the rapid quantification of thousands of proteins from biopsy-size tissue samples. As an improvement of the method, we have incorporated the PCT-MicroPestle into the PCT-SWATH workflow. The PCT-MicroPestle is a novel, miniaturized, disposable mechanical tissue homogenizer that fits directly into the microTube sample container. We optimized the pressure-cycling conditions for tissue lysis with the PCT-MicroPestle and benchmarked the performance of the system against the conventional PCT-MicroCap method using mouse liver, heart, brain, and human kidney tissues as test samples. The data indicate that the digestion of the PCT-MicroPestle-extracted proteins yielded 20-40% more MS-ready peptide mass from all tissues tested with a comparable reproducibility when compared to the conventional PCT method. Subsequent SWATH-MS analysis identified a higher number of biologically informative proteins from a given sample. In conclusion, we have developed a new device that can be seamlessly integrated into the PCT-SWATH workflow, leading to increased sample throughput and improved reproducibility at both the protein extraction and proteomic analysis levels when applied to the quantitative proteomic analysis of biopsy-level samples.

X-ray Phase Contrast Imaging of Calcified Tissue and Biomaterial Structure in Bioreactor Engineered Tissues

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

Appel, Alyssa A.; Larson, Jeffery C.; Garson, III, Alfred B.

2014-11-04

Tissues engineered in bioreactor systems have been used clinically to replace damaged tissues and organs. In addition, these systems are under continued development for many tissue engineering applications. The ability to quantitatively assess material structure and tissue formation is critical for evaluating bioreactor efficacy and for preimplantation assessment of tissue quality. These techniques allow for the nondestructive and longitudinal monitoring of large engineered tissues within the bioreactor systems and will be essential for the translation of these strategies to viable clinical therapies. X-ray Phase Contrast (XPC) imaging techniques have shown tremendous promise for a number of biomedical applications owing tomore » their ability to provide image contrast based on multiple X-ray properties, including absorption, refraction, and scatter. In this research, mesenchymal stem cell-seeded alginate hydrogels were prepared and cultured under osteogenic conditions in a perfusion bioreactor. The constructs were imaged at various time points using XPC microcomputed tomography (µCT). Imaging was performed with systems using both synchrotron- and tube-based X-ray sources. XPC µCT allowed for simultaneous three-dimensional (3D) quantification of hydrogel size and mineralization, as well as spatial information on hydrogel structure and mineralization. Samples were processed for histological evaluation and XPC showed similar features to histology and quantitative analysis consistent with the histomorphometry. Furthermore, these results provide evidence of the significant potential of techniques based on XPC for noninvasive 3D imaging engineered tissues grown in bioreactors.« less

Assessing the reporting of categorised quantitative variables in observational epidemiological studies.

PubMed

Mabikwa, Onkabetse V; Greenwood, Darren C; Baxter, Paul D; Fleming, Sarah J

2017-03-14

One aspect to consider when reporting results of observational studies in epidemiology is how quantitative risk factors are analysed. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines recommend that researchers describe how they handle quantitative variables when analysing data. For categorised quantitative variables, the authors are required to provide reasons and justifications informing their practice. We investigated and assessed the practices and reporting of categorised quantitative variables in epidemiology. The assessment was based on five medical journals that publish epidemiological research. Observational studies published between April and June 2015 and investigating the relationships between quantitative exposures (or risk factors) and the outcomes were considered for assessment. A standard form was used to collect the data, and the reporting patterns amongst eligible studies were quantified and described. Out of 61 articles assessed for eligibility, 23 observational studies were included in the assessment. Categorisation of quantitative exposures occurred in 61% of these studies and reasons informing the practice were rarely provided. Only one article explained the choice of categorisation in the analysis. Transformation of quantitative exposures into four or five groups was common and dominant amongst studies using equally spaced categories. Dichotomisation was not popular; the practice featured in one article. Overall, the majority (86%) of the studies preferred ordered or arbitrary group categories. Other criterions used to decide categorical boundaries were based on established guidelines such as consensus statements and WHO standards. Categorisation of continuous variables remains a dominant practice in epidemiological studies. The reasons informing the practice of categorisation within published work are limited and remain unknown in most articles. The existing STROBE guidelines could provide stronger

Quantitative brain tissue oximetry, phase spectroscopy and imaging the range of homeostasis in piglet brain.

PubMed

Chance, Britton; Ma, Hong Yan; Nioka, Shoko

2003-01-01

The quantification of tissue oxygen by frequency or time domain methods has been discussed in a number of prior publications where the meaning of the tissue hemoglobin oxygen saturation was unclear and where the CW instruments were unsuitable for proper quantitative measurements [1, 2]. The development of the IQ Phase Meter has greatly simplified and made reliable the difficult determination of precise phase and amplitude signals from brain. This contribution reports on the calibration of the instrument in model systems and the use of the instrument to measure tissue saturation (StO2) in a small animal model. In addition, a global interpretation of the meaning of tissue oxygen has been formulated based on the idea that autoregulation will maintain tissue oxygen at a fixed value over a range of arterial and venous oxygen values over the range of autoregulation. Beyond that range, the tissue oxygen is still correctly measured but, as expected, approaches the arterial saturation at low metabolic rates and the venous saturation at high metabolic rates of mitochondria.

Quantitative Prediction of Paravalvular Leak in Transcatheter Aortic Valve Replacement Based on Tissue-Mimicking 3D Printing.

PubMed

Qian, Zhen; Wang, Kan; Liu, Shizhen; Zhou, Xiao; Rajagopal, Vivek; Meduri, Christopher; Kauten, James R; Chang, Yung-Hang; Wu, Changsheng; Zhang, Chuck; Wang, Ben; Vannan, Mani A

2017-07-01

This study aimed to develop a procedure simulation platform for in vitro transcatheter aortic valve replacement (TAVR) using patient-specific 3-dimensional (3D) printed tissue-mimicking phantoms. We investigated the feasibility of using these 3D printed phantoms to quantitatively predict the occurrence, severity, and location of any degree of post-TAVR paravalvular leaks (PVL). We have previously shown that metamaterial 3D printing technique can be used to create patient-specific phantoms that mimic the mechanical properties of biological tissue. This may have applications in procedural planning for cardiovascular interventions. This retrospective study looked at 18 patients who underwent TAVR. Patient-specific aortic root phantoms were created using the tissue-mimicking 3D printing technique using pre-TAVR computed tomography. The CoreValve (self-expanding valve) prostheses were deployed in the phantoms to simulate the TAVR procedure, from which post-TAVR aortic root strain was quantified in vitro. A novel index, the annular bulge index, was measured to assess the post-TAVR annular strain unevenness in the phantoms. We tested the comparative predictive value of the bulge index and other known predictors of post-TAVR PVL. The maximum annular bulge index was significantly different among patient subgroups that had no PVL, trace-to-mild PVL, and moderate-to-severe PVL (p = 0.001). Compared with other known PVL predictors, bulge index was the only significant predictor of moderate-severe PVL (area under the curve = 95%; p < 0.0001). Also, in 12 patients with post-TAVR PVL, the annular bulge index predicted the major PVL location in 9 patients (accuracy = 75%). In this proof-of-concept study, we have demonstrated the feasibility of using 3D printed tissue-mimicking phantoms to quantitatively assess the post-TAVR aortic root strain in vitro. A novel indicator of the post-TAVR annular strain unevenness, the annular bulge index, outperformed the other

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Quantitative Measurement of Protease-Activity with Correction of Probe Delivery and Tissue Absorption Effects

PubMed Central

Salthouse, Christopher D.; Reynolds, Fred; Tam, Jenny M.; Josephson, Lee; Mahmood, Umar

2009-01-01

Proteases play important roles in a variety of pathologies from heart disease to cancer. Quantitative measurement of protease activity is possible using a novel spectrally matched dual fluorophore probe and a small animal lifetime imager. The recorded fluorescence from an activatable fluorophore, one that changes its fluorescent amplitude after biological target interaction, is also influenced by other factors including imaging probe delivery and optical tissue absorption of excitation and emission light. Fluorescence from a second spectrally matched constant (non-activatable) fluorophore on each nanoparticle platform can be used to correct for both probe delivery and tissue absorption. The fluorescence from each fluorophore is separated using fluorescence lifetime methods. PMID:20161242

MO-DE-303-03: Session on quantitative imaging for assessment of tumor response to radiation therapy

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

Bowen, S.

This session will focus on quantitative imaging for assessment of tumor response to radiation therapy. This is a technically challenging method to translate to practice in radiation therapy. In the new era of precision medicine, however, delivering the right treatment, to the right patient, and at the right time, can positively impact treatment choices and patient outcomes. Quantitative imaging provides the spatial sensitivity required by radiation therapy for precision medicine that is not available by other means. In this Joint ESTRO -AAPM Symposium, three leading-edge investigators will present specific motivations for quantitative imaging biomarkers in radiation therapy of esophageal, headmore » and neck, locally advanced non-small cell lung cancer, and hepatocellular carcinoma. Experiences with the use of dynamic contrast enhanced (DCE) MRI, diffusion- weighted (DW) MRI, PET/CT, and SPECT/CT will be presented. Issues covered will include: response prediction, dose-painting, timing between therapy and imaging, within-therapy biomarkers, confounding effects, normal tissue sparing, dose-response modeling, and association with clinical biomarkers and outcomes. Current information will be presented from investigational studies and clinical practice. Learning Objectives: Learn motivations for the use of quantitative imaging biomarkers for assessment of response to radiation therapy Review the potential areas of application in cancer therapy Examine the challenges for translation, including imaging confounds and paucity of evidence to date Compare exemplary examples of the current state of the art in DCE-MRI, DW-MRI, PET/CT and SPECT/CT imaging for assessment of response to radiation therapy Van der Heide: Research grants from the Dutch Cancer Society and the European Union (FP7) Bowen: RSNA Scholar grant.« less

A quantitative swab is a good non-invasive alternative to a quantitative biopsy for quantifying bacterial load in wounds healing by second intention in horses.

PubMed

Van Hecke, L L; Hermans, K; Haspeslagh, M; Chiers, K; Pint, E; Boyen, F; Martens, A M

2017-07-01

The aim of this study was to evaluate different techniques for diagnosing wound infection in wounds healing by second intention in horses and to assess the effect of a vortex and sonication protocol on quantitative bacteriology in specimens with a histologically confirmed biofilm. In 50 wounds healing by second intention, a clinical assessment, a quantitative swab, a semi-quantitative swab, and a swab for cytology were compared to a quantitative tissue biopsy (reference standard). Part of the biopsy specimen was examined histologically for evidence of a biofilm. There was a significant, high correlation (P<0.001; r=0.747) between the outcome of the quantitative swabs and the quantitative biopsies. The semi-quantitative swabs showed a significant, moderate correlation with the quantitative biopsies (P<0.001; ρ=0.524). Higher white blood cell counts for cytology were significantly associated with lower log 10 colony-forming units (CFU) in the wounds (P=0.02). Wounds with black granulation tissue showed significantly higher log 10 CFU (P=0.003). Specimens with biofilms did not yield higher bacteriological counts after a vortex and sonication protocol was performed to release bacteria from the biofilm. Based on these findings, a quantitative swab is an acceptable non-invasive alternative to a quantitative biopsy for quantifying bacterial load in equine wounds healing by second intention. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantitative assessment of reactive hyperemia using laser speckle contrast imaging at multiple wavelengths

NASA Astrophysics Data System (ADS)

Young, Anthony; Vishwanath, Karthik

2016-03-01

Reactive hyperemia refers to an increase of blood flow in tissue post release of an occlusion in the local vasculature. Measuring the temporal response of reactive hyperemia, post-occlusion in patients has the potential to shed information about microvascular diseases such as systemic sclerosis and diabetes. Laser speckle contrast imaging (LSCI) is an imaging technique capable of sensing superficial blood flow in tissue which can be used to quantitatively assess reactive hyperemia. Here, we employ LSCI using coherent sources in the blue, green and red wavelengths to evaluate reactive hyperemia in healthy human volunteers. Blood flow in the forearms of subjects were measured using LSCI to assess the time-course of reactive hyperemia that was triggered by a pressure cuff applied to the biceps of the subjects. Raw speckle images were acquired and processed to yield blood-flow parameters from a region of interest before, during and after application of occlusion. Reactive hyperemia was quantified via two measures - (1) by calculating the difference between the peak LSCI flow during the hyperemia and baseline flow, and (2) by measuring the amount of time that elapsed between the release of the occlusion and peak flow. These measurements were acquired in three healthy human participants, under the three laser wavelengths employed. The studies shed light on the utility of in vivo LSCI-based flow sensing for non-invasive assessment of reactive hyperemia responses and how they varied with the choice source wavelength influences the measured parameters.

Assessment of FUS-Tissue Interactions In Vivo

NASA Astrophysics Data System (ADS)

Haritonova, Alyona V.

Focused ultrasound (FUS) has been proposed for a variety of minimally invasive therapeutic applications, including tumor ablation, neuromodulation, targeted drug delivery and blood brain barrier opening. To date, FUS beams have been primarily monitored through MR and ultrasound diagnostic imaging modalities. The recent introduction of real-time dual-mode ultrasound array (DMUA) systems offers a new paradigm for the guidance of therapeutic focused ultrasound. The DMUA approach allows for inherent registration between the therapeutic and imaging coordinate systems. In this thesis we investigated the use of ultrasound-based thermography to assess FUS-tissue interactions. Specifically, we focused on two aspects of image-guided therapy: 1) monitoring and localization of FUS-tissue interactions, and 2) tissue damage assessment. Towards this end, we presented first experimental results of ultrasound-guided transcranial FUS in a rat brain, both ex vivo and in vivo. DMUA imaging was used to monitor and localize FUS-tissue thermal interactions in real-time. The transcranial echo data allowed for a reliable estimation of temperature change in brain tissue, which had never been done before using ultrasound image guidance. Despite some measurable distortion and loss in focusing gain, transcranial FUS beams at 3.2 MHz were localized axially and laterally. This confirms the results obtained using DMUA-based transcranial ultrasound thermography. A high degree of focusing with the DMUA was then successfully leveraged to perform localized tissue damage assessment in both ex vivo and in vivo. The experimental results presented in this thesis demonstrate some of the unique aspects of image guidance using DMUAs, especially when FUS is subject to significant distortions as in transcranial applications.

Traction force microscopy of engineered cardiac tissues.

PubMed

Pasqualini, Francesco Silvio; Agarwal, Ashutosh; O'Connor, Blakely Bussie; Liu, Qihan; Sheehy, Sean P; Parker, Kevin Kit

2018-01-01

Cardiac tissue development and pathology have been shown to depend sensitively on microenvironmental mechanical factors, such as extracellular matrix stiffness, in both in vivo and in vitro systems. We present a novel quantitative approach to assess cardiac structure and function by extending the classical traction force microscopy technique to tissue-level preparations. Using this system, we investigated the relationship between contractile proficiency and metabolism in neonate rat ventricular myocytes (NRVM) cultured on gels with stiffness mimicking soft immature (1 kPa), normal healthy (13 kPa), and stiff diseased (90 kPa) cardiac microenvironments. We found that tissues engineered on the softest gels generated the least amount of stress and had the smallest work output. Conversely, cardiomyocytes in tissues engineered on healthy- and disease-mimicking gels generated significantly higher stresses, with the maximal contractile work measured in NRVM engineered on gels of normal stiffness. Interestingly, although tissues on soft gels exhibited poor stress generation and work production, their basal metabolic respiration rate was significantly more elevated than in other groups, suggesting a highly ineffective coupling between energy production and contractile work output. Our novel platform can thus be utilized to quantitatively assess the mechanotransduction pathways that initiate tissue-level structural and functional remodeling in response to substrate stiffness.

Non-invasive tissue temperature measurements based on quantitative diffuse optical spectroscopy (DOS) of water.

PubMed

Chung, S H; Cerussi, A E; Merritt, S I; Ruth, J; Tromberg, B J

2010-07-07

We describe the development of a non-invasive method for quantitative tissue temperature measurements using Broadband diffuse optical spectroscopy (DOS). Our approach is based on well-characterized opposing shifts in near-infrared (NIR) water absorption spectra that appear with temperature and macromolecular binding state. Unlike conventional reflectance methods, DOS is used to generate scattering-corrected tissue water absorption spectra. This allows us to separate the macromolecular bound water contribution from the thermally induced spectral shift using the temperature isosbestic point at 996 nm. The method was validated in intralipid tissue phantoms by correlating DOS with thermistor measurements (R=0.96) with a difference of 1.1+/-0.91 degrees C over a range of 28-48 degrees C. Once validated, thermal and hemodynamic (i.e. oxy- and deoxy-hemoglobin concentration) changes were measured simultaneously and continuously in human subjects (forearm) during mild cold stress. DOS-measured arm temperatures were consistent with previously reported invasive deep tissue temperature studies. These results suggest that DOS can be used for non-invasive, co-registered measurements of absolute temperature and hemoglobin parameters in thick tissues, a potentially important approach for optimizing thermal diagnostics and therapeutics.

Multiview hyperspectral topography of tissue structural and functional characteristics

NASA Astrophysics Data System (ADS)

Zhang, Shiwu; Liu, Peng; Huang, Jiwei; Xu, Ronald

2012-12-01

Accurate and in vivo characterization of structural, functional, and molecular characteristics of biological tissue will facilitate quantitative diagnosis, therapeutic guidance, and outcome assessment in many clinical applications, such as wound healing, cancer surgery, and organ transplantation. However, many clinical imaging systems have limitations and fail to provide noninvasive, real time, and quantitative assessment of biological tissue in an operation room. To overcome these limitations, we developed and tested a multiview hyperspectral imaging system. The multiview hyperspectral imaging system integrated the multiview and the hyperspectral imaging techniques in a single portable unit. Four plane mirrors are cohered together as a multiview reflective mirror set with a rectangular cross section. The multiview reflective mirror set was placed between a hyperspectral camera and the measured biological tissue. For a single image acquisition task, a hyperspectral data cube with five views was obtained. The five-view hyperspectral image consisted of a main objective image and four reflective images. Three-dimensional topography of the scene was achieved by correlating the matching pixels between the objective image and the reflective images. Three-dimensional mapping of tissue oxygenation was achieved using a hyperspectral oxygenation algorithm. The multiview hyperspectral imaging technique is currently under quantitative validation in a wound model, a tissue-simulating blood phantom, and an in vivo biological tissue model. The preliminary results have demonstrated the technical feasibility of using multiview hyperspectral imaging for three-dimensional topography of tissue functional properties.

Histological Assessment of PAXgene Tissue Fixation and Stabilization Reagents

PubMed Central

Kap, Marcel; Smedts, Frank; Oosterhuis, Wolter; Winther, Rosa; Christensen, Nanna; Reischauer, Bilge; Viertler, Christian; Groelz, Daniel; Becker, Karl-Friedrich; Zatloukal, Kurt; Langer, Rupert; Slotta-Huspenina, Julia; Bodo, Koppany; de Jong, Bas; Oelmuller, Uwe; Riegman, Peter

2011-01-01

Within SPIDIA, an EC FP7 project aimed to improve pre analytic procedures, the PAXgene Tissue System (PAXgene), was designed to improve tissue quality for parallel molecular and morphological analysis. Within the SPIDIA project promising results were found in both genomic and proteomic experiments with PAXgene-fixed and paraffin embedded tissue derived biomolecules. But, for this technology to be accepted for use in both clinical and basic research, it is essential that its adequacy for preserving morphology and antigenicity is validated relative to formalin fixation. It is our aim to assess the suitability of PAXgene tissue fixation for (immuno)histological methods. Normal human tissue specimens (n = 70) were collected and divided into equal parts for fixation either with formalin or PAXgene. Sections of the obtained paraffin-embedded tissue were cut and stained. Morphological aspects of PAXgene-fixed tissue were described and also scored relative to formalin-fixed tissue. Performance of PAXgene-fixed tissue in immunohistochemical and in situ hybridization assays was also assessed relative to the corresponding formalin-fixed tissues. Morphology of PAXgene-fixed paraffin embedded tissue was well preserved and deemed adequate for diagnostics in most cases. Some antigens in PAXgene-fixed and paraffin embedded sections were detectable without the need for antigen retrieval, while others were detected using standard, formalin fixation based, immunohistochemistry protocols. Comparable results were obtained with in situ hybridization and histochemical stains. Basically all assessed histological techniques were found to be applicable to PAXgene-fixed and paraffin embedded tissue. In general results obtained with PAXgene-fixed tissue are comparable to those of formalin-fixed tissue. Compromises made in morphology can be called minor compared to the advantages in the molecular pathology possibilities. PMID:22110732

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

PubMed

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

2015-04-01

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

A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues.

PubMed

Ying, Dingge; Li, Mulin Jun; Sham, Pak Chung; Li, Miaoxin

2018-04-26

Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach. The approach has a powerful design of reducing computational burden by the utilization of regulatory predictions for candidate SNP selection and multiple testing corrections on non-independent haplotypes. The application results in multiple tissues showed that haplotype-based eQTLs not only increased the number of eQTL genes in a tissue specific manner, but were also enriched in loci that associated with complex traits in a tissue-matched manner. In addition, we found that tag SNPs of eQTL haplotypes from whole blood were selectively enriched in certain combination of regulatory elements (e.g. promoters and enhancers) according to predicted chromatin states. In summary, this eQTL haplotype detection approach, together with the application results, shed insights into synergistic effect of sequence variants on gene expression and their susceptibility to complex diseases. The executable application "eHaplo" is implemented in Java and is publicly available at http://grass.cgs.hku.hk/limx/ehaplo/. jonsonfox@gmail.com, limiaoxin@mail.sysu.edu.cn. Supplementary data are available at Bioinformatics online.

Assessment of deep tissue hyperalgesia in the groin - a method comparison of electrical vs. pressure stimulation.

PubMed

Aasvang, E K; Werner, M U; Kehlet, H

2014-09-01

Deep pain complaints are more frequent than cutaneous in post-surgical patients, and a prevalent finding in quantitative sensory testing studies. However, the preferred assessment method - pressure algometry - is indirect and tissue unspecific, hindering advances in treatment and preventive strategies. Thus, there is a need for development of methods with direct stimulation of suspected hyperalgesic tissues to identify the peripheral origin of nociceptive input. We compared the reliability of an ultrasound-guided needle stimulation protocol of electrical detection and pain thresholds to pressure algometry, by performing identical test-retest sequences 10 days apart, in deep tissues in the groin region. Electrical stimulation was performed by five up-and-down staircase series of single impulses of 0.04 ms duration, starting from 0 mA in increments of 0.2 mA until a threshold was reached and descending until sensation was lost. Method reliability was assessed by Bland-Altman plots, descriptive statistics, coefficients of variance and intraclass correlation coefficients. The electrical stimulation method was comparable to pressure algometry regarding 10 days test-retest repeatability, but with superior same-day reliability for electrical stimulation (P < 0.05). Between-subject variance rather than within-subject variance was the main source for test variation. There were no systematic differences in electrical thresholds across tissues and locations (P > 0.05). The presented tissue-specific direct deep tissue electrical stimulation technique has equal or superior reliability compared with the indirect tissue-unspecific stimulation by pressure algometry. This method may facilitate advances in mechanism based preventive and treatment strategies in acute and chronic post-surgical pain states. © 2014 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Rock Slide Risk Assessment: A Semi-Quantitative Approach

NASA Astrophysics Data System (ADS)

Duzgun, H. S. B.

2009-04-01

Rock slides can be better managed by systematic risk assessments. Any risk assessment methodology for rock slides involves identification of rock slide risk components, which are hazard, elements at risk and vulnerability. For a quantitative/semi-quantitative risk assessment for rock slides, a mathematical value the risk has to be computed and evaluated. The quantitative evaluation of risk for rock slides enables comparison of the computed risk with the risk of other natural and/or human-made hazards and providing better decision support and easier communication for the decision makers. A quantitative/semi-quantitative risk assessment procedure involves: Danger Identification, Hazard Assessment, Elements at Risk Identification, Vulnerability Assessment, Risk computation, Risk Evaluation. On the other hand, the steps of this procedure require adaptation of existing or development of new implementation methods depending on the type of landslide, data availability, investigation scale and nature of consequences. In study, a generic semi-quantitative risk assessment (SQRA) procedure for rock slides is proposed. The procedure has five consecutive stages: Data collection and analyses, hazard assessment, analyses of elements at risk and vulnerability and risk assessment. The implementation of the procedure for a single rock slide case is illustrated for a rock slope in Norway. Rock slides from mountain Ramnefjell to lake Loen are considered to be one of the major geohazards in Norway. Lake Loen is located in the inner part of Nordfjord in Western Norway. Ramnefjell Mountain is heavily jointed leading to formation of vertical rock slices with height between 400-450 m and width between 7-10 m. These slices threaten the settlements around Loen Valley and tourists visiting the fjord during summer season, as the released slides have potential of creating tsunami. In the past, several rock slides had been recorded from the Mountain Ramnefjell between 1905 and 1950. Among them

Qualitative and quantitative observations of bone tissue reactions to anodised implants.

PubMed

Sul, Young-Taeg; Johansson, Carina B; Röser, Kerstin; Albrektsson, Tomas

2002-04-01

Research projects focusing on biomaterials related factors; the bulk implant material, the macro-design of the implant and the microsurface roughness are routinely being conducted at our laboratories. In this study, we have investigated the bone tissue reactions to turned commercially pure (c.p.) titanium implants with various thicknesses of the oxide films after 6 weeks of insertion in rabbit bone. The control c.p. titanium implants had an oxide thickness of 17-200 nm while the test implants revealed an oxide thickness between 600 and 1000 nm. Routine histological investigations of the tissue reactions around the implants and enzyme histochemical detections of alkaline and acid phosphatase activities demonstrated similar findings around both the control and test implants. In general, the histomorphometrical parameters (bone to implant contact and newly formed bone) revealed significant quantitative differences between the control and test implants. The test implants demonstrated a greater bone response histomorphometrically than control implants and the osteoconductivity was more pronounced around the test implant surfaces. The parameters that differed between the implant surfaces, i.e. the oxide thickness, the pore size distribution, the porosity and the crystallinity of the surface oxides may represent factors that have an influence on the histomorphometrical results indicated by a stronger bone tissue response to the test implant surfaces, with an oxide thickness of more than 600 nm.

Cartilage T2 assessment: differentiation of normal hyaline cartilage and reparative tissue after arthroscopic cartilage repair in equine subjects.

PubMed

White, Lawrence M; Sussman, Marshall S; Hurtig, Mark; Probyn, Linda; Tomlinson, George; Kandel, Rita

2006-11-01

To prospectively assess T2 mapping characteristics of normal articular cartilage and of cartilage at sites of arthroscopic repair, including comparison with histologic results and collagen organization assessed at polarized light microscopy (PLM). Study protocol was compliant with the Canadian Council on Animal Care Guidelines and approved by the institutional animal care committee. Arthroscopic osteochondral autograft transplantation (OAT) and microfracture arthroplasty (MFx) were performed in knees of 10 equine subjects (seven female, three male; age range, 3-5 years). A site of arthroscopically normal cartilage was documented in each joint as a control site. Joints were harvested at 12 (n = 5) and 24 (n = 5) weeks postoperatively and were imaged at 1.5-T magnetic resonance (MR) with a 10-echo sagittal fast spin-echo acquisition. T2 maps of each site (21 OAT harvest, 10 MFx, 12 OAT plug, and 10 control sites) were calculated with linear least-squares curve fitting. Cartilage T2 maps were qualitatively graded as "organized" (normal transition of low-to-high T2 signal from deep to superficial cartilage zones) or "disorganized." Quantitative mean T2 values were calculated for deep, middle, and superficial cartilage at each location. Results were compared with histologic and PLM assessments by using kappa analysis. T2 maps were qualitatively graded as organized at 20 of 53 sites and as disorganized at 33 sites. Perfect agreement was seen between organized T2 and histologic findings of hyaline cartilage and between disorganized T2 and histologic findings of fibrous reparative tissue (kappa = 1.0). Strong agreement was seen between organized T2 and normal PLM findings and between disorganized T2 and abnormal PLM findings (kappa = .92). Quantitative assessment of the deep, middle, and superficial cartilage, respectively, showed mean T2 values of 53.3, 58.6, and 54.9 msec at reparative fibrous tissue sites and 40.7, 53.6, and 61.6 msec at hyaline cartilage sites. A

Quantitative Assessment of the Heterogeneity of PD-L1 Expression in Non-Small-Cell Lung Cancer.

PubMed

McLaughlin, Joseph; Han, Gang; Schalper, Kurt A; Carvajal-Hausdorf, Daniel; Pelekanou, Vasiliki; Rehman, Jamaal; Velcheti, Vamsidhar; Herbst, Roy; LoRusso, Patricia; Rimm, David L

2016-01-01

Early-phase trials with monoclonal antibodies targeting PD-1 (programmed cell death protein 1) and PD-L1 (programmed cell death 1 ligand 1) have demonstrated durable clinical responses in patients with non-small-cell lung cancer (NSCLC). However, current assays for the prognostic and/or predictive role of tumor PD-L1 expression are not standardized with respect to either quantity or distribution of expression. To demonstrate PD-L1 protein distribution in NSCLC tumors using both conventional immunohistochemistry (IHC) and quantitative immunofluorescence (QIF) and compare results obtained using 2 different PD-L1 antibodies. PD-L1 was measured using E1L3N and SP142, 2 rabbit monoclonal antibodies, in 49 NSCLC whole-tissue sections and a corresponding tissue microarray with the same 49 cases. Non-small-cell lung cancer biopsy specimens from 2011 to 2012 were collected retrospectively from the Yale Thoracic Oncology Program Tissue Bank. Human melanoma Mel 624 cells stably transfected with PD-L1 as well as Mel 624 parental cells, and human term placenta whole tissue sections were used as controls and for antibody validation. PD-L1 protein expression in tumor and stroma was assessed using chromogenic IHC and the AQUA (Automated Quantitative Analysis) method of QIF. Tumor-infiltrating lymphocytes (TILs) were scored in hematoxylin-eosin slides using current consensus guidelines. The association between PD-L1 protein expression, TILs, and clinicopathological features were determined. PD-L1 expression discordance or heterogeneity using the diaminobenzidine chromogen and QIF was the main outcome measure selected prior to performing the study. Using chromogenic IHC, both antibodies showed fair to poor concordance. The PD-L1 antibodies showed poor concordance (Cohen κ range, 0.124-0.340) using conventional chromogenic IHC and showed intra-assay heterogeneity (E1L3N coefficient of variation [CV], 6.75%-75.24%; SP142 CV, 12.17%-109.61%) and significant interassay discordance

Some suggested future directions of quantitative resource assessments

USGS Publications Warehouse

Singer, D.A.

2001-01-01

Future quantitative assessments will be expected to estimate quantities, values, and locations of undiscovered mineral resources in a form that conveys both economic viability and uncertainty associated with the resources. Historically, declining metal prices point to the need for larger deposits over time. Sensitivity analysis demonstrates that the greatest opportunity for reducing uncertainty in assessments lies in lowering uncertainty associated with tonnage estimates. Of all errors possible in assessments, those affecting tonnage estimates are by far the most important. Selecting the correct deposit model is the most important way of controlling errors because the dominance of tonnage-deposit models are the best known predictor of tonnage. Much of the surface is covered with apparently barren rocks and sediments in many large regions. Because many exposed mineral deposits are believed to have been found, a prime concern is the presence of possible mineralized rock under cover. Assessments of areas with resources under cover must rely on extrapolation from surrounding areas, new geologic maps of rocks under cover, or analogy with other well-explored areas that can be considered training tracts. Cover has a profound effect on uncertainty and on methods and procedures of assessments because geology is seldom known and geophysical methods typically have attenuated responses. Many earlier assessment methods were based on relationships of geochemical and geophysical variables to deposits learned from deposits exposed on the surface-these will need to be relearned based on covered deposits. Mineral-deposit models are important in quantitative resource assessments for two reasons: (1) grades and tonnages of most deposit types are significantly different, and (2) deposit types are present in different geologic settings that can be identified from geologic maps. Mineral-deposit models are the keystone in combining the diverse geoscience information on geology, mineral

The quantitative assessment of epicardial fat distribution on human hearts: Implications for epicardial electrophysiology.

PubMed

Mattson, Alexander R; Soto, Mario J; Iaizzo, Paul A

2018-07-01

Epicardial electrophysiological procedures rely on dependable interfacing with the myocardial tissue. For example, epicardial pacing systems must generate sustainable chronic pacing capture, while epicardial ablations must effectively deliver energy to the target hyper-excitable myocytes. The human heart has a significant adipose layer which may impede epicardial procedures. The objective of this study was to quantitatively assess the relative location of epicardial adipose on the human heart, to define locations where epicardial therapies might be performed successfully. We studied perfusion-fixed human hearts (n = 105) in multiple isolated planes including: left ventricular margin, diaphragmatic surface, and anterior right ventricle. Relative adipose distribution was quantitatively assessed via planar images, using a custom-generated image analysis algorithm. In these specimens, 76.7 ± 13.8% of the left ventricular margin, 72.7 ± 11.3% of the diaphragmatic surface, and 92.1 ± 8.7% of the anterior right margin were covered with superficial epicardial adipose layers. Percent adipose coverage significantly increased with age (P < 0.001) and history of coronary artery disease (P < 0.05). No significant relationships were identified between relative percent adipose coverage and gender, body weight or height, BMI, history of hypertension, and/or history of congestive heart failure. Additionally, we describe two-dimensional probability distributions of epicardial adipose coverage for each of the three analysis planes. In this study, we detail the quantitative assessment and probabilistic mapping of the distribution of superficial epicardial adipose on the adult human heart. These findings have implications relative to performing epicardial procedures and/or designing procedures or tools to successfully perform such treatments. Clin. Anat. 31:661-666, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging.

PubMed

Bonekamp, S; Ghosh, P; Crawford, S; Solga, S F; Horska, A; Brancati, F L; Diehl, A M; Smith, S; Clark, J M

2008-01-01

To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Feature evaluation and test-retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. A random sample of 15 obese adults with type 2 diabetes. Axial T1-weighted spin echo images centered at vertebral bodies of L2-L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test-retest reliability. Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test-retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could

Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging

PubMed Central

Bonekamp, S; Ghosh, P; Crawford, S; Solga, SF; Horska, A; Brancati, FL; Diehl, AM; Smith, S; Clark, JM

2009-01-01

Objective To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Design Feature evaluation and test–retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. Subjects A random sample of 15 obese adults with type 2 diabetes. Measurements Axial T1-weighted spin echo images centered at vertebral bodies of L2–L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test–retest reliability. Results Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test–retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Conclusion Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

Distinguishing nanomaterial particles from background airborne particulate matter for quantitative exposure assessment

NASA Astrophysics Data System (ADS)

Ono-Ogasawara, Mariko; Serita, Fumio; Takaya, Mitsutoshi

2009-10-01

As the production of engineered nanomaterials quantitatively expands, the chance that workers involved in the manufacturing process will be exposed to nanoparticles also increases. A risk management system is needed for workplaces in the nanomaterial industry based on the precautionary principle. One of the problems in the risk management system is difficulty of exposure assessment. In this article, examples of exposure assessment in nanomaterial industries are reviewed with a focus on distinguishing engineered nanomaterial particles from background nanoparticles in workplace atmosphere. An approach by JNIOSH (Japan National Institute of Occupational Safety and Health) to quantitatively measure exposure to carbonaceous nanomaterials is also introduced. In addition to real-time measurements and qualitative analysis by electron microscopy, quantitative chemical analysis is necessary for quantitatively assessing exposure to nanomaterials. Chemical analysis is suitable for quantitative exposure measurement especially at facilities with high levels of background NPs.

Investigation of the feasibility of non-invasive optical sensors for the quantitative assessment of dehydration.

PubMed

Visser, Cobus; Kieser, Eduard; Dellimore, Kiran; van den Heever, Dawie; Smith, Johan

2017-10-01

This study explores the feasibility of prospectively assessing infant dehydration using four non-invasive, optical sensors based on the quantitative and objective measurement of various clinical markers of dehydration. The sensors were investigated to objectively and unobtrusively assess the hydration state of an infant based on the quantification of capillary refill time (CRT), skin recoil time (SRT), skin temperature profile (STP) and skin tissue hydration by means of infrared spectrometry (ISP). To evaluate the performance of the sensors a clinical study was conducted on a cohort of 10 infants (aged 6-36 months) with acute gastroenteritis. High sensitivity and specificity were exhibited by the sensors, in particular the STP and SRT sensors, when combined into a fusion regression model (sensitivity: 0.90, specificity: 0.78). The SRT and STP sensors and the fusion model all outperformed the commonly used "gold standard" clinical dehydration scales including the Gorelick scale (sensitivity: 0.56, specificity: 0.56), CDS scale (sensitivity: 1.0, specificity: 0.2) and WHO scale (sensitivity: 0.13, specificity: 0.79). These results suggest that objective and quantitative assessment of infant dehydration may be possible using the sensors investigated. However, further evaluation of the sensors on a larger sample population is needed before deploying them in a clinical setting. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Characterization of human oral tissues based on quantitative analysis of optical coherence tomography images

NASA Astrophysics Data System (ADS)

Salehi, Hassan S.; Kosa, Ali; Mahdian, Mina; Moslehpour, Saeid; Alnajjar, Hisham; Tadinada, Aditya

2017-02-01

In this paper, five types of tissues, human enamel, human cortical bone, human trabecular bone, muscular tissue, and fatty tissue were imaged ex vivo using optical coherence tomography (OCT). The specimens were prepared in blocks of 5 x 5 x 3 mm (width x length x height). The OCT imaging system was a swept source OCT system operating at wavelengths ranging between 1250 nm and 1360 nm with an average power of 18 mW and a scan rate of 50 to 100 kHz. The imaging probe was placed on top of a 2 x 2 cm stabilizing device to maintain a standard distance from the samples. Ten image samples from each type of tissue were obtained. To acquire images with minimum inhomogeneity, imaging was performed multiple times at different points. Based on the observed texture differences between OCT images of soft and hard tissues, spatial and spectral features were quantitatively extracted from the OCT images. The Radon transform from angles of 0 deg to 90 deg was computed, averaged over all the angles, normalized to peak at unity, and then fitted with Gaussian function. The mean absolute values of the spatial frequency components of the OCT image were considered as a feature, where 2-D fast Fourier transform (FFT) was done to OCT images. These OCT features can reliably differentiate between a range of hard and soft tissues, and could be extremely valuable in assisting dentists for in vivo evaluation of oral tissues and early detection of pathologic changes in tissues.

Method for accurate quantitation of background tissue optical properties in the presence of emission from a strong fluorescence marker

NASA Astrophysics Data System (ADS)

Bravo, Jaime; Davis, Scott C.; Roberts, David W.; Paulsen, Keith D.; Kanick, Stephen C.

2015-03-01

Quantification of targeted fluorescence markers during neurosurgery has the potential to improve and standardize surgical distinction between normal and cancerous tissues. However, quantitative analysis of marker fluorescence is complicated by tissue background absorption and scattering properties. Correction algorithms that transform raw fluorescence intensity into quantitative units, independent of absorption and scattering, require a paired measurement of localized white light reflectance to provide estimates of the optical properties. This study focuses on the unique problem of developing a spectral analysis algorithm to extract tissue absorption and scattering properties from white light spectra that contain contributions from both elastically scattered photons and fluorescence emission from a strong fluorophore (i.e. fluorescein). A fiber-optic reflectance device was used to perform measurements in a small set of optical phantoms, constructed with Intralipid (1% lipid), whole blood (1% volume fraction) and fluorescein (0.16-10 μg/mL). Results show that the novel spectral analysis algorithm yields accurate estimates of tissue parameters independent of fluorescein concentration, with relative errors of blood volume fraction, blood oxygenation fraction (BOF), and the reduced scattering coefficient (at 521 nm) of <7%, <1%, and <22%, respectively. These data represent a first step towards quantification of fluorescein in tissue in vivo.

Basic investigation on acoustic velocity change imaging method for quantitative assessment of fat content in human liver

NASA Astrophysics Data System (ADS)

Mano, Kazune; Tanigawa, Shohei; Hori, Makoto; Yokota, Daiki; Wada, Kenji; Matsunaka, Toshiyuki; Morikawa, Hiroyasu; Horinaka, Hiromichi

2016-07-01

Fatty liver is a disease caused by the excess accumulation of fat in the human liver. The early diagnosis of fatty liver is very important, because fatty liver is the major marker linked to metabolic syndrome. We already proposed the ultrasonic velocity change imaging method to diagnose fatty liver by using the fact that the temperature dependence of ultrasonic velocity is different in water and in fat. For the diagonosis of a fatty liver stage, we attempted a feasibility study of the quantitative assessment of the fat content in the human liver using our ultrasonic velocity change imaging method. Experimental results showed that the fat content in the tissue mimic phantom containing lard was determined by its ultrasonic velocity change in the flat temperature region formed by a circular warming ultrasonic transducer with an acoustic lens having an appropriate focal length. By considering the results of our simulation using a thermal diffusion equation, we determined whether this method could be applied to fatty liver assessment under the condition that the tissue had the thermal relaxation effect caused by blood flow.

Quantitatively characterizing microstructural variations of skin tissues during ultraviolet radiation damaging process based on Mueller matrix polarimetry

NASA Astrophysics Data System (ADS)

Sheng, Wei; He, Honghui; Dong, Yang; Ma, Hui

2018-02-01

As one of the most fundamental features of light, polarization can be used to develop imaging techniques which can provide insight into the optical and structural properties of tissues. Especially, the Mueller matrix polarimetry is suitable to detect the changes in collagen and elastic fibres, which are the main compositions of skin tissue. Here we demonstrate a novel quantitative, non-contact and in situ technique to monitor the microstructural variations of skin tissue during ultraviolet radiation (UVR) induced photoaging based on Mueller matrix polarimetry. Specifically, we measure the twodimensional (2D) backscattering Mueller matrices of nude mouse skin samples, then calculate and analyze the Mueller matrix derived parameters during the skin photoaging and self-repairing processes. To induce three-day skin photoaging, the back skin of each mouse is irradiated with UVR (0.05J/cm2) for five minutes per day. After UVR, the microstructures of the nude mouse skin are damaged. During the process of UV damage, we measure the backscattering Mueller matrices of the mouse skin samples and examine the relationship between the Mueller matrix parameters and the microstructural variations of skin tissue quantitatively. The comparisons between the UVR damaged groups with and without sunscreens show that the Mueller matrix derived parameters are potential indicators for fibrous microstructure variation in skin tissue. The pathological examinations and Monte Carlo simulations confirm the relationship between the values of Mueller matrix parameters and the changes of fibrous structures. Combined with smart phones or wearable devices, this technique may have a good application prospect in the fields of cosmetics and dermatological health.

Imaging challenges in biomaterials and tissue engineering

PubMed Central

Appel, Alyssa A.; Anastasio, Mark A.; Larson, Jeffery C.; Brey, Eric M.

2013-01-01

Biomaterials are employed in the fields of tissue engineering and regenerative medicine (TERM) in order to enhance the regeneration or replacement of tissue function and/or structure. The unique environments resulting from the presence of biomaterials, cells, and tissues result in distinct challenges in regards to monitoring and assessing the results of these interventions. Imaging technologies for three-dimensional (3D) analysis have been identified as a strategic priority in TERM research. Traditionally, histological and immunohistochemical techniques have been used to evaluate engineered tissues. However, these methods do not allow for an accurate volume assessment, are invasive, and do not provide information on functional status. Imaging techniques are needed that enable non-destructive, longitudinal, quantitative, and three-dimensional analysis of TERM strategies. This review focuses on evaluating the application of available imaging modalities for assessment of biomaterials and tissue in TERM applications. Included is a discussion of limitations of these techniques and identification of areas for further development. PMID:23768903

Simple preparation of plant epidermal tissue for laser microdissection and downstream quantitative proteome and carbohydrate analysis.

PubMed

Falter, Christian; Ellinger, Dorothea; von Hülsen, Behrend; Heim, René; Voigt, Christian A

2015-01-01

The outwardly directed cell wall and associated plasma membrane of epidermal cells represent the first layers of plant defense against intruding pathogens. Cell wall modifications and the formation of defense structures at sites of attempted pathogen penetration are decisive for plant defense. A precise isolation of these stress-induced structures would allow a specific analysis of regulatory mechanism and cell wall adaption. However, methods for large-scale epidermal tissue preparation from the model plant Arabidopsis thaliana, which would allow proteome and cell wall analysis of complete, laser-microdissected epidermal defense structures, have not been provided. We developed the adhesive tape - liquid cover glass technique (ACT) for simple leaf epidermis preparation from A. thaliana, which is also applicable on grass leaves. This method is compatible with subsequent staining techniques to visualize stress-related cell wall structures, which were precisely isolated from the epidermal tissue layer by laser microdissection (LM) coupled to laser pressure catapulting. We successfully demonstrated that these specific epidermal tissue samples could be used for quantitative downstream proteome and cell wall analysis. The development of the ACT for simple leaf epidermis preparation and the compatibility to LM and downstream quantitative analysis opens new possibilities in the precise examination of stress- and pathogen-related cell wall structures in epidermal cells. Because the developed tissue processing is also applicable on A. thaliana, well-established, model pathosystems that include the interaction with powdery mildews can be studied to determine principal regulatory mechanisms in plant-microbe interaction with their potential outreach into crop breeding.

Simple preparation of plant epidermal tissue for laser microdissection and downstream quantitative proteome and carbohydrate analysis

PubMed Central

Falter, Christian; Ellinger, Dorothea; von Hülsen, Behrend; Heim, René; Voigt, Christian A.

2015-01-01

The outwardly directed cell wall and associated plasma membrane of epidermal cells represent the first layers of plant defense against intruding pathogens. Cell wall modifications and the formation of defense structures at sites of attempted pathogen penetration are decisive for plant defense. A precise isolation of these stress-induced structures would allow a specific analysis of regulatory mechanism and cell wall adaption. However, methods for large-scale epidermal tissue preparation from the model plant Arabidopsis thaliana, which would allow proteome and cell wall analysis of complete, laser-microdissected epidermal defense structures, have not been provided. We developed the adhesive tape – liquid cover glass technique (ACT) for simple leaf epidermis preparation from A. thaliana, which is also applicable on grass leaves. This method is compatible with subsequent staining techniques to visualize stress-related cell wall structures, which were precisely isolated from the epidermal tissue layer by laser microdissection (LM) coupled to laser pressure catapulting. We successfully demonstrated that these specific epidermal tissue samples could be used for quantitative downstream proteome and cell wall analysis. The development of the ACT for simple leaf epidermis preparation and the compatibility to LM and downstream quantitative analysis opens new possibilities in the precise examination of stress- and pathogen-related cell wall structures in epidermal cells. Because the developed tissue processing is also applicable on A. thaliana, well-established, model pathosystems that include the interaction with powdery mildews can be studied to determine principal regulatory mechanisms in plant–microbe interaction with their potential outreach into crop breeding. PMID:25870605

Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM).

PubMed

Narumi, Ryohei; Tomonaga, Takeshi

2016-01-01

Mass spectrometry-based phosphoproteomics is an indispensible technique used in the discovery and quantification of phosphorylation events on proteins in biological samples. The application of this technique to tissue samples is especially useful for the discovery of biomarkers as well as biological studies. We herein describe the application of a large-scale phosphoproteome analysis and SRM/MRM-based quantitation to develop a strategy for the systematic discovery and validation of biomarkers using tissue samples.

Populational analysis of suspended microtissues for high-throughput, multiplexed 3D tissue engineering

PubMed Central

Chen, Alice A.; Underhill, Gregory H.; Bhatia, Sangeeta N.

2014-01-01

Three-dimensional (3D) tissue models have significantly improved our understanding of structure/function relationships and promise to lead to new advances in regenerative medicine. However, despite the expanding diversity of 3D tissue fabrication methods, approaches for functional assessment have been relatively limited. Here, we describe the fabrication of microtissue (μ-tissue) suspensions and their quantitative evaluation with techniques capable of analyzing large sample numbers and performing multiplexed parallel analysis. We applied this platform to 3D μ-tissues representing multiple stages of liver development and disease including: embryonic stem cells, bipotential hepatic progenitors, mature hepatocytes, and hepatoma cells photoencapsulated in polyethylene glycol hydrogels. Multiparametric μ-tissue cytometry enabled quantitation of fluorescent reporter expression within populations of intact μ-tissues (n≥102-103) and sorting-based enrichment of subsets for subsequent studies. Further, 3D μ-tissues could be implanted in vivo, respond to systemic stimuli, retrieved and quantitatively assessed. In order to facilitate multiplexed ‘pooled’ experimentation, fluorescent labeling strategies were developed and utilized to investigate the impact of μ-tissue composition and exposure to soluble factors. In particular, examination of drug/gene interactions on collections of 3D hepatoma μ-tissues indicated synergistic influence of doxorubicin and knockdown of the anti-apoptotic gene BCL-XL. Collectively, these studies highlight the broad utility of μ-tissue suspensions as an enabling approach for high n, populational analysis of 3D tissue biology in vitro and in vivo. PMID:20820630

Development and validation of a LC-MS method for quantitation of ergot alkaloids in lateral saphenous vein tissue

USDA-ARS?s Scientific Manuscript database

A liquid chromatography-mass spectrometry (LC/MS) method for simultaneous quantitation of seven ergot alkaloids (lysergic acid, ergonovine, ergovaline, ergocornine, ergotamine, ergocryptine and ergocrystine) in vascular tissue was developed and validated. Reverse-phase chromatography, coupled to an...

Isolating specific cell and tissue compartments from 3D images for quantitative regional distribution analysis using novel computer algorithms.

PubMed

Fenrich, Keith K; Zhao, Ethan Y; Wei, Yuan; Garg, Anirudh; Rose, P Ken

2014-04-15

Isolating specific cellular and tissue compartments from 3D image stacks for quantitative distribution analysis is crucial for understanding cellular and tissue physiology under normal and pathological conditions. Current approaches are limited because they are designed to map the distributions of synapses onto the dendrites of stained neurons and/or require specific proprietary software packages for their implementation. To overcome these obstacles, we developed algorithms to Grow and Shrink Volumes of Interest (GSVI) to isolate specific cellular and tissue compartments from 3D image stacks for quantitative analysis and incorporated these algorithms into a user-friendly computer program that is open source and downloadable at no cost. The GSVI algorithm was used to isolate perivascular regions in the cortex of live animals and cell membrane regions of stained spinal motoneurons in histological sections. We tracked the real-time, intravital biodistribution of injected fluorophores with sub-cellular resolution from the vascular lumen to the perivascular and parenchymal space following a vascular microlesion, and mapped the precise distributions of membrane-associated KCC2 and gephyrin immunolabeling in dendritic and somatic regions of spinal motoneurons. Compared to existing approaches, the GSVI approach is specifically designed for isolating perivascular regions and membrane-associated regions for quantitative analysis, is user-friendly, and free. The GSVI algorithm is useful to quantify regional differences of stained biomarkers (e.g., cell membrane-associated channels) in relation to cell functions, and the effects of therapeutic strategies on the redistributions of biomolecules, drugs, and cells in diseased or injured tissues. Copyright © 2014 Elsevier B.V. All rights reserved.

A framework for organizing and selecting quantitative approaches for benefit-harm assessment.

PubMed

Puhan, Milo A; Singh, Sonal; Weiss, Carlos O; Varadhan, Ravi; Boyd, Cynthia M

2012-11-19

Several quantitative approaches for benefit-harm assessment of health care interventions exist but it is unclear how the approaches differ. Our aim was to review existing quantitative approaches for benefit-harm assessment and to develop an organizing framework that clarifies differences and aids selection of quantitative approaches for a particular benefit-harm assessment. We performed a review of the literature to identify quantitative approaches for benefit-harm assessment. Our team, consisting of clinicians, epidemiologists, and statisticians, discussed the approaches and identified their key characteristics. We developed a framework that helps investigators select quantitative approaches for benefit-harm assessment that are appropriate for a particular decisionmaking context. Our framework for selecting quantitative approaches requires a concise definition of the treatment comparison and population of interest, identification of key benefit and harm outcomes, and determination of the need for a measure that puts all outcomes on a single scale (which we call a benefit and harm comparison metric). We identified 16 quantitative approaches for benefit-harm assessment. These approaches can be categorized into those that consider single or multiple key benefit and harm outcomes, and those that use a benefit-harm comparison metric or not. Most approaches use aggregate data and can be used in the context of single studies or systematic reviews. Although the majority of approaches provides a benefit and harm comparison metric, only four approaches provide measures of uncertainty around the benefit and harm comparison metric (such as a 95 percent confidence interval). None of the approaches considers the actual joint distribution of benefit and harm outcomes, but one approach considers competing risks when calculating profile-specific event rates. Nine approaches explicitly allow incorporating patient preferences. The choice of quantitative approaches depends on the

A framework for organizing and selecting quantitative approaches for benefit-harm assessment

PubMed Central

2012-01-01

Background Several quantitative approaches for benefit-harm assessment of health care interventions exist but it is unclear how the approaches differ. Our aim was to review existing quantitative approaches for benefit-harm assessment and to develop an organizing framework that clarifies differences and aids selection of quantitative approaches for a particular benefit-harm assessment. Methods We performed a review of the literature to identify quantitative approaches for benefit-harm assessment. Our team, consisting of clinicians, epidemiologists, and statisticians, discussed the approaches and identified their key characteristics. We developed a framework that helps investigators select quantitative approaches for benefit-harm assessment that are appropriate for a particular decisionmaking context. Results Our framework for selecting quantitative approaches requires a concise definition of the treatment comparison and population of interest, identification of key benefit and harm outcomes, and determination of the need for a measure that puts all outcomes on a single scale (which we call a benefit and harm comparison metric). We identified 16 quantitative approaches for benefit-harm assessment. These approaches can be categorized into those that consider single or multiple key benefit and harm outcomes, and those that use a benefit-harm comparison metric or not. Most approaches use aggregate data and can be used in the context of single studies or systematic reviews. Although the majority of approaches provides a benefit and harm comparison metric, only four approaches provide measures of uncertainty around the benefit and harm comparison metric (such as a 95 percent confidence interval). None of the approaches considers the actual joint distribution of benefit and harm outcomes, but one approach considers competing risks when calculating profile-specific event rates. Nine approaches explicitly allow incorporating patient preferences. Conclusion The choice of

[Evaluation of intraventricular dyssynchrony by quantitative tissue velocity imaging in rats of post-infarction heart failure].

PubMed

Wang, Yan; Zhu, Wenhui; Duan, Xingxing; Zhao, Yongfeng; Liu, Wengang; Li, Ruizhen

2011-04-01

To evaluate intraventricular systolic dyssynchrony in rats with post-infarction heart failure by quantitative tissue velocity imaging combining synchronous electrocardiograph. A total of 60 male SD rats were randomly assigned to 3 groups: a 4 week post-operative group and an 8 week post-operation group (each n=25, with anterior descending branch of the left coronary artery ligated), and a sham operation group (n=10, with thoracotomy and open pericardium, but no ligation of the artery). The time to peak systolic velocity of regional myocardial in the rats was measured and the index of the left intraventricular dyssynchrony was calculated. All indexes of the heart function became lower as the heart failure worsened except the left ventricle index in the post-operative groups. All indexes of the dyssynchrony got longer in the post-operative groups (P<0.05), while the changes in the sham operation group were not significantly different (P>0.05). Quantitative tissue velocity imaging combining synchronous electrocardiograph can analyse the intraventricular systolic dyssynchrony accurately.

Critical temperature: A quantitative method of assessing cold tolerance

Treesearch

D.H. DeHayes; M.W., Jr. Williams

1989-01-01

Critical temperature (Tc), defined as the highest temperature at which freezing injury to plant tissues can be detected, provides a biologically meaningful and statistically defined assessment of the relative cold tolerance of plant tissues. A method is described for calculating critical temperatures in laboratory freezing studies that use...

MR-ARFI-based method for the quantitative measurement of tissue elasticity: application for monitoring HIFU therapy

NASA Astrophysics Data System (ADS)

Vappou, Jonathan; Bour, Pierre; Marquet, Fabrice; Ozenne, Valery; Quesson, Bruno

2018-05-01

Monitoring thermal therapies through medical imaging is essential in order to ensure that they are safe, efficient and reliable. In this paper, we propose a new approach, halfway between MR acoustic radiation force imaging (MR-ARFI) and MR elastography (MRE), allowing for the quantitative measurement of the elastic modulus of tissue in a highly localized manner. It relies on the simulation of the MR-ARFI profile, which depends on tissue biomechanical properties, and on the identification of tissue elasticity through the fitting of experimental displacement images measured using rapid MR-ARFI. This method was specifically developed to monitor MR-guided high intensity focused ultrasound (MRgHIFU) therapy. Elasticity changes were followed during HIFU ablations (N  =  6) performed ex vivo in porcine muscle samples, and were compared to temperature changes measured by MR-thermometry. Shear modulus was found to increase consistently and steadily a few seconds after the heating started, and such changes were found to be irreversible. The shear modulus was found to increase from 1.49  ±  0.48 kPa (before ablation) to 3.69  ±  0.93 kPa (after ablation and cooling). Thanks to its ability to perform quantitative elasticity measurements in a highly localized manner around the focal spot, this method proved to be particularly attractive for monitoring HIFU ablations.

Is epicardial adipose tissue, assessed by echocardiography, a reliable method for visceral adipose tissue prediction?

PubMed

Silaghi, Alina Cristina; Poantă, Laura; Valea, Ana; Pais, Raluca; Silaghi, Horatiu

2011-03-01

Epicardial adipose tissue is an ectopic fat storage at the heart surface in direct contact with the coronary arteries. It is considered a metabolically active tissue, being a local source of pro-inflammatory factors that contribute to the pathogenesis of coronary artery disease. The AIM of our study was to establish correlations between echocardiographic assessment of epicardial adipose tissue and anthropometric and ultrasound measurements of the central and peripheral fat depots. The study was conducted on 22 patients with or without coronaropathy. Epicardial adipose tissue was measured using Aloka Prosound α 10 machine with a 3.5-7.5 MHz variable-frequency transducer and subcutaneous and visceral fat with Esaote Megas GPX machine and 3.5-7.5 MHz variable frequency transducer. Epicardial adipose tissue measured by echocardiography is correlated with waist circumference (p < 0.05), visceral adipose tissue thickness measured by ultrasonography (US) and is not correlated with body mass index (p = 0.315), hip and thigh circumference or subcutaneous fat thickness measured by US. Our study confirms that US assessment of epicardial fat correlates with anthropometric and US measurements of the central fat, representing an indirect but reliable marker of the visceral fat.

Quantitative MRI and strength measurements in the assessment of muscle quality in Duchenne muscular dystrophy.

PubMed

Wokke, B H; van den Bergen, J C; Versluis, M J; Niks, E H; Milles, J; Webb, A G; van Zwet, E W; Aartsma-Rus, A; Verschuuren, J J; Kan, H E

2014-05-01

The purpose of this study was to assess leg muscle quality and give a detailed description of leg muscle involvement in a series of Duchenne muscular dystrophy patients using quantitative MRI and strength measurements. Fatty infiltration, as well as total and contractile (not fatty infiltrated) cross sectional areas of various leg muscles were determined in 16 Duchenne patients and 11 controls (aged 8-15). To determine specific muscle strength, four leg muscle groups (quadriceps femoris, hamstrings, anterior tibialis and triceps surae) were measured and related to the amount of contractile tissue. In patients, the quadriceps femoris showed decreased total and contractile cross sectional area, attributable to muscle atrophy. The total, but not the contractile, cross sectional area of the triceps surae was increased in patients, corresponding to hypertrophy. Specific strength decreased in all four muscle groups of Duchenne patients, indicating reduced muscle quality. This suggests that muscle hypertrophy and fatty infiltration are two distinct pathological processes, differing between muscle groups. Additionally, the quality of remaining muscle fibers is severely reduced in the legs of Duchenne patients. The combination of quantitative MRI and quantitative muscle testing could be a valuable outcome parameter in longitudinal studies and in the follow-up of therapeutic effects. Copyright © 2014 Elsevier B.V. All rights reserved.

Segmentation and Quantitative Analysis of Epithelial Tissues.

PubMed

Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

2016-01-01

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

Quantitation of Na+, K+-atpase Enzymatic Activity in Tissues of the Mammalian Vestibular System

NASA Technical Reports Server (NTRS)

Kerr, T. P.

1985-01-01

In order to quantify vestibular Na(+), K(+)-ATPase, a microassay technique was developed which is sufficiently sensitive to measure the enzymatic activity in tissue from a single animal. The assay was used to characterize ATPase in he vestibular apparatus of the Mongolian gerbil. The quantitative procedure employs NPP (5 mM) as synthetic enzyme substrate. The assay relies upon spectrophotometric measurement (410 nm) of nitrophenol (NP) released by enzymatic hydrolysis of the substrate. Product formation in the absence of ouabain reflects both specific (Na(+), K(+)-ATPase) and non-specific (Mg(++)-ATPase) enzymatic activity. By measuring the accumulation of reaction product (NP) at three-minute intervals during the course of incubation, it is found that the overall enzymatic reaction proceeds linearly for at least 45 minutes. It is therefore possible to determine two separate reaction rates from a single set of tissues. Initial results indicate that total activity amounts to 53.3 + or - 11.2 (S.E.M.) nmol/hr/mg dry tissue, of which approximately 20% is ouabain-sensitive.

Quantitative Susceptibility Mapping of Human Brain Reflects Spatial Variation in Tissue Composition

PubMed Central

Li, Wei; Wu, Bing; Liu, Chunlei

2011-01-01

Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter microarchitectures. PMID:21224002

Towards quantitative condition assessment of biodiversity outcomes: Insights from Australian marine protected areas.

PubMed

Addison, Prue F E; Flander, Louisa B; Cook, Carly N

2017-08-01

Protected area management effectiveness (PAME) evaluation is increasingly undertaken to evaluate governance, assess conservation outcomes and inform evidence-based management of protected areas (PAs). Within PAME, quantitative approaches to assess biodiversity outcomes are now emerging, where biological monitoring data are directly assessed against quantitative (numerically defined) condition categories (termed quantitative condition assessments). However, more commonly qualitative condition assessments are employed in PAME, which use descriptive condition categories and are evaluated largely with expert judgement that can be subject to a range of biases, such as linguistic uncertainty and overconfidence. Despite the benefits of increased transparency and repeatability of evaluations, quantitative condition assessments are rarely used in PAME. To understand why, we interviewed practitioners from all Australian marine protected area (MPA) networks, which have access to long-term biological monitoring data and are developing or conducting PAME evaluations. Our research revealed that there is a desire within management agencies to implement quantitative condition assessment of biodiversity outcomes in Australian MPAs. However, practitioners report many challenges in transitioning from undertaking qualitative to quantitative condition assessments of biodiversity outcomes, which are hampering progress. Challenges include a lack of agency capacity (staff numbers and money), knowledge gaps, and diminishing public and political support for PAs. We point to opportunities to target strategies that will assist agencies overcome these challenges, including new decision support tools, approaches to better finance conservation efforts, and to promote more management relevant science. While a single solution is unlikely to achieve full evidence-based conservation, we suggest ways for agencies to target strategies and advance PAME evaluations toward best practice. Copyright �

Assessment of regional adipose tissue depots: a DXA and CT comparison in cadavers of elderly persons.

PubMed

Scafoglieri, Aldo; Deklerck, Rudi; Tresignie, Jonathan; De Mey, Johan; Clarys, Jan Pieter; Bautmans, Ivan

2013-09-01

Since dual energy X-ray absorptiometry (DXA) cannot distinguish between different adipose tissue (AT) deposits, it remains unclear how DXA-derived body composition variables relate to anatomical tissue (sub)compartments. The aim of the present study was to compare and relate regional DXA variables with absolute tissue masses obtained by computer tomography (CT) scanning of the lower limbs in elderly persons. Eleven well-preserved white Caucasian adults (seven male and four female cadavers) with a median age of 79.0 years (ranging from 68 to 96 years) were fully scanned with DXA and CT. Separate densities of skin tissue, AT, muscle tissue and bone were obtained by hydrostatic weighing. The leg DXA-variables were significantly related (rho-values between 0.60 and 0.98, P < 0.01) to CT-derived tissue counterparts, but showed significant systematic differences except for subcutaneous AT mass (P = 0.773). After controlling for other AT depots, fat as measured by DXA (fat(DXA)) related only to intermuscular AT (rho = 0.82, P < 0.01) in males and to subcutaneous AT (rho = 0.84, P < 0.05) in females. Although significantly interrelated, DXA and CT variables should not be used interchangeably since they have different quantitative and physiological significance. Our results suggest that fat(DXA) represents different parts of AT depots in elderly men and women. Since DXA is not appropriate for assessing tissue variability cautious clinical interpretation is warranted. © 2013.

Three-dimensional modeling and quantitative analysis of gap junction distributions in cardiac tissue.

PubMed

Lackey, Daniel P; Carruth, Eric D; Lasher, Richard A; Boenisch, Jan; Sachse, Frank B; Hitchcock, Robert W

2011-11-01

Gap junctions play a fundamental role in intercellular communication in cardiac tissue. Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions. Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements. In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions. In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing. We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes. The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles. The methodology was tested in rat ventricular myocardium. Our analysis yielded novel quantitative data on gap junction distributions. In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis. We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium. Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction.

Fuzzy logic algorithm for quantitative tissue characterization of diffuse liver diseases from ultrasound images.

PubMed

Badawi, A M; Derbala, A S; Youssef, A M

1999-08-01

Computerized ultrasound tissue characterization has become an objective means for diagnosis of liver diseases. It is difficult to differentiate diffuse liver diseases, namely cirrhotic and fatty liver by visual inspection from the ultrasound images. The visual criteria for differentiating diffused diseases are rather confusing and highly dependent upon the sonographer's experience. This often causes a bias effects in the diagnostic procedure and limits its objectivity and reproducibility. Computerized tissue characterization to assist quantitatively the sonographer for the accurate differentiation and to minimize the degree of risk is thus justified. Fuzzy logic has emerged as one of the most active area in classification. In this paper, we present an approach that employs Fuzzy reasoning techniques to automatically differentiate diffuse liver diseases using numerical quantitative features measured from the ultrasound images. Fuzzy rules were generated from over 140 cases consisting of normal, fatty, and cirrhotic livers. The input to the fuzzy system is an eight dimensional vector of feature values: the mean gray level (MGL), the percentile 10%, the contrast (CON), the angular second moment (ASM), the entropy (ENT), the correlation (COR), the attenuation (ATTEN) and the speckle separation. The output of the fuzzy system is one of the three categories: cirrhosis, fatty or normal. The steps done for differentiating the pathologies are data acquisition and feature extraction, dividing the input spaces of the measured quantitative data into fuzzy sets. Based on the expert knowledge, the fuzzy rules are generated and applied using the fuzzy inference procedures to determine the pathology. Different membership functions are developed for the input spaces. This approach has resulted in very good sensitivities and specificity for classifying diffused liver pathologies. This classification technique can be used in the diagnostic process, together with the history

New methods to improve the safety assessment of cryopreserved ovarian tissue for fertility preservation in breast cancer patients.

PubMed

Rodríguez-Iglesias, Beatriz; Novella-Maestre, Edurne; Herraiz, Sonia; Díaz-García, César; Pellicer, Nuria; Pellicer, Antonio

2015-12-01

To develop a novel molecular panel of markers to detect breast cancer (BC) disseminated malignant cells in ovarian tissue, and to improve the safety of ovarian tissue transplantation. Experimental study. University hospital. Ten ovarian biopsies from healthy patients, 13 biopsies with diagnosed BC metastasis, and 4 biopsies from primary BC tumor for designing a diagnostic panel of BC cell contamination; 60 ovarian biopsies from BC patients undergoing fertility preservation for validating the panel. Female nude mice. A novel panel for BC malignant cell detection by reverse-transcription polymerase chain reaction (RT-PCR), inmmunohistochemical analysis, in vitro invasion assay and xenotransplantation assayed in ovarian tissue from BC patients. Expression of GCDFP15, MGB1, SBEM, MUC1, WT-1, and NY-BR-01, selected as markers, assessed by quantitative RT-PCR in samples with confirmed BC metastasis. The most sensitive markers were confirmed by immunohistochemistry, and tested in vitro and in vivo. GCDFP15, MGB1, and SBEM were the most sensitive and specific markers to detect BC metastatic cells when at least one was expressed by quantitative RT-PCR. The panel was validated in 60 patients and confirmed in an in vitro invasion assay, where no invasive cells were observed. Samples negative for BC cells cannot develop disease when xenografted. GCDFP15, MGB1, and SBEM were the most sensitive molecules to create a diagnostic panel for BC malignant cell contamination, which may make ovarian tissue cryopreservation and transplantation a safe technique for fertility preservation in BC patients. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

ASSESSING FISH TISSUE CONTAMINATION ON A REGIONAL SCALE

EPA Science Inventory

The selection of target fish species for assessing the extent of fish tissue contaminants is a critical consideration in regional stream surveys such as the Environmental Monitoring and Assessment Program (EMAP). The ideal species would be widely distributed and common, bioaccumu...

Correlation of X-ray computed tomography with quantitative nuclear magnetic resonance methods for pre-clinical measurement of adipose and lean tissues in living mice.

PubMed

Metzinger, Matthew N; Miramontes, Bernadette; Zhou, Peng; Liu, Yueying; Chapman, Sarah; Sun, Lucy; Sasser, Todd A; Duffield, Giles E; Stack, M Sharon; Leevy, W Matthew

2014-10-08

Numerous obesity studies have coupled murine models with non-invasive methods to quantify body composition in longitudinal experiments, including X-ray computed tomography (CT) or quantitative nuclear magnetic resonance (QMR). Both microCT and QMR have been separately validated with invasive techniques of adipose tissue quantification, like post-mortem fat extraction and measurement. Here we report a head-to-head study of both protocols using oil phantoms and mouse populations to determine the parameters that best align CT data with that from QMR. First, an in vitro analysis of oil/water mixtures was used to calibrate and assess the overall accuracy of microCT vs. QMR data. Next, experiments were conducted with two cohorts of living mice (either homogenous or heterogeneous by sex, age and genetic backgrounds) to assess the microCT imaging technique for adipose tissue segmentation and quantification relative to QMR. Adipose mass values were obtained from microCT data with three different resolutions, after which the data were analyzed with different filter and segmentation settings. Strong linearity was noted between the adipose mass values obtained with microCT and QMR, with optimal parameters and scan conditions reported herein. Lean tissue (muscle, internal organs) was also segmented and quantified using the microCT method relative to the analogous QMR values. Overall, the rigorous calibration and validation of the microCT method for murine body composition, relative to QMR, ensures its validity for segmentation, quantification and visualization of both adipose and lean tissues.

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples

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

Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora

Global proteomics approaches allow characterization of whole tissue lysates to an impressive depth. However, it is now increasingly recognized that to better understand the complexity of multicellular organisms, global protein profiling of specific spatially defined regions/substructures of tissues (i.e. spatially-resolved proteomics) is essential. Laser capture microdissection (LCM) enables microscopic isolation of defined regions of tissues preserving crucial spatial information. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, and that impact measurement robustness, quantification, and throughput. Here, we coupled LCM with a fully automated sample preparation workflow thatmore » with a single manual step allows: protein extraction, tryptic digestion, peptide cleanup and LC-MS/MS analysis of proteomes from microdissected tissues. Benchmarking against the current state of the art in ultrasensitive global proteomic analysis, our approach demonstrated significant improvements in quantification and throughput. Using our LCM-SNaPP proteomics approach, we characterized to a depth of more than 3,400 proteins, the ontogeny of protein changes during normal lung development in laser capture microdissected alveolar tissue containing ~4,000 cells per sample. Importantly, the data revealed quantitative changes for 350 low abundance transcription factors and signaling molecules, confirming earlier transcript-level observations and defining seven modules of coordinated transcription factor/signaling molecule expression patterns, suggesting that a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes. Our LCM-proteomics approach facilitates efficient, spatially-resolved, ultrasensitive global proteomics analyses in high-throughput that will be enabling for several

High-level expression of podoplanin in benign and malignant soft tissue tumors: immunohistochemical and quantitative real-time RT-PCR analysis.

PubMed

Xu, Yongjun; Ogose, Akira; Kawashima, Hiroyuki; Hotta, Tetsuo; Ariizumi, Takashi; Li, Guidong; Umezu, Hajime; Endo, Naoto

2011-03-01

Podoplanin is a 38 kDa mucin-type transmembrane glycoprotein that was first identified in rat glomerular epithelial cells (podocytes). It is expressed in normal lymphatic endothelium, but is absent from vascular endothelial cells. D2-40 is a commercially available mouse monoclonal antibody which binds to an epitope on human podoplanin. D2-40 immunoreactivity is therefore highly sensitive and specific for lymphatic endothelium. Recent investigations have shown widespread applications of immunohistochemical staining with D2-40 in evaluating podoplanin expression as an immunohistochemical marker for diagnosis and prognosis in various tumors. To determine whether the podoplanin (D2-40) antibody may be useful for the diagnosis of soft tissue tumors, 125 cases, including 4 kinds of benign tumors, 15 kinds of malignant tumors and 3 kinds of tumor-like lesions were immunostained using the D2-40 antibody. Total RNA was extracted from frozen tumor tissue obtained from 41 corresponding soft tissue tumor patients and 12 kinds of soft tissue tumor cell lines. Quantitative real-time PCR reactions were performed. Immunohistochemical and quantitative real-time RT-PCR analyses demonstrated the expression of the podoplanin protein and mRNA in the majority of benign and malignant soft tissue tumors and tumor-like lesions examined, with the exception of alveolar soft part sarcoma, embryonal and alveolar rhabdomyosarcoma, extraskeletal Ewing's sarcoma/peripheral primitive neuro-ectodermal tumor and lipoma, which were completely negative for podoplanin. Since it is widely and highly expressed in nearly all kinds of soft tissue tumors, especially in spindle cell sarcoma, myxoid type soft tissue tumors and soft tissue tumors of the nervous system, podoplanin is considered to have little value in the differential diagnosis of soft tissue tumors.

Quantitative clinical nonpulsatile and localized visible light oximeter: design of the T-Stat tissue oximeter

NASA Astrophysics Data System (ADS)

Benaron, David A.; Parachikov, Ilian H.; Cheong, Wai-Fung; Friedland, Shai; Duckworth, Joshua L.; Otten, David M.; Rubinsky, Boris E.; Horchner, Uwe B.; Kermit, Eben L.; Liu, Frank W.; Levinson, Carl J.; Murphy, Aileen L.; Price, John W.; Talmi, Yair; Weersing, James P.

2003-07-01

We report the development of a general, quantitative, and localized visible light clinical tissue oximeter, sensitive to both hypoxemia and ischemia. Monitor design and operation were optimized over four instrument generations. A range of clinical probes were developed, including non-contact wands, invasive catheters, and penetrating needles with injection ports. Real-time data were collected (a) from probes, standards, and reference solutions to optimize each component, (b) from ex vivo hemoglobin solutions co-analyzed for StO2% and pO2 during deoxygenation, and (c) from normoxic human subject skin and mucosal tissue surfaces. Results show that (a) differential spectroscopy allows extraction of features with minimization of the effects of scattering, (b) in vitro oximetry produces a hemoglobin saturation binding curve of expected sigmoid shape and values, and (c) that monitoring human tissues allows real-time tissue spectroscopic features to be monitored. Unlike with near-infrared (NIRS) or pulse oximetry (SpO2%) methods, we found non-pulsatile, diffusion-based tissue oximetry (StO2%) to work most reliably for non-contact reflectance monitoring and for invasive catheter- or needle-based monitoring, using blue to orange light (475-600 nm). Measured values were insensitive to motion artifact. Down time was non-existent. We conclude that the T-Stat oximeter design is suitable for the collection of spectroscopic data from human subjects, and that the oximeter may have application in the monitoring of regional hemoglobin oxygen saturation in the capillary tissue spaces of human subjects.

Selective, quantitative measurement of releasable synaptic zinc in human autopsy hippocampal brain tissue from Alzheimer’s disease patients

PubMed Central

Bjorklund, Nicole L.; Sadagoparamanujam, V.M.; Taglialatela, Giulio

2011-01-01

Aberrant central nervous system zinc homeostasis has been reported in Alzheimer’s disease (AD). However, there are conflicting reports describing zinc concentration either increased or decreased in the brain of AD patients. Such discrepancies may be due to differences in the brain area examined, zinc detection method, and/or tissue composition. Furthermore, detection and measurement of the releasable zinc pool in autopsy tissue is difficult and usually unreliable. Obtaining an adequate assessment of this releasable zinc pool is of particular significance in AD research in that zinc can coordinate with and stabilize toxic amyloid beta oligomers, which are believed to play a key role in AD neuropathology. In addition, zinc released into the synaptic cleft can interact with the postsynaptic neurons causing altered signaling and synaptic dysfunction, which is a well established event in AD. The method presented here combines two approaches, biochemical fractionation and atomic absorption spectrophotometry, to allow, in addition to extracellular zinc concentration, the reliable and quantitative measurement of zinc specifically localized in synaptic vesicles, which contain the majority of the neuronal releasable zinc. Using this methodology, we found that synaptic vesicle zinc concentrations were increased in AD hippocampi compared to age-matched controls and that this increase in releasable zinc matched increased concentration of zinc in the extracellular space. PMID:21945000

Short communication: quantitative comparison of iodothyronine deiodinase I and II mRNA expression in ovine tissues.

PubMed

Foroughi, Mohammad Ali; Dehghani, Hesam

2013-12-01

Iodothyronine deiodinases I and II (DIO1 and DIO2) remove iodine from T4 to convert it to a more biologically active T3. The relative contribution of different tissue deiodinases to the establishment of a euthyroid state in sheep is not known. The objective of this study was to quantitate the amounts of transcription of DIO1 and DIO2 deiodinases in different ovine tissues. Using RT-qPCR, we found that DIO1 deiodinase is transcribed in skeletal muscle, kidney, and heart, more than thyroid, in diaphragm in quantities very similar to thyroid, and in liver, spleen, lung, and mammary gland lower than thyroid. We also found that the level of DIO2 transcription in all other tissues was lower than that in thyroid. In clinical settings, measurement of DIO1 and DIO2 expression in a given tissue may provide important clues on the intensity of selenium deficiency and its effects on the metabolism of thyroid hormones. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health.Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper,we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameter scan provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues

NASA Astrophysics Data System (ADS)

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health. Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper, we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameters can provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Quantitative RT-PCR analysis of estrogen receptor gene expression in laser microdissected prostate cancer tissue.

PubMed

Walton, Thomas J; Li, Geng; McCulloch, Thomas A; Seth, Rashmi; Powe, Desmond G; Bishop, Michael C; Rees, Robert C

2009-06-01

Real-time quantitative RT-PCR analysis of laser microdissected tissue is considered the most accurate technique for determining tissue gene expression. The discovery of estrogen receptor beta (ERbeta) has focussed renewed interest on the role of estrogen receptors in prostate cancer, yet few studies have utilized the technique to analyze estrogen receptor gene expression in prostate cancer. Fresh tissue was obtained from 11 radical prostatectomy specimens and from 6 patients with benign prostate hyperplasia. Pure populations of benign and malignant prostate epithelium were laser microdissected, followed by RNA isolation and electrophoresis. Quantitative RT-PCR was performed using primers for androgen receptor (AR), estrogen receptor beta (ERbeta), estrogen receptor alpha (ERalpha), progesterone receptor (PGR) and prostate specific antigen (PSA), with normalization to two housekeeping genes. Differences in gene expression were analyzed using the Mann-Whitney U-test. Correlation coefficients were analyzed using Spearman's test. Significant positive correlations were seen when AR and AR-dependent PSA, and ERalpha and ERalpha-dependent PGR were compared, indicating a representative population of RNA transcripts. ERbeta gene expression was significantly over-expressed in the cancer group compared with benign controls (P < 0.01). In contrast, PGR expression was significantly down-regulated in the cancer group (P < 0.05). There were no significant differences in AR, ERalpha or PSA expression between the groups. This study represents the first to show an upregulation of ERbeta gene expression in laser microdissected prostate cancer specimens. In concert with recent studies the findings suggest differential production of ERbeta splice variants, which may play important roles in the genesis of prostate cancer. (c) 2009 Wiley-Liss, Inc.

Ultrasound elastography assessment of bone/soft tissue interface

NASA Astrophysics Data System (ADS)

Parmar, Biren J.; Yang, Xu; Chaudhry, Anuj; Shafeeq Shajudeen, Peer; Nair, Sanjay P.; Weiner, Bradley K.; Tasciotti, Ennio; Krouskop, Thomas A.; Righetti, Raffaella

2016-01-01

We report on the use of elastographic imaging techniques to assess the bone/soft tissue interface, a region that has not been previously investigated but may provide important information about fracture and bone healing. The performance of axial strain elastograms and axial shear strain elastograms at the bone/soft tissue interface was studied ex vivo on intact and fractured canine and ovine tibias. Selected ex vivo results were corroborated on intact sheep tibias in vivo. The elastography results were statistically analyzed using elastographic image quality tools. The results of this study demonstrate distinct patterns in the distribution of the normalized local axial strains and axial shear strains at the bone/soft tissue interface with respect to the background soft tissue. They also show that the relative strength and distribution of the elastographic parameters change in the presence of a fracture and depend on the degree of misalignment between the fracture fragments. Thus, elastographic imaging modalities might be used in the future to obtain information regarding the integrity of bones and to assess the severity of fractures, alignment of bone fragments as well as to follow bone healing.

Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis.

PubMed

Stack, Edward C; Wang, Chichung; Roman, Kristin A; Hoyt, Clifford C

2014-11-01

Tissue sections offer the opportunity to understand a patient's condition, to make better prognostic evaluations and to select optimum treatments, as evidenced by the place pathology holds today in clinical practice. Yet, there is a wealth of information locked up in a tissue section that is only partially accessed, due mainly to the limitations of tools and methods. Often tissues are assessed primarily based on visual analysis of one or two proteins, or 2-3 DNA or RNA molecules. Even while analysis is still based on visual perception, image analysis is starting to address the variability of human perception. This is in contrast to measuring characteristics that are substantially out of reach of human perception, such as parameters revealed through co-expression, spatial relationships, heterogeneity, and low abundance molecules. What is not routinely accessed is the information revealed through simultaneous detection of multiple markers, the spatial relationships among cells and tissue in disease, and the heterogeneity now understood to be critical to developing effective therapeutic strategies. Our purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software. A key aspect of our approach is presenting imagery in a workflow that engages the pathologist to utilize the strengths of human perception and judgment, while significantly expanding the range of metrics collectable from tissue sections and also provide a level of consistency and precision needed to support the complexities of personalized medicine. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Towards in vivo focal cortical dysplasia phenotyping using quantitative MRI.

PubMed

Adler, Sophie; Lorio, Sara; Jacques, Thomas S; Benova, Barbora; Gunny, Roxana; Cross, J Helen; Baldeweg, Torsten; Carmichael, David W

2017-01-01

Focal cortical dysplasias (FCDs) are a range of malformations of cortical development each with specific histopathological features. Conventional radiological assessment of standard structural MRI is useful for the localization of lesions but is unable to accurately predict the histopathological features. Quantitative MRI offers the possibility to probe tissue biophysical properties in vivo and may bridge the gap between radiological assessment and ex-vivo histology. This review will cover histological, genetic and radiological features of FCD following the ILAE classification and will explain how quantitative voxel- and surface-based techniques can characterise these features. We will provide an overview of the quantitative MRI measures available, their link with biophysical properties and finally the potential application of quantitative MRI to the problem of FCD subtyping. Future research linking quantitative MRI to FCD histological properties should improve clinical protocols, allow better characterisation of lesions in vivo and tailored surgical planning to the individual.

Her-2/neu expression in node-negative breast cancer: direct tissue quantitation by computerized image analysis and association of overexpression with increased risk of recurrent disease.

PubMed

Press, M F; Pike, M C; Chazin, V R; Hung, G; Udove, J A; Markowicz, M; Danyluk, J; Godolphin, W; Sliwkowski, M; Akita, R

1993-10-15

The HER-2/neu proto-oncogene (also known as c-erb B-2) is homologous with, but distinct from, the epidermal growth factor receptor. Amplification of this gene in node-positive breast cancers has been shown to correlate with both earlier relapse and shorter overall survival. In node-negative breast cancer patients, the subgroup for which accurate prognostic data could make a significant contribution to treatment decisions, the prognostic utility of HER-2/neu amplification and/or overexpression has been controversial. The purpose of this report is to address the issues surrounding this controversy and to evaluate the prognostic utility of overexpression in a carefully followed group of patients using appropriately characterized reagents and methods. In this report we present data from a study of HER-2/neu expression designed specifically to test whether or not overexpression is associated with an increased risk of recurrence in node-negative breast cancers. From a cohort of 704 women with node-negative breast cancer who experienced recurrent disease (relapsed cases) 105 were matched with 105 women with no recurrence (disease-free controls) after the equivalent follow-up period. Immunohistochemistry was used to assess HER-2/neu expression in archival tissue blocks from both relapsed cases and their matched disease-free controls. Importantly, a series of molecularly characterized breast cancer specimens were used to confirm that the antibody used was of sufficient sensitivity and specificity to identify those cancers overexpressing the HER-2/neu protein in this formalin-fixed, paraffin-embedded tissue cohort. In addition, a quantitative approach was developed to more accurately assess the amount of HER-2/neu protein identified by immunostaining tumor tissue. This was done using a purified HER-2/neu protein synthesized in a bacterial expression vector and protein lysates derived from a series of cell lines, engineered to express a defined range of HER-2/neu oncoprotein

Quantitative mass spectrometry imaging of emtricitabine in cervical tissue model using infrared matrix-assisted laser desorption electrospray ionization

PubMed Central

Bokhart, Mark T.; Rosen, Elias; Thompson, Corbin; Sykes, Craig; Kashuba, Angela D. M.; Muddiman, David C.

2015-01-01

A quantitative mass spectrometry imaging (QMSI) technique using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is demonstrated for the antiretroviral (ARV) drug emtricitabine in incubated human cervical tissue. Method development of the QMSI technique leads to a gain in sensitivity and removal of interferences for several ARV drugs. Analyte response was significantly improved by a detailed evaluation of several cationization agents. Increased sensitivity and removal of an isobaric interference was demonstrated with sodium chloride in the electrospray solvent. Voxel-to-voxel variability was improved for the MSI experiments by normalizing analyte abundance to a uniformly applied compound with similar characteristics to the drug of interest. Finally, emtricitabine was quantified in tissue with a calibration curve generated from the stable isotope-labeled analog of emtricitabine followed by cross-validation using liquid chromatography tandem mass spectrometry (LC-MS/MS). The quantitative IR-MALDESI analysis proved to be reproducible with an emtricitabine concentration of 17.2±1.8 μg/gtissue. This amount corresponds to the detection of 7 fmol/voxel in the IR-MALDESI QMSI experiment. Adjacent tissue slices were analyzed using LC-MS/MS which resulted in an emtricitabine concentration of 28.4±2.8 μg/gtissue. PMID:25318460

[The development of a computer model in the quantitative assessment of thallium-201 myocardial scintigraphy].

PubMed

Raineri, M; Traina, M; Rotolo, A; Candela, B; Lombardo, R M; Raineri, A A

1993-05-01

Thallium-201 scintigraphy is a widely used noninvasive procedure for the detection and prognostic assessment of patients with suspected or proven coronary artery disease. Thallium uptake can be evaluated by a visual analysis or by a quantitative interpretation. Quantitative scintigraphy enhances disease detection in individual coronary arteries, provides a more precise estimate of the amount of ischemic myocardium, distinguishing scar from hypoperfused tissue. Due to the great deal of data, analysis, interpretation and comparison of thallium uptake can be very complex. We designed a computer-based system for the interpretation of quantitative thallium-201 scintigraphy data uptake. We used a database (DataEase 4.2-DataEase Italia). Our software has the following functions: data storage; calculation; conversion of numerical data into different definitions classifying myocardial perfusion; uptake data comparison; automatic conclusion; comparison of different scintigrams for the same patient. Our software is made up by 4 sections: numeric analysis, descriptive analysis, automatic conclusion, clinical remarks. We introduced in the computer system appropriate information, "logical paths", that use the "IF ... THEN" rules. The software executes these rules in order to analyze the myocardial regions in the 3 phases of scintigraphic analysis (stress, redistribution, re-injection), in the 3 projections (LAO 45 degrees, LAT,ANT), considering our uptake cutoff, obtaining, finally, the automatic conclusions. For these reasons, our computer-based system could be considered a real "expert system".

Extraction efficiency and implications for absolute quantitation of propranolol in mouse brain, liver and kidney thin tissue sections using droplet-based liquid microjunction surface sampling-HPLC ESI-MS/MS

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

Kertesz, Vilmos; Weiskittel, Taylor M.; Vavek, Marissa

Currently, absolute quantitation aspects of droplet-based surface sampling for thin tissue analysis using a fully automated autosampler/HPLC-ESI-MS/MS system are not fully evaluated. Knowledge of extraction efficiency and its reproducibility is required to judge the potential of the method for absolute quantitation of analytes from thin tissue sections. Methods: Adjacent thin tissue sections of propranolol dosed mouse brain (10- μm-thick), kidney (10- μm-thick) and liver (8-, 10-, 16- and 24- μm-thick) were obtained. Absolute concentration of propranolol was determined in tissue punches from serial sections using standard bulk tissue extraction protocols and subsequent HPLC separations and tandem mass spectrometric analysis. Thesemore » values were used to determine propranolol extraction efficiency from the tissues with the droplet-based surface sampling approach. Results: Extraction efficiency of propranolol using 10- μm-thick brain, kidney and liver thin tissues using droplet-based surface sampling varied between ~45-63%. Extraction efficiency decreased from ~65% to ~36% with liver thickness increasing from 8 μm to 24 μm. Randomly selecting half of the samples as standards, precision and accuracy of propranolol concentrations obtained for the other half of samples as quality control metrics were determined. Resulting precision ( ±15%) and accuracy ( ±3%) values, respectively, were within acceptable limits. In conclusion, comparative quantitation of adjacent mouse thin tissue sections of different organs and of various thicknesses by droplet-based surface sampling and by bulk extraction of tissue punches showed that extraction efficiency was incomplete using the former method, and that it depended on the organ and tissue thickness. However, once extraction efficiency was determined and applied, the droplet-based approach provided the required quantitation accuracy and precision for assay validations. Furthermore, this means that once the extraction

Extraction efficiency and implications for absolute quantitation of propranolol in mouse brain, liver and kidney thin tissue sections using droplet-based liquid microjunction surface sampling-HPLC ESI-MS/MS

DOE PAGES

Kertesz, Vilmos; Weiskittel, Taylor M.; Vavek, Marissa; ...

2016-06-22

Currently, absolute quantitation aspects of droplet-based surface sampling for thin tissue analysis using a fully automated autosampler/HPLC-ESI-MS/MS system are not fully evaluated. Knowledge of extraction efficiency and its reproducibility is required to judge the potential of the method for absolute quantitation of analytes from thin tissue sections. Methods: Adjacent thin tissue sections of propranolol dosed mouse brain (10- μm-thick), kidney (10- μm-thick) and liver (8-, 10-, 16- and 24- μm-thick) were obtained. Absolute concentration of propranolol was determined in tissue punches from serial sections using standard bulk tissue extraction protocols and subsequent HPLC separations and tandem mass spectrometric analysis. Thesemore » values were used to determine propranolol extraction efficiency from the tissues with the droplet-based surface sampling approach. Results: Extraction efficiency of propranolol using 10- μm-thick brain, kidney and liver thin tissues using droplet-based surface sampling varied between ~45-63%. Extraction efficiency decreased from ~65% to ~36% with liver thickness increasing from 8 μm to 24 μm. Randomly selecting half of the samples as standards, precision and accuracy of propranolol concentrations obtained for the other half of samples as quality control metrics were determined. Resulting precision ( ±15%) and accuracy ( ±3%) values, respectively, were within acceptable limits. In conclusion, comparative quantitation of adjacent mouse thin tissue sections of different organs and of various thicknesses by droplet-based surface sampling and by bulk extraction of tissue punches showed that extraction efficiency was incomplete using the former method, and that it depended on the organ and tissue thickness. However, once extraction efficiency was determined and applied, the droplet-based approach provided the required quantitation accuracy and precision for assay validations. Furthermore, this means that once the extraction

Assessment of tissue viability by polarization spectroscopy

NASA Astrophysics Data System (ADS)

Nilsson, G.; Anderson, C.; Henricson, J.; Leahy, M.; O'Doherty, J.; Sjöberg, F.

2008-09-01

A new and versatile method for tissue viability imaging based on polarization spectroscopy of blood in superficial tissue structures such as the skin is presented in this paper. Linearly polarized light in the visible wavelength region is partly reflected directly by the skin surface and partly diffusely backscattered from the dermal tissue matrix. Most of the directly reflected light preserves its polarization state while the light returning from the deeper tissue layers is depolarized. By the use of a polarization filter positioned in front of a sensitive CCD-array, the light directly reflected from the tissue surface is blocked, while the depolarized light returning from the deeper tissue layers reaches the detector array. By separating the colour planes of the detected image, spectroscopic information about the amount of red blood cells (RBCs) in the microvascular network of the tissue under investigation can be derived. A theory that utilizes the differences in light absorption of RBCs and bloodless tissue in the red and green wavelength region forms the basis of an algorithm for displaying a colour coded map of the RBC distribution in a tissue. Using a fluid model, a linear relationship (cc. = 0.99) between RBC concentration and the output signal was demonstrated within the physiological range 0-4%. In-vivo evaluation using transepidermal application of acetylcholine by the way of iontophoresis displayed the heterogeneity pattern of the vasodilatation produced by the vasoactive agent. Applications of this novel technology are likely to be found in drug and skin care product development as well as in the assessment of skin irritation and tissue repair processes and even ultimately in a clinic case situation.

A simultaneous multimodal imaging system for tissue functional parameters

NASA Astrophysics Data System (ADS)

Ren, Wenqi; Zhang, Zhiwu; Wu, Qiang; Zhang, Shiwu; Xu, Ronald

2014-02-01

Simultaneous and quantitative assessment of skin functional characteristics in different modalities will facilitate diagnosis and therapy in many clinical applications such as wound healing. However, many existing clinical practices and multimodal imaging systems are subjective, qualitative, sequential for multimodal data collection, and need co-registration between different modalities. To overcome these limitations, we developed a multimodal imaging system for quantitative, non-invasive, and simultaneous imaging of cutaneous tissue oxygenation and blood perfusion parameters. The imaging system integrated multispectral and laser speckle imaging technologies into one experimental setup. A Labview interface was developed for equipment control, synchronization, and image acquisition. Advanced algorithms based on a wide gap second derivative reflectometry and laser speckle contrast analysis (LASCA) were developed for accurate reconstruction of tissue oxygenation and blood perfusion respectively. Quantitative calibration experiments and a new style of skinsimulating phantom were designed to verify the accuracy and reliability of the imaging system. The experimental results were compared with a Moor tissue oxygenation and perfusion monitor. For In vivo testing, a post-occlusion reactive hyperemia (PORH) procedure in human subject and an ongoing wound healing monitoring experiment using dorsal skinfold chamber models were conducted to validate the usability of our system for dynamic detection of oxygenation and perfusion parameters. In this study, we have not only setup an advanced multimodal imaging system for cutaneous tissue oxygenation and perfusion parameters but also elucidated its potential for wound healing assessment in clinical practice.

Stroke onset time estimation from multispectral quantitative magnetic resonance imaging in a rat model of focal permanent cerebral ischemia.

PubMed

McGarry, Bryony L; Rogers, Harriet J; Knight, Michael J; Jokivarsi, Kimmo T; Sierra, Alejandra; Gröhn, Olli Hj; Kauppinen, Risto A

2016-08-01

Quantitative T2 relaxation magnetic resonance imaging allows estimation of stroke onset time. We aimed to examine the accuracy of quantitative T1 and quantitative T2 relaxation times alone and in combination to provide estimates of stroke onset time in a rat model of permanent focal cerebral ischemia and map the spatial distribution of elevated quantitative T1 and quantitative T2 to assess tissue status. Permanent middle cerebral artery occlusion was induced in Wistar rats. Animals were scanned at 9.4T for quantitative T1, quantitative T2, and Trace of Diffusion Tensor (Dav) up to 4 h post-middle cerebral artery occlusion. Time courses of differentials of quantitative T1 and quantitative T2 in ischemic and non-ischemic contralateral brain tissue (ΔT1, ΔT2) and volumes of tissue with elevated T1 and T2 relaxation times (f1, f2) were determined. TTC staining was used to highlight permanent ischemic damage. ΔT1, ΔT2, f1, f2, and the volume of tissue with both elevated quantitative T1 and quantitative T2 (V(Overlap)) increased with time post-middle cerebral artery occlusion allowing stroke onset time to be estimated. V(Overlap) provided the most accurate estimate with an uncertainty of ±25 min. At all times-points regions with elevated relaxation times were smaller than areas with Dav defined ischemia. Stroke onset time can be determined by quantitative T1 and quantitative T2 relaxation times and tissue volumes. Combining quantitative T1 and quantitative T2 provides the most accurate estimate and potentially identifies irreversibly damaged brain tissue. © 2016 World Stroke Organization.

Quantitative assessment of hyaline cartilage elasticity during optical clearing using optical coherence elastography

NASA Astrophysics Data System (ADS)

Liu, Chih-Hao; Singh, Manmohan; Li, Jiasong; Han, Zhaolong; Wu, Chen; Wang, Shang; Idugboe, Rita; Raghunathan, Raksha; Zakharov, Valery P.; Sobol, Emil N.; Tuchin, Valery V.; Twa, Michael; Larin, Kirill V.

2015-03-01

We report the first study on using optical coherence elastography (OCE) to quantitatively monitor the elasticity change of the hyaline cartilage during the optical clearing administrated by glucose solution. The measurement of the elasticity is verified using uniaxial compression test, demonstrating the feasibility of using OCE to quantify the Young's modulus of the cartilage tissue. As the results, we found that the stiffness of the hyaline cartilage increases during the optical clearing of the tissue. This study might be potentially useful for the early detection of osteoarthritis disease.

Quantitative Procedures for the Assessment of Quality in Higher Education Institutions.

ERIC Educational Resources Information Center

Moran, Tom; Rowse, Glenwood

The development of procedures designed to provide quantitative assessments of quality in higher education institutions are reviewed. These procedures employ a systems framework and utilize quantitative data to compare institutions or programs of similar types with one another. Three major elements essential in the development of models focusing on…

Fiber optic based multiparametric spectroscopy in vivo: Toward a new quantitative tissue vitality index

NASA Astrophysics Data System (ADS)

Kutai-Asis, Hofit; Barbiro-Michaely, Efrat; Deutsch, Assaf; Mayevsky, Avraham

2006-02-01

In our previous publication (Mayevsky et al SPIE 5326: 98-105, 2004) we described a multiparametric fiber optic system enabling the evaluation of 4 physiological parameters as indicators of tissue vitality. Since the correlation between the various parameters may differ in various pathophysiological conditions there is a need for an objective quantitative index that will integrate the relative changes measured in real time by the multiparametric monitoring system into a single number-vitality index. Such an approach to calculate tissue vitality index is critical for the possibility to use such an instrument in clinical environments. In the current presentation we are reporting our preliminary results indicating that calculation of an objective tissue vitality index is feasible. We used an intuitive empirical approach based on the comparison between the calculated index by the computer and the subjective evaluation made by an expert in the field of physiological monitoring. We used the in vivo brain of rats as an animal model in our current studies. The rats were exposed to anoxia, ischemia and cortical spreading depression and the responses were recorded in real time. At the end of the monitoring session the results were analyzed and the tissue vitality index was calculated offline. Mitochondrial NADH, tissue blood flow and oxy-hemoglobin were used to calculate the vitality index of the brain in vivo, where each parameter received a different weight, in each experiment type based on their significance. It was found that the mitochondrial NADH response was the main factor affected the calculated vitality index.

Boron concentration measurements by alpha spectrometry and quantitative neutron autoradiography in cells and tissues treated with different boronated formulations and administration protocols.

PubMed

Bortolussi, Silva; Ciani, Laura; Postuma, Ian; Protti, Nicoletta; Luca Reversi; Bruschi, Piero; Ferrari, Cinzia; Cansolino, Laura; Panza, Luigi; Ristori, Sandra; Altieri, Saverio

2014-06-01

The possibility to measure boron concentration with high precision in tissues that will be irradiated represents a fundamental step for a safe and effective BNCT treatment. In Pavia, two techniques have been used for this purpose, a quantitative method based on charged particles spectrometry and a boron biodistribution imaging based on neutron autoradiography. A quantitative method to determine boron concentration by neutron autoradiography has been recently set-up and calibrated for the measurement of biological samples, both solid and liquid, in the frame of the feasibility study of BNCT. This technique was calibrated and the obtained results were cross checked with those of α spectrometry, in order to validate them. The comparisons were performed using tissues taken form animals treated with different boron administration protocols. Subsequently the quantitative neutron autoradiography was employed to measure osteosarcoma cell samples treated with BPA and with new boronated formulations. © 2013 Published by Elsevier Ltd.

A gradient method for the quantitative analysis of cell movement and tissue flow and its application to the analysis of multicellular Dictyostelium development.

PubMed

Siegert, F; Weijer, C J; Nomura, A; Miike, H

1994-01-01

We describe the application of a novel image processing method, which allows quantitative analysis of cell and tissue movement in a series of digitized video images. The result is a vector velocity field showing average direction and velocity of movement for every pixel in the frame. We apply this method to the analysis of cell movement during different stages of the Dictyostelium developmental cycle. We analysed time-lapse video recordings of cell movement in single cells, mounds and slugs. The program can correctly assess the speed and direction of movement of either unlabelled or labelled cells in a time series of video images depending on the illumination conditions. Our analysis of cell movement during multicellular development shows that the entire morphogenesis of Dictyostelium is characterized by rotational cell movement. The analysis of cell and tissue movement by the velocity field method should be applicable to the analysis of morphogenetic processes in other systems such as gastrulation and neurulation in vertebrate embryos.

[Research progress and development trend of quantitative assessment techniques for urban thermal environment.

PubMed

Sun, Tie Gang; Xiao, Rong Bo; Cai, Yun Nan; Wang, Yao Wu; Wu, Chang Guang

2016-08-01

Quantitative assessment of urban thermal environment has become a focus for urban climate and environmental science since the concept of urban heat island has been proposed. With the continual development of space information and computer simulation technology, substantial progresses have been made on quantitative assessment techniques and methods of urban thermal environment. The quantitative assessment techniques have been developed to dynamics simulation and forecast of thermal environment at various scales based on statistical analysis of thermal environment on urban-scale using the historical data of weather stations. This study reviewed the development progress of ground meteorological observation, thermal infrared remote sensing and numerical simulation. Moreover, the potential advantages and disadvantages, applicability and the development trends of these techniques were also summarized, aiming to add fundamental knowledge of understanding the urban thermal environment assessment and optimization.

Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue.

PubMed

Percy, Andrew J; Michaud, Sarah A; Jardim, Armando; Sinclair, Nicholas J; Zhang, Suping; Mohammed, Yassene; Palmer, Andrea L; Hardie, Darryl B; Yang, Juncong; LeBlanc, Andre M; Borchers, Christoph H

2017-04-01

The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards. Protein quantitation was performed using reverse standard curves, with LC-MS platform and curve performance evaluated by quality control standards. The assays comprising the final panel (101 peptides for 81 proteins in plasma; 227 peptides for 159 proteins in heart tissue) have been rigorously developed under a fit-for-purpose approach and utilize stable-isotope labeled peptides for every analyte to provide high-quality, precise relative quantitation. In addition, the peptides have been tested to be interference-free and the assay is highly multiplexed, with reproducibly determined protein concentrations spanning >4 orders of magnitude. The developed assays have been used in a small pilot study to demonstrate their application to molecular phenotyping or biomarker discovery/verification studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detection of Nanophyetus salmincola in water, snails, and fish tissues by quantitative polymerase chain reaction

USGS Publications Warehouse

Purcell, Maureen K.; Powers, Rachel L.; Besijn, Bonnie; Hershberger, Paul K.

2017-01-01

We report the development and validation of two quantitative PCR (qPCR) assays to detect Nanophyetus salmincola DNA in water samples and in fish and snail tissues. Analytical and diagnostic validation demonstrated good sensitivity, specificity, and repeatability of both qPCR assays. The N. salmincola DNA copy number in kidney tissue was significantly correlated with metacercaria counts based on microscopy. Extraction methods were optimized for the sensitive qPCR detection of N. salmincola DNA in settled water samples. Artificially spiked samples suggested that the 1-cercaria/L threshold corresponded to an estimated log10 copies per liter ≥ 6.0. Significant correlation of DNA copy number per liter and microscopic counts indicated that the estimated qPCR copy number was a good predictor of the number of waterborne cercariae. However, the detection of real-world samples below the estimated 1-cercaria/L threshold suggests that the assays may also detect other N. salmincola life stages, nonintact cercariae, or free DNA that settles with the debris. In summary, the qPCR assays reported here are suitable for identifying and quantifying all life stages of N. salmincola that occur in fish tissues, snail tissues, and water.

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues.

PubMed

Molenaar, Remco J; Khurshed, Mohammed; Hira, Vashendriya V V; Van Noorden, Cornelis J F

2018-05-26

Altered cellular metabolism is a hallmark of many diseases, including cancer, cardiovascular diseases and infection. The metabolic motor units of cells are enzymes and their activity is heavily regulated at many levels, including the transcriptional, mRNA stability, translational, post-translational and functional level. This complex regulation means that conventional quantitative or imaging assays, such as quantitative mRNA experiments, Western Blots and immunohistochemistry, yield incomplete information regarding the ultimate activity of enzymes, their function and/or their subcellular localization. Quantitative enzyme cytochemistry and histochemistry (i.e., metabolic mapping) show in-depth information on in situ enzymatic activity and its kinetics, function and subcellular localization in an almost true-to-nature situation. We describe a protocol to detect the activity of dehydrogenases, which are enzymes that perform redox reactions to reduce cofactors such as NAD(P) + and FAD. Cells and tissue sections are incubated in a medium that is specific for the enzymatic activity of one dehydrogenase. Subsequently, the dehydrogenase that is the subject of investigation performs its enzymatic activity in its subcellular site. In a chemical reaction with the reaction medium, this ultimately generates blue-colored formazan at the site of the dehydrogenase's activity. The formazan's absorbance is therefore a direct measure of the dehydrogenase's activity and can be quantified using monochromatic light microscopy and image analysis. The quantitative aspect of this protocol enables researchers to draw statistical conclusions from these assays. Besides observational studies, this technique can be used for inhibition studies of specific enzymes. In this context, studies benefit from the true-to-nature advantages of metabolic mapping, giving in situ results that may be physiologically more relevant than in vitro enzyme inhibition studies. In all, metabolic mapping is an

Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging

NASA Astrophysics Data System (ADS)

Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.

2010-02-01

We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.

Non-invasive Assessments of Adipose Tissue Metabolism In Vitro.

PubMed

Abbott, Rosalyn D; Borowsky, Francis E; Quinn, Kyle P; Bernstein, David L; Georgakoudi, Irene; Kaplan, David L

2016-03-01

Adipose tissue engineering is a diverse area of research where the developed tissues can be used to study normal adipose tissue functions, create disease models in vitro, and replace soft tissue defects in vivo. Increasing attention has been focused on the highly specialized metabolic pathways that regulate energy storage and release in adipose tissues which affect local and systemic outcomes. Non-invasive, dynamic measurement systems are useful to track these metabolic pathways in the same tissue model over time to evaluate long term cell growth, differentiation, and development within tissue engineering constructs. This approach reduces costs and time in comparison to more traditional destructive methods such as biochemical and immunochemistry assays and proteomics assessments. Towards this goal, this review will focus on important metabolic functions of adipose tissues and strategies to evaluate them with non-invasive in vitro methods. Current non-invasive methods, such as measuring key metabolic markers and endogenous contrast imaging will be explored.

Non-invasive assessments of adipose tissue metabolism in vitro

PubMed Central

Abbott, Rosalyn D.; Borowsky, Francis E.; Quinn, Kyle P.; Bernstein, David L.; Georgakoudi, Irene; Kaplan, David L.

2015-01-01

Adipose tissue engineering is a diverse area of research where the developed tissues can be used to study normal adipose tissue functions, create disease models in vitro, and replace soft tissue defects in vivo. Increasing attention has been focused on the highly specialized metabolic pathways that regulate energy storage and release in adipose tissues which affect local and systemic outcomes. Non-invasive, dynamic measurement systems are useful to track these metabolic pathways in the same tissue model over time to evaluate long term cell growth, differentiation, and development within tissue engineering constructs. This approach reduces costs and time in comparison to more traditional destructive methods such as biochemical and immunochemistry assays and proteomics assessments. Towards this goal, this review will focus on important metabolic functions of adipose tissues and strategies to evaluate them with noninvasive in vitro methods. Current non-invasive methods, such as measuring key metabolic markers and endogenous contrast imaging will be explored. PMID:26399988

Relationship between Plaque Echo, Thickness and Neovascularization Assessed by Quantitative and Semi-quantitative Contrast-Enhanced Ultrasonography in Different Stenosis Groups.

PubMed

Song, Yan; Feng, Jun; Dang, Ying; Zhao, Chao; Zheng, Jie; Ruan, Litao

2017-12-01

The aim of this study was to determine the relationship between plaque echo, thickness and neovascularization in different stenosis groups using quantitative and semi-quantitative contrast-enhanced ultrasound (CEUS) in patients with carotid atherosclerosis plaque. A total of 224 plaques were divided into mild stenosis (<50%; 135 plaques, 60.27%), moderate stenosis (50%-69%; 39 plaques, 17.41%) and severe stenosis (70%-99%; 50 plaques, 22.32%) groups. Quantitative and semi-quantitative methods were used to assess plaque neovascularization and determine the relationship between plaque echo, thickness and neovascularization. Correlation analysis revealed no relationship of neovascularization with plaque echo in the groups using either quantitative or semi-quantitative methods. Furthermore, there was no correlation of neovascularization with plaque thickness using the semi-quantitative method. The ratio of areas under the curve (RAUC) was negatively correlated with plaque thickness (r = -0.317, p = 0.001) in the mild stenosis group. With the quartile method, plaque thickness of the mild stenosis group was divided into four groups, with significant differences between the 1.5-2.2 mm and ≥3.5 mm groups (p = 0.002), 2.3-2.8 mm and ≥3.5 mm groups (p <0.001) and 2.9-3.4 mm and ≥3.5 mm groups (p <0.001). Both semi-quantitative and quantitative CEUS methods characterizing neovascularization of plaque are equivalent with respect to assessing relationships between neovascularization, echogenicity and thickness. However, the quantitative method could fail for plaque <3.5 mm because of motion artifacts. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

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.

The Use of Quantitative SPECT/CT Imaging to Assess Residual Limb Health

DTIC Science & Technology

2016-10-01

AWARD NUMBER: W81XWH-15-1-0669 TITLE: The Use of Quantitative SPECT/CT Imaging to Assess Residual Limb Health PRINCIPAL INVESTIGATOR...3. DATES COVERED 30 Sep 2015 - 29 Sep 2016 4. TITLE AND SUBTITLE The Use of Quantitative SPECT/CT Imaging to Assess Residual Limb Health 5a...amputation and subsequently evaluate the utility of non-invasive imaging for evaluating the impact of next-generation socket technologies on the health of

Assessing framing assumptions in quantitative health impact assessments: a housing intervention example.

PubMed

Mesa-Frias, Marco; Chalabi, Zaid; Foss, Anna M

2013-09-01

Health impact assessment (HIA) is often used to determine ex ante the health impact of an environmental policy or an environmental intervention. Underpinning any HIA is the framing assumption, which defines the causal pathways mapping environmental exposures to health outcomes. The sensitivity of the HIA to the framing assumptions is often ignored. A novel method based on fuzzy cognitive map (FCM) is developed to quantify the framing assumptions in the assessment stage of a HIA, and is then applied to a housing intervention (tightening insulation) as a case-study. Framing assumptions of the case-study were identified through a literature search of Ovid Medline (1948-2011). The FCM approach was used to identify the key variables that have the most influence in a HIA. Changes in air-tightness, ventilation, indoor air quality and mould/humidity have been identified as having the most influence on health. The FCM approach is widely applicable and can be used to inform the formulation of the framing assumptions in any quantitative HIA of environmental interventions. We argue that it is necessary to explore and quantify framing assumptions prior to conducting a detailed quantitative HIA during the assessment stage. Copyright © 2013 Elsevier Ltd. All rights reserved.

A qualitative and quantitative assessment for a bone marrow harvest simulator.

PubMed

Machado, Liliane S; Moraes, Ronei M

2009-01-01

Several approaches to perform assessment in training simulators based on virtual reality have been proposed. There are two kinds of assessment methods: offline and online. The main requirements related to online training assessment methodologies applied to virtual reality systems are the low computational complexity and the high accuracy. In the literature it can be found several approaches for general cases which can satisfy such requirements. An inconvenient about those approaches is related to an unsatisfactory solution for specific cases, as in some medical procedures, where there are quantitative and qualitative information available to perform the assessment. In this paper, we present an approach to online training assessment based on a Modified Naive Bayes which can manipulate qualitative and quantitative variables simultaneously. A special medical case was simulated in a bone marrow harvest simulator. The results obtained were satisfactory and evidenced the applicability of the method.

Material Properties of Human Ocular Tissue at 7-µm Resolution.

PubMed

Rohrbach, Daniel; Ito, Kazuyo; Lloyd, Harriet O; Silverman, Ronald H; Yoshida, Kenji; Yamaguchi, Tadashi; Mamou, Jonathan

2017-09-01

Quantitative assessment of the material properties of ocular tissues can provide valuable information for investigating several ophthalmic diseases. Quantitative acoustic microscopy (QAM) offers a means of obtaining such information, but few QAM investigations have been conducted on human ocular tissue. We imaged the optic nerve (ON) and iridocorneal angle in 12-µm deparaffinized sections of the human eye using a custom-built acoustic microscope with a 250-MHz transducer (7-µm lateral resolution). The two-dimensional QAM maps of ultrasound attenuation (α), speed of sound ( c), acoustic impedance ( Z), bulk modulus ( K), and mass density (ρ) were generated. Scanned samples were then stained and imaged by light microscopy for comparison with QAM maps. The spatial resolution and contrast of scanning acoustic microscopy (SAM) maps were sufficient to resolve anatomic layers of the retina (Re); anatomic features in SAM maps corresponded to those seen by light microscopy. Significant variations of the acoustic parameters were found. For example, the sclera was 220 MPa stiffer than Re, choroid, and ON tissue. To the authors' knowledge, this is the first systematic study to assess c, Z, K, ρ, and α of human ocular tissue at the high ultrasound frequencies used in this study.

Doppler Fourier Domain Optical Coherence Tomography for Label-Free Tissue Angiography

NASA Astrophysics Data System (ADS)

Leitgeb, Rainer A.; Szkulmowski, Maciej; Blatter, Cedric; Wojtkowski, Maciej

Information about tissue perfusion and the vascular structure is certainly most important for assessment of tissue state or personal health and the diagnosis of any pathological conditions. It is therefore of key medical interest to have tools available for both quantitative blood flow assessment as well as qualitative vascular imaging. The strength of optical techniques is the unprecedented level of detail even for small capillary structures or microaneurysms and the possibility to combine different techniques for additional tissue spectroscopy giving insight into tissue metabolism. There is an immediate diagnostic and pharmacological demand for high-resolution, label-free, tissue angiography and flow assessment that in addition allow for precise depth gating of flow information. The most promising candidate is Doppler optical coherence tomography (DOCT) being noncontact, label free, and without employing hazardous radiation. DOCT provides fully quantitative volumetric information about blood flow together with the vascular and structural anatomy. Besides flow quantification, analysis of OCT signal fluctuations allows to contrast moving scatterers in tissue such as red blood cells from static tissue. This allows for non-invasive optical angiography and yields high resolution even for smallest capillaries. Because of the huge potential of DOCT and lable-free optical angiography for diagnosis, the last years saw a rapid increase of publications in this field with many different approaches. The present chapter gives an overview over existing Doppler OCT approaches and angiography techniques. It furthermore discusses limitations and noise issues, and gives examples for angiography in the eye and the skin.

Repeatability Assessment by ISO 11843-7 in Quantitative HPLC for Herbal Medicines.

PubMed

Chen, Liangmian; Kotani, Akira; Hakamata, Hideki; Tsutsumi, Risa; Hayashi, Yuzuru; Wang, Zhimin; Kusu, Fumiyo

2015-01-01

We have proposed an assessment methods to estimate the measurement relative standard deviation (RSD) of chromatographic peaks in quantitative HPLC for herbal medicines by the methodology of ISO 11843 Part 7 (ISO 11843-7:2012), which provides detection limits stochastically. In quantitative HPLC with UV detection (HPLC-UV) of Scutellaria Radix for the determination of baicalin, the measurement RSD of baicalin by ISO 11843-7:2012 stochastically was within a 95% confidence interval of the statistically obtained RSD by repetitive measurements (n = 6). Thus, our findings show that it is applicable for estimating of the repeatability of HPLC-UV for determining baicalin without repeated measurements. In addition, the allowable limit of the "System repeatability" in "Liquid Chromatography" regulated in a pharmacopoeia can be obtained by the present assessment method. Moreover, the present assessment method was also successfully applied to estimate the measurement RSDs of quantitative three-channel liquid chromatography with electrochemical detection (LC-3ECD) of Chrysanthemi Flos for determining caffeoylquinic acids and flavonoids. By the present repeatability assessment method, reliable measurement RSD was obtained stochastically, and the experimental time was remarkably reduced.

Tissue Preservation Assessment Preliminary Results

NASA Technical Reports Server (NTRS)

Globus, Ruth; Costes, Sylvain

2017-01-01

Pre-flight groundbased testing done to prepare for the first Rodent Research mission validation flight, RR1 (Choi et al, 2016 PlosOne). We purified RNA and measured RIN values to assess quality of the samples. For protein, we measured liver enzyme activities. We tested protocol and methods of preservation to date. Here we present an overview of results related to tissue preservation from the RR1 validation mission and a summary of findings to date from investigators who received RR1 teissues various Biospecimen Sharing Program.

An integrated environmental modeling framework for performing Quantitative Microbial Risk Assessments

EPA Science Inventory

Standardized methods are often used to assess the likelihood of a human-health effect from exposure to a specified hazard, and inform opinions and decisions about risk management and communication. A Quantitative Microbial Risk Assessment (QMRA) is specifically adapted to detail ...

Tissue polarimetry: concepts, challenges, applications, and outlook.

PubMed

Ghosh, Nirmalya; Vitkin, I Alex

2011-11-01

Polarimetry has a long and successful history in various forms of clear media. Driven by their biomedical potential, the use of the polarimetric approaches for biological tissue assessment has also recently received considerable attention. Specifically, polarization can be used as an effective tool to discriminate against multiply scattered light (acting as a gating mechanism) in order to enhance contrast and to improve tissue imaging resolution. Moreover, the intrinsic tissue polarimetry characteristics contain a wealth of morphological and functional information of potential biomedical importance. However, in a complex random medium-like tissue, numerous complexities due to multiple scattering and simultaneous occurrences of many scattering and polarization events present formidable challenges both in terms of accurate measurements and in terms of analysis of the tissue polarimetry signal. In order to realize the potential of the polarimetric approaches for tissue imaging and characterization/diagnosis, a number of researchers are thus pursuing innovative solutions to these challenges. In this review paper, we summarize these and other issues pertinent to the polarized light methodologies in tissues. Specifically, we discuss polarized light basics, Stokes-Muller formalism, methods of polarization measurements, polarized light modeling in turbid media, applications to tissue imaging, inverse analysis for polarimetric results quantification, applications to quantitative tissue assessment, etc.

Quantitative measurement of intact alpha-synuclein proteoforms from post-mortem control and Parkinson's disease brain tissue by intact protein mass spectrometry.

PubMed

Kellie, John F; Higgs, Richard E; Ryder, John W; Major, Anthony; Beach, Thomas G; Adler, Charles H; Merchant, Kalpana; Knierman, Michael D

2014-07-23

A robust top down proteomics method is presented for profiling alpha-synuclein species from autopsied human frontal cortex brain tissue from Parkinson's cases and controls. The method was used to test the hypothesis that pathology associated brain tissue will have a different profile of post-translationally modified alpha-synuclein than the control samples. Validation of the sample processing steps, mass spectrometry based measurements, and data processing steps were performed. The intact protein quantitation method features extraction and integration of m/z data from each charge state of a detected alpha-synuclein species and fitting of the data to a simple linear model which accounts for concentration and charge state variability. The quantitation method was validated with serial dilutions of intact protein standards. Using the method on the human brain samples, several previously unreported modifications in alpha-synuclein were identified. Low levels of phosphorylated alpha synuclein were detected in brain tissue fractions enriched for Lewy body pathology and were marginally significant between PD cases and controls (p = 0.03).

NecroQuant: quantitative assessment of radiological necrosis

NASA Astrophysics Data System (ADS)

Hwang, Darryl H.; Mohamed, Passant; Varghese, Bino A.; Cen, Steven Y.; Duddalwar, Vinay

2017-11-01

Clinicians can now objectively quantify tumor necrosis by Hounsfield units and enhancement characteristics from multiphase contrast enhanced CT imaging. NecroQuant has been designed to work as part of a radiomics pipelines. The software is a departure from the conventional qualitative assessment of tumor necrosis, as it provides the user (radiologists and researchers) a simple interface to precisely and interactively define and measure necrosis in contrast-enhanced CT images. Although, the software is tested here on renal masses, it can be re-configured to assess tumor necrosis across variety of tumors from different body sites, providing a generalized, open, portable, and extensible quantitative analysis platform that is widely applicable across cancer types to quantify tumor necrosis.

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

PubMed Central

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

2014-01-01

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

Quantitative characterization of mechanically indented in vivo human skin in adults and infants using optical coherence tomography

NASA Astrophysics Data System (ADS)

Huang, Pin-Chieh; Pande, Paritosh; Shelton, Ryan L.; Joa, Frank; Moore, Dave; Gillman, Elisa; Kidd, Kimberly; Nolan, Ryan M.; Odio, Mauricio; Carr, Andrew; Boppart, Stephen A.

2017-03-01

Influenced by both the intrinsic viscoelasticity of the tissue constituents and the time-evolved redistribution of fluid within the tissue, the biomechanical response of skin can reflect not only localized pathology but also systemic physiology of an individual. While clinical diagnosis of skin pathologies typically relies on visual inspection and manual palpation, a more objective and quantitative approach for tissue characterization is highly desirable. Optical coherence tomography (OCT) is an interferometry-based imaging modality that enables in vivo assessment of cross-sectional tissue morphology with micron-scale resolution, which surpasses those of most standard clinical imaging tools, such as ultrasound imaging and magnetic resonance imaging. This pilot study investigates the feasibility of characterizing the biomechanical response of in vivo human skin using OCT. OCT-based quantitative metrics were developed and demonstrated on the human subject data, where a significant difference between deformed and nondeformed skin was revealed. Additionally, the quantified postindentation recovery results revealed differences between aged (adult) and young (infant) skin. These suggest that OCT has the potential to quantitatively assess the mechanically perturbed skin as well as distinguish different physiological conditions of the skin, such as changes with age or disease.

Combined visual and semi-quantitative assessment of 123I-FP-CIT SPECT for the diagnosis of dopaminergic neurodegenerative diseases.

PubMed

Ueda, Jun; Yoshimura, Hajime; Shimizu, Keiji; Hino, Megumu; Kohara, Nobuo

2017-07-01

Visual and semi-quantitative assessments of 123 I-FP-CIT single-photon emission computed tomography (SPECT) are useful for the diagnosis of dopaminergic neurodegenerative diseases (dNDD), including Parkinson's disease, dementia with Lewy bodies, progressive supranuclear palsy, multiple system atrophy, and corticobasal degeneration. However, the diagnostic value of combined visual and semi-quantitative assessment in dNDD remains unclear. Among 239 consecutive patients with a newly diagnosed possible parkinsonian syndrome who underwent 123 I-FP-CIT SPECT in our medical center, 114 patients with a disease duration less than 7 years were diagnosed as dNDD with the established criteria or as non-dNDD according to clinical judgment. We retrospectively examined their clinical characteristics and visual and semi-quantitative assessments of 123 I-FP-CIT SPECT. The striatal binding ratio (SBR) was used as a semi-quantitative measure of 123 I-FP-CIT SPECT. We calculated the sensitivity and specificity of visual assessment alone, semi-quantitative assessment alone, and combined visual and semi-quantitative assessment for the diagnosis of dNDD. SBR was correlated with visual assessment. Some dNDD patients with a normal visual assessment had an abnormal SBR, and vice versa. There was no statistically significant difference between sensitivity of the diagnosis with visual assessment alone and semi-quantitative assessment alone (91.2 vs. 86.8%, respectively, p = 0.29). Combined visual and semi-quantitative assessment demonstrated superior sensitivity (96.7%) to visual assessment (p = 0.03) or semi-quantitative assessment (p = 0.003) alone with equal specificity. Visual and semi-quantitative assessments of 123 I-FP-CIT SPECT are helpful for the diagnosis of dNDD, and combined visual and semi-quantitative assessment shows superior sensitivity with equal specificity.

Objective, Quantitative, Data-Driven Assessment of Chemical Probes.

PubMed

Antolin, Albert A; Tym, Joseph E; Komianou, Angeliki; Collins, Ian; Workman, Paul; Al-Lazikani, Bissan

2018-02-15

Chemical probes are essential tools for understanding biological systems and for target validation, yet selecting probes for biomedical research is rarely based on objective assessment of all potential compounds. Here, we describe the Probe Miner: Chemical Probes Objective Assessment resource, capitalizing on the plethora of public medicinal chemistry data to empower quantitative, objective, data-driven evaluation of chemical probes. We assess >1.8 million compounds for their suitability as chemical tools against 2,220 human targets and dissect the biases and limitations encountered. Probe Miner represents a valuable resource to aid the identification of potential chemical probes, particularly when used alongside expert curation. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Label-free tissue scanner for colorectal cancer screening

NASA Astrophysics Data System (ADS)

Kandel, Mikhail E.; Sridharan, Shamira; Liang, Jon; Luo, Zelun; Han, Kevin; Macias, Virgilia; Shah, Anish; Patel, Roshan; Tangella, Krishnarao; Kajdacsy-Balla, Andre; Guzman, Grace; Popescu, Gabriel

2017-06-01

The current practice of surgical pathology relies on external contrast agents to reveal tissue architecture, which is then qualitatively examined by a trained pathologist. The diagnosis is based on the comparison with standardized empirical, qualitative assessments of limited objectivity. We propose an approach to pathology based on interferometric imaging of "unstained" biopsies, which provides unique capabilities for quantitative diagnosis and automation. We developed a label-free tissue scanner based on "quantitative phase imaging," which maps out optical path length at each point in the field of view and, thus, yields images that are sensitive to the "nanoscale" tissue architecture. Unlike analysis of stained tissue, which is qualitative in nature and affected by color balance, staining strength and imaging conditions, optical path length measurements are intrinsically quantitative, i.e., images can be compared across different instruments and clinical sites. These critical features allow us to automate the diagnosis process. We paired our interferometric optical system with highly parallelized, dedicated software algorithms for data acquisition, allowing us to image at a throughput comparable to that of commercial tissue scanners while maintaining the nanoscale sensitivity to morphology. Based on the measured phase information, we implemented software tools for autofocusing during imaging, as well as image archiving and data access. To illustrate the potential of our technology for large volume pathology screening, we established an "intrinsic marker" for colorectal disease that detects tissue with dysplasia or colorectal cancer and flags specific areas for further examination, potentially improving the efficiency of existing pathology workflows.

Assessment of imaging quality in magnified phase CT of human bone tissue at the nanoscale

NASA Astrophysics Data System (ADS)

Yu, Boliang; Langer, Max; Pacureanu, Alexandra; Gauthier, Remy; Follet, Helene; Mitton, David; Olivier, Cecile; Cloetens, Peter; Peyrin, Francoise

2017-10-01

Bone properties at all length scales have a major impact on the fracture risk in disease such as osteoporosis. However, quantitative 3D data on bone tissue at the cellular scale are still rare. Here we propose to use magnified X-ray phase nano-CT to quantify bone ultra-structure in human bone, on the new setup developed on the beamline ID16A at the ESRF, Grenoble. Obtaining 3D images requires the application of phase retrieval prior to tomographic reconstruction. Phase retrieval is an ill-posed problem for which various approaches have been developed. Since image quality has a strong impact on the further quantification of bone tissue, our aim here is to evaluate different phase retrieval methods for imaging bone samples at the cellular scale. Samples from femurs of female donors were scanned using magnified phase nano-CT at voxel sizes of 120 and 30 nm with an energy of 33 keV. Four CT scans at varying sample-to-detector distances were acquired for each sample. We evaluated three phase retrieval methods adapted to these conditions: Paganin's method at single distance, Paganin's method extended to multiple distances, and the contrast transfer function (CTF) approach for pure phase objects. These methods were used as initialization to an iterative refinement step. Our results based on visual and quantitative assessment show that the use of several distances (as opposed to single one) clearly improves image quality and the two multi-distance phase retrieval methods give similar results. First results on the segmentation of osteocyte lacunae and canaliculi from such images are presented.

Multiparametric Quantitative Ultrasound Imaging in Assessment of Chronic Kidney Disease.

PubMed

Gao, Jing; Perlman, Alan; Kalache, Safa; Berman, Nathaniel; Seshan, Surya; Salvatore, Steven; Smith, Lindsey; Wehrli, Natasha; Waldron, Levi; Kodali, Hanish; Chevalier, James

2017-11-01

To evaluate the value of multiparametric quantitative ultrasound imaging in assessing chronic kidney disease (CKD) using kidney biopsy pathologic findings as reference standards. We prospectively measured multiparametric quantitative ultrasound markers with grayscale, spectral Doppler, and acoustic radiation force impulse imaging in 25 patients with CKD before kidney biopsy and 10 healthy volunteers. Based on all pathologic (glomerulosclerosis, interstitial fibrosis/tubular atrophy, arteriosclerosis, and edema) scores, the patients with CKD were classified into mild (no grade 3 and <2 of grade 2) and moderate to severe (at least 2 of grade 2 or 1 of grade 3) CKD groups. Multiparametric quantitative ultrasound parameters included kidney length, cortical thickness, pixel intensity, parenchymal shear wave velocity, intrarenal artery peak systolic velocity (PSV), end-diastolic velocity (EDV), and resistive index. We tested the difference in quantitative ultrasound parameters among mild CKD, moderate to severe CKD, and healthy controls using analysis of variance, analyzed correlations of quantitative ultrasound parameters with pathologic scores and the estimated glomerular filtration rate (GFR) using Pearson correlation coefficients, and examined the diagnostic performance of quantitative ultrasound parameters in determining moderate CKD and an estimated GFR of less than 60 mL/min/1.73 m 2 using receiver operating characteristic curve analysis. There were significant differences in cortical thickness, pixel intensity, PSV, and EDV among the 3 groups (all P < .01). Among quantitative ultrasound parameters, the top areas under the receiver operating characteristic curves for PSV and EDV were 0.88 and 0.97, respectively, for determining pathologic moderate to severe CKD, and 0.76 and 0.86 for estimated GFR of less than 60 mL/min/1.73 m 2 . Moderate to good correlations were found for PSV, EDV, and pixel intensity with pathologic scores and estimated GFR. The

Proof of the quantitative potential of immunofluorescence by mass spectrometry.

PubMed

Toki, Maria I; Cecchi, Fabiola; Hembrough, Todd; Syrigos, Konstantinos N; Rimm, David L

2017-03-01

Protein expression in formalin-fixed, paraffin-embedded patient tissue is routinely measured by Immunohistochemistry (IHC). However, IHC has been shown to be subject to variability in sensitivity, specificity and reproducibility, and is generally, at best, considered semi-quantitative. Mass spectrometry (MS) is considered by many to be the criterion standard for protein measurement, offering high sensitivity, specificity, and objective molecular quantification. Here, we seek to show that quantitative immunofluorescence (QIF) with standardization can achieve quantitative results comparable to MS. Epidermal growth factor receptor (EGFR) was measured by quantitative immunofluorescence in 15 cell lines with a wide range of EGFR expression, using different primary antibody concentrations, including the optimal signal-to-noise concentration after quantitative titration. QIF target measurement was then compared to the absolute EGFR concentration measured by Liquid Tissue-selected reaction monitoring mass spectrometry. The best agreement between the two assays was found when the EGFR primary antibody was used at the optimal signal-to-noise concentration, revealing a strong linear regression (R 2 =0.88). This demonstrates that quantitative optimization of titration by calculation of signal-to-noise ratio allows QIF to be standardized to MS and can therefore be used to assess absolute protein concentration in a linear and reproducible manner.

The Quantitative Reasoning for College Science (QuaRCS) Assessment: Emerging Themes from 5 Years of Data

NASA Astrophysics Data System (ADS)

Follette, Katherine; Dokter, Erin; Buxner, Sanlyn

2018-01-01

The Quantitative Reasoning for College Science (QuaRCS) Assessment is a validated assessment instrument that was designed to measure changes in students' quantitative reasoning skills, attitudes toward mathematics, and ability to accurately assess their own quantitative abilities. It has been administered to more than 5,000 students at a variety of institutions at the start and end of a semester of general education college science instruction. I will begin by briefly summarizing our published work surrounding validation of the instrument and identification of underlying attitudinal factors (composite variables identified via factor analysis) that predict 50% of the variation in students' scores on the assessment. I will then discuss more recent unpublished work, including: (1) Development and validation of an abbreviated version of the assessment (The QuaRCS Light), which results in marked improvements in students' ability to maintain a high effort level throughout the assessment and has broad implications for quantitative reasoning assessments in general, and (2) Our efforts to revise the attitudinal portion of the assessment to better assess math anxiety level, another key factor in student performance on numerical assessments.

Development of a new quantitative gas permeability method for dental implant-abutment connection tightness assessment

PubMed Central

2011-01-01

Background Most dental implant systems are presently made of two pieces: the implant itself and the abutment. The connection tightness between those two pieces is a key point to prevent bacterial proliferation, tissue inflammation and bone loss. The leak has been previously estimated by microbial, color tracer and endotoxin percolation. Methods A new nitrogen flow technique was developed for implant-abutment connection leakage measurement, adapted from a recent, sensitive, reproducible and quantitative method used to assess endodontic sealing. Results The results show very significant differences between various sealing and screwing conditions. The remaining flow was lower after key screwing compared to hand screwing (p = 0.03) and remained different from the negative test (p = 0.0004). The method reproducibility was very good, with a coefficient of variation of 1.29%. Conclusions Therefore, the presented new gas flow method appears to be a simple and robust method to compare different implant systems. It allows successive measures without disconnecting the abutment from the implant and should in particular be used to assess the behavior of the connection before and after mechanical stress. PMID:21492459

Diffuse Optics for Tissue Monitoring and Tomography

PubMed Central

Durduran, T; Choe, R; Baker, W B; Yodh, A G

2015-01-01

This review describes the diffusion model for light transport in tissues and the medical applications of diffuse light. Diffuse optics is particularly useful for measurement of tissue hemodynamics, wherein quantitative assessment of oxy- and deoxy-hemoglobin concentrations and blood flow are desired. The theoretical basis for near-infrared or diffuse optical spectroscopy (NIRS or DOS, respectively) is developed, and the basic elements of diffuse optical tomography (DOT) are outlined. We also discuss diffuse correlation spectroscopy (DCS), a technique whereby temporal correlation functions of diffusing light are transported through tissue and are used to measure blood flow. Essential instrumentation is described, and representative brain and breast functional imaging and monitoring results illustrate the workings of these new tissue diagnostics. PMID:26120204

An integrated environmental modeling framework for performing quantitative microbial risk assessments

USDA-ARS?s Scientific Manuscript database

Standardized methods are often used to assess the likelihood of a human-health effect from exposure to a specified hazard, and inform opinions and decisions about risk management and communication. A Quantitative Microbial Risk Assessment (QMRA) is specifically adapted to detail potential human-heal...

Quantitation of stress echocardiography by tissue Doppler and strain rate imaging: a dream come true?

PubMed

Galderisi, Maurizio; Mele, Donato; Marino, Paolo Nicola

2005-01-01

Tissue Doppler (TD) is an ultrasound tool providing a quantitative agreement of left ventricular regional myocardial function in different modalities. Spectral pulsed wave (PW) TD, performed online during the examination, measures instantaneous myocardial velocities. By means of color TD, velocity images are digitally stored for subsequent off-line analysis and mean myocardial velocities are measured. An implementation of color TD includes strain rate imaging (SRI), based on post-processing conversion of regional velocities in local myocardial deformation rate (strain rate) and percent deformation (strain). These three modalities have been applied to stress echocardiography for quantitative evaluation of regional left ventricular function and detection of ischemia and viability. They present advantages and limitations. PWTD does not permit the simultaneous assessment of multiple walls and therefore is not compatible with clinical stress echocardiography while it could be used in a laboratory setting. Color TD provides a spatial map of velocity throughout the myocardium but its results are strongly affected by the frame rate. Both color TD and PWTD are also influenced by overall cardiac motion and tethering from adjacent segments and require reference velocity values for interpretation of regional left ventricular function. High frame rate (i.e. > 150 ms) post-processing-derived SRI can potentially overcome these limitations, since measurements of myocardial deformation have not any significant apex-to-base gradient. Preliminary studies have shown encouraging results about the ability of SRI to detect ischemia and viability, in terms of both strain rate changes and/or evidence of post-systolic thickening. SRI is, however, Doppler-dependent and time-consuming. Further technical refinements are needed to improve its application and introduce new ultrasound modalities to overcome the limitations of the Doppler-derived deformation analysis.

Fluorescence of Picrosirius Red Multiplexed With Immunohistochemistry for the Quantitative Assessment of Collagen in Tissue Sections.

PubMed

Wegner, Kyle A; Keikhosravi, Adib; Eliceiri, Kevin W; Vezina, Chad M

2017-08-01

The low cost and simplicity of picrosirius red (PSR) staining have driven its popularity for collagen detection in tissue sections. We extended the versatility of this method by using fluorescent imaging to detect the PSR signal and applying automated quantification tools. We also developed the first PSR protocol that is fully compatible with multiplex immunostaining, making it possible to test whether collagen structure differs across immunohistochemically labeled regions of the tissue landscape. We compared our imaging method with two gold standards in collagen imaging, linear polarized light microscopy and second harmonic generation imaging, and found that it is at least as sensitive and robust to changes in sample orientation. As proof of principle, we used a genetic approach to overexpress beta catenin in a patchy subset of mouse prostate epithelial cells distinguished only by immunolabeling. We showed that collagen fiber length is significantly greater near beta catenin overexpressing cells than near control cells. Our fluorescent PSR imaging method is sensitive, reproducible, and offers a new way to guide region of interest selection for quantifying collagen in tissue sections.

Coexistence of Epstein-Barr virus and Parvovirus B19 in tonsillar tissue samples: quantitative measurement by real-time PCR.

PubMed

Sahiner, Fatih; Gümral, Ramazan; Yildizoğlu, Üzeyir; Babayiğit, Mustafa Alparslan; Durmaz, Abdullah; Yiğit, Nuri; Saraçli, Mehmet Ali; Kubar, Ayhan

2014-08-01

In this study, we aimed to investigate the presence and copy number of six different viruses in tonsillar tissue samples removed surgically because of chronic recurrent tonsillitis or chronic obstructive tonsillar hypertrophy. In total, 56 tissue samples (tonsillar core) collected from 44 children and 12 adults were included in this study. The presence of viruses was investigated using a new TaqMan-based quantitative real-time PCR assay. Of the 56 tissue samples, 67.9% (38/56) were positive for at least one of the six viruses. Epstein-Barr virus was the most frequently detected virus, being found in 53.6% (30/56), followed by human Parvovirus B19 21.4% (12/56), human adenovirus 12.5% (7/56), human Cytomegalovirus 5.4% (3/56), BK polyomavirus 1.8% (1/56), and Herpes simplex virus 1.8% (1/56). Precancerous or cancerous changes were not detected in the tonsillar tissue samples by pathologic examination, whereas lymphoid hyperplasia was observed in 24 patients. In contrast to other viruses, B19 virus was present in high copy number in tonsillar tissues. The rates of EBV and B19 virus with high copy number (>500.000 copies/ml) were higher in children than in adults, and a positive relationship was also found between the presence of EBV and the presence of B19 virus with high copy number (P=0.037). It is previously reported that some viral agents are associated with different chronic tonsillar pathologies. In the present study, the presence of B19 virus in tonsillar core samples was investigated quantitatively for the first time, and our data suggests that EBV infections could be associated with B19 virus infections or could facilitate B19 virus replication. However, further detailed studies are needed to clarify this observation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quantitative method to assess caries via fluorescence imaging from the perspective of autofluorescence spectral analysis

NASA Astrophysics Data System (ADS)

Chen, Q. G.; Zhu, H. H.; Xu, Y.; Lin, B.; Chen, H.

2015-08-01

A quantitative method to discriminate caries lesions for a fluorescence imaging system is proposed in this paper. The autofluorescence spectral investigation of 39 teeth samples classified by the International Caries Detection and Assessment System levels was performed at 405 nm excitation. The major differences in the different caries lesions focused on the relative spectral intensity range of 565-750 nm. The spectral parameter, defined as the ratio of wavebands at 565-750 nm to the whole spectral range, was calculated. The image component ratio R/(G + B) of color components was statistically computed by considering the spectral parameters (e.g. autofluorescence, optical filter, and spectral sensitivity) in our fluorescence color imaging system. Results showed that the spectral parameter and image component ratio presented a linear relation. Therefore, the image component ratio was graded as <0.66, 0.66-1.06, 1.06-1.62, and >1.62 to quantitatively classify sound, early decay, established decay, and severe decay tissues, respectively. Finally, the fluorescence images of caries were experimentally obtained, and the corresponding image component ratio distribution was compared with the classification result. A method to determine the numerical grades of caries using a fluorescence imaging system was proposed. This method can be applied to similar imaging systems.

Hydrogen quantitative risk assessment workshop proceedings.

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

Groth, Katrina M.; Harris, Aaron P.

2013-09-01

The Quantitative Risk Assessment (QRA) Toolkit Introduction Workshop was held at Energetics on June 11-12. The workshop was co-hosted by Sandia National Laboratories (Sandia) and HySafe, the International Association for Hydrogen Safety. The objective of the workshop was twofold: (1) Present a hydrogen-specific methodology and toolkit (currently under development) for conducting QRA to support the development of codes and standards and safety assessments of hydrogen-fueled vehicles and fueling stations, and (2) Obtain feedback on the needs of early-stage users (hydrogen as well as potential leveraging for Compressed Natural Gas [CNG], and Liquefied Natural Gas [LNG]) and set priorities for %E2%80%9CVersionmore » 1%E2%80%9D of the toolkit in the context of the commercial evolution of hydrogen fuel cell electric vehicles (FCEV). The workshop consisted of an introduction and three technical sessions: Risk Informed Development and Approach; CNG/LNG Applications; and Introduction of a Hydrogen Specific QRA Toolkit.« less

Does peripheral quantitative computed tomography ignore tissue density of cancellous bone?

PubMed

Banse, X; Devogelaer, J P

2002-01-01

The purpose of this work was to determine the capacity of peripheral quantitative computed tomography (pQCT) to accurately measure the true physical properties of vertebral cancellous bone samples and to predict their stiffness. pQCT bone mineral density (BMD) was first measured in ideal conditions. Ten cubic specimens of vertebral cancellous bone (10 x 10 x 10 mm) were washed with a water jet, defatted, and scanned in saline after elimination of air bubbles; thirteen slices were obtained. Seventy-one unprepared cylindrical samples were scanned in more realistic conditions, which allow further biomechanical testing. After extraction from the vertebral body, the samples were pushed into a plastic tube (no effort was made to remove the marrow or air bubbles), and only four slices were obtained to reduce the duration of scan. For the 81 samples, the true bone volume fraction (BV/TV, %), true apparent density (rho(app), g/cm(3)), and tissue density (rho(tiss), g/cm(3)) (an indicator of the degree of mineralization of the matrix) were then measured using Archimedes principle. rho(app) was closely correlated to BV/TV (r(2) = 0.97). rho(tiss) (1.58 +/- 0.08 g/cm(2)) was almost constant but had some influence on rho(app) (r(2) = 0.03, p < 0.001). The pQCT BMD predicted accurately rho(app) (r(2) = 0.96) and BV/TV (r(2) = 0.93) for the cylinders. For the cubes, in ideal conditions, the same correlations were even better (r(2) > 0.99, both). Analysis of covariance indicated no difference (p > 0.05) in the regressions due to preparation of the samples. The stiffness was better predicted by the true rho(app) (r(2) = 0.87) than by BV/TV (r(2) = 0.83), indicating that stiffness was influenced by small differences in the tissue density. Consequently, the correlation between pQCT BMD and stiffness was excellent (r(2) = 0.84). The fact that pQCT did not ignore this tissue density information compensated for the inaccuracies linked to realistic scanning conditions of the cylinder.

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

PubMed Central

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

2017-01-01

One consequence of demographic change is the increasing demand for biocompatible materials for use in implants and prostheses. This is accompanied by a growing number of experimental animals because the interactions between new biomaterials and its host tissue have to be investigated. To evaluate novel materials and engineered tissues the use of non-destructive imaging modalities have been identified as a strategic priority. This provides the opportunity for studying interactions repeatedly with individual animals, along with the advantages of reduced biological variability and decreased number of laboratory animals. However, histological techniques are still the golden standard in preclinical biomaterial research. The present article demonstrates a detailed method comparison between histology and magnetic resonance imaging. This includes the presentation of their image qualities as well as the detailed statistical analysis for assessing agreement between quantitative measures. Exemplarily, the bony ingrowth of tissue engineered bone substitutes for treatment of a cleft-like maxillary bone defect has been evaluated. By using a graphical concordance analysis the mean difference between MRI results and histomorphometrical measures has been examined. The analysis revealed a slightly but significant bias in the case of the bone volume (biasHisto−MRI:Bone volume=2.40 %, p<0.005) and a clearly significant deviation for the remaining defect width (biasHisto−MRI:Defect width=−6.73 %, p≪0.005). But the study although showed a considerable effect of the analyzed section position to the quantitative result. It could be proven, that the bias of the data sets was less originated due to the imaging modalities, but mainly on the evaluation of different slice positions. The article demonstrated that method comparisons not always need the use of an independent animal study, additionally. PMID:28666026

Quantitative detection of astaxanthin and cantaxanthin in Atlantic salmon by resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Ermakov, Igor V.; Ermakova, Maia R.; Gellermann, Werner

2006-02-01

Two major carotenoids species found in salmonids muscle tissues are astaxanthin and cantaxanthin. They are taken up from fish food and are responsible for the attractive red-orange color of salmon filet. Since carotenoids are powerful antioxidants and biomarkers of nutrient consumption, they are thought to indicate fish health and resistance to diseases in fish farm environments. Therefore, a rapid, accurate, quantitative optical technique for measuring carotenoid content in salmon tissues is of economic interest. We demonstrate the possibility of using fast, selective, quantitative detection of astaxanthin and cantaxanthin in salmon muscle tissues, employing resonance Raman spectroscopy. Analyzing strong Raman signals originating from the carbon-carbon double bond stretch vibrations of the carotenoid molecules under blue laser excitation, we are able to characterize quantitatively the concentrations of carotenoids in salmon muscle tissue. To validate the technique, we compared Raman data with absorption measurements of carotenoid extracts in acetone. A close correspondence was observed in absorption spectra for tissue extract in acetone and a pure astaxanthin solution. Raman results show a linear dependence between Raman and absorption data. The proposed technique holds promise as a method of rapid screening of carotenoid levels in fish muscle tissues and may be attractive for the fish farm industry to assess the dietary status of salmon, risk for infective diseases, and product quality control.

Estimation of whole body fat from appendicular soft tissue from peripheral quantitative computed tomography in adolescent girls

PubMed Central

Lee, Vinson R.; Blew, Rob M.; Farr, Josh N.; Tomas, Rita; Lohman, Timothy G.; Going, Scott B.

2013-01-01

Objective Assess the utility of peripheral quantitative computed tomography (pQCT) for estimating whole body fat in adolescent girls. Research Methods and Procedures Our sample included 458 girls (aged 10.7 ± 1.1y, mean BMI = 18.5 ± 3.3 kg/m2) who had DXA scans for whole body percent fat (DXA %Fat). Soft tissue analysis of pQCT scans provided thigh and calf subcutaneous percent fat and thigh and calf muscle density (muscle fat content surrogates). Anthropometric variables included weight, height and BMI. Indices of maturity included age and maturity offset. The total sample was split into validation (VS; n = 304) and cross-validation (CS; n = 154) samples. Linear regression was used to develop prediction equations for estimating DXA %Fat from anthropometric variables and pQCT-derived soft tissue components in VS and the best prediction equation was applied to CS. Results Thigh and calf SFA %Fat were positively correlated with DXA %Fat (r = 0.84 to 0.85; p <0.001) and thigh and calf muscle densities were inversely related to DXA %Fat (r = −0.30 to −0.44; p < 0.001). The best equation for estimating %Fat included thigh and calf SFA %Fat and thigh and calf muscle density (adj. R2 = 0.90; SEE = 2.7%). Bland-Altman analysis in CS showed accurate estimates of percent fat (adj. R2 = 0.89; SEE = 2.7%) with no bias. Discussion Peripheral QCT derived indices of adiposity can be used to accurately estimate whole body percent fat in adolescent girls. PMID:25147482

In vivo quantitative NMR imaging of fruit tissues during growth using Spoiled Gradient Echo sequence.

PubMed

Kenouche, S; Perrier, M; Bertin, N; Larionova, J; Ayadi, A; Zanca, M; Long, J; Bezzi, N; Stein, P C; Guari, Y; Cieslak, M; Godin, C; Goze-Bac, C

2014-12-01

Nondestructive studies of physiological processes in agronomic products require increasingly higher spatial and temporal resolutions. Nuclear Magnetic Resonance (NMR) imaging is a non-invasive technique providing physiological and morphological information on biological tissues. The aim of this study was to design a robust and accurate quantitative measurement method based on NMR imaging combined with contrast agent (CA) for mapping and quantifying water transport in growing cherry tomato fruits. A multiple flip-angle Spoiled Gradient Echo (SGE) imaging sequence was used to evaluate the intrinsic parameters maps M0 and T1 of the fruit tissues. Water transport and paths flow were monitored using Gd(3+)/[Fe(CN)6](3-)/D-mannitol nanoparticles as a tracer. This dynamic study was carried out using a compartmental modeling. The CA was preferentially accumulated in the surrounding tissues of columella and in the seed envelopes. The total quantities and the average volume flow of water estimated are: 198 mg, 1.76 mm(3)/h for the columella and 326 mg, 2.91 mm(3)/h for the seed envelopes. We demonstrate in this paper that the NMR imaging technique coupled with efficient and biocompatible CA in physiological medium has the potential to become a major tool in plant physiology research. Copyright © 2014 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2006-07-01

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

Assessing fundamental 2-dimensional understanding of basic soft tissue techniques.

PubMed

Jabbour, Noel; Dobratz, Eric J; Dresner, Harley S; Hilger, Peter A

2011-01-01

To develop a written practical examination and scoring system for assessing trainee skills in basic soft-tissue techniques. A brief written practical examination was developed to assess the ability of trainees to sketch preoperative plans and postoperative results for common soft-tissue techniques: simple-excision, M-plasty, geometric broken line closure, Z-plasty, V-to-Y flap, and rhombic flap. A scoring system was developed to assign 0 to 5 points to each of 10 items on the examination for a total score of 0-50. The 15-minute examination was administered as a pretest, posttest, and 3-month posttest assessment as part of a soft-tissue course at our institution. University of Minnesota, Otolaryngology Department. Three raters reviewed all examination answer sheets independently. The pretest scores of examinees correlated strongly with their level of training; the average pretest for junior residents (PGY 1-2) compared with senior residents (PGY 4-5) was 17.3 (of 50) versus 26.0 (p < 0.01). The scoring system showed a high intrarater reliability and high interrater reliability with correlation coefficients of r = 0.99 and r = 0.95, respectively and agreement coefficients of κ = 0.82 and κ = 0.77, respectively. This written practical examination and scoring system may be used to assess the skills of trainees accurately in basic soft tissue techniques and to expose areas of deficiency that can be addressed in future training sessions. Copyright © 2011 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Phase-contrast CT: Qualitative and Quantitative Evaluation of Capillarized Sinusoids and Trabecular Structure in Human Hepatocellular Carcinoma Tissues.

PubMed

Jian, Jianbo; Zhang, Wenxue; Yang, Hao; Zhao, Xinyan; Xuan, Ruijiao; Li, Dongyue; Hu, Chunhong

2017-01-01

Capillarization of sinusoids and change of trabecular thickness are the main histologic features in hepatocellular carcinoma (HCC). Of particular interest are the three-dimensional (3D) visualization and quantitative evaluation of such alterations in the HCC progression. X-ray phase-contrast computed tomography (PCCT) is an emerging imaging method that provides excellent image contrast for soft tissues. This study aimed to explore the potential of in-line PCCT in microstructure imaging of capillarized sinusoids and trabecular structure in human HCC tissues and to quantitatively evaluate the alterations of those fine structures during the development of HCC. This project was designed as an ex vivo experimental study. The study was approved by the institutional review board, and informed consent was obtained from the patients. Eight human resected HCC tissue samples were imaged using in-line PCCT. After histologic processing, PCCT images and histopathologic data were matched. Fine structures in HCC tissues were revealed. Quantitative analyses of capillarized sinusoids (ie, percentage of sinusoidal area [PSA], sinusoidal volume) and trabecular structure (ie, trabecular thickness, surface-area-to-volume ratio [SA/V]) in low-grade (well or moderately differentiated) and high-grade (poorly differentiated) HCC groups were performed. Using PCCT, the alterations of capillarized sinusoids and trabecular structure were clearly observed in 3D geometry, which was confirmed by the corresponding histologic sections. The 3D qualitative analyses of sinusoids in the high-grade HCC group were significantly different (P < 0.05) in PSA (7.8 ± 2.5%) and sinusoidal volume (2.9 ± 0.6 × 10 7  µm 3 ) from those in the low-grade HCC group (PSA, 12.9 ± 2.2%; sinusoidal volume, 2.4 ± 0.3 × 10 7  µm 3 ). Moreover, the 3D quantitative evaluation of the trabecular structure in the high-grade HCC group showed a significant change (P < 0.05) in the

Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses

ERIC Educational Resources Information Center

Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

2016-01-01

Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory…

DiOlistic Labeling of Neurons in Tissue Slices: A Qualitative and Quantitative Analysis of Methodological Variations.

PubMed

Staffend, Nancy A; Meisel, Robert L

2011-01-01

Fine neuronal morphology, such as dendritic spines, classically has been studied using the Golgi technique; however, Golgi staining is difficult to combine with other histological techniques. With the increasing popularity of fluorescent imaging, a number of fluorescent dyes have been developed that enable the coupling of multiple fluorescent labels in a single preparation. These fluorescent dyes include the lipophilic dialkylcarbocyanine, DiI; traditionally used for anterograde and retrograde neuronal tracing. More recently, DiI labeling has been used in combination with the Gene Gun for "DiOlistic" labeling of neurons in slice preparations. DiI sequesters itself within and diffuses laterally along the neuronal membrane, however once the cell is permeabilized, the DiI begins to leak from the cell membrane. A DiI derivative, Cell Tracker™ CM-DiI, increases dye stability and labeling half-life in permeabilized tissue, however at much greater expense. Here, the DiI and CM-DiI DiOlistic labeling techniques were tested in side-by-side experiments evaluating dye stability within dendritic architecture in medium spiny neurons of the dorsal stratum in both non-permeabilized and permeabilized tissue sections. In tissue sections that were not permeabilized, spine density in DiI labeled sections was higher than in CM-DiI labeling. In contrast, tissue sections that were permeabilized had higher spine densities in CM-DiI labeled neurons. These results suggest that for experiments involving non-permeabilized tissue, traditional DiI will suffice, however for experiments involving permeabilized tissue CM-DiI provides more consistent data. These experiments provide the first quantitative analyses of the impact of methodological permutations on neuronal labeling with DiI.

[Evaluation of left ventricular diastolic function in canine acute myocardial ischemia using velocity vector imaging and quantitative tissue velocity imaging].

PubMed

Zhang, Chuan; Zha, Dao-Gang; DU, Rong-Sheng; Hu, Feng; Li, Sheng-Hui; Wu, Xiao-Yuan; Liu, Yi-Li

2009-07-01

To assess the value of velocity vector imaging (VVI) and quantitative tissue velocity imaging (QTVI) in assessing left ventricular diastolic function of the dogs with acute myocardial ischemia. Six healthy mongrel dogs were subjected to ligation of the left circumflex artery or left anterior descending artery to induce coronary artery stenosis of varying degrees. The mean peak diastolic velocity (Em) of the ventricular walls around the mitral annulus was recorded with VVI or QTVI in the coronary blood flow. The left ventricular end diastolic pressure (LVEDP) was measured with pigtail catheter in the left ventricle. As the coronary blood flow decreased, LVEDP was gradually increased, and Em measured by VVI or QTVI were also gradually decreased. A good linear correlation was shown between Em measured by VVI or QTVI and LVEDP (r=-0.834, P<0.001, and r=-0.68, P<0.001, respectively). A significant difference was observed in the correlation coefficient between VVI and QTVI (Z=2.625, P=0.0087). VVI and QTVI both provide good noninvasive means for measuring left ventricular diastolic function. VVI, a new echocardiographic modality without angular dependence, is better than QTVI in evaluating left ventricular diastolic function.

Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

USGS Publications Warehouse

Chase, D.M.; Elliott, D.G.; Pascho, R.J.

2006-01-01

Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

Quantitative background parenchymal uptake on molecular breast imaging and breast cancer risk: a case-control study.

PubMed

Hruska, Carrie B; Geske, Jennifer R; Swanson, Tiffinee N; Mammel, Alyssa N; Lake, David S; Manduca, Armando; Conners, Amy Lynn; Whaley, Dana H; Scott, Christopher G; Carter, Rickey E; Rhodes, Deborah J; O'Connor, Michael K; Vachon, Celine M

2018-06-05

Background parenchymal uptake (BPU), which refers to the level of Tc-99m sestamibi uptake within normal fibroglandular tissue on molecular breast imaging (MBI), has been identified as a breast cancer risk factor, independent of mammographic density. Prior analyses have used subjective categories to describe BPU. We evaluate a new quantitative method for assessing BPU by testing its reproducibility, comparing quantitative results with previously established subjective BPU categories, and determining the association of quantitative BPU with breast cancer risk. Two nonradiologist operators independently performed region-of-interest analysis on MBI images viewed in conjunction with corresponding digital mammograms. Quantitative BPU was defined as a unitless ratio of the average pixel intensity (counts/pixel) within the fibroglandular tissue versus the average pixel intensity in fat. Operator agreement and the correlation of quantitative BPU measures with subjective BPU categories assessed by expert radiologists were determined. Percent density on mammograms was estimated using Cumulus. The association of quantitative BPU with breast cancer (per one unit BPU) was examined within an established case-control study of 62 incident breast cancer cases and 177 matched controls. Quantitative BPU ranged from 0.4 to 3.2 across all subjects and was on average higher in cases compared to controls (1.4 versus 1.2, p < 0.007 for both operators). Quantitative BPU was strongly correlated with subjective BPU categories (Spearman's r = 0.59 to 0.69, p < 0.0001, for each paired combination of two operators and two radiologists). Interoperator and intraoperator agreement in the quantitative BPU measure, assessed by intraclass correlation, was 0.92 and 0.98, respectively. Quantitative BPU measures showed either no correlation or weak negative correlation with mammographic percent density. In a model adjusted for body mass index and percent density, higher quantitative BPU was

I Vivo Quantitative Ultrasound Imaging and Scatter Assessments.

NASA Astrophysics Data System (ADS)

Lu, Zheng Feng

There is evidence that "instrument independent" measurements of ultrasonic scattering properties would provide useful diagnostic information that is not available with conventional ultrasound imaging. This dissertation is a continuing effort to test the above hypothesis and to incorporate quantitative ultrasound methods into clinical examinations for early detection of diffuse liver disease. A well-established reference phantom method was employed to construct quantitative ultrasound images of tissue in vivo. The method was verified by extensive phantom tests. A new method was developed to measure the effective attenuation coefficient of the body wall. The method relates the slope of the difference between the echo signal power spectrum from a uniform region distal to the body wall and the echo signal power spectrum from a reference phantom to the body wall attenuation. The accuracy obtained from phantom tests suggests further studies with animal experiments. Clinically, thirty-five healthy subjects and sixteen patients with diffuse liver disease were studied by these quantitative ultrasound methods. The average attenuation coefficient in normals agreed with previous investigators' results; in vivo backscatter coefficients agreed with the results from normals measured by O'Donnell. Strong discriminating power (p < 0.001) was found for both attenuation and backscatter coefficients between fatty livers and normals; a significant difference (p < 0.01) was observed in the backscatter coefficient but not in the attenuation coefficient between cirrhotic livers and normals. An in vivo animal model of steroid hepatopathy was used to investigate the system sensitivity in detecting early changes in canine liver resulting from corticosteroid administration. The average attenuation coefficient slope increased from 0.7 dB/cm/MHz in controls to 0.82 dB/cm/MHz (at 6 MHz) in treated animals on day 14 into the treatment, and the backscatter coefficient was 26times 10^{ -4}cm^{-1}sr

The effects of tissue processing on markers for T and B cells from solid tissues.

PubMed

Millard, P R; Rabin, B S; Whiteside, T L; Hubbard, J D

1977-03-01

Suspensions of lymphoid cells from tissues have been used for the determination of the quantitative relationship between the T and B cell populations. The distribution of the lymphocytes within a given tissue, however, cannot be demonstrated once such a suspension has been prepared. Various methods of characterizing lymphocytes within tissues were evaluated. The method of tissue preparation can alter the capability of detecting the lymphocyte markers. Fluorescein-labeled anti-immunoglobulin sera reacted equally well with lymphocytes in tissue regardless of the method of tissue preparation. Complement-coated sheep erythrocytes were less effective in detecting lymphocyte markers in tissue sections than in cell suspensions. Quantitative assays of lymphocytes could be done in suspensions only. Unaltered sheep erythrocytes did not bind to T lymphocytes in tissue. T lymphocytes could be identified in tissue sections, however, by the use of anti-human T cell serum.

A fiber-optic-based imaging system for nondestructive assessment of cell-seeded tissue-engineered scaffolds.

PubMed

Hofmann, Matthias C; Whited, Bryce M; Criswell, Tracy; Rylander, Marissa Nichole; Rylander, Christopher G; Soker, Shay; Wang, Ge; Xu, Yong

2012-09-01

A major limitation in tissue engineering is the lack of nondestructive methods that assess the development of tissue scaffolds undergoing preconditioning in bioreactors. Due to significant optical scattering in most scaffolding materials, current microscope-based imaging methods cannot "see" through thick and optically opaque tissue constructs. To address this deficiency, we developed a fiber-optic-based imaging method that is capable of nondestructive imaging of fluorescently labeled cells through a thick and optically opaque scaffold, contained in a bioreactor. This imaging modality is based on the local excitation of fluorescent cells, the acquisition of fluorescence through the scaffold, and fluorescence mapping based on the position of the excitation light. To evaluate the capability and accuracy of the imaging system, human endothelial cells (ECs), stably expressing green fluorescent protein (GFP), were imaged through a fibrous scaffold. Without sacrificing the scaffolds, we nondestructively visualized the distribution of GFP-labeled cells through a ~500 μm thick scaffold with cell-level resolution and distinct localization. These results were similar to control images obtained using an optical microscope with direct line-of-sight access. Through a detailed quantitative analysis, we demonstrated that this method achieved a resolution on the order of 20-30 μm, with 10% or less deviation from standard optical microscopy. Furthermore, we demonstrated that the penetration depth of the imaging method exceeded that of confocal laser scanning microscopy by more than a factor of 2. Our imaging method also possesses a working distance (up to 8 cm) much longer than that of a standard confocal microscopy system, which can significantly facilitate bioreactor integration. This method will enable the nondestructive monitoring of ECs seeded on the lumen of a tissue-engineered vascular graft during preconditioning in vitro, as well as for other tissue-engineered constructs

Evaluation of coronary stenosis with the aid of quantitative image analysis in histological cross sections.

PubMed

Dulohery, Kate; Papavdi, Asteria; Michalodimitrakis, Manolis; Kranioti, Elena F

2012-11-01

Coronary artery atherosclerosis is a hugely prevalent condition in the Western World and is often encountered during autopsy. Atherosclerotic plaques can cause luminal stenosis: which, if over a significant level (75%), is said to contribute to cause of death. Estimation of stenosis can be macroscopically performed by the forensic pathologists at the time of autopsy or by microscopic examination. This study compares macroscopic estimation with quantitative microscopic image analysis with a particular focus on the assessment of significant stenosis (>75%). A total of 131 individuals were analysed. The sample consists of an atherosclerotic group (n=122) and a control group (n=9). The results of the two methods were significantly different from each other (p=0.001) and the macroscopic method gave a greater percentage stenosis by an average of 3.5%. Also, histological examination of coronary artery stenosis yielded a difference in significant stenosis in 11.5% of cases. The differences were attributed to either histological quantitative image analysis underestimation; gross examination overestimation; or, a combination of both. The underestimation may have come from tissue shrinkage during tissue processing for histological specimen. The overestimation from the macroscopic assessment can be attributed to the lumen shape, to the examiner observer error or to a possible bias to diagnose coronary disease when no other cause of death is apparent. The results indicate that the macroscopic estimation is open to more biases and that histological quantitative image analysis only gives a precise assessment of stenosis ex vivo. Once tissue shrinkage, if any, is accounted for then histological quantitative image analysis will yield a more accurate assessment of in vivo stenosis. It may then be considered a complementary tool for the examination of coronary stenosis. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

A Hertzian contact mechanics based formulation to improve ultrasound elastography assessment of uterine cervical tissue stiffness.

PubMed

Briggs, Brandi N; Stender, Michael E; Muljadi, Patrick M; Donnelly, Meghan A; Winn, Virginia D; Ferguson, Virginia L

2015-06-25

Clinical practice requires improved techniques to assess human cervical tissue properties, especially at the internal os, or orifice, of the uterine cervix. Ultrasound elastography (UE) holds promise for non-invasively monitoring cervical stiffness throughout pregnancy. However, this technique provides qualitative strain images that cannot be linked to a material property (e.g., Young's modulus) without knowledge of the contact pressure under a rounded transvaginal transducer probe and correction for the resulting non-uniform strain dissipation. One technique to standardize elastogram images incorporates a material of known properties and uses one-dimensional, uniaxial Hooke's law to calculate Young's modulus within the compressed material half-space. However, this method does not account for strain dissipation and the strains that evolve in three-dimensional space. We demonstrate that an analytical approach based on 3D Hertzian contact mechanics provides a reasonable first approximation to correct for UE strain dissipation underneath a round transvaginal transducer probe and thus improves UE-derived estimates of tissue modulus. We validate the proposed analytical solution and evaluate sources of error using a finite element model. As compared to 1D uniaxial Hooke's law, the Hertzian contact-based solution yields significantly improved Young's modulus predictions in three homogeneous gelatin tissue phantoms possessing different moduli. We also demonstrate the feasibility of using this technique to image human cervical tissue, where UE-derived moduli estimations for the uterine cervix anterior lip agreed well with published, experimentally obtained values. Overall, UE with an attached reference standard and a Hertzian contact-based correction holds promise for improving quantitative estimates of cervical tissue modulus. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

Desset, Sophie; Poulet, Axel; Tatout, Christophe

2018-01-01

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

Quantitative Analysis of TDLUs using Adaptive Morphological Shape Techniques

PubMed Central

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

2014-01-01

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

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

DOE PAGES

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.; ...

2015-11-03

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

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

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Genetic toxicology at the crossroads-from qualitative hazard evaluation to quantitative risk assessment.

PubMed

White, Paul A; Johnson, George E

2016-05-01

Applied genetic toxicology is undergoing a transition from qualitative hazard identification to quantitative dose-response analysis and risk assessment. To facilitate this change, the Health and Environmental Sciences Institute (HESI) Genetic Toxicology Technical Committee (GTTC) sponsored a workshop held in Lancaster, UK on July 10-11, 2014. The event included invited speakers from several institutions and the contents was divided into three themes-1: Point-of-departure Metrics for Quantitative Dose-Response Analysis in Genetic Toxicology; 2: Measurement and Estimation of Exposures for Better Extrapolation to Humans and 3: The Use of Quantitative Approaches in Genetic Toxicology for human health risk assessment (HHRA). A host of pertinent issues were discussed relating to the use of in vitro and in vivo dose-response data, the development of methods for in vitro to in vivo extrapolation and approaches to use in vivo dose-response data to determine human exposure limits for regulatory evaluations and decision-making. This Special Issue, which was inspired by the workshop, contains a series of papers that collectively address topics related to the aforementioned themes. The Issue includes contributions that collectively evaluate, describe and discuss in silico, in vitro, in vivo and statistical approaches that are facilitating the shift from qualitative hazard evaluation to quantitative risk assessment. The use and application of the benchmark dose approach was a central theme in many of the workshop presentations and discussions, and the Special Issue includes several contributions that outline novel applications for the analysis and interpretation of genetic toxicity data. Although the contents of the Special Issue constitutes an important step towards the adoption of quantitative methods for regulatory assessment of genetic toxicity, formal acceptance of quantitative methods for HHRA and regulatory decision-making will require consensus regarding the

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

ERIC Educational Resources Information Center

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

2014-01-01

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

Synchrotron microCT imaging of soft tissue in juvenile zebrafish reveals retinotectal projections

NASA Astrophysics Data System (ADS)

Xin, Xuying; Clark, Darin; Ang, Khai Chung; van Rossum, Damian B.; Copper, Jean; Xiao, Xianghui; La Riviere, Patrick J.; Cheng, Keith C.

2017-02-01

Biomedical research and clinical diagnosis would benefit greatly from full volume determinations of anatomical phenotype. Comprehensive tools for morphological phenotyping are central for the emerging field of phenomics, which requires high-throughput, systematic, accurate, and reproducible data collection from organisms affected by genetic, disease, or environmental variables. Theoretically, complete anatomical phenotyping requires the assessment of every cell type in the whole organism, but this ideal is presently untenable due to the lack of an unbiased 3D imaging method that allows histopathological assessment of any cell type despite optical opacity. Histopathology, the current clinical standard for diagnostic phenotyping, involves the microscopic study of tissue sections to assess qualitative aspects of tissue architecture, disease mechanisms, and physiological state. However, quantitative features of tissue architecture such as cellular composition and cell counting in tissue volumes can only be approximated due to characteristics of tissue sectioning, including incomplete sampling and the constraints of 2D imaging of 5 micron thick tissue slabs. We have used a small, vertebrate organism, the zebrafish, to test the potential of microCT for systematic macroscopic and microscopic morphological phenotyping. While cell resolution is routinely achieved using methods such as light sheet fluorescence microscopy and optical tomography, these methods do not provide the pancellular perspective characteristic of histology, and are constrained by the limited penetration of visible light through pigmented and opaque specimens, as characterizes zebrafish juveniles. Here, we provide an example of neuroanatomy that can be studied by microCT of stained soft tissue at 1.43 micron isotropic voxel resolution. We conclude that synchrotron microCT is a form of 3D imaging that may potentially be adopted towards more reproducible, large-scale, morphological phenotyping of optically

Qualitative and quantitative ultrasound attributes of maternal-foetal structures in pregnant ewes.

PubMed

da Silva, Pda; Uscategui, Rar; Santos, Vjc; Taira, A R; Mariano, Rsg; Rodrigues, Mgk; Simões, Apr; Maronezi, M C; Avante, M L; Vicente, Wrr; Feliciano, Mar

2018-06-01

The aim of this study was to examine foetal organs and placental tissue to establish a correlation between the changes in the composition of these structures associated with their maturation and the ultrasonographic characteristics of the images. Twenty-four pregnant ewes were included in the study. Ultrasonography assessments were performed in B-mode, from the ninth gestational week until parturition. The lungs, liver and kidneys of foetuses and placentomes were located in transverse and longitudinal sections to evaluate the echogenicity (hypoechoic, isoechoic, hyperechoic or mixed) and echotexture (homogeneous and heterogeneous) of the tissues of interest. For quantitative evaluation of the ultrasonographic characteristics, it was performed a computerized image analysis using a commercial software (Image ProPlus ® ). Mean numerical pixel values (NPVs), pixel heterogeneity (standard deviation of NPVs) and minimum and maximum pixel values were measured by selecting five circular regions of interest in each assessed tissue. All evaluated tissues presented significant variations in the NPVs, except for the liver. Pulmonary NPVmean, NPVmin and NPVmax decreased gradually through gestational weeks. The renal parameters gradually decreased with the advancement of the gestational weeks until the 17th week and later stabilized. The placentome NPVmean, NPVmin and NPVmax decreased gradually over the course of weeks. The hepatic tissue did not show echogenicity and echotexture variations and presented medium echogenicity and homogeneous echotexture throughout the experimental period. It was concluded that pixels numerical evaluation of maternal-foetal tissues was applicable and allowed the identification of quantitative ultrasonographic characteristics showing changes in echogenicity related to gestational age. © 2018 Blackwell Verlag GmbH.

Towards intraoperative surgical margin assessment and visualization using bioimpedance properties of the tissue

NASA Astrophysics Data System (ADS)

Khan, Shadab; Mahara, Aditya; Hyams, Elias S.; Schned, Alan; Halter, Ryan

2015-03-01

Prostate cancer (PCa) has a high 10-year recurrence rate, making PCa the second leading cause of cancer-specific mortality among men in the USA. PCa recurrences are often predicted by assessing the status of surgical margins (SM) with positive surgical margins (PSM) increasing the chances of biochemical recurrence by 2-4 times. To this end, an SM assessment system using Electrical Impedance Spectroscopy (EIS) was developed with a microendoscopic probe. This system measures the tissue bioimpedance over a range of frequencies (1 kHz to 1MHz), and computes a Composite Impedance Metric (CIM). CIM can be used to classify tissue as benign or cancerous. The system was used to collect the impedance spectra from excised prostates, which were obtained from men undergoing radical prostatectomy. The data revealed statistically significant (p<0.05) differences in the impedance properties of the benign and tumorous tissues, and between different tissue morphologies. To visualize the results of SM-assessment, a visualization tool using da Vinci stereo laparoscope is being developed. Together with the visualization tool, the EIS-based SM assessment system can be potentially used to intraoperatively classify tissues and display the results on the surgical console with a video feed of the surgical site, thereby augmenting a surgeon's view of the site and providing a potential solution to the intraoperative SM assessment needs.

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. | Office of Cancer Genomics

Cancer.gov

We and others have shown that transition and maintenance of biological states is controlled by master regulator proteins, which can be inferred by interrogating tissue-specific regulatory models (interactomes) with transcriptional signatures, using the VIPER algorithm. Yet, some tissues may lack molecular profiles necessary for interactome inference (orphan tissues), or, as for single cells isolated from heterogeneous samples, their tissue context may be undetermined.

Quantitative and qualitative 5-aminolevulinic acid–induced protoporphyrin IX fluorescence in skull base meningiomas

PubMed Central

Bekelis, Kimon; Valdés, Pablo A.; Erkmen, Kadir; Leblond, Frederic; Kim, Anthony; Wilson, Brian C.; Harris, Brent T.; Paulsen, Keith D.; Roberts, David W.

2011-01-01

Object Complete resection of skull base meningiomas provides patients with the best chance for a cure; however, surgery is frequently difficult given the proximity of lesions to vital structures, such as cranial nerves, major vessels, and venous sinuses. Accurate discrimination between tumor and normal tissue is crucial for optimal tumor resection. Qualitative assessment of protoporphyrin IX (PpIX) fluorescence following the exogenous administration of 5-aminolevulinic acid (ALA) has demonstrated utility in malignant glioma resection but limited use in meningiomas. Here the authors demonstrate the use of ALA-induced PpIX fluorescence guidance in resecting a skull base meningioma and elaborate on the advantages and disadvantages provided by both quantitative and qualitative fluorescence methodologies in skull base meningioma resection. Methods A 52-year-old patient with a sphenoid wing WHO Grade I meningioma underwent tumor resection as part of an institutional review board–approved prospective study of fluorescence-guided resection. A surgical microscope modified for fluorescence imaging was used for the qualitative assessment of visible fluorescence, and an intraoperative probe for in situ fluorescence detection was utilized for quantitative measurements of PpIX. The authors assessed the detection capabilities of both the qualitative and quantitative fluorescence approaches. Results The patient harboring a sphenoid wing meningioma with intraorbital extension underwent radical resection of the tumor with both visibly and nonvisibly fluorescent regions. The patient underwent a complete resection without any complications. Some areas of the tumor demonstrated visible fluorescence. The quantitative probe detected neoplastic tissue better than the qualitative modified surgical microscope. The intraoperative probe was particularly useful in areas that did not reveal visible fluorescence, and tissue from these areas was confirmed as tumor following histopathological

Quantitative Segmentation of Fluorescence Microscopy Images of Heterogeneous Tissue: Application to the Detection of Residual Disease in Tumor Margins.

PubMed

Mueller, Jenna L; Harmany, Zachary T; Mito, Jeffrey K; Kennedy, Stephanie A; Kim, Yongbaek; Dodd, Leslie; Geradts, Joseph; Kirsch, David G; Willett, Rebecca M; Brown, J Quincy; Ramanujam, Nimmi

2013-01-01

To develop a robust tool for quantitative in situ pathology that allows visualization of heterogeneous tissue morphology and segmentation and quantification of image features. TISSUE EXCISED FROM A GENETICALLY ENGINEERED MOUSE MODEL OF SARCOMA WAS IMAGED USING A SUBCELLULAR RESOLUTION MICROENDOSCOPE AFTER TOPICAL APPLICATION OF A FLUORESCENT ANATOMICAL CONTRAST AGENT: acriflavine. An algorithm based on sparse component analysis (SCA) and the circle transform (CT) was developed for image segmentation and quantification of distinct tissue types. The accuracy of our approach was quantified through simulations of tumor and muscle images. Specifically, tumor, muscle, and tumor+muscle tissue images were simulated because these tissue types were most commonly observed in sarcoma margins. Simulations were based on tissue characteristics observed in pathology slides. The potential clinical utility of our approach was evaluated by imaging excised margins and the tumor bed in a cohort of mice after surgical resection of sarcoma. Simulation experiments revealed that SCA+CT achieved the lowest errors for larger nuclear sizes and for higher contrast ratios (nuclei intensity/background intensity). For imaging of tumor margins, SCA+CT effectively isolated nuclei from tumor, muscle, adipose, and tumor+muscle tissue types. Differences in density were correctly identified with SCA+CT in a cohort of ex vivo and in vivo images, thus illustrating the diagnostic potential of our approach. The combination of a subcellular-resolution microendoscope, acriflavine staining, and SCA+CT can be used to accurately isolate nuclei and quantify their density in anatomical images of heterogeneous tissue.

The phenomenon of cathodoluminescence in tooth hard tissues

NASA Astrophysics Data System (ADS)

Bessudnova, Nadezda O.; Matasov, Maxim D.

2012-03-01

The phenomenon of luminescence in tooth hard tissues under the hits of electrons accelerated up to 3keV has been investigated and the nature of luminescence has been described. It has been discovered that the change in luminescence color depends on the place of the impingement of primary electrons. The latter could be explained by different chemical compositions of compounds and complexes where luminescence is observed. Based on the analysis of RGB color bar charts, the correlation between the color of luminescence and calcium-phosphorus ratio in tooth hard tissues has been investigated. Thus, cathodoluminescence can be considered as a tool for in vitro quantitative assessment of tooth hard tissues compositions.

A Quantitative MR Imaging Assessment of Leukoencephalopathy in Children Treated for Acute Lymphoblastic Leukemia without Irradiation

PubMed Central

Reddick, Wilburn E.; Glass, John O.; Helton, Kathleen J.; Langston, James W.; Li, Chin-Shang; Pui, Ching-Hon

2008-01-01

PURPOSE Intravenous methotrexate (IV-MTX), an effective treatment for acute lymphoblastic leukemia (ALL), has a significant toxic effect on the central nervous system, with leukoencephalopathy (LE) being the most common form. The purpose of this study was to use objective quantitative MR imaging to prospectively assess the temporal evolution of LE extent and intensity. METHODS Forty-five children (low-risk, 10 mol/L/12F; mean age, 5.0 years at diagnosis; standard/high-risk, 11 mol/L/12F; mean age, 9.2 years at diagnosis) treated for ALL on a single institutional protocol were evaluated longitudinally to assess the extent of LE (proportion of white matter impacted) through tissue segmentation and the relative intensity of LE through relative elevations in T1 and T2 relaxation rates. One-sided Wilcoxon-Mann-Whitney tests were used to assess differences in quantitative measures at 4 different points in therapy both within and between risk arms. RESULTS The proportion of white matter affected in both patient groups increased significantly with additional courses of IV-MTX, whereas the intensity of LE also increased steadily; however, both the intensity and extent of LE declined significantly ∼1.5 years after completion of IV-MTX. Increases in the T1 and T2 relaxation rates above normal-appearing white matter were significantly correlated with each other and were dependent on the proportion of white matter affected. CONCLUSION Higher doses and more courses of IV-MTX were associated with increased intensity and extent of LE. There was a significant reduction in both the intensity and extent of LE after completion of therapy. The impact of these changes on neurocognitive functioning and quality of life in survivors remains to be determined. PMID:16219848

Quantitative metabolic imaging using endogenous fluorescence to detect stem cell differentiation

NASA Astrophysics Data System (ADS)

Quinn, Kyle P.; Sridharan, Gautham V.; Hayden, Rebecca S.; Kaplan, David L.; Lee, Kyongbum; Georgakoudi, Irene

2013-12-01

The non-invasive high-resolution spatial mapping of cell metabolism within tissues could provide substantial advancements in assessing the efficacy of stem cell therapy and understanding tissue development. Here, using two-photon excited fluorescence microscopy, we elucidate the relationships among endogenous cell fluorescence, cell redox state, and the differentiation of human mesenchymal stem cells into adipogenic and osteoblastic lineages. Using liquid chromatography/mass spectrometry and quantitative PCR, we evaluate the sensitivity of an optical redox ratio of FAD/(NADH + FAD) to metabolic changes associated with stem cell differentiation. Furthermore, we probe the underlying physiological mechanisms, which relate a decrease in the redox ratio to the onset of differentiation. Because traditional assessments of stem cells and engineered tissues are destructive, time consuming, and logistically intensive, the development and validation of a non-invasive, label-free approach to defining the spatiotemporal patterns of cell differentiation can offer a powerful tool for rapid, high-content characterization of cell and tissue cultures.

Optimization of Evans blue quantitation in limited rat tissue samples

PubMed Central

Wang, Hwai-Lee; Lai, Ted Weita

2014-01-01

Evans blue dye (EBD) is an inert tracer that measures plasma volume in human subjects and vascular permeability in animal models. Quantitation of EBD can be difficult when dye concentration in the sample is limited, such as when extravasated dye is measured in the blood-brain barrier (BBB) intact brain. The procedure described here used a very small volume (30 µl) per sample replicate, which enabled high-throughput measurements of the EBD concentration based on a standard 96-well plate reader. First, ethanol ensured a consistent optic path length in each well and substantially enhanced the sensitivity of EBD fluorescence spectroscopy. Second, trichloroacetic acid (TCA) removed false-positive EBD measurements as a result of biological solutes and partially extracted EBD into the supernatant. Moreover, a 1:2 volume ratio of 50% TCA ([TCA final] = 33.3%) optimally extracted EBD from the rat plasma protein-EBD complex in vitro and in vivo, and 1:2 and 1:3 weight-volume ratios of 50% TCA optimally extracted extravasated EBD from the rat brain and liver, respectively, in vivo. This procedure is particularly useful in the detection of EBD extravasation into the BBB-intact brain, but it can also be applied to detect dye extravasation into tissues where vascular permeability is less limiting. PMID:25300427

Optimization of Evans blue quantitation in limited rat tissue samples

NASA Astrophysics Data System (ADS)

Wang, Hwai-Lee; Lai, Ted Weita

2014-10-01

Evans blue dye (EBD) is an inert tracer that measures plasma volume in human subjects and vascular permeability in animal models. Quantitation of EBD can be difficult when dye concentration in the sample is limited, such as when extravasated dye is measured in the blood-brain barrier (BBB) intact brain. The procedure described here used a very small volume (30 µl) per sample replicate, which enabled high-throughput measurements of the EBD concentration based on a standard 96-well plate reader. First, ethanol ensured a consistent optic path length in each well and substantially enhanced the sensitivity of EBD fluorescence spectroscopy. Second, trichloroacetic acid (TCA) removed false-positive EBD measurements as a result of biological solutes and partially extracted EBD into the supernatant. Moreover, a 1:2 volume ratio of 50% TCA ([TCA final] = 33.3%) optimally extracted EBD from the rat plasma protein-EBD complex in vitro and in vivo, and 1:2 and 1:3 weight-volume ratios of 50% TCA optimally extracted extravasated EBD from the rat brain and liver, respectively, in vivo. This procedure is particularly useful in the detection of EBD extravasation into the BBB-intact brain, but it can also be applied to detect dye extravasation into tissues where vascular permeability is less limiting.

76 FR 19311 - Update of the 2003 Interagency Quantitative Assessment of the Relative Risk to Public Health From...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-07

... the 2003 Interagency Quantitative Assessment of the Relative Risk to Public Health From Foodborne... quantitative targets established in ``Healthy People 2010.'' In 2005, FoodNet data showed 0.30 L. monocytogenes... 4). In 2003, FDA and FSIS published a quantitative assessment of the relative risk to public health...

Assessment of tumor response to oxygen challenge using quantitative diffusion MRI in an animal model.

PubMed

Zhang, Zhongwei; Yuan, Qing; Zhou, Heling; Zhao, Dawen; Li, Li; Gerberich, Jenifer L; Mason, Ralph P

2015-11-01

To assess tumor response to oxygen challenge using quantitative diffusion magnetic resonance imaging (MRI). A well-characterized Dunning R3327-AT1 rat prostate cancer line was implanted subcutaneously in the right thigh of male Copenhagen rats (n = 8). Diffusion-weighted images (DWI) with multiple b values (0, 25, 50, 100, 150, 200, 300, 500, 1000, 1500 s/mm(2) ) in three orthogonal directions were obtained using a multishot FSE-based Stejskal-Tanner DWI sequence (FSE-DWI) at 4.7T, while rats breathed medical air (21% oxygen) and with 100% oxygen challenge. Stretched-exponential and intravoxel incoherent motion (IVIM) models were used to calculate and compare quantitative diffusion parameters: diffusion heterogeneity index (α), intravoxel distribution of diffusion coefficients (DDC), tissue diffusivity (Dt), pseudo-diffusivity (Dp), and perfusion fraction (f) on a voxel-by-voxel basis. A significant increase of α (73.9 ± 4.7% in air vs. 78.1 ± 4.5% in oxygen, P = 0.0198) and a significant decrease of f (13.4 ± 3.7% in air vs. 10.4 ± 2.7% in oxygen, P = 0.0201) were observed to accompany oxygen challenge. Correlations between f and α during both air and oxygen breathing were found; the correlation coefficients (r) were -0.90 and -0.96, respectively. Positive correlations between Dt and DDC with oxygen breathing (r = 0.95, P = 0.0003), f and DDC with air breathing were also observed (r = 0.95, P = 0.0004). Quantitative diffusion MRI demonstrated changes in tumor perfusion in response to oxygen challenge. © 2015 Wiley Periodicals, Inc.

Quantitative determination of selenium and mercury, and an ICP-MS semi-quantitative scan of other elements in samples of eagle tissues collected from the Pacific Northwest--Summer 2011

USGS Publications Warehouse

May, Thomas; Walther, Mike; Brumbaugh, William

2013-01-01

Eagle tissues from dead eagle carcasses were collected by U.S. Fish and Wildlife Service personnel at various locations in the Pacific Northwest as part of a study to document the occurrence of metal and metalloid contaminants. A group of 182 eagle tissue samples, consisting of liver, kidney, brain, talon, feather, femur, humerus, and stomach contents, were quantitatively analyzed for concentrations of selenium and mercury by atomic absorption techniques, and for other elements by semi-quantitative scan with an inductively coupled plasma-mass spectrometer. For the various tissue matrices analyzed by an ICP-MS semiquantitative scan, some elemental concentrations (micrograms per gram dry weight) were quite variable within a particular matrix; notable observations were as follows: lead concentrations ranged from 0.2 to 31 in femurs, 0.1 to 29 in humeri, 0.1 to 54 in talons, less than (<) 0.05 to 120 in livers, <0.05 to 34 in kidneys, and 0.05 to 8 in brains; copper concentrations ranged from 5 to 9 in feathers, 8 to 47 in livers, 7 to 43 in kidneys, and 7 to 28 in brains; cadmium concentrations ranged from 0.1 to 10 in kidneys. In stomach contents, concentrations of vanadium ranged from 0.08 to 5, chromium 2 to 34, manganese 1 to 57, copper 2 to 69, arsenic <0.05 to 6, rubidium 1 to 13, and barium <0.5 to 18. Selenium concentrations from highest to lowest based on the matrix mean were as follows: kidney, liver, feather, brain, stomach content, talon, femur, and humerus. For mercury, the highest to lowest concentrations were feather, liver, talon, brain, stomach content, femur, and humerus.

Quantitative analysis of polyethylene glycol (PEG) and PEGylated proteins in animal tissues by LC-MS/MS coupled with in-source CID.

PubMed

Gong, Jiachang; Gu, Xiaomei; Achanzar, William E; Chadwick, Kristina D; Gan, Jinping; Brock, Barry J; Kishnani, Narendra S; Humphreys, W Griff; Iyer, Ramaswamy A

2014-08-05

The covalent conjugation of polyethylene glycol (PEG, typical MW > 10k) to therapeutic peptides and proteins is a well-established approach to improve their pharmacokinetic properties and diminish the potential for immunogenicity. Even though PEG is generally considered biologically inert and safe in animals and humans, the slow clearance of large PEGs raises concerns about potential adverse effects resulting from PEG accumulation in tissues following chronic administration, particularly in the central nervous system. The key information relevant to the issue is the disposition and fate of the PEG moiety after repeated dosing with PEGylated proteins. Here, we report a novel quantitative method utilizing LC-MS/MS coupled with in-source CID that is highly selective and sensitive to PEG-related materials. Both (40K)PEG and a tool PEGylated protein (ATI-1072) underwent dissociation in the ionization source of mass spectrometer to generate a series of PEG-specific ions, which were subjected to further dissociation through conventional CID. To demonstrate the potential application of the method to assess PEG biodistribution following PEGylated protein administration, a single dose study of ATI-1072 was conducted in rats. Plasma and various tissues were collected, and the concentrations of both (40K)PEG and ATI-1072 were determined using the LC-MS/MS method. The presence of (40k)PEG in plasma and tissue homogenates suggests the degradation of PEGylated proteins after dose administration to rats, given that free PEG was absent in the dosing solution. The method enables further studies for a thorough characterization of disposition and fate of PEGylated proteins.

Status and future of Quantitative Microbiological Risk Assessment in China

PubMed Central

Dong, Q.L.; Barker, G.C.; Gorris, L.G.M.; Tian, M.S.; Song, X.Y.; Malakar, P.K.

2015-01-01

Since the implementation of the Food Safety Law of the People's Republic of China in 2009 use of Quantitative Microbiological Risk Assessment (QMRA) has increased. QMRA is used to assess the risk posed to consumers by pathogenic bacteria which cause the majority of foodborne outbreaks in China. This review analyses the progress of QMRA research in China from 2000 to 2013 and discusses 3 possible improvements for the future. These improvements include planning and scoping to initiate QMRA, effectiveness of microbial risk assessment utility for risk management decision making, and application of QMRA to establish appropriate Food Safety Objectives. PMID:26089594

Identification and quantitative evaluation of the fiber structure in the pathological tissue using Mueller matrix microscope

NASA Astrophysics Data System (ADS)

Zhou, Jialing; He, Honghui; Wang, Ye; Ma, Hui

2017-02-01

Fiber structure changes in the various pathological processes, such as the increase of fibrosis in liver diseases, the derangement of fiber in cervical cancer and so on. Currently, clinical pathologic diagnosis is regarded as the golden criterion, but different doctors with discrepancy in knowledge and experience may obtain different conclusions. Up to a point, quantitative evaluation of the fiber structure in the pathological tissue can be of great service to quantitative diagnosis. Mueller matrix measurement is capable of probing comprehensive microstructural information of samples and different wavelength of lights can provide more information. In this paper, we use a Mueller matrix microscope with light sources in six different wavelength. We use unstained, dewaxing liver tissue slices in four stages and the pathological biopsy of the filtration channels from rabbit eyes as samples. We apply the Mueller matrix polar decomposition (MMPD) parameter δ which corresponds to retardance to liver slices. The mean value of abnormal region get bigger when the level of fibrosis get higher and light in short wavelength is more sensitive to the microstructure of fiber. On the other hand, we use the Mueller matrix transformation (MMT) parameter Φ which is associated to the angel of fast axis in the analysis of the slices of the filtration channels from rabbit eyes. The value of kurtosis and the value of skewness shows big difference between new born region and normal region and can reveal the arrangement of fiber. These results indicate that the Mueller matrix microscope has great potential in auxiliary diagnosis.

Quantitative analysis of wet-heat inactivation in bovine spongiform encephalopathy

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

Matsuura, Yuichi; Ishikawa, Yukiko; Bo, Xiao

2013-03-01

Highlights: ► We quantitatively analyzed wet-heat inactivation of the BSE agent. ► Infectivity of the BSE macerate did not survive 155 °C wet-heat treatment. ► Once the sample was dehydrated, infectivity was observed even at 170 °C. ► A quantitative PMCA assay was used to evaluate the degree of BSE inactivation. - Abstract: The bovine spongiform encephalopathy (BSE) agent is resistant to conventional microbial inactivation procedures and thus threatens the safety of cattle products and by-products. To obtain information necessary to assess BSE inactivation, we performed quantitative analysis of wet-heat inactivation of infectivity in BSE-infected cattle spinal cords. Using amore » highly sensitive bioassay, we found that infectivity in BSE cattle macerates fell with increase in temperatures from 133 °C to 150 °C and was not detected in the samples subjected to temperatures above 155 °C. In dry cattle tissues, infectivity was detected even at 170 °C. Thus, BSE infectivity reduces with increase in wet-heat temperatures but is less affected when tissues are dehydrated prior to the wet-heat treatment. The results of the quantitative protein misfolding cyclic amplification assay also demonstrated that the level of the protease-resistant prion protein fell below the bioassay detection limit by wet-heat at 155 °C and higher and could help assess BSE inactivation. Our results show that BSE infectivity is strongly resistant to wet-heat inactivation and that it is necessary to pay attention to BSE decontamination in recycled cattle by-products.« less

Quantitative colorectal cancer perfusion measurement by multidetector-row CT: does greater tumour coverage improve measurement reproducibility?

PubMed

Goh, V; Halligan, S; Gartner, L; Bassett, P; Bartram, C I

2006-07-01

The purpose of this study was to determine if greater z-axis tumour coverage improves the reproducibility of quantitative colorectal cancer perfusion measurements using CT. A 65 s perfusion study was acquired following intravenous contrast administration in 10 patients with proven colorectal cancer using a four-detector row scanner. This was repeated within 48 h using identical technical parameters to allow reproducibility assessment. Quantitative tumour blood volume, blood flow, mean transit time and permeability measurements were determined using commercially available software (Perfusion 3.0; GE Healthcare, Waukesha, WI) for data obtained from a 5 mm z-axis tumour coverage, and from a 20 mm z-axis tumour coverage. Measurement reproducibility was assessed using Bland-Altman statistics, for a 5 mm z-axis tumour coverage, and 20 mm z-axis tumour coverage, respectively. The mean difference (95% limits of agreement) for blood volume, blood flow, mean transit time and permeability were 0.04 (-2.50 to +2.43) ml/100 g tissue; +8.80 (-50.5 to +68.0) ml/100 g tissue/min; -0.99 (-8.19 to +6.20) seconds; and +1.20 (-5.42 to +7.83) ml/100 g tissue/min, respectively, for a 5 mm coverage, and -0.04 (-2.61 to +2.53) ml/100 g tissue; +7.40 (-50.3 to +65.0) ml/100 g tissue/min; -2.46 (-12.61 to +7.69) seconds; and -0.23 (-8.31 to +7.85) ml/100 g tissue/min, respectively, for a 20 mm coverage, indicating similar levels of agreement. In conclusion, increasing z-axis coverage does not improve reproducibility of quantitative colorectal cancer perfusion measurements.

Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling.

PubMed

Vlot, Anna H C; de Witte, Wilhelmus E A; Danhof, Meindert; van der Graaf, Piet H; van Westen, Gerard J P; de Lange, Elizabeth C M

2017-12-04

Selectivity is an important attribute of effective and safe drugs, and prediction of in vivo target and tissue selectivity would likely improve drug development success rates. However, a lack of understanding of the underlying (pharmacological) mechanisms and availability of directly applicable predictive methods complicates the prediction of selectivity. We explore the value of combining physiologically based pharmacokinetic (PBPK) modeling with quantitative structure-activity relationship (QSAR) modeling to predict the influence of the target dissociation constant (K D ) and the target dissociation rate constant on target and tissue selectivity. The K D values of CB1 ligands in the ChEMBL database are predicted by QSAR random forest (RF) modeling for the CB1 receptor and known off-targets (TRPV1, mGlu5, 5-HT1a). Of these CB1 ligands, rimonabant, CP-55940, and Δ 8 -tetrahydrocanabinol, one of the active ingredients of cannabis, were selected for simulations of target occupancy for CB1, TRPV1, mGlu5, and 5-HT1a in three brain regions, to illustrate the principles of the combined PBPK-QSAR modeling. Our combined PBPK and target binding modeling demonstrated that the optimal values of the K D and k off for target and tissue selectivity were dependent on target concentration and tissue distribution kinetics. Interestingly, if the target concentration is high and the perfusion of the target site is low, the optimal K D value is often not the lowest K D value, suggesting that optimization towards high drug-target affinity can decrease the benefit-risk ratio. The presented integrative structure-pharmacokinetic-pharmacodynamic modeling provides an improved understanding of tissue and target selectivity.

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women.

PubMed

Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C; Joseph, Gabby B; Yap, Samuel P; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M

2012-07-01

The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 ± 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. Fat infiltration of muscle commonly occurs in many metabolic and neuromuscular diseases. • Image-based semi-quantitative classifications for assessing fat infiltration are not well validated. • Quantitative MRI techniques provide an accurate assessment of muscle fat.

Qualitative assessment of connective tissue graft with epithelial component. A microsurgical periodontal plastic surgical technique for soft tissue esthetics.

PubMed

Rossi, Roberto; Pilloni, Andrea; Morales, Regina Santos

2009-01-01

Connective tissue grafts have been used successfully in the treatment of gingival recession. In the mid 80s and late 90s, the periodontal literature presented various techniques such as free gingival grafts, pedicle flaps, subepithelial connective tissue grafts, acellular dermal matrix grafts, and guided tissue regeneration to cover denuded root surfaces. Currently, connective tissue grafting is a reliable treatment for esthetic root coverage. This paper presents a qualitative assessment of a surgical technique that uses a connective tissue graft, including a portion of epithelium in the shape of the defect. This procedure enhances the healing of the covered root surface, increases the thickness of the soft tissue and improves esthetics. The criteria used for evaluation were: color, volume, texture, and blending. This evaluation demonstrated encouraging results from an esthetic viewpoint.

Short Course Introduction to Quantitative Mineral Resource Assessments

USGS Publications Warehouse

Singer, Donald A.

2007-01-01

This is an abbreviated text supplementing the content of three sets of slides used in a short course that has been presented by the author at several workshops. The slides should be viewed in the order of (1) Introduction and models, (2) Delineation and estimation, and (3) Combining estimates and summary. References cited in the slides are listed at the end of this text. The purpose of the three-part form of mineral resource assessments discussed in the accompanying slides is to make unbiased quantitative assessments in a format needed in decision-support systems so that consequences of alternative courses of action can be examined. The three-part form of mineral resource assessments was developed to assist policy makers evaluate the consequences of alternative courses of action with respect to land use and mineral-resource development. The audience for three-part assessments is a governmental or industrial policy maker, a manager of exploration, a planner of regional development, or similar decision-maker. Some of the tools and models presented here will be useful for selection of exploration sites, but that is a side benefit, not the goal. To provide unbiased information, we recommend the three-part form of mineral resource assessments where general locations of undiscovered deposits are delineated from a deposit type's geologic setting, frequency distributions of tonnages and grades of well-explored deposits serve as models of grades and tonnages of undiscovered deposits, and number of undiscovered deposits are estimated probabilistically by type. The internally consistent descriptive, grade and tonnage, deposit density, and economic models used in the design of the three-part form of assessments reduce the chances of biased estimates of the undiscovered resources. What and why quantitative resource assessments: The kind of assessment recommended here is founded in decision analysis in order to provide a framework for making decisions concerning mineral

Brillouin microscopy: assessing ocular tissue biomechanics.

PubMed

Yun, Seok Hyun; Chernyak, Dimitri

2018-07-01

Assessment of corneal biomechanics has been an unmet clinical need in ophthalmology for many years. Many researchers and clinicians have identified corneal biomechanics as source of variability in refractive procedures and one of the main factors in keratoconus. However, it has been difficult to accurately characterize corneal biomechanics in patients. The recent development of Brillouin light scattering microscopy heightens the promise of bringing biomechanics into the clinic. The aim of this review is to overview the progress and discuss prospective applications of this new technology. Brillouin microscopy uses a low-power near-infrared laser beam to determine longitudinal modulus or mechanical compressibility of tissue by analyzing the return signal spectrum. Human clinical studies have demonstrated significant difference in the elastic properties of normal corneas versus corneas diagnosed with mild and severe keratoconus. Clinical data have also shown biomechanical changes after corneal cross-linking treatment of keratoconus patients. Brillouin measurements of the crystalline lens and sclera have also been demonstrated. Brillouin microscopy is a promising technology under commercial development at present. The technique enables physicians to characterize the biomechanical properties of ocular tissues.

A simple hemostasis model for the quantitative evaluation of hydrogel-based local hemostatic biomaterials on tissue surface.

PubMed

Murakami, Yoshihiko; Yokoyama, Masayuki; Nishida, Hiroshi; Tomizawa, Yasuko; Kurosawa, Hiromi

2008-09-01

Several hemostat hydrogels are clinically used, and some other agents are studied for safer, more facile, and more efficient hemostasis. In the present paper, we proposed a novel method to evaluate local hemostat hydrogel on tissue surface. The procedure consisted of the following steps: (step 1) a mouse was fixed on a cork board, and its abdomen was incised; (step 2) serous fluid was carefully removed because it affected the estimation of the weight gained by the filter paper, and parafilm and preweighted filter paper were placed beneath the liver (parafilm prevented the filter paper's absorption of gradually oozing serous fluid); (step 3) the cork board was tilted and maintained at an angle of about 45 degrees so that the bleeding would more easily flow from the liver toward the filter paper; and (step 4) the bleeding lasted for 3 min. In this step, a hemostat was applied to the liver wound immediately after the liver was pricked with a needle. We found that (1) a careful removal of serous fluid prior to a bleeding and (2) a quantitative determination of the amount of excess aqueous solution that oozed out from a hemostat were important to a rigorous evaluation of hemostat efficacy. We successfully evaluated the efficacy of a fibrin-based hemostat hydrogel by using our method. The method proposed in the present study enabled the quantitative, accurate, and easy evaluation of the efficacy of local hemostatic hydrogel which acts as tissue-adhesive agent on biointerfaces.

Functional imaging and assessment of the glucose diffusion rate in epithelial tissues in optical coherence tomography

NASA Astrophysics Data System (ADS)

Larin, K. V.; Tuchin, V. V.

2008-06-01

Functional imaging, monitoring and quantitative description of glucose diffusion in epithelial and underlying stromal tissues in vivo and controlling of the optical properties of tissues are extremely important for many biomedical applications including the development of noninvasive or minimally invasive glucose sensors as well as for therapy and diagnostics of various diseases, such as cancer, diabetic retinopathy, and glaucoma. Recent progress in the development of a noninvasive molecular diffusion biosensor based on optical coherence tomography (OCT) is described. The diffusion of glucose was studied in several epithelial tissues both in vitro and in vivo. Because OCT provides depth-resolved imaging of tissues with high in-depth resolution, the glucose diffusion is described not only as a function of time but also as a function of depth.

Quantitative shear wave imaging optical coherence tomography for noncontact mechanical characterization of myocardium

NASA Astrophysics Data System (ADS)

Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

2015-03-01

Optical coherence elastography (OCE) is an emerging low-coherence imaging technique that provides noninvasive assessment of tissue biomechanics with high spatial resolution. Among various OCE methods, the capability of quantitative measurement of tissue elasticity is of great importance for tissue characterization and pathology detection across different samples. Here we report a quantitative OCE technique, termed quantitative shear wave imaging optical coherence tomography (Q-SWI-OCT), which enables noncontact measurement of tissue Young's modulus based on the ultra-fast imaging of the shear wave propagation inside the sample. A focused air-puff device is used to interrogate the tissue with a low-pressure short-duration air stream that stimulates a localized displacement with the scale at micron level. The propagation of this tissue deformation in the form of shear wave is captured by a phase-sensitive OCT system running with the scan of the M-mode imaging over the path of the wave propagation. The temporal characteristics of the shear wave is quantified based on the cross-correlation of the tissue deformation profiles at all the measurement locations, and linear regression is utilized to fit the data plotted in the domain of time delay versus wave propagation distance. The wave group velocity is thus calculated, which results in the quantitative measurement of the Young's modulus. As the feasibility demonstration, experiments are performed on tissuemimicking phantoms with different agar concentrations and the quantified elasticity values with Q-SWI-OCT agree well with the uniaxial compression tests. For functional characterization of myocardium with this OCE technique, we perform our pilot experiments on ex vivo mouse cardiac muscle tissues with two studies, including 1) elasticity difference of cardiac muscle under relaxation and contract conditions and 2) mechanical heterogeneity of the heart introduced by the muscle fiber orientation. Our results suggest the

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry.

PubMed

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J; Kertesz, Vilmos; Gan, Jinping

2016-03-25

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites were studied. Major organs (brain, lung, liver, kidney and muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed the same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. In addition, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative Segmentation of Fluorescence Microscopy Images of Heterogeneous Tissue: Application to the Detection of Residual Disease in Tumor Margins

PubMed Central

Mueller, Jenna L.; Harmany, Zachary T.; Mito, Jeffrey K.; Kennedy, Stephanie A.; Kim, Yongbaek; Dodd, Leslie; Geradts, Joseph; Kirsch, David G.; Willett, Rebecca M.; Brown, J. Quincy; Ramanujam, Nimmi

2013-01-01

Purpose To develop a robust tool for quantitative in situ pathology that allows visualization of heterogeneous tissue morphology and segmentation and quantification of image features. Materials and Methods Tissue excised from a genetically engineered mouse model of sarcoma was imaged using a subcellular resolution microendoscope after topical application of a fluorescent anatomical contrast agent: acriflavine. An algorithm based on sparse component analysis (SCA) and the circle transform (CT) was developed for image segmentation and quantification of distinct tissue types. The accuracy of our approach was quantified through simulations of tumor and muscle images. Specifically, tumor, muscle, and tumor+muscle tissue images were simulated because these tissue types were most commonly observed in sarcoma margins. Simulations were based on tissue characteristics observed in pathology slides. The potential clinical utility of our approach was evaluated by imaging excised margins and the tumor bed in a cohort of mice after surgical resection of sarcoma. Results Simulation experiments revealed that SCA+CT achieved the lowest errors for larger nuclear sizes and for higher contrast ratios (nuclei intensity/background intensity). For imaging of tumor margins, SCA+CT effectively isolated nuclei from tumor, muscle, adipose, and tumor+muscle tissue types. Differences in density were correctly identified with SCA+CT in a cohort of ex vivo and in vivo images, thus illustrating the diagnostic potential of our approach. Conclusion The combination of a subcellular-resolution microendoscope, acriflavine staining, and SCA+CT can be used to accurately isolate nuclei and quantify their density in anatomical images of heterogeneous tissue. PMID:23824589

Improving the Linkages between Air Pollution Epidemiology and Quantitative Risk Assessment

PubMed Central

Bell, Michelle L.; Walker, Katy; Hubbell, Bryan

2011-01-01

Background: Air pollution epidemiology plays an integral role in both identifying the hazards of air pollution as well as supplying the risk coefficients that are used in quantitative risk assessments. Evidence from both epidemiology and risk assessments has historically supported critical environmental policy decisions. The extent to which risk assessors can properly specify a quantitative risk assessment and characterize key sources of uncertainty depends in part on the availability, and clarity, of data and assumptions in the epidemiological studies. Objectives: We discuss the interests shared by air pollution epidemiology and risk assessment communities in ensuring that the findings of epidemiological studies are appropriately characterized and applied correctly in risk assessments. We highlight the key input parameters for risk assessments and consider how modest changes in the characterization of these data might enable more accurate risk assessments that better represent the findings of epidemiological studies. Discussion: We argue that more complete information regarding the methodological choices and input data used in epidemiological studies would support more accurate risk assessments—to the benefit of both disciplines. In particular, we suggest including additional details regarding air quality, demographic, and health data, as well as certain types of data-rich graphics. Conclusions: Relatively modest changes to the data reported in epidemiological studies will improve the quality of risk assessments and help prevent the misinterpretation and mischaracterization of the results of epidemiological studies. Such changes may also benefit epidemiologists undertaking meta-analyses. We suggest workshops as a way to improve the dialogue between the two communities. PMID:21816702

Determination of optimal glycerol concentration for optical tissue clearing

NASA Astrophysics Data System (ADS)

Youn, Eungjun; Son, Taeyoon; Kim, Han-Sung; Jung, Byungjo

2012-02-01

The laser scattering in tissue is significant in diagnostic and therapeutic purposes of laser. Many studies have been conducted to minimize laser scattering in tissue and therefore, to maximize the clinical efficacy by enhancing photon density. Optical clearing agents (OCAs) have been employed for optical tissue clearing (OTC). This study was aimed to investigate the optimal concentration of an OCA, glycerol, in topical application,, so that it can be utilized for clinical diagnosis and therapy in dermatology. Glycerol was topically applied to avoid possible edema caused by dermal injection. The effect of OTC was quantitatively evaluated as a function of the concentration of glycerol with various methods. Optical methods such as optical coherence tomography (OCT) and an integrating sphere were used to assess the enhancement of light penetration depth and refractive index matching. In addition, a non-optical method, ultrasound scanner, was utilized to evaluate quantitatively collagen dissociation. The results revealed that 70 % glycerol was the optimal concentration of OTC for topical application. This study may provide a guideline regarding to the use of glycerol for optimal diagnostic and therapeutic effects in dermatology.

Quantitation of tissue loss during prolonged space flight

NASA Technical Reports Server (NTRS)

Leonard, J. I.

1979-01-01

Data from Skylab missions related to tissue loss in space were analyzed. Significant changes in gross body composition occur during spaceflight, these include: alterations in water balance resulting from headward shifts of fluid, loss of musculoskeletal tissue, and alterations in fat depending upon the balance between caloric intake and energy expenditure. An effort was made to control the more essential components of body weight on the Skylab missions.

Assessing covariate balance when using the generalized propensity score with quantitative or continuous exposures.

PubMed

Austin, Peter C

2018-01-01

Propensity score methods are increasingly being used to estimate the effects of treatments and exposures when using observational data. The propensity score was initially developed for use with binary exposures (e.g., active treatment vs. control). The generalized propensity score is an extension of the propensity score for use with quantitative exposures (e.g., dose or quantity of medication, income, years of education). A crucial component of any propensity score analysis is that of balance assessment. This entails assessing the degree to which conditioning on the propensity score (via matching, weighting, or stratification) has balanced measured baseline covariates between exposure groups. Methods for balance assessment have been well described and are frequently implemented when using the propensity score with binary exposures. However, there is a paucity of information on how to assess baseline covariate balance when using the generalized propensity score. We describe how methods based on the standardized difference can be adapted for use with quantitative exposures when using the generalized propensity score. We also describe a method based on assessing the correlation between the quantitative exposure and each covariate in the sample when weighted using generalized propensity score -based weights. We conducted a series of Monte Carlo simulations to evaluate the performance of these methods. We also compared two different methods of estimating the generalized propensity score: ordinary least squared regression and the covariate balancing propensity score method. We illustrate the application of these methods using data on patients hospitalized with a heart attack with the quantitative exposure being creatinine level.

A Framework for General Education Assessment: Assessing Information Literacy and Quantitative Literacy with ePortfolios

ERIC Educational Resources Information Center

Hubert, David A.; Lewis, Kati J.

2014-01-01

This essay presents the findings of an authentic and holistic assessment, using a random sample of one hundred student General Education ePortfolios, of two of Salt Lake Community College's (SLCC) college-wide learning outcomes: quantitative literacy (QL) and information literacy (IL). Performed by four faculty from biology, humanities, and…

[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

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.

Quantitative Ultrasound Imaging Using Acoustic Backscatter Coefficients.

NASA Astrophysics Data System (ADS)

Boote, Evan Jeffery

Current clinical ultrasound scanners render images which have brightness levels related to the degree of backscattered energy from the tissue being imaged. These images offer the interpreter a qualitative impression of the scattering characteristics of the tissue being examined, but due to the complex factors which affect the amplitude and character of the echoed acoustic energy, it is difficult to make quantitative assessments of scattering nature of the tissue, and thus, difficult to make precise diagnosis when subtle disease effects are present. In this dissertation, a method of data reduction for determining acoustic backscatter coefficients is adapted for use in forming quantitative ultrasound images of this parameter. In these images, the brightness level of an individual pixel corresponds to the backscatter coefficient determined for the spatial position represented by that pixel. The data reduction method utilized rigorously accounts for extraneous factors which affect the scattered echo waveform and has been demonstrated to accurately determine backscatter coefficients under a wide range of conditions. The algorithms and procedures used to form backscatter coefficient images are described. These were tested using tissue-mimicking phantoms which have regions of varying scattering levels. Another phantom has a fat-mimicking layer for testing these techniques under more clinically relevant conditions. Backscatter coefficient images were also formed of in vitro human liver tissue. A clinical ultrasound scanner has been adapted for use as a backscatter coefficient imaging platform. The digital interface between the scanner and the computer used for data reduction are described. Initial tests, using phantoms are presented. A study of backscatter coefficient imaging of in vivo liver was performed using several normal, healthy human subjects.

Development of a quantitative PCR assay for monitoring Streptococcus agalactiae colonization and tissue tropism in experimentally infected tilapia.

PubMed

Su, Y-L; Feng, J; Li, Y-W; Bai, J-S; Li, A-X

2016-02-01

Streptococcus agalactiae has become one of the most important emerging pathogens in the aquaculture industry and has resulted in large economic losses for tilapia farms in China. In this study, three pairs of specific primers were designed and tested for their specificities and sensitivities in quantitative real-time polymerase chain reactions (qPCRs) after optimization of the annealing temperature. The primer pair IGS-s/IGS-a, which targets the 16S-23S rRNA intergenic spacer region, was finally chosen, having a detection limit of 8.6 copies of S. agalactiae DNA in a 20 μL reaction mixture. Bacterial tissue tropism was demonstrated by qPCR in Oreochromis niloticus 5 days post-injection with a virulent S. agalactiae strain. Bacterial loads were detected at the highest level in brain, followed by moderately high levels in kidney, heart, spleen, intestines, and eye. Significantly lower bacterial loads were observed in muscle, gill and liver. In addition, significantly lower bacterial loads were observed in the brain of convalescent O. niloticus 14 days post-injection with several different S. agalactiae strains. The qPCR for the detection of S. agalactiae developed in this study provides a quantitative tool for investigating bacterial tissue tropism in infected fish, as well as for monitoring bacterial colonization in convalescent fish. © 2015 John Wiley & Sons Ltd.

Quantification of HCV RNA in Liver Tissue by bDNA Assay.

PubMed

Dailey, P J; Collins, M L; Urdea, M S; Wilber, J C

1999-01-01

With this statement, Sherlock and Dooley have described two of the three major challenges involved in quantitatively measuring any analyte in tissue samples: the distribution of the analyte in the tissue; and the standard of reference, or denominator, with which to make comparisons between tissue samples. The third challenge for quantitative measurement of an analyte in tissue is to ensure reproducible and quantitative recovery of the analyte on extraction from tissue samples. This chapter describes a method that can be used to measure HCV RNA quantitatively in liver biopsy and tissue samples using the bDNA assay. All three of these challenges-distribution, denominator, and recovery-apply to the measurement of HCV RNA in liver biopsies.

Single-cell quantitative HER2 measurement identifies heterogeneity and distinct subgroups within traditionally defined HER2-positive patients.

PubMed

Onsum, Matthew D; Geretti, Elena; Paragas, Violette; Kudla, Arthur J; Moulis, Sharon P; Luus, Lia; Wickham, Thomas J; McDonagh, Charlotte F; MacBeath, Gavin; Hendriks, Bart S

2013-11-01

Human epidermal growth factor receptor 2 (HER2) is an important biomarker for breast and gastric cancer prognosis and patient treatment decisions. HER2 positivity, as defined by IHC or fluorescent in situ hybridization testing, remains an imprecise predictor of patient response to HER2-targeted therapies. Challenges to correct HER2 assessment and patient stratification include intratumoral heterogeneity, lack of quantitative and/or objective assays, and differences between measuring HER2 amplification at the protein versus gene level. We developed a novel immunofluorescence method for quantitation of HER2 protein expression at the single-cell level on FFPE patient samples. Our assay uses automated image analysis to identify and classify tumor versus non-tumor cells, as well as quantitate the HER2 staining for each tumor cell. The HER2 staining level is converted to HER2 protein expression using a standard cell pellet array stained in parallel with the tissue sample. This approach allows assessment of HER2 expression and heterogeneity within a tissue section at the single-cell level. By using this assay, we identified distinct subgroups of HER2 heterogeneity within traditional definitions of HER2 positivity in both breast and gastric cancers. Quantitative assessment of intratumoral HER2 heterogeneity may offer an opportunity to improve the identification of patients likely to respond to HER2-targeted therapies. The broad applicability of the assay was demonstrated by measuring HER2 expression profiles on multiple tumor types, and on normal and diseased heart tissues. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

A new method of quantitative cavitation assessment in the field of a lithotripter.

PubMed

Jöchle, K; Debus, J; Lorenz, W J; Huber, P

1996-01-01

Transient cavitation seems to be a very important effect regarding the interaction of pulsed high-energy ultrasound with biologic tissues. Using a newly developed laser optical system we are able to determine the life-span of transient cavities (relative error less than +/- 5%) in the focal region of a lithotripter (Lithostar, Siemens). The laser scattering method is based on the detection of scattered laser light reflected during a bubble's life. This method requires no sort of sensor material in the pathway of the sound field. Thus, the method avoids any interference with bubble dynamics during the measurement. The knowledge of the time of bubble decay allows conclusions to be reached on the destructive power of the cavities. By combining the results of life-span measurements with the maximum bubble radius using stroboscopic photographs we found that the measured time of bubble decay and the predicted time using Rayleigh's law only differs by about 13% even in the case of complex bubble fields. It can be shown that the laser scattering method is feasible to assess cavitation events quantitatively. Moreover, it will enable us to compare different medical ultrasound sources that have the capability to generate cavitation.

Exploring a new quantitative image marker to assess benefit of chemotherapy to ovarian cancer patients

NASA Astrophysics Data System (ADS)

Mirniaharikandehei, Seyedehnafiseh; Patil, Omkar; Aghaei, Faranak; Wang, Yunzhi; Zheng, Bin

2017-03-01

Accurately assessing the potential benefit of chemotherapy to cancer patients is an important prerequisite to developing precision medicine in cancer treatment. The previous study has shown that total psoas area (TPA) measured on preoperative cross-section CT image might be a good image marker to predict long-term outcome of pancreatic cancer patients after surgery. However, accurate and automated segmentation of TPA from the CT image is difficult due to the fuzzy boundary or connection of TPA to other muscle areas. In this study, we developed a new interactive computer-aided detection (ICAD) scheme aiming to segment TPA from the abdominal CT images more accurately and assess the feasibility of using this new quantitative image marker to predict the benefit of ovarian cancer patients receiving Bevacizumab-based chemotherapy. ICAD scheme was applied to identify a CT image slice of interest, which is located at the level of L3 (vertebral spines). The cross-sections of the right and left TPA are segmented using a set of adaptively adjusted boundary conditions. TPA is then quantitatively measured. In addition, recent studies have investigated that muscle radiation attenuation which reflects fat deposition in the tissue might be a good image feature for predicting the survival rate of cancer patients. The scheme and TPA measurement task were applied to a large national clinical trial database involving 1,247 ovarian cancer patients. By comparing with manual segmentation results, we found that ICAD scheme could yield higher accuracy and consistency for this task. Using a new ICAD scheme can provide clinical researchers a useful tool to more efficiently and accurately extract TPA as well as muscle radiation attenuation as new image makers, and allow them to investigate the discriminatory power of it to predict progression-free survival and/or overall survival of the cancer patients before and after taking chemotherapy.

Improved cancer risk stratification and diagnosis via quantitative phase microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Liu, Yang; Uttam, Shikhar; Pham, Hoa V.; Hartman, Douglas J.

2017-02-01

Pathology remains the gold standard for cancer diagnosis and in some cases prognosis, in which trained pathologists examine abnormality in tissue architecture and cell morphology characteristic of cancer cells with a bright-field microscope. The limited resolution of conventional microscope can result in intra-observer variation, missed early-stage cancers, and indeterminate cases that often result in unnecessary invasive procedures in the absence of cancer. Assessment of nanoscale structural characteristics via quantitative phase represents a promising strategy for identifying pre-cancerous or cancerous cells, due to its nanoscale sensitivity to optical path length, simple sample preparation (i.e., label-free) and low cost. I will present the development of quantitative phase microscopy system in transmission and reflection configuration to detect the structural changes in nuclear architecture, not be easily identifiable by conventional pathology. Specifically, we will present the use of transmission-mode quantitative phase imaging to improve diagnostic accuracy of urine cytology and the nuclear dry mass is progressively correlate with negative, atypical, suspicious and positive cytological diagnosis. In a second application, we will present the use of reflection-mode quantitative phase microscopy for depth-resolved nanoscale nuclear architecture mapping (nanoNAM) of clinically prepared formalin-fixed, paraffin-embedded tissue sections. We demonstrated that the quantitative phase microscopy system detects a gradual increase in the density alteration of nuclear architecture during malignant transformation in animal models of colon carcinogenesis and in human patients with ulcerative colitis, even in tissue that appears histologically normal according to pathologists. We evaluated the ability of nanoNAM to predict "future" cancer progression in patients with ulcerative colitis.

EQUIFAT: A novel scoring system for the semi-quantitative evaluation of regional adipose tissues in Equidae.

PubMed

Morrison, Philippa K; Harris, Patricia A; Maltin, Charlotte A; Grove-White, Dai; Argo, Caroline McG

2017-01-01

Anatomically distinct adipose tissues represent variable risks to metabolic health in man and some other mammals. Quantitative-imaging of internal adipose depots is problematic in large animals and associations between regional adiposity and health are poorly understood. This study aimed to develop and test a semi-quantitative system (EQUIFAT) which could be applied to regional adipose tissues. Anatomically-defined, photographic images of adipose depots (omental, mesenteric, epicardial, rump) were collected from 38 animals immediately post-mortem. Images were ranked and depot-specific descriptors were developed (1 = no fat visible; 5 = excessive fat present). Nuchal-crest and ventro-abdominal-retroperitoneal adipose depot depths (cm) were transformed to categorical 5 point scores. The repeatability and reliability of EQUIFAT was independently tested by 24 observers. When half scores were permitted, inter-observer agreement was substantial (average κw: mesenteric, 0.79; omental, 0.79; rump 0.61) or moderate (average κw; epicardial, 0.60). Intra-observer repeatability was tested by 8 observers on 2 occasions. Kappa analysis indicated perfect (omental and mesenteric) and substantial agreement (epicardial and rump) between attempts. A further 207 animals were evaluated ante-mortem (age, height, breed-type, gender, body condition score [BCS]) and again immediately post-mortem (EQUIFAT scores, carcass weight). Multivariable, random effect linear regression models were fitted (breed as random effect; BCS as outcome variable). Only height, carcass weight, omental and retroperitoneal EQUIFAT scores remained as explanatory variables in the final model. The EQUIFAT scores developed here demonstrate clear functional differences between regional adipose depots and future studies could be directed towards describing associations between adiposity and disease risk in surgical and post-mortem situations.

EQUIFAT: A novel scoring system for the semi-quantitative evaluation of regional adipose tissues in Equidae

PubMed Central

Morrison, Philippa K.; Harris, Patricia A.; Maltin, Charlotte A.; Grove-White, Dai; Argo, Caroline McG.

2017-01-01

Anatomically distinct adipose tissues represent variable risks to metabolic health in man and some other mammals. Quantitative-imaging of internal adipose depots is problematic in large animals and associations between regional adiposity and health are poorly understood. This study aimed to develop and test a semi-quantitative system (EQUIFAT) which could be applied to regional adipose tissues. Anatomically-defined, photographic images of adipose depots (omental, mesenteric, epicardial, rump) were collected from 38 animals immediately post-mortem. Images were ranked and depot-specific descriptors were developed (1 = no fat visible; 5 = excessive fat present). Nuchal-crest and ventro-abdominal-retroperitoneal adipose depot depths (cm) were transformed to categorical 5 point scores. The repeatability and reliability of EQUIFAT was independently tested by 24 observers. When half scores were permitted, inter-observer agreement was substantial (average κw: mesenteric, 0.79; omental, 0.79; rump 0.61) or moderate (average κw; epicardial, 0.60). Intra-observer repeatability was tested by 8 observers on 2 occasions. Kappa analysis indicated perfect (omental and mesenteric) and substantial agreement (epicardial and rump) between attempts. A further 207 animals were evaluated ante-mortem (age, height, breed-type, gender, body condition score [BCS]) and again immediately post-mortem (EQUIFAT scores, carcass weight). Multivariable, random effect linear regression models were fitted (breed as random effect; BCS as outcome variable). Only height, carcass weight, omental and retroperitoneal EQUIFAT scores remained as explanatory variables in the final model. The EQUIFAT scores developed here demonstrate clear functional differences between regional adipose depots and future studies could be directed towards describing associations between adiposity and disease risk in surgical and post-mortem situations. PMID:28296956

Can we predict necrosis intra-operatively? Real-time optical quantitative perfusion imaging in surgery: study protocol for a prospective, observational, in vivo pilot study.

PubMed

Jansen, Sanne M; de Bruin, Daniel M; van Berge Henegouwen, Mark I; Strackee, Simon D; Veelo, Denise P; van Leeuwen, Ton G; Gisbertz, Suzanne S

2017-01-01

Compromised perfusion as a result of surgical intervention causes a reduction of oxygen and nutrients in tissue and therefore decreased tissue vitality. Quantitative imaging of tissue perfusion during reconstructive surgery, therefore, may reduce the incidence of complications. Non-invasive optical techniques allow real-time tissue imaging, with high resolution and high contrast. The objectives of this study are, first, to assess the feasibility and accuracy of optical coherence tomography (OCT), sidestream darkfield microscopy (SDF), laser speckle contrast imaging (LSCI), and fluorescence imaging (FI) for quantitative perfusion imaging and, second, to identify/search for criteria that enable risk prediction of necrosis during gastric tube and free flap reconstruction. This prospective, multicenter, observational in vivo pilot study will assess tissue perfusion using four optical technologies: OCT, SDF, LSCI, and FI in 40 patients: 20 patients who will undergo gastric tube reconstruction after esophagectomy and 20 patients who will undergo free flap surgery. Intra-operative images of gastric perfusion will be obtained directly after reconstruction at four perfusion areas. Feasibility of perfusion imaging will be analyzed per technique. Quantitative parameters directly related to perfusion will be scored per perfusion area, and differences between biologically good versus reduced perfusion will be tested statistically. Patient outcome will be correlated to images and perfusion parameters. Differences in perfusion parameters before and after a bolus of ephedrine will be tested for significance. This study will identify quantitative perfusion-related parameters for an objective assessment of tissue perfusion during surgery. This will likely allow early risk stratification of necrosis development, which will aid in achieving a reduction of complications in gastric tube reconstruction and free flap transplantation. Clinicaltrials.gov registration number NCT02902549

Characterization of human myoblast differentiation for tissue-engineering purposes by quantitative gene expression analysis.

PubMed

Stern-Straeter, Jens; Bonaterra, Gabriel Alejandro; Kassner, Stefan S; Zügel, Stefanie; Hörmann, Karl; Kinscherf, Ralf; Goessler, Ulrich Reinhart

2011-08-01

Tissue engineering of skeletal muscle is an encouraging possibility for the treatment of muscle loss through the creation of functional muscle tissue in vitro from human stem cells. Currently, the preferred stem cells are primary, non-immunogenic satellite cells ( = myoblasts). The objective of this study was to determine the expression patterns of myogenic markers within the human satellite cell population during their differentiation into multinucleated myotubes for an accurate characterization of stem cell behaviour. Satellite cells were incubated (for 1, 4, 8, 12 or 16 days) with a culture medium containing either a low [ = differentiation medium (DM)] or high [ = growth medium (GM)] concentration of growth factors. Furthermore, we performed a quantitative gene expression analysis of well-defined differentiation makers: myogenic factor 5 (MYF5), myogenin (MYOG), skeletal muscle αactin1 (ACTA1), embryonic (MYH3), perinatal (MYH8) and adult skeletal muscle myosin heavy chain (MYH1). Additionally, the fusion indices of forming myotubes of MYH1, MYH8 and ACTA1 were calculated. We show that satellite cells incubated with DM expressed multiple characteriztic features of mature skeletal muscles, verified by time-dependent upregulation of MYOG, MYH1, MYH3, MYH8 and ACTA1. However, satellite cells incubated with GM did not reveal all morphological aspects of muscle differentiation. Immunocytochemical investigations with antibodies directed against the differentiation markers showed correlations between the gene expression and differentiation. Our data provide information about time-dependent gene expression of differentiation markers in human satellite cells, which can be used for maturation analyses in skeletal muscle tissue-engineering applications. Copyright © 2011 John Wiley & Sons, Ltd.

Fatigue Damage of Collagenous Tissues: Experiment, Modeling and Simulation Studies

PubMed Central

Martin, Caitlin; Sun, Wei

2017-01-01

Mechanical fatigue damage is a critical issue for soft tissues and tissue-derived materials, particularly for musculoskeletal and cardiovascular applications; yet, our understanding of the fatigue damage process is incomplete. Soft tissue fatigue experiments are often difficult and time-consuming to perform, which has hindered progress in this area. However, the recent development of soft-tissue fatigue-damage constitutive models has enabled simulation-based fatigue analyses of tissues under various conditions. Computational simulations facilitate highly controlled and quantitative analyses to study the distinct effects of various loading conditions and design features on tissue durability; thus, they are advantageous over complex fatigue experiments. Although significant work to calibrate the constitutive models from fatigue experiments and to validate predictability remains, further development in these areas will add to our knowledge of soft-tissue fatigue damage and will facilitate the design of durable treatments and devices. In this review, the experimental, modeling, and simulation efforts to study collagenous tissue fatigue damage are summarized and critically assessed. PMID:25955007

Novel diffuse optics system for continuous tissue viability monitoring: extended recovery in vivo testing in a porcine flap model

NASA Astrophysics Data System (ADS)

Lee, Seung Yup; Pakela, Julia M.; Hedrick, Taylor L.; Vishwanath, Karthik; Helton, Michael C.; Chung, Yooree; Kolodziejski, Noah J.; Stapels, Christopher J.; McAdams, Daniel R.; Fernandez, Daniel E.; Christian, James F.; O'Reilly, Jameson; Farkas, Dana; Ward, Brent B.; Feinberg, Stephen E.; Mycek, Mary-Ann

2017-02-01

In reconstructive surgery, tissue perfusion/vessel patency is critical to the success of microvascular free tissue flaps. Early detection of flap failure secondary to compromise of vascular perfusion would significantly increase the chances of flap salvage. We have developed a compact, clinically-compatible monitoring system to enable automated, minimally-invasive, continuous, and quantitative assessment of flap viability/perfusion. We tested the system's continuous monitoring capability during extended non-recovery surgery using an in vivo porcine free flap model. Initial results indicated that the system could assess flap viability/perfusion in a quantitative and continuous manner. With proven performance, the compact form constructed with cost-effective components would make this system suitable for clinical translation.

Quantitative Assessment of Heterogeneity in Tumor Metabolism Using FDG-PET

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

Vriens, Dennis, E-mail: d.vriens@nucmed.umcn.nl; Disselhorst, Jonathan A.; Oyen, Wim J.G.

2012-04-01

Purpose: [{sup 18}F]-fluorodeoxyglucose-positron emission tomography (FDG-PET) images are usually quantitatively analyzed in 'whole-tumor' volumes of interest. Also parameters determined with dynamic PET acquisitions, such as the Patlak glucose metabolic rate (MR{sub glc}) and pharmacokinetic rate constants of two-tissue compartment modeling, are most often derived per lesion. We propose segmentation of tumors to determine tumor heterogeneity, potentially useful for dose-painting in radiotherapy and elucidating mechanisms of FDG uptake. Methods and Materials: In 41 patients with 104 lesions, dynamic FDG-PET was performed. On MR{sub glc} images, tumors were segmented in quartiles of background subtracted maximum MR{sub glc} (0%-25%, 25%-50%, 50%-75%, and 75%-100%).more » Pharmacokinetic analysis was performed using an irreversible two-tissue compartment model in the three segments with highest MR{sub glc} to determine the rate constants of FDG metabolism. Results: From the highest to the lowest quartile, significant decreases of uptake (K{sub 1}), washout (k{sub 2}), and phosphorylation (k{sub 3}) rate constants were seen with significant increases in tissue blood volume fraction (V{sub b}). Conclusions: Tumor regions with highest MR{sub glc} are characterized by high cellular uptake and phosphorylation rate constants with relatively low blood volume fractions. In regions with less metabolic activity, the blood volume fraction increases and cellular uptake, washout, and phosphorylation rate constants decrease. These results support the hypothesis that regional tumor glucose phosphorylation rate is not dependent on the transport of nutrients (i.e., FDG) to the tumor.« less

Quantitative assessment of brain tissue oxygenation in porcine models of cardiac arrest and cardiopulmonary resuscitation using hyperspectral near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Lotfabadi, Shahin S.; Toronov, Vladislav; Ramadeen, Andrew; Hu, Xudong; Kim, Siwook; Dorian, Paul; Hare, Gregory M. T.

2014-03-01

Near-infrared spectroscopy (NIRS) is a non-invasive tool to measure real-time tissue oxygenation in the brain. In an invasive animal experiment we were able to directly compare non-invasive NIRS measurements on the skull with invasive measurements directly on the brain dura matter. We used a broad-band, continuous-wave hyper-spectral approach to measure tissue oxygenation in the brain of pigs under the conditions of cardiac arrest, cardiopulmonary resuscitation (CPR), and defibrillation. An additional purpose of this research was to find a correlation between mortality due to cardiac arrest and inadequacy of the tissue perfusion during attempts at resuscitation. Using this technique we measured the changes in concentrations of oxy-hemoglobin [HbO2] and deoxy-hemoglobin [HHb] to quantify the tissue oxygenation in the brain. We also extracted cytochrome c oxidase changes Δ[Cyt-Ox] under the same conditions to determine increase or decrease in cerebral oxygen delivery. In this paper we proved that applying CPR, [HbO2] concentration and tissue oxygenation in the brain increase while [HHb] concentration decreases which was not possible using other measurement techniques. We also discovered a similar trend in changes of both [Cyt-Ox] concentration and tissue oxygen saturation (StO2). Both invasive and non-invasive measurements showed similar results.

Quantitative susceptibility mapping (QSM): Decoding MRI data for a tissue magnetic biomarker

PubMed Central

Wang, Yi; Liu, Tian

2015-01-01

In MRI, the main magnetic field polarizes the electron cloud of a molecule, generating a chemical shift for observer protons within the molecule and a magnetic susceptibility inhomogeneity field for observer protons outside the molecule. The number of water protons surrounding a molecule for detecting its magnetic susceptibility is vastly greater than the number of protons within the molecule for detecting its chemical shift. However, the study of tissue magnetic susceptibility has been hindered by poor molecular specificities of hitherto used methods based on MRI signal phase and T2* contrast, which depend convolutedly on surrounding susceptibility sources. Deconvolution of the MRI signal phase can determine tissue susceptibility but is challenged by the lack of MRI signal in the background and by the zeroes in the dipole kernel. Recently, physically meaningful regularizations, including the Bayesian approach, have been developed to enable accurate quantitative susceptibility mapping (QSM) for studying iron distribution, metabolic oxygen consumption, blood degradation, calcification, demyelination, and other pathophysiological susceptibility changes, as well as contrast agent biodistribution in MRI. This paper attempts to summarize the basic physical concepts and essential algorithmic steps in QSM, to describe clinical and technical issues under active development, and to provide references, codes, and testing data for readers interested in QSM. Magn Reson Med 73:82–101, 2015. © 2014 The Authors. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance. This is an open access article under the terms of the Creative commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited. PMID:25044035

Online quantitative analysis of multispectral images of human body tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.

2013-08-01

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

Comparison study on qualitative and quantitative risk assessment methods for urban natural gas pipeline network.

PubMed

Han, Z Y; Weng, W G

2011-05-15

In this paper, a qualitative and a quantitative risk assessment methods for urban natural gas pipeline network are proposed. The qualitative method is comprised of an index system, which includes a causation index, an inherent risk index, a consequence index and their corresponding weights. The quantitative method consists of a probability assessment, a consequences analysis and a risk evaluation. The outcome of the qualitative method is a qualitative risk value, and for quantitative method the outcomes are individual risk and social risk. In comparison with previous research, the qualitative method proposed in this paper is particularly suitable for urban natural gas pipeline network, and the quantitative method takes different consequences of accidents into consideration, such as toxic gas diffusion, jet flame, fire ball combustion and UVCE. Two sample urban natural gas pipeline networks are used to demonstrate these two methods. It is indicated that both of the two methods can be applied to practical application, and the choice of the methods depends on the actual basic data of the gas pipelines and the precision requirements of risk assessment. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

Diagnostic accuracy of stress perfusion CMR in comparison with quantitative coronary angiography: fully quantitative, semiquantitative, and qualitative assessment.

PubMed

Mordini, Federico E; Haddad, Tariq; Hsu, Li-Yueh; Kellman, Peter; Lowrey, Tracy B; Aletras, Anthony H; Bandettini, W Patricia; Arai, Andrew E

2014-01-01

This study's primary objective was to determine the sensitivity, specificity, and accuracy of fully quantitative stress perfusion cardiac magnetic resonance (CMR) versus a reference standard of quantitative coronary angiography. We hypothesized that fully quantitative analysis of stress perfusion CMR would have high diagnostic accuracy for identifying significant coronary artery stenosis and exceed the accuracy of semiquantitative measures of perfusion and qualitative interpretation. Relatively few studies apply fully quantitative CMR perfusion measures to patients with coronary disease and comparisons to semiquantitative and qualitative methods are limited. Dual bolus dipyridamole stress perfusion CMR exams were performed in 67 patients with clinical indications for assessment of myocardial ischemia. Stress perfusion images alone were analyzed with a fully quantitative perfusion (QP) method and 3 semiquantitative methods including contrast enhancement ratio, upslope index, and upslope integral. Comprehensive exams (cine imaging, stress/rest perfusion, late gadolinium enhancement) were analyzed qualitatively with 2 methods including the Duke algorithm and standard clinical interpretation. A 70% or greater stenosis by quantitative coronary angiography was considered abnormal. The optimum diagnostic threshold for QP determined by receiver-operating characteristic curve occurred when endocardial flow decreased to <50% of mean epicardial flow, which yielded a sensitivity of 87% and specificity of 93%. The area under the curve for QP was 92%, which was superior to semiquantitative methods: contrast enhancement ratio: 78%; upslope index: 82%; and upslope integral: 75% (p = 0.011, p = 0.019, p = 0.004 vs. QP, respectively). Area under the curve for QP was also superior to qualitative methods: Duke algorithm: 70%; and clinical interpretation: 78% (p < 0.001 and p < 0.001 vs. QP, respectively). Fully quantitative stress perfusion CMR has high diagnostic accuracy for

Myocardial Tissue Characterization by Magnetic Resonance Imaging

PubMed Central

Ferreira, Vanessa M.; Piechnik, Stefan K.; Robson, Matthew D.; Neubauer, Stefan

2014-01-01

Cardiac magnetic resonance (CMR) imaging is a well-established noninvasive imaging modality in clinical cardiology. Its unsurpassed accuracy in defining cardiac morphology and function and its ability to provide tissue characterization make it well suited for the study of patients with cardiac diseases. Late gadolinium enhancement was a major advancement in the development of tissue characterization techniques, allowing the unique ability of CMR to differentiate ischemic heart disease from nonischemic cardiomyopathies. Using T2-weighted techniques, areas of edema and inflammation can be identified in the myocardium. A new generation of myocardial mapping techniques are emerging, enabling direct quantitative assessment of myocardial tissue properties in absolute terms. This review will summarize recent developments involving T1-mapping and T2-mapping techniques and focus on the clinical applications and future potential of these evolving CMR methodologies. PMID:24576837

Quantitative detection of Toxoplasma gondii in tissues of experimentally infected turkeys and in retail turkey products by magnetic-capture PCR.

PubMed

Koethe, Martin; Straubinger, Reinhard K; Pott, Susan; Bangoura, Berit; Geuthner, Anne-Catrin; Daugschies, Arwid; Ludewig, Martina

2015-12-01

Magnetic-capture PCR was applied for the quantitative detection of Toxoplasma gondii in tissues of experimentally infected turkeys and retail turkey meat products. For experimental infection, three T. gondii strains (ME49, CZ-Tiger, NED), varying infectious doses in different matrices (organisms in single mouse brains or 10(3), 10(5), or 10(6) oocysts in buffer) were used. From all animals, breast, thigh, and drumstick muscle tissues and for CZ-Tiger-infected animals additionally brains and hearts were analyzed. Using the magnetic-capture PCR large volumes of up to 100 g were examined. Our results show that most T. gondii parasites are present in brain and heart tissue. Of the three skeletal muscle types, drumsticks were affected at the highest and breast at the lowest level. Type III strain (NED) seems to be less efficient in infecting turkeys compared to type II strains, because only few tissues of NED infected animals contained T. gondii DNA. Furthermore, the number of detected parasitic stages increased with the level of infectious dose. Infection mode by either oocyst or tissue cyst stage did not have an effect on the amount of T. gondii present in tissues. In retail turkey meat products T. gondii DNA was not detectable although a contact with the parasite was inferred by serology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Novel quantitative assessment of metamorphopsia in maculopathy.

PubMed

Wiecek, Emily; Lashkari, Kameran; Dakin, Steven C; Bex, Peter

2014-11-18

Patients with macular disease often report experiencing metamorphopsia (visual distortion). Although typically measured with Amsler charts, more quantitative assessments of perceived distortion are desirable to effectively monitor the presence, progression, and remediation of visual impairment. Participants with binocular (n = 33) and monocular (n = 50) maculopathy across seven disease groups, and control participants (n = 10) with no identifiable retinal disease completed a modified Amsler grid assessment (presented on a computer screen with eye tracking to ensure fixation compliance) and two novel assessments to measure metamorphopsia in the central 5° of visual field. A total of 81% (67/83) of participants completed a hyperacuity task where they aligned eight dots in the shape of a square, and 64% (32/50) of participants with monocular distortion completed a spatial alignment task using dichoptic stimuli. Ten controls completed all tasks. Horizontal and vertical distortion magnitudes were calculated for each of the three assessments. Distortion magnitudes were significantly higher in patients than controls in all assessments. There was no significant difference in magnitude of distortion across different macular diseases. There were no significant correlations between overall magnitude of distortion among any of the three measures and no significant correlations in localized measures of distortion. Three alternative quantifications of monocular spatial distortion in the central visual field generated uncorrelated estimates of visual distortion. It is therefore unlikely that metamorphopsia is caused solely by retinal displacement, but instead involves additional top-down information, knowledge about the scene, and perhaps, cortical reorganization. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

QUANTITATIVE CANCER RISK ASSESSMENT METHODOLOGY USING SHORT-TERM GENETIC BIOASSAYS: THE COMPARATIVE POTENCY METHOD

EPA Science Inventory

Quantitative risk assessment is fraught with many uncertainties. The validity of the assumptions underlying the methods employed are often difficult to test or validate. Cancer risk assessment has generally employed either human epidemiological data from relatively high occupatio...

Assessing Anticalcification Treatments in Bioprosthetic Tissue by Using the New Zealand Rabbit Intramuscular Model

PubMed Central

Wright, Gregory A; Faught, Joelle M; Olin, Jane M

2009-01-01

The objective of this work was to demonstrate that the New Zealand White (NZW) rabbit intramuscular model can be used for detecting calcification in bioprosthetic tissue and to compare the calcification in the rabbit to that of native human valves. The rabbit model was compared with the commonly used Sprague–Dawley rat subcutaneous model. Eighteen rabbits and 18 rats were used to assess calcification in bioprosthetic tissue over time (7, 14, 30, and 90 d). The explanted rabbit and rat tissue discs were measured for calcium by using atomic absorption and Raman spectroscopy. Calcium deposits on the human valve explants were assessed by using Raman spectroscopy. The results showed that the NZW rabbit model is robust for detecting calcification in a shorter duration (14 d), with less infection complications, more space to implant tissue groups (thereby reducing animal use numbers), and a more metabolically and mechanically dynamic environment than the rat subcutaneous model . The human explanted valves and rabbit explanted tissue both showed Raman peaks at 960 cm−1 which is representative of hydroxyapatite. Hydroxyapatite is the final calcium and phosphate species in the calcification of bioprosthetic heart valves and rabbit intramuscular implants. The NZW rabbit intramuscular model is an effective model for assessing calcification in bioprosthetic tissue. PMID:19619417

Quantitative imaging biomarkers: a review of statistical methods for technical performance assessment.

PubMed

Raunig, David L; McShane, Lisa M; Pennello, Gene; Gatsonis, Constantine; Carson, Paul L; Voyvodic, James T; Wahl, Richard L; Kurland, Brenda F; Schwarz, Adam J; Gönen, Mithat; Zahlmann, Gudrun; Kondratovich, Marina V; O'Donnell, Kevin; Petrick, Nicholas; Cole, Patricia E; Garra, Brian; Sullivan, Daniel C

2015-02-01

Technological developments and greater rigor in the quantitative measurement of biological features in medical images have given rise to an increased interest in using quantitative imaging biomarkers to measure changes in these features. Critical to the performance of a quantitative imaging biomarker in preclinical or clinical settings are three primary metrology areas of interest: measurement linearity and bias, repeatability, and the ability to consistently reproduce equivalent results when conditions change, as would be expected in any clinical trial. Unfortunately, performance studies to date differ greatly in designs, analysis method, and metrics used to assess a quantitative imaging biomarker for clinical use. It is therefore difficult or not possible to integrate results from different studies or to use reported results to design studies. The Radiological Society of North America and the Quantitative Imaging Biomarker Alliance with technical, radiological, and statistical experts developed a set of technical performance analysis methods, metrics, and study designs that provide terminology, metrics, and methods consistent with widely accepted metrological standards. This document provides a consistent framework for the conduct and evaluation of quantitative imaging biomarker performance studies so that results from multiple studies can be compared, contrasted, or combined. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

High Resolution Peripheral Quantitative Computed Tomography for Assessment of Bone Quality

NASA Astrophysics Data System (ADS)

Kazakia, Galateia

2014-03-01

The study of bone quality is motivated by the high morbidity, mortality, and societal cost of skeletal fractures. Over 10 million people are diagnosed with osteoporosis in the US alone, suffering 1.5 million osteoporotic fractures and costing the health care system over 17 billion annually. Accurate assessment of fracture risk is necessary to ensure that pharmacological and other interventions are appropriately administered. Currently, areal bone mineral density (aBMD) based on 2D dual-energy X-ray absorptiometry (DXA) is used to determine osteoporotic status and predict fracture risk. Though aBMD is a significant predictor of fracture risk, it does not completely explain bone strength or fracture incidence. The major limitation of aBMD is the lack of 3D information, which is necessary to distinguish between cortical and trabecular bone and to quantify bone geometry and microarchitecture. High resolution peripheral quantitative computed tomography (HR-pQCT) enables in vivo assessment of volumetric BMD within specific bone compartments as well as quantification of geometric and microarchitectural measures of bone quality. HR-pQCT studies have documented that trabecular bone microstructure alterations are associated with fracture risk independent of aBMD.... Cortical bone microstructure - specifically porosity - is a major determinant of strength, stiffness, and fracture toughness of cortical tissue and may further explain the aBMD-independent effect of age on bone fragility and fracture risk. The application of finite element analysis (FEA) to HR-pQCT data permits estimation of patient-specific bone strength, shown to be associated with fracture incidence independent of aBMD. This talk will describe the HR-pQCT scanner, established metrics of bone quality derived from HR-pQCT data, and novel analyses of bone quality currently in development. Cross-sectional and longitudinal HR-pQCT studies investigating the impact of aging, disease, injury, gender, race, and

Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model

PubMed Central

Velikina, Julia V.; Block, Walter F.; Kijowski, Richard; Samsonov, Alexey A.

2017-01-01

We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexibl representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplifie treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed ∼200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure. PMID:28113746

Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model.

PubMed

Liu, Fang; Velikina, Julia V; Block, Walter F; Kijowski, Richard; Samsonov, Alexey A

2017-02-01

We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexible representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplified treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed  ∼ 200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure.

Quantitative Imaging of D-2-Hydroxyglutarate in Selected Histological Tissue Areas by a Novel Bioluminescence Technique.

PubMed

Voelxen, Nadine F; Walenta, Stefan; Proescholdt, Martin; Dettmer, Katja; Pusch, Stefan; Mueller-Klieser, Wolfgang

2016-01-01

Patients with malignant gliomas have a poor prognosis with average survival of less than 1 year. Whereas in other tumor entities the characteristics of tumor metabolism are successfully used for therapeutic approaches, such developments are very rare in brain tumors, notably in gliomas. One metabolic feature characteristic of gliomas, in particular diffuse astrocytomas and oligodendroglial tumors, is the variable content of D-2-hydroxyglutarate (D2HG), a metabolite that was discovered first in this tumor entity. D2HG is generated in large amounts due to various "gain-of-function" mutations in the isocitrate dehydrogenases IDH1 and IDH2. Meanwhile, D2HG has been detected in several other tumor entities, including intrahepatic bile-duct cancer, chondrosarcoma, acute myeloid leukemia, and angioimmunoblastic T-cell lymphoma. D2HG is barely detectable in healthy tissue (<0.1 mM), but its concentration increases up to 35 mM in malignant tumor tissues. Consequently, the "oncometabolite" D2HG has gained increasing interest in the field of tumor metabolism. To facilitate its quantitative measurement without loss of spatial resolution at a microscopical level, we have developed a novel bioluminescence assay for determining D2HG in sections of snap-frozen tissue. The assay was verified independently by photometric tests and liquid chromatography/mass spectrometry. The novel technique allows the microscopically resolved determination of D2HG in a concentration range of 0-10 μmol/g tissue (wet weight). In combination with the already established bioluminescence imaging techniques for ATP, glucose, pyruvate, and lactate, the novel D2HG assay enables a comparative characterization of the metabolic profile of individual tumors in a further dimension.

Arrhenius parameters for primary thermal injury in human tonsillar tissue

NASA Astrophysics Data System (ADS)

McMillan, Kathleen; Radabaugh, Rebecca; Coad, James E.

2011-03-01

Clinical implementation of a thermal therapy requires the ability to predict tissue injury following exposures to specific thermal histories. As part of an effort to develop a nonexcisional alternative to tonsillectomy, the degree of primary hyperthermic tissue injury in human tonsil was characterized. Fifteen fresh pediatric hypertrophic tonsillectomy specimens were sectioned and treated in a NIST-calibrated saline bath at temperatures of 40 to 70°C with hold times of one to seven minutes. The treated tissues were subsequently nitroblue tetrazolium (NBT) stained to assess for thermal respiratory enzyme inactivation as a marker of cellular injury/death. The NBT stains were quantitatively image analyzed and used to calculate Arrhenius parameters for primary thermal injury in human tonsils.

Two-photon Microscopy and Polarimetry for Assessment of Myocardial Tissue Organization

NASA Astrophysics Data System (ADS)

Archambault-Wallenburg, Marika

Optical methods can provide useful tissue characterization tools. For this project, two-photon microscopy and polarized light examinations (polarimetry) were used to assess the organizational state of myocardium in healthy, infarcted, and stem-cell regenerated states. Two-photon microscopy visualizes collagen through second-harmonic generation and myocytes through two-photon excitation autofluorescence, providing information on the composition and structure/organization of the tissue. Polarimetry measurements yield a value of linear retardance that can serve as an indicator of tissue anisotropy, and with a dual-projection method, information about the anisotropy axis orientation can also be extracted. Two-photon microscopy results reveal that stem-cell treated tissue retains more myocytes and structure than infarcted myocardium, while polarimetry findings suggest that the injury caused by temporary ligation of a coronary artery is less severe and more diffuse that than caused by a permanent ligation. Both these methods show potential for tissue characterization.

[Quantitative data analysis for live imaging of bone.

PubMed

Seno, Shigeto

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

Elucidating the Burden of HIV in Tissues Using Multiplexed Immunofluorescence and In Situ Hybridization: Methods for the Single-Cell Phenotypic Characterization of Cells Harboring HIV In Situ.

PubMed

Vasquez, Joshua J; Hussien, Rajaa; Aguilar-Rodriguez, Brandon; Junger, Henrik; Dobi, Dejan; Henrich, Timothy J; Thanh, Cassandra; Gibson, Erica; Hogan, Louise E; McCune, Joseph; Hunt, Peter W; Stoddart, Cheryl A; Laszik, Zoltan G

2018-06-01

Persistent tissue reservoirs of HIV present a major barrier to cure. Defining subsets of infected cells in tissues is a major focus of HIV cure research. Herein, we describe a novel multiplexed in situ hybridization (ISH) (RNAscope) protocol to detect HIV-DNA (vDNA) and HIV-RNA (vRNA) in formalin-fixed paraffin-embedded (FFPE) human tissues in combination with immunofluorescence (IF) phenotyping of the infected cells. We show that multiplexed IF and ISH (mIFISH) is suitable for quantitative assessment of HIV vRNA and vDNA and that multiparameter IF phenotyping allows precise identification of the cellular source of the ISH signal. We also provide semi-quantitative data on the impact of various tissue fixatives on the detectability of vDNA and vRNA with RNAscope technology. Finally, we describe methods to quantitate the ISH signal on whole-slide digital images and validation of the quantitative ISH data with quantitative real-time PCR for vRNA. It is our hope that this approach will provide insight into the biology of HIV tissue reservoirs and to inform strategies aimed at curing HIV.

Functional and morphological ultrasonic biomicroscopy for tissue engineers

NASA Astrophysics Data System (ADS)

Mallidi, S.; Aglyamov, S. R.; Karpiouk, A. B.; Park, S.; Emelianov, S. Y.

2006-03-01

Tissue engineering is an interdisciplinary field that combines various aspects of engineering and life sciences and aims to develop biological substitutes to restore, repair or maintain tissue function. Currently, the ability to have quantitative functional assays of engineered tissues is limited to existing invasive methods like biopsy. Hence, an imaging tool for non-invasive and simultaneous evaluation of the anatomical and functional properties of the engineered tissue is needed. In this paper we present an advanced in-vivo imaging technology - ultrasound biomicroscopy combined with complementary photoacoustic and elasticity imaging techniques, capable of accurate visualization of both structural and functional changes in engineered tissues, sequential monitoring of tissue adaptation and/or regeneration, and possible assistance of drug delivery and treatment planning. The combined imaging at microscopic resolution was evaluated on tissue mimicking phantoms imaged with 25 MHz single element focused transducer. The results of our study demonstrate that the ultrasonic, photoacoustic and elasticity images synergistically complement each other in detecting features otherwise imperceptible using the individual techniques. Finally, we illustrate the feasibility of the combined ultrasound, photoacoustic and elasticity imaging techniques in accurately assessing the morphological and functional changes occurring in engineered tissue.

Quantitative Assessment of Breast Cosmetic Outcome After Whole-Breast Irradiation

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

Reddy, Jay P.; Lei, Xiudong; Huang, Sheng-Cheng

Purpose: To measure, by quantitative analysis of digital photographs, breast cosmetic outcome within the setting of a randomized trial of conventionally fractionated (CF) and hypofractionated (HF) whole-breast irradiation (WBI), to identify how quantitative cosmesis metrics were associated with patient- and physician-reported cosmesis and whether they differed by treatment arm. Methods and Materials: From 2011 to 2014, 287 women aged ≥40 with ductal carcinoma in situ or early invasive breast cancer were randomized to HF-WBI (42.56 Gy/16 fractions [fx] + 10-12.5 Gy/4-5 fx boost) or CF-WBI (50 Gy/25 fx + 10-14 Gy/5-7 fx). At 1 year after treatment we collected digital photographs, patient-reported cosmesis using the Breast Cancer Treatment and Outcomesmore » Scale, and physician-reported cosmesis using the Radiation Therapy Oncology Group scale. Six quantitative measures of breast symmetry, labeled M1-M6, were calculated from anteroposterior digital photographs. For each measure, values closer to 1 imply greater symmetry, and values closer to 0 imply greater asymmetry. Associations between M1-M6 and patient- and physician-reported cosmesis and treatment arm were evaluated using the Kruskal-Wallis test. Results: Among 245 evaluable patients, patient-reported cosmesis was strongly associated with M1 (vertical symmetry measure) (P<.01). Physician-reported cosmesis was similarly correlated with M1 (P<.01) and also with M2 (vertical symmetry, P=.01) and M4 (horizontal symmetry, P=.03). At 1 year after treatment, HF-WBI resulted in better values of M2 (P=.02) and M3 (P<.01) than CF-WBI; treatment arm was not significantly associated with M1, M4, M5, or M6 (P≥.12). Conclusions: Quantitative assessment of breast photographs reveals similar to improved cosmetic outcome with HF-WBI compared with CF-WBI 1 year after treatment. Assessing cosmetic outcome using these measures could be useful for future comparative effectiveness studies and outcome reporting.« less

Quantitative Assessment of Breast Cosmetic Outcome After Whole-Breast Irradiation.

PubMed

Reddy, Jay P; Lei, Xiudong; Huang, Sheng-Cheng; Nicklaus, Krista M; Fingeret, Michelle C; Shaitelman, Simona F; Hunt, Kelly K; Buchholz, Thomas A; Merchant, Fatima; Markey, Mia K; Smith, Benjamin D

2017-04-01

To measure, by quantitative analysis of digital photographs, breast cosmetic outcome within the setting of a randomized trial of conventionally fractionated (CF) and hypofractionated (HF) whole-breast irradiation (WBI), to identify how quantitative cosmesis metrics were associated with patient- and physician-reported cosmesis and whether they differed by treatment arm. From 2011 to 2014, 287 women aged ≥40 with ductal carcinoma in situ or early invasive breast cancer were randomized to HF-WBI (42.56 Gy/16 fractions [fx] + 10-12.5 Gy/4-5 fx boost) or CF-WBI (50 Gy/25 fx + 10-14 Gy/5-7 fx). At 1 year after treatment we collected digital photographs, patient-reported cosmesis using the Breast Cancer Treatment and Outcomes Scale, and physician-reported cosmesis using the Radiation Therapy Oncology Group scale. Six quantitative measures of breast symmetry, labeled M1-M6, were calculated from anteroposterior digital photographs. For each measure, values closer to 1 imply greater symmetry, and values closer to 0 imply greater asymmetry. Associations between M1-M6 and patient- and physician-reported cosmesis and treatment arm were evaluated using the Kruskal-Wallis test. Among 245 evaluable patients, patient-reported cosmesis was strongly associated with M1 (vertical symmetry measure) (P<.01). Physician-reported cosmesis was similarly correlated with M1 (P<.01) and also with M2 (vertical symmetry, P=.01) and M4 (horizontal symmetry, P=.03). At 1 year after treatment, HF-WBI resulted in better values of M2 (P=.02) and M3 (P<.01) than CF-WBI; treatment arm was not significantly associated with M1, M4, M5, or M6 (P≥.12). Quantitative assessment of breast photographs reveals similar to improved cosmetic outcome with HF-WBI compared with CF-WBI 1 year after treatment. Assessing cosmetic outcome using these measures could be useful for future comparative effectiveness studies and outcome reporting. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantitative MRI of kidneys in renal disease.

PubMed

Kline, Timothy L; Edwards, Marie E; Garg, Ishan; Irazabal, Maria V; Korfiatis, Panagiotis; Harris, Peter C; King, Bernard F; Torres, Vicente E; Venkatesh, Sudhakar K; Erickson, Bradley J

2018-03-01

To evaluate the reproducibility and utility of quantitative magnetic resonance imaging (MRI) sequences for the assessment of kidneys in young adults with normal renal function (eGFR ranged from 90 to 130 mL/min/1.73 m 2 ) and patients with early renal disease (autosomal dominant polycystic kidney disease). This prospective case-control study was performed on ten normal young adults (18-30 years old) and ten age- and sex-matched patients with early renal parenchymal disease (autosomal dominant polycystic kidney disease). All subjects underwent a comprehensive kidney MRI protocol, including qualitative imaging: T1w, T2w, FIESTA, and quantitative imaging: 2D cine phase contrast of the renal arteries, and parenchymal diffusion weighted imaging (DWI), magnetization transfer imaging (MTI), blood oxygen level dependent (BOLD) imaging, and magnetic resonance elastography (MRE). The normal controls were imaged on two separate occasions ≥24 h apart (range 24-210 h) to assess reproducibility of the measurements. Quantitative MR imaging sequences were found to be reproducible. The mean ± SD absolute percent difference between quantitative parameters measured ≥24 h apart were: MTI-derived ratio = 4.5 ± 3.6%, DWI-derived apparent diffusion coefficient (ADC) = 6.5 ± 3.4%, BOLD-derived R2* = 7.4 ± 5.9%, and MRE-derived tissue stiffness = 7.6 ± 3.3%. Compared with controls, the ADPKD patient's non-cystic renal parenchyma (NCRP) had statistically significant differences with regard to quantitative parenchymal measures: lower MTI percent ratios (16.3 ± 4.4 vs. 23.8 ± 1.2, p < 0.05), higher ADCs (2.46 ± 0.20 vs. 2.18 ± 0.10 × 10 -3  mm 2 /s, p < 0.05), lower R2*s (14.9 ± 1.7 vs. 18.1 ± 1.6 s -1 , p < 0.05), and lower tissue stiffness (3.2 ± 0.3 vs. 3.8 ± 0.5 kPa, p < 0.05). Excellent reproducibility of the quantitative measurements was obtained in all cases. Significantly different quantitative MR parenchymal

A Quantitative Needs Assessment Technique for Cross-Cultural Work Adjustment Training.

ERIC Educational Resources Information Center

Selmer, Lyn

2000-01-01

A study of 67 Swedish expatriate bosses and 104 local Hong Kong middle managers tested a quantitative needs assessment technique measuring work values. Two-thirds of middle managers' work values were not correctly estimated by their bosses, especially instrumental values (pay, benefits, security, working hours and conditions), indicating a need…

Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia

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

Tholouli, Eleni; MacDermott, Sarah; Hoyland, Judith

2012-08-24

Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection inmore » archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.« less

Study on quantitative risk assessment model of the third party damage for natural gas pipelines based on fuzzy comprehensive assessment

NASA Astrophysics Data System (ADS)

Qiu, Zeyang; Liang, Wei; Wang, Xue; Lin, Yang; Zhang, Meng

2017-05-01

As an important part of national energy supply system, transmission pipelines for natural gas are possible to cause serious environmental pollution, life and property loss in case of accident. The third party damage is one of the most significant causes for natural gas pipeline system accidents, and it is very important to establish an effective quantitative risk assessment model of the third party damage for reducing the number of gas pipelines operation accidents. Against the third party damage accident has the characteristics such as diversity, complexity and uncertainty, this paper establishes a quantitative risk assessment model of the third party damage based on Analytic Hierarchy Process (AHP) and Fuzzy Comprehensive Evaluation (FCE). Firstly, risk sources of third party damage should be identified exactly, and the weight of factors could be determined via improved AHP, finally the importance of each factor is calculated by fuzzy comprehensive evaluation model. The results show that the quantitative risk assessment model is suitable for the third party damage of natural gas pipelines and improvement measures could be put forward to avoid accidents based on the importance of each factor.

Food Consumption and Handling Survey for Quantitative Microbiological Consumer Phase Risk Assessments.

PubMed

Chardon, Jurgen; Swart, Arno

2016-07-01

In the consumer phase of a typical quantitative microbiological risk assessment (QMRA), mathematical equations identify data gaps. To acquire useful data we designed a food consumption and food handling survey (2,226 respondents) for QMRA applications that is especially aimed at obtaining quantitative data. For a broad spectrum of food products, the survey covered the following topics: processing status at retail, consumer storage, preparation, and consumption. Questions were designed to facilitate distribution fitting. In the statistical analysis, special attention was given to the selection of the most adequate distribution to describe the data. Bootstrap procedures were used to describe uncertainty. The final result was a coherent quantitative consumer phase food survey and parameter estimates for food handling and consumption practices in The Netherlands, including variation over individuals and uncertainty estimates.

Handheld Tissue Hardness Meters for Assessing the Mechanical Properties of Skeletal Muscle: A Feasibility Study.

PubMed

Chino, Kentaro; Takahashi, Hideyuki

2016-09-01

The purpose of this study was to examine the feasibility of using handheld tissue hardness meters to assess the mechanical properties of skeletal muscle. This observational study included 33 healthy men (age, 22.4 ± 4.4 years) and 33 healthy women (age, 23.7 ± 4.2 years). Participants were placed in a supine position, and tissue hardness overlying the rectus femoris and the shear modulus of the muscle were measured on the right side of the body at 50% thigh length. In the same position, subcutaneous adipose tissue thickness and muscle thickness were measured using B-mode ultrasonography. To examine the associations of subcutaneous adipose tissue thickness, muscle thickness, and muscle shear modulus with tissue hardness, linear regression using a stepwise bidirectional elimination approach was performed. Stepwise linear regression revealed that subcutaneous adipose tissue thickness (r = -0.38, P = .002) and muscle shear modulus (r = 0.27, P = .03) were significantly associated with tissue hardness. Significant associations among adipose tissue thickness, muscle shear modulus, and tissue hardness show the limitations and feasibility of handheld tissue hardness meters for assessing the mechanical properties of skeletal muscles. Copyright © 2016. Published by Elsevier Inc.

A quantitative microbial risk assessment for center pivot irrigation of dairy wastewaters

USDA-ARS?s Scientific Manuscript database

In the western United States where livestock wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks from inhaling pathogens aerosolized dur...

Quantitative in vivo imaging of tissue factor expression in glioma using dynamic contrast-enhanced MRI derived parameters.

PubMed

Chen, Xiao; Xie, Tian; Fang, Jingqin; Xue, Wei; Tong, Haipeng; Kang, Houyi; Wang, Sumei; Yang, Yizeng; Xu, Minhui; Zhang, Weiguo

2017-08-01

Tissue Factor (TF) has been well established in angiogenesis, invasion, metastasis, and prognosis in glioma. A noninvasive assessment of TF expression status in glioma is therefore of obvious clinical relevance. Dynamic contrast-enhanced (DCE) MRI parameters have been used to evaluate microvascular characteristics and predict molecular expression status in tumors. Our aim is to investigate whether quantitative DCE-MRI parameters could assess TF expression in glioma. Thirty-two patients with histopathologically diagnosed supratentorial glioma who underwent DCE-MRI were retrospectively recruited. Extended Tofts linear model was used for DCE-MRI post-processing. Hot-spot, whole tumor cross-sectional approaches, and histogram were used for analysis of model based parameters. Four serial paraffin sections of each case were stained with TF, CD105, CD34 and α-Sooth Muscle Actin, respectively for evaluating the association of TF and microvascular properties. Pearson correlation was performed between percentage of TF expression area and DCE-MRI parameters, multiple microvascular indexes. Volume transfer constant (K trans ) hot-spot value best correlated with TF (r=0.886, p<0.001), followed by 90th percentile K trans value (r=0.801, p<0.001). Moreover, histogram analysis of K trans value demonstrated that weak TF expression was associated with less heterogeneous and positively skewed distribution. Finally, pathology analysis revealed TF was associated with glioma grade and significantly correlated with these two dynamic angiogenic indexes which could be used to explain the strong correlation between K trans and TF expression. Our results indicate that K trans may serve as a potential clinical imaging biomarker to predict TF expression status preoperatively in gliomas. Copyright © 2017 Elsevier B.V. All rights reserved.

A Quantitative Three-Dimensional Image Analysis Tool for Maximal Acquisition of Spatial Heterogeneity Data.

PubMed

Allenby, Mark C; Misener, Ruth; Panoskaltsis, Nicki; Mantalaris, Athanasios

2017-02-01

Three-dimensional (3D) imaging techniques provide spatial insight into environmental and cellular interactions and are implemented in various fields, including tissue engineering, but have been restricted by limited quantification tools that misrepresent or underutilize the cellular phenomena captured. This study develops image postprocessing algorithms pairing complex Euclidean metrics with Monte Carlo simulations to quantitatively assess cell and microenvironment spatial distributions while utilizing, for the first time, the entire 3D image captured. Although current methods only analyze a central fraction of presented confocal microscopy images, the proposed algorithms can utilize 210% more cells to calculate 3D spatial distributions that can span a 23-fold longer distance. These algorithms seek to leverage the high sample cost of 3D tissue imaging techniques by extracting maximal quantitative data throughout the captured image.

Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices.

PubMed Central

Christensen, G D; Simpson, W A; Younger, J J; Baddour, L M; Barrett, F F; Melton, D M; Beachey, E H

1985-01-01

The adherence of coagulase-negative staphylococci to smooth surfaces was assayed by measuring the optical densities of stained bacterial films adherent to the floors of plastic tissue culture plates. The optical densities correlated with the weight of the adherent bacterial film (r = 0.906; P less than 0.01). The measurements also agreed with visual assessments of bacterial adherence to culture tubes, microtiter plates, and tissue culture plates. Selected clinical strains were passed through a mouse model for foreign body infections and a rat model for catheter-induced endocarditis. The adherence measurements of animal passed strains remained the same as those of the laboratory-maintained parent strain. Spectrophotometric classification of coagulase-negative staphylococci into nonadherent and adherent categories according to these measurements had a sensitivity, specificity, and accuracy of 90.6, 80.8, and 88.4%, respectively. We examined a previously described collection of 127 strains of coagulase-negative staphylococci isolated from an outbreak of intravascular catheter-associated sepsis; strains associated with sepsis were more adherent than blood culture contaminants and cutaneous strains (P less than 0.001). We also examined a collection of 84 strains isolated from pediatric patients with cerebrospinal fluid (CSF) shunts; once again, pathogenic strains were more adherent than were CSF contaminants (P less than 0.01). Finally, we measured the adherence of seven endocarditis strains. As opposed to strains associated with intravascular catheters and CSF shunts, endocarditis strains were less adherent than were saprophytic strains of coagulase-negative staphylococci. The optical densities of bacterial films adherent to plastic tissue culture plates serve as a quantitative model for the study of the adherence of coagulase-negative staphylococci to medical devices, a process which may be important in the pathogenesis of foreign body infections. Images PMID:3905855

Monitoring temporal microstructural variations of skeletal muscle tissues by multispectral Mueller matrix polarimetry

NASA Astrophysics Data System (ADS)

Dong, Yang; He, Honghui; He, Chao; Ma, Hui

2017-02-01

Mueller matrix polarimetry is a powerful tool for detecting microscopic structures, therefore can be used to monitor physiological changes of tissue samples. Meanwhile, spectral features of scattered light can also provide abundant microstructural information of tissues. In this paper, we take the 2D multispectral backscattering Mueller matrix images of bovine skeletal muscle tissues, and analyze their temporal variation behavior using multispectral Mueller matrix parameters. The 2D images of the Mueller matrix elements are reduced to the multispectral frequency distribution histograms (mFDHs) to reveal the dominant structural features of the muscle samples more clearly. For quantitative analysis, the multispectral Mueller matrix transformation (MMT) parameters are calculated to characterize the microstructural variations during the rigor mortis and proteolysis processes of the skeletal muscle tissue samples. The experimental results indicate that the multispectral MMT parameters can be used to judge different physiological stages for bovine skeletal muscle tissues in 24 hours, and combining with the multispectral technique, the Mueller matrix polarimetry and FDH analysis can monitor the microstructural variation features of skeletal muscle samples. The techniques may be used for quick assessment and quantitative monitoring of meat qualities in food industry.

The Quantitative Reasoning for College Science (QuaRCS) Assessment in non-Astro 101 Courses

NASA Astrophysics Data System (ADS)

Kirkman, Thomas W.; Jensen, Ellen

2016-06-01

The innumeracy of American students and adults is a much lamented educational problem. The quantitative reasoning skills of college students may be particularly addressed and improved in "general education" science courses like Astro 101. Demonstrating improvement requires a standardized instrument. Among the non-proprietary instruments the Quantitative Literacy and Reasoning Assessment[1] (QRLA) and the Quantitative Reasoning for College Science (QuaRCS) Assessment[2] stand out.Follette et al. developed the QuaRCS in the context of Astro 101 at University of Arizona. We report on QuaRCS results in different contexts: pre-med physics and pre-nursing microbiology at a liberal arts college. We report on the mismatch between students' contemporaneous report of a question's difficulty and the actual probability of success. We report correlations between QuaRCS and other assessments of overall student performance in the class. We report differences in attitude towards mathematics in these two different but health-related student populations .[1] QLRA, Gaze et al., 2014, DOI: http://dx.doi.org/10.5038/1936-4660.7.2.4[2] QuaRCS, Follette, et al., 2015, DOI: http://dx.doi.org/10.5038/1936-4660.8.2.2

76 FR 2901 - Cellu Tissue Corporation; Notice of Availability of Environmental Assessment

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-18

... Tissue Corporation; Notice of Availability of Environmental Assessment January 11, 2011. In accordance with the National Environmental Policy Act of 1969 and the Federal Energy Regulatory Commission... Assessment (EA) for the project. The EA contains the staff's analysis of the potential environmental impacts...

Functional imaging and assessment of the glucose diffusion rate in epithelial tissues in optical coherence tomography

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

Larin, K V; Tuchin, V V

2008-06-30

Functional imaging, monitoring and quantitative description of glucose diffusion in epithelial and underlying stromal tissues in vivo and controlling of the optical properties of tissues are extremely important for many biomedical applications including the development of noninvasive or minimally invasive glucose sensors as well as for therapy and diagnostics of various diseases, such as cancer, diabetic retinopathy, and glaucoma. Recent progress in the development of a noninvasive molecular diffusion biosensor based on optical coherence tomography (OCT) is described. The diffusion of glucose was studied in several epithelial tissues both in vitro and in vivo. Because OCT provides depth-resolved imaging ofmore » tissues with high in-depth resolution, the glucose diffusion is described not only as a function of time but also as a function of depth. (special issue devoted to application of laser technologies in biophotonics and biomedical studies)« less

Automated characterization of normal and pathologic lung tissue by topological texture analysis of multidetector CT

NASA Astrophysics Data System (ADS)

Boehm, H. F.; Fink, C.; Becker, C.; Reiser, M.

2007-03-01

Reliable and accurate methods for objective quantitative assessment of parenchymal alterations in the lung are necessary for diagnosis, treatment and follow-up of pulmonary diseases. Two major types of alterations are pulmonary emphysema and fibrosis, emphysema being characterized by abnormal enlargement of the air spaces distal to the terminal, nonrespiratory bronchiole, accompanied by destructive changes of the alveolar walls. The main characteristic of fibrosis is coursening of the interstitial fibers and compaction of the pulmonary tissue. With the ability to display anatomy free from superimposing structures and greater visual clarity, Multi-Detector-CT has shown to be more sensitive than the chest radiograph in identifying alterations of lung parenchyma. In automated evaluation of pulmonary CT-scans, quantitative image processing techniques are applied for objective evaluation of the data. A number of methods have been proposed in the past, most of which utilize simple densitometric tissue features based on the mean X-ray attenuation coefficients expressed in terms of Hounsfield Units [HU]. Due to partial volume effects, most of the density-based methodologies tend to fail, namely in cases, where emphysema and fibrosis occur within narrow spatial limits. In this study, we propose a methodology based upon the topological assessment of graylevel distribution in the 3D image data of lung tissue which provides a way of improving quantitative CT evaluation. Results are compared to the more established density-based methods.

Understanding outbreaks of waterborne infectious disease: quantitative microbial risk assessment vs. epidemiology

USDA-ARS?s Scientific Manuscript database

Drinking water contaminated with microbial pathogens can cause outbreaks of infectious disease, and these outbreaks are traditionally studied using epidemiologic methods. Quantitative microbial risk assessment (QMRA) can predict – and therefore help prevent – such outbreaks, but it has never been r...

QUANTITATIVE ASSESSMENT OF CORAL DISEASES IN THE FLORIDA KEYS: STRATEGY AND METHODOLOGY

EPA Science Inventory

Most studies of coral disease have focused on the incidence of a single disease within a single location. Our overall objective is to use quantitative assessments to characterize annual patterns in the distribution and frequency of scleractinian and gorgonian coral diseases over ...

Robust tissue classification for reproducible wound assessment in telemedicine environments

NASA Astrophysics Data System (ADS)

Wannous, Hazem; Treuillet, Sylvie; Lucas, Yves

2010-04-01

In telemedicine environments, a standardized and reproducible assessment of wounds, using a simple free-handled digital camera, is an essential requirement. However, to ensure robust tissue classification, particular attention must be paid to the complete design of the color processing chain. We introduce the key steps including color correction, merging of expert labeling, and segmentation-driven classification based on support vector machines. The tool thus developed ensures stability under lighting condition, viewpoint, and camera changes, to achieve accurate and robust classification of skin tissues. Clinical tests demonstrate that such an advanced tool, which forms part of a complete 3-D and color wound assessment system, significantly improves the monitoring of the healing process. It achieves an overlap score of 79.3 against 69.1% for a single expert, after mapping on the medical reference developed from the image labeling by a college of experts.

A Novel Quantitative 500-MHz Acoustic-microscopy System for Ophthalmologic Tissues

PubMed Central

Rohrbach, Daniel; Jakob, Anette; Lloyd, Harriet O.; Tretbar, Steffen H.; Silverman, Ronald H.; Mamou, Jonathan

2017-01-01

Objective This paper describes development of a novel 500-MHz scanning acoustic microscope (SAM) for assessing the mechanical properties of ocular tissues at fine resolution. The mechanical properties of some ocular tissues, such as lamina cribrosa (LC) in the optic nerve head, are believed to play a pivotal role in eye pathogenesis. Methods A novel etching technology was used to fabricate silicon-based lens for a 500-MHz transducer. The transducer was tested in a custom designed scanning system on human eyes. Two-dimensional (2D) maps of bulk modulus (K), mass density (ρ) were derived using improved versions of current state-of-the-art signal processing approaches. Results The transducer employed a lens radius of 125 μm and had a center frequency of 479 MHz with a −6-dB bandwidth of 264 MHz and a lateral resolution of 4 μm. The LC, Bruch’s membrane (BM) at the interface of the retina and choroid, and Bowman’s layer (BL) at the interface of the corneal epithelium and stroma, were successfully imaged and resolved. Analysis of the 2D parameter maps revealed average values of LC, BM and BL with KLC = 2.81 ± 0.17; GPa, KBM = 2.89 ± 0.18; GPa, K BL = 2.6 ± 0.09; GPa, ρ LC = 0.96 ± 0.03 g/cm3; ρ BM = 0.97 ± 0.04 g/cm3; ρ BL = 0.98 ± 0.04g/cm3; Significance This novel SAM was shown to be capable of measuring mechanical properties of soft biological tissues at microscopic resolution; it currently is the only system that allows Simultaneous measurement of K, ρ, and attenuation in large lateral scales (field area > 9 mm2) and at fine resolutions. PMID:27249824

Carr-Purcell-Meiboom-Gill imaging of prostate cancer: quantitative T2 values for cancer discrimination.

PubMed

Roebuck, Joseph R; Haker, Steven J; Mitsouras, Dimitris; Rybicki, Frank J; Tempany, Clare M; Mulkern, Robert V

2009-05-01

Quantitative, apparent T(2) values of suspected prostate cancer and healthy peripheral zone tissue in men with prostate cancer were measured using a Carr-Purcell-Meiboom-Gill (CPMG) imaging sequence in order to assess the cancer discrimination potential of tissue T(2) values. The CPMG imaging sequence was used to image the prostates of 18 men with biopsy-proven prostate cancer. Whole gland coverage with nominal voxel volumes of 0.54 x 1.1 x 4 mm(3) was obtained in 10.7 min, resulting in data sets suitable for generating high-quality images with variable T(2)-weighting and for evaluating quantitative T(2) values on a pixel-by-pixel basis. Region-of-interest analysis of suspected healthy peripheral zone tissue and suspected cancer, identified on the basis of both T(1)- and T(2)-weighted signal intensities and available histopathology reports, yielded significantly (P<.0001) longer apparent T(2) values in suspected healthy tissue (193+/-49 ms) vs. suspected cancer (100+/-26 ms), suggesting potential utility of this method as a tissue specific discrimination index for prostate cancer. We conclude that CPMG imaging of the prostate can be performed in reasonable scan times and can provide advantages over T(2)-weighted fast spin echo (FSE) imaging alone, including quantitative T(2) values for cancer discrimination as well as proton density maps without the point spread function degradation associated with short effective echo time FSE sequences.

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

PubMed

Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John T

2015-08-01

Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples sequencing on an Illumina GAIIx genome analyzer with the quantitative assessment of protein-RNA interactions. This assay is able to analyze interactions between one or possibly several proteins with millions of different RNAs in a single experiment. We have successfully used HiTS-RAP to analyze interactions of the EGFP and negative elongation factor subunit E (NELF-E) proteins with their corresponding canonical and mutant RNA aptamers. Here we provide a detailed protocol for HiTS-RAP that can be completed in about a month (8 d hands-on time). This includes the preparation and testing of recombinant proteins and DNA templates, clustering DNA templates on a flowcell, HiTS and protein binding with a GAIIx instrument, and finally data analysis. We also highlight aspects of HiTS-RAP that can be further improved and points of comparison between HiTS-RAP and two other recently developed methods, quantitative analysis of RNA on a massively parallel array (RNA-MaP) and RNA Bind-n-Seq (RBNS), for quantitative analysis of RNA-protein interactions.

Automated Tracking of Quantitative Assessments of Tumor Burden in Clinical Trials1

PubMed Central

Rubin, Daniel L; Willrett, Debra; O'Connor, Martin J; Hage, Cleber; Kurtz, Camille; Moreira, Dilvan A

2014-01-01

There are two key challenges hindering effective use of quantitative assessment of imaging in cancer response assessment: 1) Radiologists usually describe the cancer lesions in imaging studies subjectively and sometimes ambiguously, and 2) it is difficult to repurpose imaging data, because lesion measurements are not recorded in a format that permits machine interpretation and interoperability. We have developed a freely available software platform on the basis of open standards, the electronic Physician Annotation Device (ePAD), to tackle these challenges in two ways. First, ePAD facilitates the radiologist in carrying out cancer lesion measurements as part of routine clinical trial image interpretation workflow. Second, ePAD records all image measurements and annotations in a data format that permits repurposing image data for analyses of alternative imaging biomarkers of treatment response. To determine the impact of ePAD on radiologist efficiency in quantitative assessment of imaging studies, a radiologist evaluated computed tomography (CT) imaging studies from 20 subjects having one baseline and three consecutive follow-up imaging studies with and without ePAD. The radiologist made measurements of target lesions in each imaging study using Response Evaluation Criteria in Solid Tumors 1.1 criteria, initially with the aid of ePAD, and then after a 30-day washout period, the exams were reread without ePAD. The mean total time required to review the images and summarize measurements of target lesions was 15% (P < .039) shorter using ePAD than without using this tool. In addition, it was possible to rapidly reanalyze the images to explore lesion cross-sectional area as an alternative imaging biomarker to linear measure. We conclude that ePAD appears promising to potentially improve reader efficiency for quantitative assessment of CT examinations, and it may enable discovery of future novel image-based biomarkers of cancer treatment response. PMID:24772204

Assessment of Tissue Perfusion Following Conventional Liposuction of Perforator-Based Abdominal Flaps

PubMed Central

Saçak, Bülent; Yalçın, Doğuş; Pilancı, Özgür; Tuncer, Fatma Betül; Çelebiler, Özhan

2017-01-01

Background The effect of liposuction on the perforators of the lower abdominal wall has been investigated in several studies. There are controversial results in the literature that have primarily demonstrated the number and patency of the perforators. The aim of this study was to determine the effect of liposuction on the perfusion of perforator-based abdominal flaps using a combined laser–Doppler spectrophotometer (O2C, Oxygen to See, LEA Medizintechnik). Methods Nine female patients undergoing classical abdominoplasty were included in the study. Perforators and the perfusion zones of the deep inferior epigastric artery flap were marked on the patient's abdominal wall. Flap perfusion was quantitatively assessed by measuring blood flow, velocity, capillary oxygen saturation, and relative amount of hemoglobin for each zone preoperatively, after tumescent solution infiltration, following elevation of the flap on a single perforator, and after deep and superficial liposuction, respectively. Results The measurements taken after elevation of the flap were not significantly different than measurements taken after the liposuction procedures. Conclusions The liposuction procedure does not significantly alter the perfusion of perforator-based abdominal flaps in the early period. The abdominal tissue discarded in a classic abdominoplasty operation can be raised as a perforator flap and has been demonstrated to be a unique model for clinical research. PMID:28352599

Diffuse reflectance spectroscopy as a tool for real-time tissue assessment during colorectal cancer surgery

NASA Astrophysics Data System (ADS)

Baltussen, Elisabeth J. M.; Snaebjornsson, Petur; de Koning, Susan G. Brouwer; Sterenborg, Henricus J. C. M.; Aalbers, Arend G. J.; Kok, Niels; Beets, Geerard L.; Hendriks, Benno H. W.; Kuhlmann, Koert F. D.; Ruers, Theo J. M.

2017-10-01

Colorectal surgery is the standard treatment for patients with colorectal cancer. To overcome two of the main challenges, the circumferential resection margin and postoperative complications, real-time tissue assessment could be of great benefit during surgery. In this ex vivo study, diffuse reflectance spectroscopy (DRS) was used to differentiate tumor tissue from healthy surrounding tissues in patients with colorectal neoplasia. DRS spectra were obtained from tumor tissue, healthy colon, or rectal wall and fat tissue, for every patient. Data were randomly divided into training (80%) and test (20%) sets. After spectral band selection, the spectra were classified using a quadratic classifier and a linear support vector machine. Of the 38 included patients, 36 had colorectal cancer and 2 had an adenoma. When the classifiers were applied to the test set, colorectal cancer could be discriminated from healthy tissue with an overall accuracy of 0.95 (±0.03). This study demonstrates the possibility to separate colorectal cancer from healthy surrounding tissue by applying DRS. High classification accuracies were obtained both in homogeneous and inhomogeneous tissues. This is a fundamental step toward the development of a tool for real-time in vivo tissue assessment during colorectal surgery.

Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR

PubMed Central

2014-01-01

Background Gene expression analysis using quantitative reverse transcription PCR (qRT-PCR) is a robust method wherein the expression levels of target genes are normalised using internal control genes, known as reference genes, to derive changes in gene expression levels. Although reference genes have recently been suggested for olive tissues, combined/independent analysis on different cultivars has not yet been tested. Therefore, an assessment of reference genes was required to validate the recent findings and select stably expressed genes across different olive cultivars. Results A total of eight candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), serine/threonine-protein phosphatase catalytic subunit (PP2A), elongation factor 1 alpha (EF1-alpha), polyubiquitin (OUB2), aquaporin tonoplast intrinsic protein (TIP2), tubulin alpha (TUBA), 60S ribosomal protein L18-3 (60S RBP L18-3) and polypyrimidine tract-binding protein homolog 3 (PTB)] were chosen based on their stability in olive tissues as well as in other plants. Expression stability was examined by qRT-PCR across 12 biological samples, representing mesocarp tissues at various developmental stages in three different olive cultivars, Barnea, Frantoio and Picual, independently and together during the 2009 season with two software programs, GeNorm and BestKeeper. Both software packages identified GAPDH, EF1-alpha and PP2A as the three most stable reference genes across the three cultivars and in the cultivar, Barnea. GAPDH, EF1-alpha and 60S RBP L18-3 were found to be most stable reference genes in the cultivar Frantoio while 60S RBP L18-3, OUB2 and PP2A were found to be most stable reference genes in the cultivar Picual. Conclusions The analyses of expression stability of reference genes using qRT-PCR revealed that GAPDH, EF1-alpha, PP2A, 60S RBP L18-3 and OUB2 are suitable reference genes for expression analysis in developing Olea europaea mesocarp tissues, displaying the highest level

Quantitative tissue parameters of Achilles tendon and plantar fascia in healthy subjects using a handheld myotonometer.

PubMed

Orner, Sarah; Kratzer, Wolfgang; Schmidberger, Julian; Grüner, Beate

2018-01-01

The aim of the study was to examine the quantitative tissue properties of the Achilles tendon and plantar fascia using a handheld, non-invasive MyotonPRO device, in order to generate normal values and examine the biomechanical relationship of both structures. Prospective study of a large, healthy sample population. The study sample included 207 healthy subjects (87 males and 120 females) for the Achilles tendon and 176 healthy subjects (73 males and 103 females) for the plantar fascia. For the correlations of the tissue parameters of the Achilles tendon and plantar fascia an intersection of both groups was formed which included 150 healthy subjects (65 males and 85 females). All participants were measured in a prone position. Consecutive measurements of the Achilles tendon and plantar fascia were performed by MyotonPRO device at defined sites. For the left and right Achilles tendons and plantar fasciae all five MyotonPRO parameters (Frequency [Hz], Decrement, Stiffness [N/m], Creep and Relaxation Time [ms]) were calculated of healthy males and females. The correlation of the tissue parameters of the Achilles tendon and plantar fascia showed a significant positive correlation of all parameters on the left as well as on the right side. The MyotonPRO is a feasible device for easy measurement of passive tissue properties of the Achilles tendon and plantar fascia in a clinical setting. The generated normal values of the Achilles tendon and plantar fascia are important for detecting abnormalities in patients with Achilles tendinopathy or plantar fasciitis in the future. Biomechanically, both structures are positively correlated. This may provide new aspects in the diagnostics and therapy of plantar fasciitis and Achilles tendinopathy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantitative motor assessment of muscular weakness in myasthenia gravis: a pilot study.

PubMed

Hoffmann, Sarah; Siedler, Jana; Brandt, Alexander U; Piper, Sophie K; Kohler, Siegfried; Sass, Christian; Paul, Friedemann; Reilmann, Ralf; Meisel, Andreas

2015-12-23

Muscular weakness in myasthenia gravis (MG) is commonly assessed using Quantitative Myasthenia Gravis Score (QMG). More objective and quantitative measures may complement the use of clinical scales and might detect subclinical affection of muscles. We hypothesized that muscular weakness in patients with MG can be quantified with the non-invasive Quantitative Motor (Q-Motor) test for Grip Force Assessment (QGFA) and Involuntary Movement Assessment (QIMA) and that pathological findings correlate with disease severity as measured by QMG. This was a cross-sectional pilot study investigating patients with confirmed diagnosis of MG. Data was compared to healthy controls (HC). Subjects were asked to lift a device (250 and 500 g) equipped with electromagnetic sensors that measured grip force (GF) and three-dimensional changes in position and orientation. These were used to calculate the position index (PI) and orientation index (OI) as measures for involuntary movements due to muscular weakness. Overall, 40 MG patients and 23 HC were included. PI and OI were significantly higher in MG patients for both weights in the dominant and non-dominant hand. Subgroup analysis revealed that patients with clinically ocular myasthenia gravis (OMG) also showed significantly higher values for PI and OI in both hands and for both weights. Disease severity correlates with QIMA performance in the non-dominant hand. Q-Motor tests and particularly QIMA may be useful objective tools for measuring motor impairment in MG and seem to detect subclinical generalized motor signs in patients with OMG. Q-Motor parameters might serve as sensitive endpoints for clinical trials in MG.

IWGT report on quantitative approaches to genotoxicity risk ...

EPA Pesticide Factsheets

This is the second of two reports from the International Workshops on Genotoxicity Testing (IWGT) Working Group on Quantitative Approaches to Genetic Toxicology Risk Assessment (the QWG). The first report summarized the discussions and recommendations of the QWG related to the need for quantitative dose–response analysis of genetic toxicology data, the existence and appropriate evaluation of threshold responses, and methods to analyze exposure-response relationships and derive points of departure (PoDs) from which acceptable exposure levels could be determined. This report summarizes the QWG discussions and recommendations regarding appropriate approaches to evaluate exposure-related risks of genotoxic damage, including extrapolation below identified PoDs and across test systems and species. Recommendations include the selection of appropriate genetic endpoints and target tissues, uncertainty factors and extrapolation methods to be considered, the importance and use of information on mode of action, toxicokinetics, metabolism, and exposure biomarkers when using quantitative exposure-response data to determine acceptable exposure levels in human populations or to assess the risk associated with known or anticipated exposures. The empirical relationship between genetic damage (mutation and chromosomal aberration) and cancer in animal models was also examined. It was concluded that there is a general correlation between cancer induction and mutagenic and/or clast

A comparative study of qualitative and quantitative methods for the assessment of adhesive remnant after bracket debonding.

PubMed

Cehreli, S Burcak; Polat-Ozsoy, Omur; Sar, Cagla; Cubukcu, H Evren; Cehreli, Zafer C

2012-04-01

The amount of the residual adhesive after bracket debonding is frequently assessed in a qualitative manner, utilizing the adhesive remnant index (ARI). This study aimed to investigate whether quantitative assessment of the adhesive remnant yields more precise results compared to qualitative methods utilizing the 4- and 5-point ARI scales. Twenty debonded brackets were selected. Evaluation and scoring of the adhesive remnant on bracket bases were made consecutively using: 1. qualitative assessment (visual scoring) and 2. quantitative measurement (image analysis) on digital photographs. Image analysis was made on scanning electron micrographs (SEM) and high-precision elemental maps of the adhesive remnant as determined by energy dispersed X-ray spectrometry. Evaluations were made in accordance with the original 4-point and the modified 5-point ARI scales. Intra-class correlation coefficients (ICCs) were calculated, and the data were evaluated using Friedman test followed by Wilcoxon signed ranks test with Bonferroni correction. ICC statistics indicated high levels of agreement for qualitative visual scoring among examiners. The 4-point ARI scale was compliant with the SEM assessments but indicated significantly less adhesive remnant compared to the results of quantitative elemental mapping. When the 5-point scale was used, both quantitative techniques yielded similar results with those obtained qualitatively. These results indicate that qualitative visual scoring using the ARI is capable of generating similar results with those assessed by quantitative image analysis techniques. In particular, visual scoring with the 5-point ARI scale can yield similar results with both the SEM analysis and elemental mapping.

A hybrid approach to advancing quantitative prediction of tissue distribution of basic drugs in human

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

Poulin, Patrick, E-mail: patrick-poulin@videotron.ca; Ekins, Sean; Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201

A general toxicity of basic drugs is related to phospholipidosis in tissues. Therefore, it is essential to predict the tissue distribution of basic drugs to facilitate an initial estimate of that toxicity. The objective of the present study was to further assess the original prediction method that consisted of using the binding to red blood cells measured in vitro for the unbound drug (RBCu) as a surrogate for tissue distribution, by correlating it to unbound tissue:plasma partition coefficients (Kpu) of several tissues, and finally to predict volume of distribution at steady-state (V{sub ss}) in humans under in vivo conditions. Thismore » correlation method demonstrated inaccurate predictions of V{sub ss} for particular basic drugs that did not follow the original correlation principle. Therefore, the novelty of this study is to provide clarity on the actual hypotheses to identify i) the impact of pharmacological mode of action on the generic correlation of RBCu-Kpu, ii) additional mechanisms of tissue distribution for the outlier drugs, iii) molecular features and properties that differentiate compounds as outliers in the original correlation analysis in order to facilitate its applicability domain alongside the properties already used so far, and finally iv) to present a novel and refined correlation method that is superior to what has been previously published for the prediction of human V{sub ss} of basic drugs. Applying a refined correlation method after identifying outliers would facilitate the prediction of more accurate distribution parameters as key inputs used in physiologically based pharmacokinetic (PBPK) and phospholipidosis models.« less

Affordable, automatic quantitative fall risk assessment based on clinical balance scales and Kinect data.

PubMed

Colagiorgio, P; Romano, F; Sardi, F; Moraschini, M; Sozzi, A; Bejor, M; Ricevuti, G; Buizza, A; Ramat, S

2014-01-01

The problem of a correct fall risk assessment is becoming more and more critical with the ageing of the population. In spite of the available approaches allowing a quantitative analysis of the human movement control system's performance, the clinical assessment and diagnostic approach to fall risk assessment still relies mostly on non-quantitative exams, such as clinical scales. This work documents our current effort to develop a novel method to assess balance control abilities through a system implementing an automatic evaluation of exercises drawn from balance assessment scales. Our aim is to overcome the classical limits characterizing these scales i.e. limited granularity and inter-/intra-examiner reliability, to obtain objective scores and more detailed information allowing to predict fall risk. We used Microsoft Kinect to record subjects' movements while performing challenging exercises drawn from clinical balance scales. We then computed a set of parameters quantifying the execution of the exercises and fed them to a supervised classifier to perform a classification based on the clinical score. We obtained a good accuracy (~82%) and especially a high sensitivity (~83%).

Differentiation of malignant from benign soft tissue tumours: use of additive qualitative and quantitative diffusion-weighted MR imaging to standard MR imaging at 3.0 T.

PubMed

Lee, So-Yeon; Jee, Won-Hee; Jung, Joon-Yong; Park, Michael Y; Kim, Sun-Ki; Jung, Chan-Kwon; Chung, Yang-Guk

2016-03-01

To determine the added value of diffusion-weighted imaging (DWI) to standard magnetic resonance imaging (MRI) to differentiate malignant from benign soft tissue tumours at 3.0 T. 3.0 T MR images including DWI in 63 patients who underwent surgery for soft tissue tumours were retrospectively analyzed. Two readers independently interpreted MRI for the presence of malignancy in two steps: standard MRI alone, standard MRI and DWI with qualitative and quantitative analysis combined. There were 34 malignant and 29 non-malignant soft tissue tumours. In qualitative analysis, hyperintensity relative to skeletal muscle was more frequent in malignant than benign tumours on DWI (P=0.003). In quantitative analysis, ADCs of malignant tumours were significantly lower than those of non-malignant tumours (P≤0.002): 759±385 vs. 1188±423 μm(2)/sec minimum ADC value, 941±440 vs. 1310±440 μm(2)/sec average ADC value. The mean sensitivity, specificity and accuracy of both readers were 96%, 72%, and 85% on standard MRI alone and 97%, 90%, and 94% on standard MRI with DWI. The addition of DWI to standard MRI improves the diagnostic accuracy for differentiation of malignant from benign soft tissue tumours at 3.0 T. DWI has added value for differentiating malignant from benign soft tissue tumours. Addition of DWI to standard MRI at 3.0 T improves the diagnostic accuracy. Measurements of both ADC min within solid portion and ADC av are helpful.

The affect of tissue depth variation on craniofacial reconstructions.

PubMed

Starbuck, John M; Ward, Richard E

2007-10-25

We examined the affect of tissue depth variation on the reconstruction of facial form, through the application of the American method, utilizing published tissue depth measurements for emaciated, normal, and obese faces. In this preliminary study, three reconstructions were created on reproductions of the same skull for each set of tissue depth measurements. The resulting morphological variation was measured quantitatively using the anthropometric craniofacial variability index (CVI). This method employs 16 standard craniofacial anthropometric measurements and the results reflect "pattern variation" or facial harmony. We report no appreciable variation in the quantitative measure of the pattern facial form obtained from the three different sets of tissue depths. Facial similarity was assessed qualitatively utilizing surveys of photographs of the three reconstructions. Surveys indicated that subjects frequently perceived the reconstructions as representing different individuals. This disagreement indicates that size of the face may blind observers to similarities in facial form. This research is significant because it illustrates the confounding effect that normal human variation contributes in the successful recognition of individuals from a representational three-dimensional facial reconstruction. Research results suggest that successful identification could be increased if multiple reconstructions were created which reflect a wide range of possible outcomes for facial form. The creation of multiple facial images, from a single skull, will be facilitated as computerized versions of facial reconstruction are further developed and refined.

Near-infrared Raman spectroscopy for assessing biochemical changes of cervical tissue associated with precarcinogenic transformation.

PubMed

Duraipandian, Shiyamala; Mo, Jianhua; Zheng, Wei; Huang, Zhiwei

2014-11-07

Raman spectroscopy measures the inelastically scattered light from tissue that is capable of identifying native tissue biochemical constituents and their changes associated with disease transformation. This study aims to characterize the Raman spectroscopic properties of cervical tissue associated with the multi-stage progression of cervical precarcinogenic sequence. A rapid-acquisition fiber-optic near-infrared (NIR) Raman diagnostic system was employed for tissue Raman spectral measurements at 785 nm excitation. A total of 68 Raman spectra (23 benign, 29 low-grade squamous intraepithelial lesions (LSIL) and 16 high grade squamous intraepithelial lesions (HSIL)) were measured from 25 cervical tissue biopsy specimens, as confirmed by colposcopy-histopathology. The semi-quantitative biochemical modeling based on the major biochemicals (i.e., DNA, proteins (histone, collagen), lipid (triolein) and carbohydrates (glycogen)) in cervical tissue uncovers the stepwise accumulation of biomolecular changes associated with progressive cervical precarcinogenesis. Multi-class partial least squares-discriminant analysis (PLS-DA) together with leave-one tissue site-out, cross-validation yielded the diagnostic sensitivities of 95.7%, 82.8% and 81.3%; specificities of 100.0%, 92.3% and 88.5%,for discrimination among benign, LSIL and HSIL cervical tissues, respectively. This work suggests that the Raman spectral biomarkers have identified the potential to be used for monitoring the multi-stage cervical precarcinogenesis, forming the foundation of applying NIR Raman spectroscopy for the early diagnosis of cervical precancer in vivo at the molecular level.

Assessing diabetic foot ulcer development risk with hyperspectral tissue oximetry

NASA Astrophysics Data System (ADS)

Yudovsky, Dmitry; Nouvong, Aksone; Schomacker, Kevin; Pilon, Laurent

2011-02-01

Foot ulceration remains a serious health concern for diabetic patients and has a major impact on the cost of diabetes treatment. Early detection and preventive care, such as offloading or improved hygiene, can greatly reduce the risk of further complications. We aim to assess the use of hyperspectral tissue oximetry in predicting the risk of diabetic foot ulcer formation. Tissue oximetry measurements are performed during several visits with hyperspectral imaging of the feet in type 1 and 2 diabetes mellitus subjects that are at risk for foot ulceration. The data are retrospectively analyzed at 21 sites that ulcerated during the course of our study and an ulceration prediction index is developed. Then, an image processing algorithm based on this index is implemented. This algorithm is able to predict tissue at risk of ulceration with a sensitivity and specificity of 95 and 80%, respectively, for images taken, on average, 58 days before tissue damage is apparent to the naked eye. Receiver operating characteristic analysis is also performed to give a range of sensitivity/specificity values resulting in a Q-value of 89%.

Biomechanics and mechanobiology in functional tissue engineering

PubMed Central

Guilak, Farshid; Butler, David L.; Goldstein, Steven A.; Baaijens, Frank P.T.

2014-01-01

The field of tissue engineering continues to expand and mature, and several products are now in clinical use, with numerous other preclinical and clinical studies underway. However, specific challenges still remain in the repair or regeneration of tissues that serve a predominantly biomechanical function. Furthermore, it is now clear that mechanobiological interactions between cells and scaffolds can critically influence cell behavior, even in tissues and organs that do not serve an overt biomechanical role. Over the past decade, the field of “functional tissue engineering” has grown as a subfield of tissue engineering to address the challenges and questions on the role of biomechanics and mechanobiology in tissue engineering. Originally posed as a set of principles and guidelines for engineering of load-bearing tissues, functional tissue engineering has grown to encompass several related areas that have proven to have important implications for tissue repair and regeneration. These topics include measurement and modeling of the in vivo biomechanical environment; quantitative analysis of the mechanical properties of native tissues, scaffolds, and repair tissues; development of rationale criteria for the design and assessment of engineered tissues; investigation of the effects biomechanical factors on native and repair tissues, in vivo and in vitro; and development and application of computational models of tissue growth and remodeling. Here we further expand this paradigm and provide examples of the numerous advances in the field over the past decade. Consideration of these principles in the design process will hopefully improve the safety, efficacy, and overall success of engineered tissue replacements. PMID:24818797

Biomechanics and mechanobiology in functional tissue engineering.

PubMed

Guilak, Farshid; Butler, David L; Goldstein, Steven A; Baaijens, Frank P T

2014-06-27

The field of tissue engineering continues to expand and mature, and several products are now in clinical use, with numerous other preclinical and clinical studies underway. However, specific challenges still remain in the repair or regeneration of tissues that serve a predominantly biomechanical function. Furthermore, it is now clear that mechanobiological interactions between cells and scaffolds can critically influence cell behavior, even in tissues and organs that do not serve an overt biomechanical role. Over the past decade, the field of "functional tissue engineering" has grown as a subfield of tissue engineering to address the challenges and questions on the role of biomechanics and mechanobiology in tissue engineering. Originally posed as a set of principles and guidelines for engineering of load-bearing tissues, functional tissue engineering has grown to encompass several related areas that have proven to have important implications for tissue repair and regeneration. These topics include measurement and modeling of the in vivo biomechanical environment; quantitative analysis of the mechanical properties of native tissues, scaffolds, and repair tissues; development of rationale criteria for the design and assessment of engineered tissues; investigation of the effects biomechanical factors on native and repair tissues, in vivo and in vitro; and development and application of computational models of tissue growth and remodeling. Here we further expand this paradigm and provide examples of the numerous advances in the field over the past decade. Consideration of these principles in the design process will hopefully improve the safety, efficacy, and overall success of engineered tissue replacements. Copyright © 2014 Elsevier Ltd. All rights reserved.

Creating an anthropomorphic digital MR phantom—an extensible tool for comparing and evaluating quantitative imaging algorithms

NASA Astrophysics Data System (ADS)

Bosca, Ryan J.; Jackson, Edward F.

2016-01-01

Assessing and mitigating the various sources of bias and variance associated with image quantification algorithms is essential to the use of such algorithms in clinical research and practice. Assessment is usually accomplished with grid-based digital reference objects (DRO) or, more recently, digital anthropomorphic phantoms based on normal human anatomy. Publicly available digital anthropomorphic phantoms can provide a basis for generating realistic model-based DROs that incorporate the heterogeneity commonly found in pathology. Using a publicly available vascular input function (VIF) and digital anthropomorphic phantom of a normal human brain, a methodology was developed to generate a DRO based on the general kinetic model (GKM) that represented realistic and heterogeneously enhancing pathology. GKM parameters were estimated from a deidentified clinical dynamic contrast-enhanced (DCE) MRI exam. This clinical imaging volume was co-registered with a discrete tissue model, and model parameters estimated from clinical images were used to synthesize a DCE-MRI exam that consisted of normal brain tissues and a heterogeneously enhancing brain tumor. An example application of spatial smoothing was used to illustrate potential applications in assessing quantitative imaging algorithms. A voxel-wise Bland-Altman analysis demonstrated negligible differences between the parameters estimated with and without spatial smoothing (using a small radius Gaussian kernel). In this work, we reported an extensible methodology for generating model-based anthropomorphic DROs containing normal and pathological tissue that can be used to assess quantitative imaging algorithms.

Assessment of eye bank-prepared posterior lamellar corneal tissue for endothelial keratoplasty.

PubMed

Rose, Linda; Briceño, César A; Stark, Walter J; Gloria, Dante G; Jun, Albert S

2008-02-01

To evaluate eye bank-prepared tissue for Descemet's stripping automated endothelial keratoplasty (DSAEK). Experimental study and retrospective case series. Seventeen human donor corneas and 4 recipient patients undergoing DSAEK surgery. Corneal-scleral discs were obtained. Specular microscopy and pachymetry were performed. A designated Tissue Banks International technician used a microkeratome to prepare a flap. Posterior bed thickness was measured. The sectioned tissue was stored, and at 24 and 48 hours, pachymetry was repeated. At 48 hours, specular microscopy was repeated, and endothelial cell viability was assessed with trypan blue. Descemet's stripping automated endothelial keratoplasty was performed in 4 patients using eye bank-prepared posterior lamellar tissue. Corneal tissue was assessed with the following parameters: corneal thickness measured with ultrasonic pachymetry, cell density counts measured with a keratoanalyzer, and cell viability as observed with trypan blue exclusion. Patient outcomes were measured by changes in visual acuity (VA) and the presence of a clear graft. Donor corneal pachymetry before sectioning averaged 599+/-52 microm. Immediately after sectioning with a microkeratome set at a depth of 300 microm, mean posterior bed thickness was 328+/-95 microm. Thus, the mean cutting depth achieved by the microkeratome when set at 300 micrometers averaged 271+/-83 microm. After storage for 24 hours, the posterior beds measured 352 microm, an average swelling of 24 (7%) microm (P = 0.14). After 48 hours, the posterior beds measured 382 microm, an average swelling of 54 (16%) microm (P = 0.02). Cell counts 48 hours after sectioning decreased by an average of 11% (P = 0.10). Endothelial cell staining confirmed improvement in postsectioning morphology and survival with increased technician experience. All 4 patients receiving eye bank-prepared DSAEK tissue showed uncomplicated postoperative results, with improvement in VA. The microkeratome cutting

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

Methods of quantitative risk assessment: The case of the propellant supply system

NASA Astrophysics Data System (ADS)

Merz, H. A.; Bienz, A.

1984-08-01

As a consequence of the disastrous accident in Lapua (Finland) in 1976, where an explosion in a cartridge loading facility killed 40 and injured more than 70 persons, efforts were undertaken to examine and improve the safety of such installations. An ammunition factory in Switzerland considered the replacement of the manual supply of propellant hoppers by a new pneumatic supply system. This would reduce the maximum quantity of propellant in the hoppers to a level, where an accidental ignition would no longer lead to a detonation, and this would drastically limit the effects on persons. A quantitative risk assessment of the present and the planned supply system demonstrated that, in this particular case, the pneumatic supply system would not reduce the risk enough to justify the related costs. In addition, it could be shown that the safety of the existing system can be improved more effectively by other safety measures at considerably lower costs. Based on this practical example, the advantages of a strictly quantitative risk assessment for the safety planning in explosives factories are demonstrated. The methodological background of a risk assessment and the steps involved in the analysis are summarized. In addition, problems of quantification are discussed.

Three-dimensional micro-scale strain mapping in living biological soft tissues.

PubMed

Moo, Eng Kuan; Sibole, Scott C; Han, Sang Kuy; Herzog, Walter

2018-04-01

Non-invasive characterization of the mechanical micro-environment surrounding cells in biological tissues at multiple length scales is important for the understanding of the role of mechanics in regulating the biosynthesis and phenotype of cells. However, there is a lack of imaging methods that allow for characterization of the cell micro-environment in three-dimensional (3D) space. The aims of this study were (i) to develop a multi-photon laser microscopy protocol capable of imprinting 3D grid lines onto living tissue at a high spatial resolution, and (ii) to develop image processing software capable of analyzing the resulting microscopic images and performing high resolution 3D strain analyses. Using articular cartilage as the biological tissue of interest, we present a novel two-photon excitation imaging technique for measuring the internal 3D kinematics in intact cartilage at sub-micrometer resolution, spanning length scales from the tissue to the cell level. Using custom image processing software, we provide accurate and robust 3D micro-strain analysis that allows for detailed qualitative and quantitative assessment of the 3D tissue kinematics. This novel technique preserves tissue structural integrity post-scanning, therefore allowing for multiple strain measurements at different time points in the same specimen. The proposed technique is versatile and opens doors for experimental and theoretical investigations on the relationship between tissue deformation and cell biosynthesis. Studies of this nature may enhance our understanding of the mechanisms underlying cell mechano-transduction, and thus, adaptation and degeneration of soft connective tissues. We presented a novel two-photon excitation imaging technique for measuring the internal 3D kinematics in intact cartilage at sub-micrometer resolution, spanning from tissue length scale to cellular length scale. Using a custom image processing software (lsmgridtrack), we provide accurate and robust micro

Non-invasive terahertz imaging of tissue water content for flap viability assessment

PubMed Central

Bajwa, Neha; Au, Joshua; Jarrahy, Reza; Sung, Shijun; Fishbein, Michael C.; Riopelle, David; Ennis, Daniel B.; Aghaloo, Tara; St. John, Maie A.; Grundfest, Warren S.; Taylor, Zachary D.

2016-01-01

Accurate and early prediction of tissue viability is the most significant determinant of tissue flap survival in reconstructive surgery. Perturbation in tissue water content (TWC) is a generic component of the tissue response to such surgeries, and, therefore, may be an important diagnostic target for assessing the extent of flap viability in vivo. We have previously shown that reflective terahertz (THz) imaging, a non-ionizing technique, can generate spatially resolved maps of TWC in superficial soft tissues, such as cornea and wounds, on the order of minutes. Herein, we report the first in vivo pilot study to investigate the utility of reflective THz TWC imaging for early assessment of skin flap viability. We obtained longitudinal visible and reflective THz imagery comparing 3 bipedicled flaps (i.e. survival model) and 3 fully excised flaps (i.e. failure model) in the dorsal skin of rats over a postoperative period of 7 days. While visual differences between both models manifested 48 hr after surgery, statistically significant (p < 0.05, independent t-test) local differences in TWC contrast were evident in THz flap image sets as early as 24 hr. Excised flaps, histologically confirmed as necrotic, demonstrated a significant, yet localized, reduction in TWC in the flap region compared to non-traumatized skin. In contrast, bipedicled flaps, histologically verified as viable, displayed mostly uniform, unperturbed TWC across the flap tissue. These results indicate the practical potential of THz TWC sensing to accurately predict flap failure 24 hours earlier than clinical examination. PMID:28101431

Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the Florida Keys using real-time RT-PCR

USGS Publications Warehouse

Donaldson, K.A.; Griffin, Dale W.; Paul, J.H.

2002-01-01

A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

Use of Quantitative Microbial Risk Assessment to Improve Interpretation of a Recreational Water Epidemiological Study

EPA Science Inventory

We conducted a supplemental water quality monitoring study and quantitative microbial risk assessment (QMRA) to complement the United States Environmental Protection Agency’s (U.S. EPA) National Epidemiological and Environmental Assessment of Recreational Water study at Boquerón ...

Topographic association of angioscopic yellow plaques with coronary atherosclerotic plaque: assessment with quantitative colorimetry in human coronary artery autopsy specimens.

PubMed

Ishibashi, Fumiyuki; Lisauskas, Jennifer B; Kawamura, Akio; Waxman, Sergio

2008-01-01

Yellow plaques seen during coronary angioscopy are thought to be the surrogates for superficial intimal lipids in coronary plaque. Given diffuse and heterogeneous nature of atherosclerosis, yellow plaques in coronaries may be seen as several yellow spots on diffuse coronary plaque. We examined the topographic association of yellow plaques with coronary plaque. In 40 non-severely stenotic ex-vivo coronary segments (average length: 52.2 +/- 3.1 mm), yellow plaques were examined by angioscopy with quantitative colorimetry. The segments were cut perpendicular to the long axis of the vessel at 2 mm intervals, and 1045 slides with 5 microm thick tissue for whole segments were prepared. To construct the plaque surface, each tissue slice was considered to be representative of the adjacent 2 mm. The circumference of the lumen and the lumen border of plaque were measured in each slide, and the plaque surface region was constructed. Coronary plaque was in 37 (93%) of 40 segments, and consisted of a single mass [39.9 +/- 3.9 (0-100) mm, 311.3 +/- 47.4 (0.0-1336.2) mm2]. In 30 (75%) segments, multiple (2-9) yellow plaques were detected on a mass of coronary plaque. The number of yellow plaques correlated positively with coronary plaque surface area (r = 0.77, P < 0.0001). Yellow plaques in coronaries detected by angioscopy with quantitative colorimetry, some of them are associated with lipid cores underneath thin fibrous caps, may be used to assess the extent of coronary plaque. Further research using angioscopy could be of value to study the association of high-risk coronaries with acute coronary syndromes.

[A quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse].

PubMed

Zhang, Yu; Chen, Yuzhen; Hu, Chunguang; Zhang, Huaning; Bi, Zhenwang; Bi, Zhenqiang

2015-05-01

To construct a quantitative risk assessment model of salmonella on carcass in poultry slaughterhouse and to find out effective interventions to reduce salmonella contamination. We constructed a modular process risk model (MPRM) from evisceration to chilling in Excel Sheet using the data of the process parameters in poultry and the Salmomella concentration surveillance of Jinan in 2012. The MPRM was simulated by @ risk software. The concentration of salmonella on carcass after chilling was 1.96MPN/g which was calculated by model. The sensitive analysis indicated that the correlation coefficient of the concentration of salmonella after defeathering and in chilling pool were 0.84 and 0.34,which were the primary factors to the concentration of salmonella on carcass after chilling. The study provided a quantitative assessment model structure for salmonella on carcass in poultry slaughterhouse. The risk manager could control the contamination of salmonella on carcass after chilling by reducing the concentration of salmonella after defeathering and in chilling pool.

Comprehensive, Quantitative Risk Assessment of CO{sub 2} Geologic Sequestration

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

Lepinski, James

2013-09-30

A Quantitative Failure Modes and Effects Analysis (QFMEA) was developed to conduct comprehensive, quantitative risk assessments on CO{sub 2} capture, transportation, and sequestration or use in deep saline aquifers, enhanced oil recovery operations, or enhanced coal bed methane operations. The model identifies and characterizes potential risks; identifies the likely failure modes, causes, effects and methods of detection; lists possible risk prevention and risk mitigation steps; estimates potential damage recovery costs, mitigation costs and costs savings resulting from mitigation; and ranks (prioritizes) risks according to the probability of failure, the severity of failure, the difficulty of early failure detection and themore » potential for fatalities. The QFMEA model generates the necessary information needed for effective project risk management. Diverse project information can be integrated into a concise, common format that allows comprehensive, quantitative analysis, by a cross-functional team of experts, to determine: What can possibly go wrong? How much will damage recovery cost? How can it be prevented or mitigated? What is the cost savings or benefit of prevention or mitigation? Which risks should be given highest priority for resolution? The QFMEA model can be tailored to specific projects and is applicable to new projects as well as mature projects. The model can be revised and updated as new information comes available. It accepts input from multiple sources, such as literature searches, site characterization, field data, computer simulations, analogues, process influence diagrams, probability density functions, financial analysis models, cost factors, and heuristic best practices manuals, and converts the information into a standardized format in an Excel spreadsheet. Process influence diagrams, geologic models, financial models, cost factors and an insurance schedule were developed to support the QFMEA model. Comprehensive, quantitative risk

Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses

PubMed Central

Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

2016-01-01

Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. PMID:27146161

Carr-Purcell-Meiboom-Gill (CPMG) Imaging of Prostate Cancer: Quantitative T2 Values for Cancer Discrimination

PubMed Central

Roebuck, Joseph R.; Haker, Steven J.; Mitsouras, Dimitris; Rybicki, Frank J.; Tempany, Clare M.; Mulkern, Robert V.

2009-01-01

Quantitative, apparent T2 values of suspected prostate cancer and healthy peripheral zone tissue in men with prostate cancer were measured using a Carr-Purcell-Meiboom-Gill (CPMG) imaging sequence in order to assess the cancer discrimination potential of tissue T2 values. The CPMG imaging sequence was used to image the prostates of 18 men with biopsy proven prostate cancer. Whole gland coverage with nominal voxel volumes of 0.54 × 1.1 × 4 mm3 was obtained in 10.7 minutes, resulting in data sets suitable for generating high quality images with variable T2-weighting and for evaluating quantitative T2 values on a pixel-by-pixel basis. Region-of-interest analysis of suspected healthy peripheral zone tissue and suspected cancer, identified on the basis of both T1- and T2-weighted signal intensities and available histopathology reports, yielded significantly (p < 0.0001) longer apparent T2 values in suspected healthy tissue (193 ± 49 ms) vs. suspected cancer (100 ± 26 ms), suggesting potential utility of this method as a tissue specific discrimination index for prostate cancer. We conclude that CPMG imaging of the prostate can be performed in reasonable scan times and can provide advantages over T2-weighted fast spin echo imaging alone, including quantitative T2 values for cancer discrimination as well as proton density maps without the point spread function degradation associated with short effective echo time fast spin echo (FSE) sequences. PMID:18823731

Application of NIR spectroscopy in the assessment of diabetic foot disorders

NASA Astrophysics Data System (ADS)

Schleicher, Eckhard; Hampel, Uwe; Freyer, Richard

2001-10-01

Diabetic foot syndrome (DFS) is a common sequel of long-term diabetes mellitus. There is a urgent need of noninvasive, objective and quantitative diagnostic tools to assess tissue viability and perfusion for a successful therapy. NIR spectroscopy seems to be qualified to measure local capillary hemoglobin saturation of the outer extremities in patients with progressive diabetic disorders. We investigate how NIR spectroscopy can be applied to the assessment of diabetic foot problems such as neuropathy and angiopathy. Thereby we use spatially resolved spectroscopy in conjunction with a specially developed continuous-wave laser spectrometer. Comparison of intra- and interindividual measurements is expected to yield quantitative measures of local tissue viability which is a prerequisite for a successful therapy.

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

ERIC Educational Resources Information Center

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

2017-01-01

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

Monitoring Cartilage Tissue Engineering Using Magnetic Resonance Spectroscopy, Imaging, and Elastography

PubMed Central

Klatt, Dieter; Magin, Richard L.

2013-01-01

A key technical challenge in cartilage tissue engineering is the development of a noninvasive method for monitoring the composition, structure, and function of the tissue at different growth stages. Due to its noninvasive, three-dimensional imaging capabilities and the breadth of available contrast mechanisms, magnetic resonance imaging (MRI) techniques can be expected to play a leading role in assessing engineered cartilage. In this review, we describe the new MR-based tools (spectroscopy, imaging, and elastography) that can provide quantitative biomarkers for cartilage tissue development both in vitro and in vivo. Magnetic resonance spectroscopy can identify the changing molecular structure and alternations in the conformation of major macromolecules (collagen and proteoglycans) using parameters such as chemical shift, relaxation rates, and magnetic spin couplings. MRI provides high-resolution images whose contrast reflects developing tissue microstructure and porosity through changes in local relaxation times and the apparent diffusion coefficient. Magnetic resonance elastography uses low-frequency mechanical vibrations in conjunction with MRI to measure soft tissue mechanical properties (shear modulus and viscosity). When combined, these three techniques provide a noninvasive, multiscale window for characterizing cartilage tissue growth at all stages of tissue development, from the initial cell seeding of scaffolds to the development of the extracellular matrix during construct incubation, and finally, to the postimplantation assessment of tissue integration in animals and patients. PMID:23574498

Quantitative risk assessment for skin sensitization: Success or failure?

PubMed

Kimber, Ian; Gerberick, G Frank; Basketter, David A

2017-02-01

Skin sensitization is unique in the world of toxicology. There is a combination of reliable, validated predictive test methods for identification of skin sensitizing chemicals, a clearly documented and transparent approach to risk assessment, and effective feedback from dermatology clinics around the world delivering evidence of the success or failure of the hazard identification/risk assessment/management process. Recent epidemics of contact allergy, particularly to preservatives, have raised questions of whether the safety/risk assessment process is working in an optimal manner (or indeed is working at all!). This review has as its focus skin sensitization quantitative risk assessment (QRA). The core toxicological principles of QRA are reviewed, and evidence of use and misuse examined. What becomes clear is that skin sensitization QRA will only function adequately if two essential criteria are met. The first is that QRA is applied rigourously, and the second is that potential exposure to the sensitizing substance is assessed adequately. This conclusion will come as no surprise to any toxicologist who appreciates the basic premise that "risk = hazard x exposure". Accordingly, use of skin sensitization QRA is encouraged, not least because the essential feedback from dermatology clinics can be used as a tool to refine QRA in situations where this risk assessment tool has not been properly used. Copyright © 2016 Elsevier Inc. All rights reserved.