Absorption and scattering coefficient dependence of laser-Doppler flowmetry models for large tissue volumes.

PubMed

Binzoni, T; Leung, T S; Rüfenacht, D; Delpy, D T

2006-01-21

Based on quasi-elastic scattering theory (and random walk on a lattice approach), a model of laser-Doppler flowmetry (LDF) has been derived which can be applied to measurements in large tissue volumes (e.g. when the interoptode distance is >30 mm). The model holds for a semi-infinite medium and takes into account the transport-corrected scattering coefficient and the absorption coefficient of the tissue, and the scattering coefficient of the red blood cells. The model holds for anisotropic scattering and for multiple scattering of the photons by the moving scatterers of finite size. In particular, it has also been possible to take into account the simultaneous presence of both Brownian and pure translational movements. An analytical and simplified version of the model has also been derived and its validity investigated, for the case of measurements in human skeletal muscle tissue. It is shown that at large optode spacing it is possible to use the simplified model, taking into account only a 'mean' light pathlength, to predict the blood flow related parameters. It is also demonstrated that the 'classical' blood volume parameter, derived from LDF instruments, may not represent the actual blood volume variations when the investigated tissue volume is large. The simplified model does not need knowledge of the tissue optical parameters and thus should allow the development of very simple and cost-effective LDF hardware.

Human fetal lung morphometry at autopsy with new modeling to quantitate structural maturity.

PubMed

Lipsett, Jill

2017-06-01

To demonstrate a simplified morphometric procedure, including a new model for acinar structural maturity, applicable to autopsy fetal lung and present reference values for these parameters. Cases with autopsy consent for research were studied. To simplify analysis only critical morphometric parameters were measured to allow calculation of gas-exchange surface area. A total of 58 fetuses, 16-40 weeks were included. Subjects were rejected with any condition predisposing to pulmonary hypo/hyperplasia, significant maceration, or if lung weight/bodyweight or microscopy identified pulmonary hypoplasia or lung growth disorders. Lungs were inflation fixed, weights and volumes determined, sampled, then returned to the body. Volume densities (V V ) of parenchyma/non-parenchyma and air-space/gas-exchange tissue, gas-exchange surface density (S V ), and total surface area (SA) were determined. The number, mean radius, and septal thickness of modeled airspace-spheres were calculated. Equations were generated for each parameter function of gestation and bodyweight. From 16 to 40-week weights and volumes increased as power functions from ∼4 g/mL to ∼90 g/mL. Parenchyma/non-parenchyma changed little-75:25 (16 weeks) to 71:29 (term). Parenchyma was 10% airspace:90% tissue early and 50:50 by term. Gas-exchange S V increased from 175 to 450 cm 2 /cm 3 and total SA increased from 0.059 to 4.793 m 2 . There were 3.31 × 10 6 airspace-spheres, 12 µ radius, septal thickness 30 µ at 16 weeks, increasing to 56.92 × 10 6 , 26 µ radius, septal thickness 13 µ by term. Morphometry can feasibly be performed at autopsy, providing more informative quantitative data on lung structural development than current methods utilized. This reference data set compares well with published data. © 2017 Wiley Periodicals, Inc.

Simplified procedure for computing the absorption of sound by the atmosphere

DOT National Transportation Integrated Search

2007-10-31

This paper describes a study that resulted in the development of a simplified : method for calculating attenuation by atmospheric-absorption for wide-band : sounds analyzed by one-third octave-band filters. The new method [referred to : herein as the...

Automatic breast tissue density estimation scheme in digital mammography images

NASA Astrophysics Data System (ADS)

Menechelli, Renan C.; Pacheco, Ana Luisa V.; Schiabel, Homero

2017-03-01

Cases of breast cancer have increased substantially each year. However, radiologists are subject to subjectivity and failures of interpretation which may affect the final diagnosis in this examination. The high density features in breast tissue are important factors related to these failures. Thus, among many functions some CADx (Computer-Aided Diagnosis) schemes are classifying breasts according to the predominant density. In order to aid in such a procedure, this work attempts to describe automated software for classification and statistical information on the percentage change in breast tissue density, through analysis of sub regions (ROIs) from the whole mammography image. Once the breast is segmented, the image is divided into regions from which texture features are extracted. Then an artificial neural network MLP was used to categorize ROIs. Experienced radiologists have previously determined the ROIs density classification, which was the reference to the software evaluation. From tests results its average accuracy was 88.7% in ROIs classification, and 83.25% in the classification of the whole breast density in the 4 BI-RADS density classes - taking into account a set of 400 images. Furthermore, when considering only a simplified two classes division (high and low densities) the classifier accuracy reached 93.5%, with AUC = 0.95.

Quantitative Analysis of ¹⁸F-(E)-N-(3-Iodoprop-2-Enyl)-2β-Carbofluoroethoxy-3β-(4'-Methyl-Phenyl) Nortropane Binding to the Dopamine Transporter in Parkinson Disease.

PubMed

Fazio, Patrik; Svenningsson, Per; Forsberg, Anton; Jönsson, Erik G; Amini, Nahid; Nakao, Ryuji; Nag, Sangram; Halldin, Christer; Farde, Lars; Varrone, Andrea

2015-05-01

(18)F-(E)-N-(3-iodoprop-2-enyl)-2β-carbofluoroethoxy-3β-(4'-methyl-phenyl) nortropane ((18)F-FE-PE2I) is a recently developed radioligand for the in vivo quantification of the dopamine transporter (DAT) in the striatum and substantia nigra (SN). The aim of this study was to examine the suitability of (18)F-FE-PE2I as a tool for imaging the nigrostriatal pathway in Parkinson disease (PD) with PET. Ten PD patients (9 men and 1 woman; mean age ± SD, 60 ± 9 y; Hoehn and Yahr, 1-2; Unified Parkinson Disease Rating Scale motor, 18.9 ± 6.7) and 10 controls (9 men and 1 woman; mean age ± SD, 60 ± 7 y) were included. PET measurements with (18)F-FE-PE2I were conducted for 93 min using the High-Resolution Research Tomograph. Venous blood was drawn to compare protein binding, parent fraction, and radiometabolite composition in PD patients and controls. Regions of interest for the caudate, putamen, ventral striatum, SN, and cerebellum were drawn on coregistered MR images. The outcome measure was the binding potential (BP(ND)) estimated with the simplified reference tissue model and the Logan graphical analysis, using the cerebellum as a reference region. Time stability of BP(ND) was examined to define the shortest acquisition protocol for quantitative studies. The wavelet-aided parametric imaging method was used to obtain high-resolution BP(ND) images to compare DAT availability in the striatum and SN in PD patients and control subjects. Group differences were assessed with the unpaired t test (P < 0.05). Parent, radiometabolite fractions, plasma concentration, and cerebellar uptake of (18)F-FE-PE2I did not differ significantly between PD patients and controls. Stable estimates of BP(ND) (<8% of the 93-min value) were obtained with the simplified reference tissue model using approximately 66 min of data. BP(ND) values in PD patients were significantly lower than those in controls (P < 0.05) in the caudate (2.54 ± 0.79 vs. 3.68 ± 0.56), putamen (1.39 ± 1.04 vs. 4.41 ± 0.54), ventral striatum (2.26 ± 0.93 vs. 3.30 ± 0.46), and SN (0.46 ± 0.20 vs. 0.68 ± 0.15). (18)F-FE-PE2I is clearly a suitable radioligand for DAT quantification and imaging of the nigrostriatal pathway in PD. Similar metabolism in controls and PD patients, suitability of the cerebellum as a reference region, and accuracy of quantification using approximately 66 min of PET data are advantages for noninvasive and simplified imaging protocols for PD studies. Finally, DAT loss in PD can be measured in both the striatum and the SN, supporting the utility of (18)F-FE-PE2I as an imaging tool of the nigrostriatal pathway. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Simplified versus geometrically accurate models of forefoot anatomy to predict plantar pressures: A finite element study.

PubMed

Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R

2016-01-25

Integration of patient-specific biomechanical measurements into the design of therapeutic footwear has been shown to improve clinical outcomes in patients with diabetic foot disease. The addition of numerical simulations intended to optimise intervention design may help to build on these advances, however at present the time and labour required to generate and run personalised models of foot anatomy restrict their routine clinical utility. In this study we developed second-generation personalised simple finite element (FE) models of the forefoot with varying geometric fidelities. Plantar pressure predictions from barefoot, shod, and shod with insole simulations using simplified models were compared to those obtained from CT-based FE models incorporating more detailed representations of bone and tissue geometry. A simplified model including representations of metatarsals based on simple geometric shapes, embedded within a contoured soft tissue block with outer geometry acquired from a 3D surface scan was found to provide pressure predictions closest to the more complex model, with mean differences of 13.3kPa (SD 13.4), 12.52kPa (SD 11.9) and 9.6kPa (SD 9.3) for barefoot, shod, and insole conditions respectively. The simplified model design could be produced in <1h compared to >3h in the case of the more detailed model, and solved on average 24% faster. FE models of the forefoot based on simplified geometric representations of the metatarsal bones and soft tissue surface geometry from 3D surface scans may potentially provide a simulation approach with improved clinical utility, however further validity testing around a range of therapeutic footwear types is required. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simplified antibiotic regimens for treatment of clinical severe infection in the outpatient setting when referral is not possible for young infants in Pakistan (Simplified Antibiotic Therapy Trial [SATT]): a randomised, open-label, equivalence trial.

PubMed

Mir, Fatima; Nisar, Imran; Tikmani, Shiyam S; Baloch, Benazir; Shakoor, Sadia; Jehan, Fyezah; Ahmed, Imran; Cousens, Simon; Zaidi, Anita K M

2017-02-01

Parenteral antibiotic therapy for young infants (aged 0-59 days) with suspected sepsis is sometimes not available or feasible in countries with high neonatal mortality. Outpatient treatment could save lives in such settings. We aimed to assess the equivalence of two simplified antibiotic regimens, comprising fewer injections and oral rather than parenteral administration, compared with a reference treatment for young infants with clinical severe infection. We undertook the Simplified Antibiotic Therapy Trial (SATT), a three-arm, randomised, open-label, equivalence trial in five communities in Karachi, Pakistan. We enrolled young infants (aged 0-59 days) who either presented at a primary health-care clinic or were identified by a community health worker with signs of clinical severe infection. We included infants who were not critically ill and whose family refused admission. We randomly assigned infants to either intramuscular procaine benzylpenicillin and gentamicin once a day for 7 days (reference); oral amoxicillin twice daily and intramuscular gentamicin once a day for 7 days; or intramuscular procaine benzylpenicillin and gentamicin once a day for 2 days followed by oral amoxicillin twice daily for 5 days. The primary outcome was treatment failure within 7 days of enrolment and the primary analysis was per protocol. We judged experimental treatments as efficacious as the reference if the upper bound of the 95% CI for the difference in treatment failure was less than 5·0. This trial is registered at ClinicalTrials.gov, number NCT01027429. Between Jan 1, 2010, and Dec 26, 2013, 2780 infants were deemed eligible for the trial, of whom 2453 (88%) were enrolled. Because of inadequate clinical follow-up or treatment adherence, 2251 infants were included in the per-protocol analysis. 820 infants (747 per protocol) were assigned the reference treatment of procaine benzylpenicillin and gentamicin, 816 (751 per protocol) were allocated amoxicillin and gentamicin, and 817 (753 per protocol) were assigned procaine benzylpenicillin, gentamicin, and amoxicillin. Treatment failure within 7 days of enrolment was reported in 90 (12%) infants who received procaine benzylpenicillin and gentamicin (reference), 76 (10%) of those given amoxicillin and gentamicin (risk difference with reference -1·9, 95% CI -5·1 to 1·3), and 99 (13%) of those treated with procaine benzylpenicillin, gentamicin, and amoxicillin (risk difference with reference 1·1, -2·3 to 4·5). Two simplified antibiotic regimens requiring fewer injections are equivalent to a reference treatment for young infants with signs of clinical severe infection but without signs of critical illness. The use of these simplified regimens has the potential to increase access to treatment for sick young infants who cannot be referred to hospital. The Saving Newborn Lives initiative of Save the Children, through support from the Bill & Melinda Gates, and by WHO and USAID. Copyright © 2017 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY license. Published by Elsevier Ltd.. All rights reserved.

Experimental Study of Radiation Efficiency from an Ingested Source inside a Human Body Model^*.

PubMed

Chan, Yawen; -H Meng, Max; Wu, K-L; Wang, Xiaona

2005-01-01

The attenuation of human body trunk at frequency range of 100MHz to 6GHz from an internal source was estimated using a simplified experimental model. Antennas were placed in the model which was filled with distilled water, 0.9% NaCl saline solution, and porcine body tissue alternately to determine the attenuation of the system. Saline has greater attenuation than water due to its higher conductivity, while porcine body tissue has attenuation bounded by saline solution and water. Estimated attenuation at the four ISM bands, 434MHz, 915MHz, 2.45GHz and 5.8GHz were given and all of these bands satisfied the safety and sensitivity requirements of a biomedical telemetry system. 915MHz and 2.45GHz are good choices for the wireless link because of their relatively larger electrical size of RF components such as antenna. In addition, with the growth in wireless LAN and Bluetooth technology, miniaturized antennas, camera modules, and other RF devices have been developed which can be employed in biomedical ingested or implanted devices. This paper gives a reference of attenuation values of a human body trunk of average size. It should be noted that the attenuation values can be different for different body size and different body composition, and therefore the values in this paper serves as a reference only.

Doubled Haploid ‘CUDH2107’ as a Reference for Bulb Onion (Allium cepa L.) Research: Development of a Transcriptome Catalogue and Identification of Transcripts Associated with Male Fertility

PubMed Central

Khosa, Jiffinvir S.; Lee, Robyn; Bräuning, Sophia; Lord, Janice; Pither-Joyce, Meeghan; McCallum, John; Macknight, Richard C.

2016-01-01

Researchers working on model plants have derived great benefit from developing genomic and genetic resources using ‘reference’ genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line ‘CUDH2107’ by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue. A total of 396 million 100 base pair paired reads was assembled using the Trinity pipeline, resulting in 271,665 transcript contigs. This dataset was analysed for gene ontology and transcripts were classified on the basis of putative biological processes, molecular function and cellular localization. Significant differences were observed in transcript expression profiles between different tissues. To demonstrate the utility of our CUDH2107 transcriptome catalogue for understanding the genetic and molecular basis of various traits, we identified orthologues of rice genes involved in male fertility and flower development. These genes provide an excellent starting point for studying the molecular regulation, and the engineering of reproductive traits. PMID:27861615

Simplified models for dark matter searches at the LHC

NASA Astrophysics Data System (ADS)

Abdallah, Jalal; Araujo, Henrique; Arbey, Alexandre; Ashkenazi, Adi; Belyaev, Alexander; Berger, Joshua; Boehm, Celine; Boveia, Antonio; Brennan, Amelia; Brooke, Jim; Buchmueller, Oliver; Buckley, Matthew; Busoni, Giorgio; Calibbi, Lorenzo; Chauhan, Sushil; Daci, Nadir; Davies, Gavin; De Bruyn, Isabelle; De Jong, Paul; De Roeck, Albert; de Vries, Kees; Del Re, Daniele; De Simone, Andrea; Di Simone, Andrea; Doglioni, Caterina; Dolan, Matthew; Dreiner, Herbi K.; Ellis, John; Eno, Sarah; Etzion, Erez; Fairbairn, Malcolm; Feldstein, Brian; Flaecher, Henning; Feng, Eric; Fox, Patrick; Genest, Marie-Hélène; Gouskos, Loukas; Gramling, Johanna; Haisch, Ulrich; Harnik, Roni; Hibbs, Anthony; Hoh, Siewyan; Hopkins, Walter; Ippolito, Valerio; Jacques, Thomas; Kahlhoefer, Felix; Khoze, Valentin V.; Kirk, Russell; Korn, Andreas; Kotov, Khristian; Kunori, Shuichi; Landsberg, Greg; Liem, Sebastian; Lin, Tongyan; Lowette, Steven; Lucas, Robyn; Malgeri, Luca; Malik, Sarah; McCabe, Christopher; Mete, Alaettin Serhan; Morgante, Enrico; Mrenna, Stephen; Nakahama, Yu; Newbold, Dave; Nordstrom, Karl; Pani, Priscilla; Papucci, Michele; Pataraia, Sophio; Penning, Bjoern; Pinna, Deborah; Polesello, Giacomo; Racco, Davide; Re, Emanuele; Riotto, Antonio Walter; Rizzo, Thomas; Salek, David; Sarkar, Subir; Schramm, Steven; Skubic, Patrick; Slone, Oren; Smirnov, Juri; Soreq, Yotam; Sumner, Timothy; Tait, Tim M. P.; Thomas, Marc; Tomalin, Ian; Tunnell, Christopher; Vichi, Alessandro; Volansky, Tomer; Weiner, Neal; West, Stephen M.; Wielers, Monika; Worm, Steven; Yavin, Itay; Zaldivar, Bryan; Zhou, Ning; Zurek, Kathryn

2015-09-01

This document outlines a set of simplified models for dark matter and its interactions with Standard Model particles. It is intended to summarize the main characteristics that these simplified models have when applied to dark matter searches at the LHC, and to provide a number of useful expressions for reference. The list of models includes both ss-channel and tt-channel scenarios. For ss-channel, spin-0 and spin-1 mediations are discussed, and also realizations where the Higgs particle provides a portal between the dark and visible sectors. The guiding principles underpinning the proposed simplified models are spelled out, and some suggestions for implementation are presented.

Characterizing tissue microstructure using an ultrasound system-independent spatial autocorrelation function

NASA Astrophysics Data System (ADS)

Dong, Fang

1999-09-01

The research described in this dissertation is related to characterization of tissue microstructure using a system- independent spatial autocorrelation function (SAF). The function was determined using a reference phantom method, which employed a well-defined ``point- scatterer'' reference phantom to account for instrumental factors. The SAF's were estimated for several tissue-mimicking (TM) phantoms and fresh dog livers. Both phantom tests and in vitro dog liver measurements showed that the reference phantom method is relatively simple and fairly accurate, providing the bandwidth of the measurement system is sufficient for the size of the scatterer being involved in the scattering process. Implementation of this method in clinical scanner requires that distortions from patient's body wall be properly accounted for. The SAF's were estimated for two phantoms with body-wall-like distortions. The experimental results demonstrated that body wall distortions have little effect if echo data are acquired from a large scattering volume. One interesting application of the SAF is to form a ``scatterer size image''. The scatterer size image may help providing diagnostic tools for those diseases in which the tissue microstructure is different from the normal. Another method, the BSC method, utilizes information contained in the frequency dependence of the backscatter coefficient to estimate the scatterer size. The SAF technique produced accurate scatterer size images of homogeneous TM phantoms and the BSC method was capable of generating accurate size images for heterogeneous phantoms. In the scatterer size image of dog kidneys, the contrast-to-noise-ratio (CNR) between renal cortex and medulla was improved dramatically compared to the gray- scale image. The effect of nonlinear propagation was investigated by using a custom-designed phantom with overlaying TM fat layer. The results showed that the correlation length decreased when the transmitting power increased. The measurement results support the assumption that nonlinear propagation generates harmonic energies and causes underestimation of scatterer diameters. Nonlinear propagation can be further enhanced by those materials with high B/A value-a parameter which characterizes the degree of nonlinearity. Nine versions of TM fat and non-fat materials were measured for their B/A values using a new measurement technique, the ``simplified finite amplitude insertion substitution'' (SFAIS) method.

Criteria for personal dosimetry in mixed radiation fields in space. [analyzing trapped protons, tissue disintegration stars, and neutrons

NASA Technical Reports Server (NTRS)

Schaefer, H. J.

1974-01-01

The complexity of direct reading and passive dosimeters for monitoring radiation is studied to strike the right balance of compromise to simplify the monitoring procedure. Trapped protons, tissue disintegration stars, and neutrons are analyzed.

Simplified models for dark matter searches at the LHC

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

Abdallah, Jalal; Araujo, Henrique; Arbey, Alexandre

This document a outlines a set of simplified models for dark matter and its interactions with Standard Model particles. It is intended to summarize the main characteristics that these simplified models have when applied to dark matter searches at the LHC, and to provide a number of useful expressions for reference. The list of models includes both s-channel and t-channel scenarios. For s-channel, spin-0 and spin-1 mediations are discussed, and also realizations where the Higgs particle provides a portal between the dark and visible sectors. The guiding principles underpinning the proposed simplified models are spelled out, and some suggestions formore » implementation are presented.« less

Simplified Models for Dark Matter Searches at the LHC

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

Abdallah, Jalal

This document outlines a set of simplified models for dark matter and its interactions with Standard Model particles. It is intended to summarize the main characteristics that these simplified models have when applied to dark matter searches at the LHC, and to provide a number of useful expressions for reference. The list of models includes both s-channel and t-channel scenarios. For s-channel, spin-0 and spin-1 mediations are discussed, and also realizations where the Higgs particle provides a portal between the dark and visible sectors. The guiding principles underpinning the proposed simplified models are spelled out, and some suggestions for implementationmore » are presented.« less

Simplified Models for Dark Matter Searches at the LHC

DOE PAGES

Abdallah, Jalal

2015-08-11

This document outlines a set of simplified models for dark matter and its interactions with Standard Model particles. It is intended to summarize the main characteristics that these simplified models have when applied to dark matter searches at the LHC, and to provide a number of useful expressions for reference. The list of models includes both s-channel and t-channel scenarios. For s-channel, spin-0 and spin-1 mediations are discussed, and also realizations where the Higgs particle provides a portal between the dark and visible sectors. The guiding principles underpinning the proposed simplified models are spelled out, and some suggestions for implementationmore » are presented.« less

Silicon Carbide Metallization

NASA Astrophysics Data System (ADS)

Lescoat, F.; Tanguy, F.; Durand, P.

2016-05-01

A study has been done to assess the feasibility of metallization of Silicon Carbide (SiC) in order to simplify design and mounting of one or more ground reference rail needed to provide an electrical reference for electronics mounted on an SiC structure.

A simplified plastic embedding and immunohistologic technique for immunophenotypic analysis of human hematopoietic and lymphoid tissues.

PubMed Central

Casey, T. T.; Cousar, J. B.; Collins, R. D.

1988-01-01

Routine fixation and paraffin embedding destroys many hematopoietic and lymphoid differentiation antigens detected by flow cytometry or frozen section immunohistochemistry. On the other hand, morphologic evaluation is difficult in flow cytometric or frozen section studies. A simplified three-step plastic embedding system using acetone-fixed tissues embedded in glycol-methacrylate (GMA) resin has been found to provide both excellent morphologic and antigenic preservation. With our system, a wide variety of antigens are detected in plastic sections without trypsinization or prolonged embedding procedures; pan-B (CD19, CD22), pan-T (CD7, CD5, CD3, CD2), T-subset (CD4, CD8, CD1, CD25) markers as well as surface immunoglobulin and markers for myeloid and mononuclear-phagocyte cells are preserved. In summary, modifications of plastic embedding techniques used in this study simplify the procedure, apparently achieve excellent antigenic preservation, and facilitate evaluation of morphologic details in relation to immunocytochemical markers. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:3282442

External dose-rate conversion factors of radionuclides for air submersion, ground surface contamination and water immersion based on the new ICRP dosimetric setting.

PubMed

Yoo, Song Jae; Jang, Han-Ki; Lee, Jai-Ki; Noh, Siwan; Cho, Gyuseong

2013-01-01

For the assessment of external doses due to contaminated environment, the dose-rate conversion factors (DCFs) prescribed in Federal Guidance Report 12 (FGR 12) and FGR 13 have been widely used. Recently, there were significant changes in dosimetric models and parameters, which include the use of the Reference Male and Female Phantoms and the revised tissue weighting factors, as well as the updated decay data of radionuclides. In this study, the DCFs for effective and equivalent doses were calculated for three exposure settings: skyshine, groundshine and water immersion. Doses to the Reference Phantoms were calculated by Monte Carlo simulations with the MCNPX 2.7.0 radiation transport code for 26 mono-energy photons between 0.01 and 10 MeV. The transport calculations were performed for the source volume within the cut-off distances practically contributing to the dose rates, which were determined by a simplified calculation model. For small tissues for which the reduction of variances are difficult, the equivalent dose ratios to a larger tissue (with lower statistical errors) nearby were employed to make the calculation efficient. Empirical response functions relating photon energies, and the organ equivalent doses or the effective doses were then derived by the use of cubic-spline fitting of the resulting doses for 26 energy points. The DCFs for all radionuclides considered important were evaluated by combining the photon emission data of the radionuclide and the empirical response functions. Finally, contributions of accompanied beta particles to the skin equivalent doses and the effective doses were calculated separately and added to the DCFs. For radionuclides considered in this study, the new DCFs for the three exposure settings were within ±10 % when compared with DCFs in FGR 13.

External dose-rate conversion factors of radionuclides for air submersion, ground surface contamination and water immersion based on the new ICRP dosimetric setting

PubMed Central

Yoo, Song Jae; Jang, Han-Ki; Lee, Jai-Ki; Noh, Siwan; Cho, Gyuseong

2013-01-01

For the assessment of external doses due to contaminated environment, the dose-rate conversion factors (DCFs) prescribed in Federal Guidance Report 12 (FGR 12) and FGR 13 have been widely used. Recently, there were significant changes in dosimetric models and parameters, which include the use of the Reference Male and Female Phantoms and the revised tissue weighting factors, as well as the updated decay data of radionuclides. In this study, the DCFs for effective and equivalent doses were calculated for three exposure settings: skyshine, groundshine and water immersion. Doses to the Reference Phantoms were calculated by Monte Carlo simulations with the MCNPX 2.7.0 radiation transport code for 26 mono-energy photons between 0.01 and 10 MeV. The transport calculations were performed for the source volume within the cut-off distances practically contributing to the dose rates, which were determined by a simplified calculation model. For small tissues for which the reduction of variances are difficult, the equivalent dose ratios to a larger tissue (with lower statistical errors) nearby were employed to make the calculation efficient. Empirical response functions relating photon energies, and the organ equivalent doses or the effective doses were then derived by the use of cubic-spline fitting of the resulting doses for 26 energy points. The DCFs for all radionuclides considered important were evaluated by combining the photon emission data of the radionuclide and the empirical response functions. Finally, contributions of accompanied beta particles to the skin equivalent doses and the effective doses were calculated separately and added to the DCFs. For radionuclides considered in this study, the new DCFs for the three exposure settings were within ±10 % when compared with DCFs in FGR 13. PMID:23542764

Simplified filtered Smith predictor for MIMO processes with multiple time delays.

PubMed

Santos, Tito L M; Torrico, Bismark C; Normey-Rico, Julio E

2016-11-01

This paper proposes a simplified tuning strategy for the multivariable filtered Smith predictor. It is shown that offset-free control can be achieved with step references and disturbances regardless of the poles of the primary controller, i.e., integral action is not explicitly required. This strategy reduces the number of design parameters and simplifies tuning procedure because the implicit integrative poles are not considered for design purposes. The simplified approach can be used to design continuous-time or discrete-time controllers. Three case studies are used to illustrate the advantages of the proposed strategy if compared with the standard approach, which is based on the explicit integrative action. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

[The subject matters concerned with use of simplified analytical systems from the perspective of the Japanese Association of Medical Technologists].

PubMed

Morishita, Y

2001-05-01

The subject matters concerned with use of so-called simplified analytical systems for the purpose of useful utilizing are mentioned from the perspective of a laboratory technician. 1. The data from simplified analytical systems should to be agreed with those of particular reference methods not to occur the discrepancy of the data from different laboratories. 2. Accuracy of the measured results using simplified analytical systems is hard to be scrutinized thoroughly and correctly with the quality control surveillance procedure on the stored pooled serum or partly-processed blood. 3. It is necessary to present the guide line to follow about the contents of evaluation to guarantee on quality of simplified analytical systems. 4. Maintenance and manual performance of simplified analytical systems have to be standardized by a laboratory technician and a selling agent technician. 5. It calls attention, further that the cost of simplified analytical systems is much expensive compared to that of routine method with liquid reagents. 6. Various substances in human serum, like cytokine, hormone, tumor marker, and vitamin, etc. are also hoped to be measured by simplified analytical systems.

Simplified estimation of age-specific reference intervals for skewed data.

PubMed

Wright, E M; Royston, P

1997-12-30

Age-specific reference intervals are commonly used in medical screening and clinical practice, where interest lies in the detection of extreme values. Many different statistical approaches have been published on this topic. The advantages of a parametric method are that they necessarily produce smooth centile curves, the entire density is estimated and an explicit formula is available for the centiles. The method proposed here is a simplified version of a recent approach proposed by Royston and Wright. Basic transformations of the data and multiple regression techniques are combined to model the mean, standard deviation and skewness. Using these simple tools, which are implemented in almost all statistical computer packages, age-specific reference intervals may be obtained. The scope of the method is illustrated by fitting models to several real data sets and assessing each model using goodness-of-fit techniques.

Monte Carlo Simulations Comparing the Response of a Novel Hemispherical Tepc to Existing Spherical and Cylindrical Tepcs for Neutron Monitoring and Dosimetry.

PubMed

Broughton, David P; Waker, Anthony J

2017-05-01

Neutron dosimetry in reactor fields is currently mainly conducted with unwieldy flux monitors. Tissue Equivalent Proportional Counters (TEPCs) have been shown to have the potential to improve the accuracy of neutron dosimetry in these fields, and Multi-Element Tissue Equivalent Proportional Counters (METEPCs) could reduce the size of instrumentation required to do so. Complexity of current METEPC designs has inhibited their use beyond research. This work proposes a novel hemispherical counter with a wireless anode ball in place of the traditional anode wire as a possible solution for simplifying manufacturing. The hemispherical METEPC element was analyzed as a single TEPC to first demonstrate the potential of this new design by evaluating its performance relative to the reference spherical TEPC design and a single element from a cylindrical METEPC. Energy deposition simulations were conducted using the Monte Carlo code PHITS for both monoenergetic 2.5 MeV neutrons and the neutron energy spectrum of Cf-D2O moderated. In these neutron fields, the hemispherical counter appears to be a good alternative to the reference spherical geometry, performing slightly better than the cylindrical counter, which tends to underrespond to H*(10) for the lower neutron energies of the Cf-D2O moderated field. These computational results are promising, and if follow-up experimental work demonstrates the hemispherical counter works as anticipated, it will be ready to be incorporated into an METEPC design.

Simplified realistic human head model for simulating Tumor Treating Fields (TTFields).

PubMed

Wenger, Cornelia; Bomzon, Ze'ev; Salvador, Ricardo; Basser, Peter J; Miranda, Pedro C

2016-08-01

Tumor Treating Fields (TTFields) are alternating electric fields in the intermediate frequency range (100-300 kHz) of low-intensity (1-3 V/cm). TTFields are an anti-mitotic treatment against solid tumors, which are approved for Glioblastoma Multiforme (GBM) patients. These electric fields are induced non-invasively by transducer arrays placed directly on the patient's scalp. Cell culture experiments showed that treatment efficacy is dependent on the induced field intensity. In clinical practice, a software called NovoTalTM uses head measurements to estimate the optimal array placement to maximize the electric field delivery to the tumor. Computational studies predict an increase in the tumor's electric field strength when adapting transducer arrays to its location. Ideally, a personalized head model could be created for each patient, to calculate the electric field distribution for the specific situation. Thus, the optimal transducer layout could be inferred from field calculation rather than distance measurements. Nonetheless, creating realistic head models of patients is time-consuming and often needs user interaction, because automated image segmentation is prone to failure. This study presents a first approach to creating simplified head models consisting of convex hulls of the tissue layers. The model is able to account for anisotropic conductivity in the cortical tissues by using a tensor representation estimated from Diffusion Tensor Imaging. The induced electric field distribution is compared in the simplified and realistic head models. The average field intensities in the brain and tumor are generally slightly higher in the realistic head model, with a maximal ratio of 114% for a simplified model with reasonable layer thicknesses. Thus, the present pipeline is a fast and efficient means towards personalized head models with less complexity involved in characterizing tissue interfaces, while enabling accurate predictions of electric field distribution.

Structure and strategy in encoding simplified graphs

NASA Technical Reports Server (NTRS)

Schiano, Diane J.; Tversky, Barbara

1992-01-01

Tversky and Schiano (1989) found a systematic bias toward the 45-deg line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal 'axes' are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as 'graphs' only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

Ecological quality boundary-setting procedures: the Gulf of Riga case study.

PubMed

Aigars, Juris; Müller-Karulis, Bärbel; Martin, Georg; Jermakovs, Vadims

2008-03-01

Two approaches for setting ecological class boundaries, response curves and a simplified mathematical boundary-setting protocol, were tested for coastal, transitional and open waters in the Gulf of Riga, Baltic Sea. The simplified mathematical boundary-setting protocol defines acceptable ecological status based on expert judgment by a uniform relative deviation from reference conditions. In contrast, response curves derive class boundary definitions from observed changes in biological quality elements along environmental pressure gradients for class boundary definitions. Identification of relevant environmental pressures for the construction of response curves was based on a conceptual model of eutrophication in the Gulf of Riga. Response curves were successfully established for summer chlorophyll a and transparency, as well as for macrozoobenthos abundance in the Central Gulf, macrozoobenthos biotic coefficient in the Southern Gulf, and maximum depth of phytobenthos in the Northern Gulf. In the Gulf of Riga response curves almost always permitted a larger deviation from reference conditions than the 50% deviation applied for the simplified mathematical boundary-setting protocol. The case study clearly demonstrated that class boundary definitions should take into account the sensitivity of the target water body. Also, the class boundaries for different ecological quality elements were internally more consistent than those derived by the simplified mathematical boundary-setting protocol.

Simplified models vs. effective field theory approaches in dark matter searches

NASA Astrophysics Data System (ADS)

De Simone, Andrea; Jacques, Thomas

2016-07-01

In this review we discuss and compare the usage of simplified models and Effective Field Theory (EFT) approaches in dark matter searches. We provide a state of the art description on the subject of EFTs and simplified models, especially in the context of collider searches for dark matter, but also with implications for direct and indirect detection searches, with the aim of constituting a common language for future comparisons between different strategies. The material is presented in a form that is as self-contained as possible, so that it may serve as an introductory review for the newcomer as well as a reference guide for the practitioner.

Extended Finite Element Method with Simplified Spherical Harmonics Approximation for the Forward Model of Optical Molecular Imaging

PubMed Central

Li, Wei; Yi, Huangjian; Zhang, Qitan; Chen, Duofang; Liang, Jimin

2012-01-01

An extended finite element method (XFEM) for the forward model of 3D optical molecular imaging is developed with simplified spherical harmonics approximation (SPN). In XFEM scheme of SPN equations, the signed distance function is employed to accurately represent the internal tissue boundary, and then it is used to construct the enriched basis function of the finite element scheme. Therefore, the finite element calculation can be carried out without the time-consuming internal boundary mesh generation. Moreover, the required overly fine mesh conforming to the complex tissue boundary which leads to excess time cost can be avoided. XFEM conveniences its application to tissues with complex internal structure and improves the computational efficiency. Phantom and digital mouse experiments were carried out to validate the efficiency of the proposed method. Compared with standard finite element method and classical Monte Carlo (MC) method, the validation results show the merits and potential of the XFEM for optical imaging. PMID:23227108

Extended finite element method with simplified spherical harmonics approximation for the forward model of optical molecular imaging.

PubMed

Li, Wei; Yi, Huangjian; Zhang, Qitan; Chen, Duofang; Liang, Jimin

2012-01-01

An extended finite element method (XFEM) for the forward model of 3D optical molecular imaging is developed with simplified spherical harmonics approximation (SP(N)). In XFEM scheme of SP(N) equations, the signed distance function is employed to accurately represent the internal tissue boundary, and then it is used to construct the enriched basis function of the finite element scheme. Therefore, the finite element calculation can be carried out without the time-consuming internal boundary mesh generation. Moreover, the required overly fine mesh conforming to the complex tissue boundary which leads to excess time cost can be avoided. XFEM conveniences its application to tissues with complex internal structure and improves the computational efficiency. Phantom and digital mouse experiments were carried out to validate the efficiency of the proposed method. Compared with standard finite element method and classical Monte Carlo (MC) method, the validation results show the merits and potential of the XFEM for optical imaging.

How to Decide on Modeling Details: Risk and Benefit Assessment.

PubMed

Özilgen, Mustafa

Mathematical models based on thermodynamic, kinetic, heat, and mass transfer analysis are central to this chapter. Microbial growth, death, enzyme inactivation models, and the modeling of material properties, including those pertinent to conduction and convection heating, mass transfer, such as diffusion and convective mass transfer, and thermodynamic properties, such as specific heat, enthalpy, and Gibbs free energy of formation and specific chemical exergy are also needed in this task. The origins, simplifying assumptions, and uses of model equations are discussed in this chapter, together with their benefits. The simplified forms of these models are sometimes referred to as "laws," such as "the first law of thermodynamics" or "Fick's second law." Starting to modeling a study with such "laws" without considering the conditions under which they are valid runs the risk of ending up with erronous conclusions. On the other hand, models started with fundamental concepts and simplified with appropriate considerations may offer explanations for the phenomena which may not be obtained just with measurements or unprocessed experimental data. The discussion presented here is strengthened with case studies and references to the literature.

In vivo assessment and dosimetry of 2 novel PDE10A PET radiotracers in humans: 18F-MNI-659 and 18F-MNI-654.

PubMed

Barret, Olivier; Thomae, David; Tavares, Adriana; Alagille, David; Papin, Caroline; Waterhouse, Rikki; McCarthy, Timothy; Jennings, Danna; Marek, Ken; Russell, David; Seibyl, John; Tamagnan, Gilles

2014-08-01

Phosphodiesterase (PDE) 10A is an enzyme involved in the regulation of cyclic adenosine monophosphate and cyclic guanosine monophosphate and is highly expressed in medium-sized spiny neurons of the striatum, making it an attractive target for novel therapies for a variety of neurologic and psychiatric disorders that involve striatal function. Potential ligands for PET imaging of PDE10A have been reported. Here, we report the first-in-human characterization of 2 new PDE10A radioligands, 2-(2-(3-(1-(2-fluoroethyl)-1H-indazol-6-yl)-7-methyl-4-oxo-3,4-dihydroquinazolin-2-yl)ethyl)-4-isopropoxyisoindoline-1,3-dione ((18)F-MNI-654) and 2-(2-(3-(4-(2-fluoroethoxy)phenyl)-7-methyl-4-oxo-3,4-dihydroquinazolin-2-yl)ethyl)-4-isopropoxyisoindoline-1,3-dione ((18)F-MNI-659), with the goal of selecting the best one for use in future studies interrogating pathophysiologic changes in neuropsychiatric disorders and aiding pharmaceutical development targeting PDE10A. Eleven healthy volunteers participated in this study ((18)F-MNI-654 test-retest, 2 men; (18)F-MNI-659 test-retest, 4 men and 1 woman; (18)F-MNI-659 dosimetry, 2 men and 2 women). Brain PET images were acquired over 5.5 h for (18)F-MNI-654 and over 3.5 h for (18)F-MNI-659, and pharmacokinetic modeling with plasma- and reference-region (cerebellar cortex)-based methods was performed. Whole-body PET images were acquired over 6 h for (18)F-MNI-659 and radiation dosimetry estimated with OLINDA. Both radiotracers were similarly metabolized, with about 20% of intact parent remaining at 120 min after injection. PET time-activity data demonstrated that (18)F-MNI-654 kinetics were much slower than (18)F-MNI-659 kinetics. For (18)F-MNI-659, there was good agreement between the Logan and simplified reference tissue models for nondisplaceable binding potential (BPND), supporting noninvasive quantification, with test-retest variability less than 10% and intraclass correlation greater than 0.9. The (18)F-MNI-659 effective dose was estimated at 0.024 mSv/MBq. PET imaging in the human brain with 2 novel PDE10A (18)F tracers is being reported. Noninvasive quantification of (18)F-MNI-659 with the simplified reference tissue model using the cerebellum as a reference is possible. In addition, (18)F-MNI-659 kinetics are fast enough for a good estimate of BPND with 90 min of data, with values around 3.0 in the basal ganglia. Finally, (18)F-MNI-659 dosimetry is favorable and consistent with values reported for other PET radiotracers currently used in humans. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Selection and validation of suitable reference genes for miRNA expression normalization by quantitative RT-PCR in citrus somatic embryogenic and adult tissues.

PubMed

Kou, Shu-Jun; Wu, Xiao-Meng; Liu, Zheng; Liu, Yuan-Long; Xu, Qiang; Guo, Wen-Wu

2012-12-01

miRNAs have recently been reported to modulate somatic embryogenesis (SE), a key pathway of plant regeneration in vitro. For expression level detection and subsequent function dissection of miRNAs in certain biological processes, qRT-PCR is one of the most effective and sensitive techniques, for which suitable reference gene selection is a prerequisite. In this study, three miRNAs and eight non-coding RNAs (ncRNA) were selected as reference candidates, and their expression stability was inspected in developing citrus SE tissues cultured at 20, 25, and 30 °C. Stability of the eight non-miRNA ncRNAs was further validated in five adult tissues without temperature treatment. The best single reference gene for SE tissues was snoR14 or snoRD25, while for the adult tissues the best one was U4; although they were not as stable as the optimal multiple references snoR14 + U6 for SE tissues and snoR14 + U5 for adult tissues. For expression normalization of less abundant miRNAs in SE tissues, miR3954 was assessed as a viable reference. Single reference gene snoR14 outperformed multiple references for the overall SE and adult tissues. As one of the pioneer systematic studies on reference gene identification for plant miRNA normalization, this study benefits future exploration on miRNA function in citrus and provides valuable information for similar studies in other higher plants. Three miRNAs and eight non-coding RNAs were tested as reference candidates on developing citrus SE tissues. Best single references snoR14 or snoRD25 and optimal multiple references snoR14 + U6, snoR14 + U5 were identified.

Quantification of hyaluronan (HA) using a simplified fluorophore-assisted carbohydrate electrophoresis (FACE) procedure.

PubMed

Midura, Ronald J; Cali, Valbona; Lauer, Mark E; Calabro, Anthony; Hascall, Vincent C

2018-01-01

Hyaluronan (HA) exhibits numerous important roles in physiology and pathologies, and these facts necessitate an ability to accurately and reproducibly measure its quantities in tissues and cell cultures. Our group previously reported a rigorous and analytical procedure to quantify HA (and chondroitin sulfate, CS) using a reductive amination chemistry and separation of the fluorophore-conjugated, unsaturated disaccharides unique to HA and CS on high concentration acrylamide gels. This procedure is known as fluorophore-assisted carbohydrate electrophoresis (FACE) and has been adapted for the detection and quantification of all glycosaminoglycan types. While this previous FACE procedure is relatively straightforward to implement by carbohydrate research investigators, many nonglycoscience laboratories now studying HA biology might have difficulties establishing this prior FACE procedure as a routine assay for HA. To address this need, we have greatly simplified our prior FACE procedure for accurate and reproducible assessment of HA in tissues and cell cultures. This chapter describes in detail this simplified FACE procedure and, because it uses an enzyme that degrades both HA and CS, investigators will also gain additional insight into the quantities of CS in the same samples dedicated for HA analysis. © 2018 Elsevier Inc. All rights reserved.

3D imaging of optically cleared tissue using a simplified CLARITY method and on-chip microscopy

PubMed Central

Zhang, Yibo; Shin, Yoonjung; Sung, Kevin; Yang, Sam; Chen, Harrison; Wang, Hongda; Teng, Da; Rivenson, Yair; Kulkarni, Rajan P.; Ozcan, Aydogan

2017-01-01

High-throughput sectioning and optical imaging of tissue samples using traditional immunohistochemical techniques can be costly and inaccessible in resource-limited areas. We demonstrate three-dimensional (3D) imaging and phenotyping in optically transparent tissue using lens-free holographic on-chip microscopy as a low-cost, simple, and high-throughput alternative to conventional approaches. The tissue sample is passively cleared using a simplified CLARITY method and stained using 3,3′-diaminobenzidine to target cells of interest, enabling bright-field optical imaging and 3D sectioning of thick samples. The lens-free computational microscope uses pixel super-resolution and multi-height phase recovery algorithms to digitally refocus throughout the cleared tissue and obtain a 3D stack of complex-valued images of the sample, containing both phase and amplitude information. We optimized the tissue-clearing and imaging system by finding the optimal illumination wavelength, tissue thickness, sample preparation parameters, and the number of heights of the lens-free image acquisition and implemented a sparsity-based denoising algorithm to maximize the imaging volume and minimize the amount of the acquired data while also preserving the contrast-to-noise ratio of the reconstructed images. As a proof of concept, we achieved 3D imaging of neurons in a 200-μm-thick cleared mouse brain tissue over a wide field of view of 20.5 mm2. The lens-free microscope also achieved more than an order-of-magnitude reduction in raw data compared to a conventional scanning optical microscope imaging the same sample volume. Being low cost, simple, high-throughput, and data-efficient, we believe that this CLARITY-enabled computational tissue imaging technique could find numerous applications in biomedical diagnosis and research in low-resource settings. PMID:28819645

Accelerating non-contrast-enhanced MR angiography with inflow inversion recovery imaging by skipped phase encoding and edge deghosting (SPEED).

PubMed

Chang, Zheng; Xiang, Qing-San; Shen, Hao; Yin, Fang-Fang

2010-03-01

To accelerate non-contrast-enhanced MR angiography (MRA) with inflow inversion recovery (IFIR) with a fast imaging method, Skipped Phase Encoding and Edge Deghosting (SPEED). IFIR imaging uses a preparatory inversion pulse to reduce signals from static tissue, while leaving inflow arterial blood unaffected, resulting in sparse arterial vasculature on modest tissue background. By taking advantage of vascular sparsity, SPEED can be simplified with a single-layer model to achieve higher efficiency in both scan time reduction and image reconstruction. SPEED can also make use of information available in multiple coils for further acceleration. The techniques are demonstrated with a three-dimensional renal non-contrast-enhanced IFIR MRA study. Images are reconstructed by SPEED based on a single-layer model to achieve an undersampling factor of up to 2.5 using one skipped phase encoding direction. By making use of information available in multiple coils, SPEED can achieve an undersampling factor of up to 8.3 with four receiver coils. The reconstructed images generally have comparable quality as that of the reference images reconstructed from full k-space data. As demonstrated with a three-dimensional renal IFIR scan, SPEED based on a single-layer model is able to reduce scan time further and achieve higher computational efficiency than the original SPEED.

A novel method of genomic DNA extraction for Cactaceae1

PubMed Central

Fehlberg, Shannon D.; Allen, Jessica M.; Church, Kathleen

2013-01-01

• Premise of the study: Genetic studies of Cactaceae can at times be impeded by difficult sampling logistics and/or high mucilage content in tissues. Simplifying sampling and DNA isolation through the use of cactus spines has not previously been investigated. • Methods and Results: Several protocols for extracting DNA from spines were tested and modified to maximize yield, amplification, and sequencing. Sampling of and extraction from spines resulted in a simplified protocol overall and complete avoidance of mucilage as compared to typical tissue extractions. Sequences from one nuclear and three plastid regions were obtained across eight genera and 20 species of cacti using DNA extracted from spines. • Conclusions: Genomic DNA useful for amplification and sequencing can be obtained from cactus spines. The protocols described here are valuable for any cactus species, but are particularly useful for investigators interested in sampling living collections, extensive field sampling, and/or conservation genetic studies. PMID:25202521

Trypsin and MALDI matrix pre-coated targets simplify sample preparation for mapping proteomic distributions within biological tissues by imaging mass spectrometry

PubMed Central

Zubair, Faizan; Laibinis, Paul E.; Swisher, William G.; Yang, Junhai; Spraggins, Jeffrey M.; Norris, Jeremy L.; Caprioli, Richard M.

2017-01-01

Prefabricated surfaces containing α-cyano-4-hydroxycinnamic acid and trypsin have been developed to facilitate enzymatic digestion of endogenous tissue proteins prior to matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). Tissue sections are placed onto slides that were previously coated with α-cyano-4-hydroxycinnamic acid and trypsin. After incubation to promote enzymatic digestion, the tissue is analyzed by MALDI IMS to determine the spatial distribution of the tryptic fragments. The peptides detected in the MALDI IMS dataset were identified by Liquid chromatography-tandem mass spectrometry/mass spectrometry. Protein identification was further confirmed by correlating the localization of unique tryptic fragments originating from common parent proteins. Using this procedure, proteins with molecular weights as large as 300 kDa were identified and their distributions were imaged in sections of rat brain. In particular, large proteins such as myristoylated alanine-rich C-kinase substrate (29.8 kDa) and spectrin alpha chain, non-erythrocytic 1 (284 kDa) were detected that are not observed without trypsin. The pre-coated targets simplify workflow and increase sample throughput by decreasing the sample preparation time. Further, the approach allows imaging at higher spatial resolution compared with robotic spotters that apply one drop at a time. PMID:27676701

41 CFR 101-29.303 - All Federal executive agencies.

Code of Federal Regulations, 2010 CFR

2010-07-01

... present form and scope or whether a more simplified one can be used; (2) The existence of voluntary... CID's; and (4) The currency and applicability of reference documents included in the product...

Temperature and solute-transport simulation in streamflow using a Lagrangian reference frame

USGS Publications Warehouse

Jobson, Harvey E.

1980-01-01

A computer program for simulating one-dimensional, unsteady temperature and solute transport in a river has been developed and documented for general use. The solution approach to the convective-diffusion equation uses a moving reference frame (Lagrangian) which greatly simplifies the mathematics of the solution procedure and dramatically reduces errors caused by numerical dispersion. The model documentation is presented as a series of four programs of increasing complexity. The conservative transport model can be used to route a single conservative substance. The simplified temperature model is used to predict water temperature in rivers when only temperature and windspeed data are available. The complete temperature model is highly accurate but requires rather complete meteorological data. Finally, the 10-parameter model can be used to route as many as 10 interacting constituents through a river reach. (USGS)

Orthodontic-periodontal interactions: Orthodontic extrusion in interdisciplinary regenerative treatments.

PubMed

Paolone, Maria Giacinta; Kaitsas, Roberto

2018-06-01

Orthodontics is a periodontal treatment. "Guided orthodontic regeneration" (GOR) procedures use orthodontic movements in perio-restorative patients. The GOR technique includes a guided orthodontic "soft tissue" regeneration (GOTR) and a guided orthodontic "bone" regeneration (GOBR) with a plastic soft tissue approach and a regenerating reality. The increased amount of soft tissue gained with orthodontic movement can be used for subsequent periodontal regenerative techniques. The increased amount of bone can as well improve primary implant stability and, eventually, simplify a GTR technique to regenerate soft tissues, to restore tooth with external resorption in aesthetic zone or to extract a tooth to create new hard-soft tissue for adjacent teeth. Copyright © 2018. Published by Elsevier Masson SAS.

Rationalisation and Validation of an Acrylamide-Free Procedure in Three-Dimensional Histological Imaging

PubMed Central

Lai, Hei Ming; Liu, Alan King Lun; Ng, Wai-Lung; DeFelice, John; Lee, Wing Sang; Li, Heng; Li, Wen; Ng, Ho Man; Chang, Raymond Chuen-Chung; Lin, Bin; Wu, Wutian; Gentleman, Steve M.

2016-01-01

Three-dimensional visualization of intact tissues is now being achieved by turning tissues transparent. CLARITY is a unique tissue clearing technique, which features the use of detergents to remove lipids from fixed tissues to achieve optical transparency. To preserve tissue integrity, an acrylamide-based hydrogel has been proposed to embed the tissue. In this study, we examined the rationale behind the use of acrylamide in CLARITY, and presented evidence to suggest that the omission of acrylamide-hydrogel embedding in CLARITY does not alter the preservation of tissue morphology and molecular information in fixed tissues. We therefore propose a novel and simplified workflow for formaldehyde-fixed tissue clearing, which will facilitate the laboratory implementation of this technique. Furthermore, we have investigated the basic tissue clearing process in detail and have highlighted some areas for targeted improvement of technologies essential for the emerging subject of three-dimensional histology. PMID:27359336

Simplifying Skin Disease Diagnosis with Topical Nanotechnology.

PubMed

Yeo, David C; Xu, Chenjie

2018-05-01

A new study published in the journal Nature Biomedical Engineering 1 documents a novel diagnostic technology that exploits topically applied nanotechnology to detect skin tissue biomarkers for diagnosis. This concept is demonstrated by noninvasively imaging connective tissue growth factor (CTGF) mRNA in abnormal scar cells, whole tissue, and animal models. In this commentary, we highlight the main findings and discuss their implications. Successful implementation in the clinic could give rise to self-applied, biopsy-free diagnostic technology and significantly reduce healthcare burden. Crucially, noninvasive visualization of disease biomarkers, mobile device signal acquisition, and Internet-enabled transmission could significantly transform the diagnosis of skin disease and other superficial tissues.

Simplifying Access to Student Loan Information Act of 2014

THOMAS, 113th Congress

Sen. Shaheen, Jeanne [D-NH

2014-03-11

Senate - 03/11/2014 Read twice and referred to the Committee on Health, Education, Labor, and Pensions. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Simplifying Financial Aid for Students Act of 2014

THOMAS, 113th Congress

Sen. Booker, Cory A. [D-NJ

2014-05-14

Senate - 05/14/2014 Read twice and referred to the Committee on Health, Education, Labor, and Pensions. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Simplifying the extracellular matrix for 3-D cell culture and tissue engineering: a pragmatic approach.

PubMed

Prestwich, Glenn D

2007-08-15

The common technique of growing cells on tissue culture plastic (TCP) is gradually being supplanted by methods for culturing cells in two-dimensions (2-D) on matrices with more appropriate physical and biological properties or by encapsulation of cells in three-dimensions (3-D). The universal acceptance of the new 3-D paradigm is currently constrained by the lack of a biocompatible material in the marketplace that offers ease of use, experimental flexibility, and a seamless transition from in vitro to in vivo applications. In this Prospect, I argue that the standard for 3-D cell culture should be bio-inspired, biomimetic materials that can be used "as is" in drug discovery, toxicology, cell banking, and ultimately in medicine. Such biomaterials must therefore be highly reproducible, manufacturable, approvable, and affordable. To obtain integrated, functional, multicellular systems that recapitulate tissues and organs, the needs of the true end-users-physicians and patients-must dictate the key design criteria. Herein I describe the development of one such material that meets these requirements: a covalently crosslinked, biodegradable, simplified mimic of the extracellular matrix (ECM) that permits 3-D culture of cells in vitro and enables tissue formation in vivo. In contrast to materials that were designed for in vitro cell culture and then found unsuitable for clinical use, these semi-synthetic hyaluronan-derived materials were developed for in vivo tissue repair, and are now being re-engineered for in vitro applications in research.

Updated Lagrangian finite element formulations of various biological soft tissue non-linear material models: a comprehensive procedure and review.

PubMed

Townsend, Molly T; Sarigul-Klijn, Nesrin

2016-01-01

Simplified material models are commonly used in computational simulation of biological soft tissue as an approximation of the complicated material response and to minimize computational resources. However, the simulation of complex loadings, such as long-duration tissue swelling, necessitates complex models that are not easy to formulate. This paper strives to offer the updated Lagrangian formulation comprehensive procedure of various non-linear material models for the application of finite element analysis of biological soft tissues including a definition of the Cauchy stress and the spatial tangential stiffness. The relationships between water content, osmotic pressure, ionic concentration and the pore pressure stress of the tissue are discussed with the merits of these models and their applications.

Quantification of 18F-Fluoride Kinetics: Evaluation of Simplified Methods.

PubMed

Raijmakers, Pieter; Temmerman, Olivier P P; Saridin, Carrol P; Heyligers, Ide C; Becking, Alfred G; van Lingen, Arthur; Lammertsma, Adriaan A

2014-07-01

(18)F-fluoride PET is a promising noninvasive method for measuring bone metabolism and bone blood flow. The purpose of this study was to assess the performance of various clinically useful simplified methods by comparing them with full kinetic analysis. In addition, the validity of deriving bone blood flow from K1 of (18)F-fluoride was investigated using (15)O-H2O as a reference. Twenty-two adults (mean age ± SD, 44.8 ± 25.2 y), including 16 patients scheduled for bone surgery and 6 healthy volunteers, were studied. All patients underwent dynamic (15)O-H2O and (18)F-fluoride scans before surgery. Ten of these patients had serial PET measurements before and at 2 time points after local bone surgery. During all PET scans, arterial blood was monitored continuously. (18)F-fluoride data were analyzed using nonlinear regression (NLR) and several simplified methods (Patlak and standardized uptake value [SUV]). SUV was evaluated for different time intervals after injection and after normalizing to body weight, lean body mass, and body surface area, and simplified measurements were compared with NLR results. In addition, changes in SUV and Patlak-derived fluoride influx rate (Ki) after surgery were compared with corresponding changes in NLR-derived Ki. Finally, (18)F-fluoride K1 was compared with bone blood flow derived from (15)O-H2O data, using the standard single-tissue-compartment model. K1 of (18)F-fluoride correlated with measured blood flow, but the correlation coefficient was relatively low (r = 0.35, P < 0.001). NLR resulted in a mean Ki of 0.0160 ± 0.0122, whereas Patlak analysis, for the interval 10-60 min after injection, resulted in an almost-identical mean Ki of 0.0161 ± 0.0117. The Patlak-derived Ki, for 10-60 min after injection, showed a high correlation with the NLR-derived Ki (r = 0.976). The highest correlation between Ki and lean body mass-normalized SUV was found for the interval 50-60 min (r = 0.958). Finally, changes in SUV correlated significantly with those in Ki (r = 0.97). The present data support the use of both Patlak and SUV for assessing fluoride kinetics in humans. However, (18)F-fluoride PET has only limited accuracy in monitoring bone blood flow. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Blood flow mechanics and oxygen transport and delivery in the retinal microcirculation: multiscale mathematical modeling and numerical simulation.

PubMed

Causin, Paola; Guidoboni, Giovanna; Malgaroli, Francesca; Sacco, Riccardo; Harris, Alon

2016-06-01

The scientific community continues to accrue evidence that blood flow alterations and ischemic conditions in the retina play an important role in the pathogenesis of ocular diseases. Many factors influence retinal hemodynamics and tissue oxygenation, including blood pressure, blood rheology, oxygen arterial permeability and tissue metabolic demand. Since the influence of these factors on the retinal circulation is difficult to isolate in vivo, we propose here a novel mathematical and computational model describing the coupling between blood flow mechanics and oxygen ([Formula: see text]) transport in the retina. Albeit in a simplified manner, the model accounts for the three-dimensional anatomical structure of the retina, consisting in a layered tissue nourished by an arteriolar/venular network laying on the surface proximal to the vitreous. Capillary plexi, originating from terminal arterioles and converging into smaller venules, are embedded in two distinct tissue layers. Arteriolar and venular networks are represented by fractal trees, whereas capillary plexi are represented using a simplified lumped description. In the model, [Formula: see text] is transported along the vasculature and delivered to the tissue at a rate that depends on the metabolic demand of the various tissue layers. First, the model is validated against available experimental results to identify baseline conditions. Then, a sensitivity analysis is performed to quantify the influence of blood pressure, blood rheology, oxygen arterial permeability and tissue oxygen demand on the [Formula: see text] distribution within the blood vessels and in the tissue. This analysis shows that: (1) systemic arterial blood pressure has a strong influence on the [Formula: see text] profiles in both blood and tissue; (2) plasma viscosity and metabolic consumption rates have a strong influence on the [Formula: see text] tension at the level of the retinal ganglion cells; and (3) arterial [Formula: see text] permeability has a strong influence on the [Formula: see text] saturation in the retinal arterioles.

Note: Improved calibration of atomic force microscope cantilevers using multiple reference cantilevers.

PubMed

Sader, John E; Friend, James R

2015-05-01

Overall precision of the simplified calibration method in J. E. Sader et al., Rev. Sci. Instrum. 83, 103705 (2012), Sec. III D, is dominated by the spring constant of the reference cantilever. The question arises: How does one take measurements from multiple reference cantilevers, and combine these results, to improve uncertainty of the reference cantilever's spring constant and hence the overall precision of the method? This question is addressed in this note. Its answer enables manufacturers to specify of a single set of data for the spring constant, resonant frequency, and quality factor, from measurements on multiple reference cantilevers. With this data set, users can trivially calibrate cantilevers of the same type.

Comparative plasma and tissue distribution of Sun Pharma's generic doxorubicin HCl liposome injection versus Caelyx® (doxorubicin HCl liposome injection) in syngeneic fibrosarcoma-bearing BALB/c mice and Sprague-Dawley rats.

PubMed

Burade, Vinod; Bhowmick, Subhas; Maiti, Kuntal; Zalawadia, Rishit; Jain, Deepak; Rajamannar, Thennati

2017-05-01

The liposomal formulation of doxorubicin [doxorubicin (DXR) hydrochloride (HCl) liposome injection, Caelyx ® ] alters the tissue distribution of DXR as compared with nonliposomal DXR, resulting in an improved benefit-risk profile. We conducted studies in murine models to compare the plasma and tissue distribution of a proposed generic DXR HCl liposome injection developed by Sun Pharmaceuticals Industries Limited (SPIL DXR HCl liposome injection) with Caelyx ® . The plasma and tissue distributions of the SPIL and reference DXR HCl liposome injections were compared in syngeneic fibrosarcoma-bearing BALB/c mice and Sprague-Dawley rats. Different batches and different lots of the same batch of the reference product were also compared with each other. The SPIL and reference DXR HCl liposome injections exhibited generally comparable plasma and tissue distribution profiles in both models. While minor differences were observed between the two products in some tissues, different batches and lots of the reference product also showed some differences in the distribution of various analytes in some tissues. The ratios of estimated free to encapsulated DXR for plasma and tissue were generally comparable between the SPIL and reference DXR HCl liposome injections in both models, indicating similar extents of absorption into the tissues and similar rates of drug release from liposomes. The plasma and tissue distribution profiles of the SPIL and reference DXR HCl liposome injections were shown to be generally comparable. Inconsistencies between the products observed in some tissues were thought to be due to biological variation.

The Application of a Massively Parallel Computer to the Simulation of Electrical Wave Propagation Phenomena in the Heart Muscle Using Simplified Models

NASA Technical Reports Server (NTRS)

Karpoukhin, Mikhii G.; Kogan, Boris Y.; Karplus, Walter J.

1995-01-01

The simulation of heart arrhythmia and fibrillation are very important and challenging tasks. The solution of these problems using sophisticated mathematical models is beyond the capabilities of modern super computers. To overcome these difficulties it is proposed to break the whole simulation problem into two tightly coupled stages: generation of the action potential using sophisticated models. and propagation of the action potential using simplified models. The well known simplified models are compared and modified to bring the rate of depolarization and action potential duration restitution closer to reality. The modified method of lines is used to parallelize the computational process. The conditions for the appearance of 2D spiral waves after the application of a premature beat and the subsequent traveling of the spiral wave inside the simulated tissue are studied.

A Simplified Technique for Implant-Abutment Level Impression after Soft Tissue Adaptation around Provisional Restoration

PubMed Central

Kutkut, Ahmad; Abu-Hammad, Osama; Frazer, Robert

2016-01-01

Impression techniques for implant restorations can be implant level or abutment level impressions with open tray or closed tray techniques. Conventional implant-abutment level impression techniques are predictable for maximizing esthetic outcomes. Restoration of the implant traditionally requires the use of the metal or plastic impression copings, analogs, and laboratory components. Simplifying the dental implant restoration by reducing armamentarium through incorporating conventional techniques used daily for crowns and bridges will allow more general dentists to restore implants in their practices. The demonstrated technique is useful when modifications to implant abutments are required to correct the angulation of malpositioned implants. This technique utilizes conventional crown and bridge impression techniques. As an added benefit, it reduces costs by utilizing techniques used daily for crowns and bridges. The aim of this report is to describe a simplified conventional impression technique for custom abutments and modified prefabricated solid abutments for definitive restorations. PMID:29563457

Time-dependent diffusion MRI in cancer: tissue modeling and applications

NASA Astrophysics Data System (ADS)

Reynaud, Olivier

2017-11-01

In diffusion weighted imaging (DWI), the apparent diffusion coefficient has been recognized as a useful and sensitive surrogate for cell density, paving the way for non-invasive tumor staging, and characterization of treatment efficacy in cancer. However, microstructural parameters, such as cell size, density and/or compartmental diffusivities affect diffusion in various fashions, making of conventional DWI a sensitive but non-specific probe into changes happening at cellular level. Alternatively, tissue complexity can be probed and quantified using the time dependence of diffusion metrics, sometimes also referred to as temporal diffusion spectroscopy when only using oscillating diffusion gradients. Time-dependent diffusion (TDD) is emerging as a strong candidate for specific and non-invasive tumor characterization. Despite the lack of a general analytical solution for all diffusion times / frequencies, TDD can be probed in various regimes where systems simplify in order to extract relevant information about tissue microstructure. The fundamentals of TDD are first reviewed (a) in the short time regime, disentangling structural and diffusive tissue properties, and (b) near the tortuosity limit, assuming weakly heterogeneous media near infinitely long diffusion times. Focusing on cell bodies (as opposed to neuronal tracts), a simple but realistic model for intracellular diffusion can offer precious insight on diffusion inside biological systems, at all times. Based on this approach, the main three geometrical models implemented so far (IMPULSED, POMACE, VERDICT) are reviewed. Their suitability to quantify cell size, intra- and extracellular spaces (ICS and ECS) and diffusivities are assessed. The proper modeling of tissue membrane permeability – hardly a newcomer in the field, but lacking applications - and its impact on microstructural estimates are also considered. After discussing general issues with tissue modeling and microstructural parameter estimation (i.e. fitting), potential solutions are detailed. The in vivo applications of this new, non-invasive, specific approach in cancer are reviewed, ranging from the characterization of gliomas in rodent brains and observation of time-dependence in breast tissue lesions and prostate cancer, to the recent preclinical evaluation of new treatments efficacy. It is expected that clinical applications of TDD will strongly benefit the community in terms of non-invasive cancer screening.

Light propagation from fluorescent probes in biological tissues by coupled time-dependent parabolic simplified spherical harmonics equations

PubMed Central

Domínguez, Jorge Bouza; Bérubé-Lauzière, Yves

2011-01-01

We introduce a system of coupled time-dependent parabolic simplified spherical harmonic equations to model the propagation of both excitation and fluorescence light in biological tissues. We resort to a finite element approach to obtain the time-dependent profile of the excitation and the fluorescence light fields in the medium. We present results for cases involving two geometries in three-dimensions: a homogeneous cylinder with an embedded fluorescent inclusion and a realistically-shaped rodent with an embedded inclusion alike an organ filled with a fluorescent probe. For the cylindrical geometry, we show the differences in the time-dependent fluorescence response for a point-like, a spherical, and a spherically Gaussian distributed fluorescent inclusion. From our results, we conclude that the model is able to describe the time-dependent excitation and fluorescent light transfer in small geometries with high absorption coefficients and in nondiffusive domains, as may be found in small animal diffuse optical tomography (DOT) and fluorescence DOT imaging. PMID:21483606

Adhesive sealing of dentin surfaces in vitro: A review

PubMed Central

Abu-Nawareg, Manar M; Zidan, Ahmed Z; Zhou, Jianfeng; Agee, Kelli; Chiba, Ayaka; Tagami, Jungi; Pashley, David H

2016-01-01

Purpose The purpose of this review is to describe the evolution of the use of dental adhesives to form a tight seal of freshly prepared dentin to protect the pulp from bacterial products, during the time between crown preparation and final cementum of full crowns. The evolution of these “immediate dentin sealants” follows the evolution of dental adhesives, in general. That is, they began with multiple-step, etch-and-rinse adhesives, and then switched to the use of simplified adhesives. Methods Literature was reviewed for evidence that bacteria or bacterial products diffusing across dentin can irritate pulpal tissues before and after smear layer removal. Smear layers can be solubilized by plaque organisms within 7–10 days if they are directly exposed to oral fluids. It is likely that smear layers covered by temporary restorations may last more than one month. As long as smear layers remain in place, they can partially seal dentin. Thus, many in vitro studies evaluating the sealing ability of adhesive resins use smear layer-covered dentin as a reference condition. Surprisingly, many adhesives do not seal dentin as well as do smear layers. Results Both in vitro and in vivo studies show that resin-covered dentin allows dentinal fluid to cross polymerized resins. The use of simplified single bottle adhesives to seal dentin was a step backwards. Currently, most authorities use either 3-step adhesives such as Scotchbond Multi-Purposea or OptiBond FLb or two-step self-etching primer adhesives, such as Clearfil SEc, Unifil Bondd or AdheSEe, respectfully. PMID:26846037

Simplifying the Ambiguous Law, Keeping Everyone Reliably Safe Act of 2010

THOMAS, 111th Congress

Rep. Sanchez, Loretta [D-CA-47

2010-07-01

Senate - 07/28/2010 Received in the Senate and Read twice and referred to the Committee on the Judiciary. (All Actions) Tracker: This bill has the status Passed HouseHere are the steps for Status of Legislation:

Energy deposition at the bone-tissue interface from nuclear fragments produced by high-energy nucleons

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Hajnal, Ferenc; Wilson, John W.

1990-01-01

The transport of nuclear fragmentation recoils produced by high-energy nucleons in the region of the bone-tissue interface is considered. Results for the different flux and absorbed dose for recoils produced by 1 GeV protons are presented in a bidirectional transport model. The energy deposition in marrow cavities is seen to be enhanced by recoils produced in bone. Approximate analytic formulae for absorbed dose near the interface region are also presented for a simplified range-energy model.

Mammalian Cell Culture Simplified.

ERIC Educational Resources Information Center

Moss, Robert; Solomon, Sondra

1991-01-01

A tissue culture experiment that does not require elaborate equipment and that can be used to teach sterile technique, the principles of animal cell line maintenance, and the concept of cell growth curves is described. The differences between cancerous and normal cells can be highlighted. The procedure is included. (KR)

Patterns of control of maximum metabolic rate in humans.

PubMed

Hochachka, Peter W; Beatty, Cheryl L

2003-09-01

In this analysis, four performance phenotypes were used to compare mechanisms of control of aerobic maximum metabolic rate (MMR): (i) untrained sedentary (US) subjects, as a reference group against which to compare (ii) power trained (PT), (iii) endurance trained (ET) and (iv) high altitude adapted native (HA) subject groups. Sprinters represented the PT group; long distance runners illustrated the ET group; and Quechuas represented the HA group. Numerous recent studies have identified contributors to control on both the adenosine triphosphate (ATP) supply side and the ATP demand side of ATP turnover. Control coefficients or c(i) values were defined as fractional change in MMR/fractional change in the capacity of any given step in ATP turnover. From the best available evidence it appears that at MMR all five of the major steps in energy delivery (namely, ventilation, pulmonary diffusion, cardiac output, tissue capillary - mitochondrial O(2) transfer, and aerobic cell metabolism per se) approach an upper functional ceiling, with control strength being distributed amongst the various O(2) flux steps. On the energy demand side, the situation is somewhat simplified since at MMR approximately 90% of O(2)-based ATP synthesis is used for actomyosin (AM) and Ca(2+) ATPases; at MMR these two ATP demand rates also appear to be near an upper functional ceiling. In consequence, at MMR the control contributions or c(i) values are rather evenly divided amongst all seven major steps in ATP supply and ATP demand pathways right to the point of fatigue. Relative to US (the reference group), in PT subjects at MMR control strength shifts towards O(2) delivery steps (ventilation, pulmonary diffusion and cardiac output). In contrast in ET and HA subjects at MMR control shifts towards the energy demand steps (AM and Ca(2+) ATPases), and more control strength is focussed on tissue level ATP supply and ATP demand. One obvious advantage of the ET and HA control pattern is improved metabolite homeostasis. Another possibility is that, with some reserve capacity in the O(2) delivery steps and control focussed on ATP turnover at the tissue level, nature has designed the ideal 'endurance machine'.

Control of maximum metabolic rate in humans: dependence on performance phenotypes.

PubMed

Hochachka, Peter W; Burelle, Yan

2004-01-01

Borrowing from metabolic control analysis the concept of control coefficients or ci values, defined as fractional change in MMR/fractional change in the capacity of any given step in ATP turnover, we used four performance phenotypes to compare mechanisms of control of aerobic maximum metabolic rate (MMR): (i) untrained sedentary (US) subjects, as a reference group against which to compare (ii) power trained (PT), (iii) endurance trained (ET), and (iv) high altitude adapted native (HA) subject groups. Sprinters represented the PT group; long distance runners illustrated the ET group; and Andean natives represented the HA group. Numerous recent studies have identified contributors to control on both the adenosine triphosphate (ATP) supply side and the ATP demand side of ATP turnover. From the best available evidence it appears that at MMR all five of the major steps in energy delivery (namely, ventilation, pulmonary diffusion, cardiac output, tissue capillary--mitochondrial O2 transfer, and aerobic cell metabolism per se) approach an upper functional ceiling, with control strength being distributed amongst the various O2 flux steps. On the energy demand side, the situation is somewhat simplified since at MMR approximately 90% of O2-based ATP synthesis is used for actomyosin (AM) and Ca2+ ATPases; at MMR these two ATP demand rates also appear to be near an upper functional ceiling. In consequence, at MMR the control contributions or ci values are distributed amongst all seven major steps in ATP supply and ATP demand pathways right to the point of fatigue. Relative to US (the reference group), in PT subjects at MMR control strength shifts towards O2 delivery steps (ventilation, pulmonary diffusion, and cardiac output); here physiological regulation clearly dominates MMR control. In contrast in ET and HA subjects at MMR control shifts towards the energy demand steps (AM and Ca2+ ATPases), and more control strength is focussed on tissue level ATP supply and ATP demand. One obvious advantage of the ET and HA biochemical-level control is improved metabolite homeostasis. Additionally, with some reserve capacity in the O2 delivery steps, the focussing of control on ATP turnover at the tissue level has allowed nature to improve on an 'endurance machine' design.

Three Microstructural Exercises for Students.

ERIC Educational Resources Information Center

Means, Winthrop D.

1986-01-01

Describes laboratory exercises which demonstrate a new simplified technique for deforming thin samples of crystalline materials on the stage of a petrographic microscope. Discusses how this process allows students to see the development of microstructures resulting from cracking, slipping, thinning, and recrystallization. References and sources of…

Generalized paired-agent kinetic model for in vivo quantification of cancer cell-surface receptors under receptor saturation conditions

NASA Astrophysics Data System (ADS)

Sadeghipour, N.; Davis, S. C.; Tichauer, K. M.

2017-01-01

New precision medicine drugs oftentimes act through binding to specific cell-surface cancer receptors, and thus their efficacy is highly dependent on the availability of those receptors and the receptor concentration per cell. Paired-agent molecular imaging can provide quantitative information on receptor status in vivo, especially in tumor tissue; however, to date, published approaches to paired-agent quantitative imaging require that only ‘trace’ levels of imaging agent exist compared to receptor concentration. This strict requirement may limit applicability, particularly in drug binding studies, which seek to report on a biological effect in response to saturating receptors with a drug moiety. To extend the regime over which paired-agent imaging may be used, this work presents a generalized simplified reference tissue model (GSRTM) for paired-agent imaging developed to approximate receptor concentration in both non-receptor-saturated and receptor-saturated conditions. Extensive simulation studies show that tumor receptor concentration estimates recovered using the GSRTM are more accurate in receptor-saturation conditions than the standard simple reference tissue model (SRTM) (% error (mean  ±  sd): GSRTM 0  ±  1 and SRTM 50  ±  1) and match the SRTM accuracy in non-saturated conditions (% error (mean  ±  sd): GSRTM 5  ±  5 and SRTM 0  ±  5). To further test the approach, GSRTM-estimated receptor concentration was compared to SRTM-estimated values extracted from tumor xenograft in vivo mouse model data. The GSRTM estimates were observed to deviate from the SRTM in tumors with low receptor saturation (which are likely in a saturated regime). Finally, a general ‘rule-of-thumb’ algorithm is presented to estimate the expected level of receptor saturation that would be achieved in a given tissue provided dose and pharmacokinetic information about the drug or imaging agent being used, and physiological information about the tissue. These studies suggest that the GSRTM is necessary when receptor saturation exceeds 20% and highlight the potential for GSRTM to accurately measure receptor concentrations under saturation conditions, such as might be required during high dose drug studies, or for imaging applications where high concentrations of imaging agent are required to optimize signal-to-noise conditions. This model can also be applied to PET and SPECT imaging studies that tend to suffer from noisier data, but require one less parameter to fit if images are converted to imaging agent concentration (quantitative PET/SPECT).

Feasibility of implementation of a "simplified, No-X-Ray, no-lead apron, two-catheter approach" for ablation of supraventricular arrhythmias in children and adults.

PubMed

Stec, Sebastian; Śledź, Janusz; Mazij, Mariusz; Raś, Małgorzata; Ludwik, Bartosz; Chrabąszcz, Michał; Śledź, Arkadiusz; Banasik, Małgorzata; Bzymek, Magdalena; Młynarczyk, Krzysztof; Deutsch, Karol; Labus, Michał; Śpikowski, Jerzy; Szydłowski, Lesław

2014-08-01

Although the "near-zero-X-Ray" or "No-X-Ray" catheter ablation (CA) approach has been reported for treatment of various arrhythmias, few prospective studies have strictly used "No-X-Ray," simplified 2-catheter approaches for CA in patients with supraventricular tachycardia (SVT). We assessed the feasibility of a minimally invasive, nonfluoroscopic (MINI) CA approach in such patients. Data were obtained from a prospective multicenter CA registry of patients with regular SVTs. After femoral access, 2 catheters were used to create simple, 3D electroanatomic maps and to perform electrophysiologic studies. Medical staff did not use lead aprons after the first 10 MINI CA cases. A total of 188 patients (age, 45 ± 21 years; 17% <19 years; 55% women) referred for the No-X-Ray approach were included. They were compared to 714 consecutive patients referred for a simplified approach using X-rays (age, 52 ± 18 years; 7% <19 years; 55% women). There were 9 protocol exceptions that necessitated the use of X-rays. Ultimately, 179/188 patients underwent the procedure without fluoroscopy, with an acute success rate of 98%. The procedure times (63 ± 26 vs. 63 ± 29 minutes, P > 0.05), major complications (0% vs. 0%, P > 0.05) and acute (98% vs. 98%, P > 0.05) and long-term (93% vs. 94%, P > 0.05) success rates were similar in the "No-X-Ray" and control groups. Implementation of a strict "No-X-Ray, simplified 2-catheter" CA approach is safe and effective in majority of the patients with SVT. This modified approach for SVTs should be prospectively validated in a multicenter study. © 2014 Wiley Periodicals, Inc.

Reference-tissue correction of T2-weighted signal intensity for prostate cancer detection

NASA Astrophysics Data System (ADS)

Peng, Yahui; Jiang, Yulei; Oto, Aytekin

2014-03-01

The purpose of this study was to investigate whether correction with respect to reference tissue of T2-weighted MRimage signal intensity (SI) improves its effectiveness for classification of regions of interest (ROIs) as prostate cancer (PCa) or normal prostatic tissue. Two image datasets collected retrospectively were used in this study: 71 cases acquired with GE scanners (dataset A), and 59 cases acquired with Philips scanners (dataset B). Through a consensus histology- MR correlation review, 175 PCa and 108 normal-tissue ROIs were identified and drawn manually. Reference-tissue ROIs were selected in each case from the levator ani muscle, urinary bladder, and pubic bone. T2-weighted image SI was corrected as the ratio of the average T2-weighted image SI within an ROI to that of a reference-tissue ROI. Area under the receiver operating characteristic curve (AUC) was used to evaluate the effectiveness of T2-weighted image SIs for differentiation of PCa from normal-tissue ROIs. AUC (+/- standard error) for uncorrected T2-weighted image SIs was 0.78+/-0.04 (datasets A) and 0.65+/-0.05 (datasets B). AUC for corrected T2-weighted image SIs with respect to muscle, bladder, and bone reference was 0.77+/-0.04 (p=1.0), 0.77+/-0.04 (p=1.0), and 0.75+/-0.04 (p=0.8), respectively, for dataset A; and 0.81+/-0.04 (p=0.002), 0.78+/-0.04 (p<0.001), and 0.79+/-0.04 (p<0.001), respectively, for dataset B. Correction in reference to the levator ani muscle yielded the most consistent results between GE and Phillips images. Correction of T2-weighted image SI in reference to three types of extra-prostatic tissue can improve its effectiveness for differentiation of PCa from normal-tissue ROIs, and correction in reference to the levator ani muscle produces consistent T2-weighted image SIs between GE and Phillips MR images.

Simplified Model and Response Analysis for Crankshaft of Air Compressor

NASA Astrophysics Data System (ADS)

Chao-bo, Li; Jing-jun, Lou; Zhen-hai, Zhang

2017-11-01

The original model of crankshaft is simplified to the appropriateness to balance the calculation precision and calculation speed, and then the finite element method is used to analyse the vibration response of the structure. In order to study the simplification and stress concentration for crankshaft of air compressor, this paper compares calculative mode frequency and experimental mode frequency of the air compressor crankshaft before and after the simplification, the vibration response of reference point constraint conditions is calculated by using the simplified model, and the stress distribution of the original model is calculated. The results show that the error between calculative mode frequency and experimental mode frequency is controlled in less than 7%, the constraint will change the model density of the system, the position between the crank arm and the shaft appeared stress concentration, so the part of the crankshaft should be treated in the process of manufacture.

Characterization of [11C]Lu AE92686 as a PET radioligand for phosphodiesterase 10A in the nonhuman primate brain.

PubMed

Yang, Kai-Chun; Stepanov, Vladimir; Amini, Nahid; Martinsson, Stefan; Takano, Akihiro; Nielsen, Jacob; Bundgaard, Christoffer; Bang-Andersen, Benny; Grimwood, Sarah; Halldin, Christer; Farde, Lars; Finnema, Sjoerd J

2017-02-01

[ 11 C]Lu AE92686 is a positron emission tomography (PET) radioligand that has recently been validated for examining phosphodiesterase 10A (PDE10A) in the human striatum. [ 11 C]Lu AE92686 has high affinity for PDE10A (IC 50  = 0.39 nM) and may also be suitable for examination of the substantia nigra, a region with low density of PDE10A. Here, we report characterization of regional [ 11 C]Lu AE92686 binding to PDE10A in the nonhuman primate (NHP) brain. A total of 11 PET measurements, seven baseline and four following pretreatment with unlabeled Lu AE92686 or the structurally unrelated PDE10A inhibitor MP-10, were performed in five NHPs using a high resolution research tomograph (HRRT). [ 11 C]Lu AE92686 binding was quantified using a radiometabolite-corrected arterial input function and compartmental and graphical modeling approaches. Regional time-activity curves were best described with the two-tissue compartment model (2TCM). However, the distribution volume (V T ) values for all regions were obtained by the Logan plot analysis, as reliable cerebellar V T values could not be derived by the 2TCM. For cerebellum, a proposed reference region, V T values increased by ∼30 % with increasing PET measurement duration from 63 to 123 min, while V T values in target regions remained stable. Both pretreatment drugs significantly decreased [ 11 C]Lu AE92686 binding in target regions, while no significant effect on cerebellum was observed. Binding potential (BP ND ) values, derived with the simplified reference tissue model (SRTM), were 13-17 in putamen and 3-5 in substantia nigra and correlated well to values from the Logan plot analysis. The method proposed for quantification of [ 11 C]Lu AE92686 binding in applied studies in NHP is based on 63 min PET data and SRTM with cerebellum as a reference region. The study supports that [ 11 C]Lu AE92686 can be used for PET examinations of PDE10A binding also in substantia nigra.

Note: Improved calibration of atomic force microscope cantilevers using multiple reference cantilevers

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

Sader, John E., E-mail: jsader@unimelb.edu.au; Friend, James R.

2015-05-15

Overall precision of the simplified calibration method in J. E. Sader et al., Rev. Sci. Instrum. 83, 103705 (2012), Sec. III D, is dominated by the spring constant of the reference cantilever. The question arises: How does one take measurements from multiple reference cantilevers, and combine these results, to improve uncertainty of the reference cantilever’s spring constant and hence the overall precision of the method? This question is addressed in this note. Its answer enables manufacturers to specify of a single set of data for the spring constant, resonant frequency, and quality factor, from measurements on multiple reference cantilevers. Withmore » this data set, users can trivially calibrate cantilevers of the same type.« less

A lapping apparatus for hard tissue sections.

PubMed

Malcolm, A S

1975-02-01

A Lapping Apparatus is described which enables sections both embedded and unembedded to be ground plano parallel within +/- 1 micron. Sections cemented to steel subplates are retained by a magnetic holder which simplifies loading and unloading. Good surface and edge finish can be obtained and only short lapping times are required.

RILS: What are they, what are they good for, and do we have any?

USDA-ARS?s Scientific Manuscript database

RILs, or recombinant inbred lines, are a set of genetically related individuals that can simplify the gene discovery process. They are constructed using regular breeding processes rather than using tissue culture or other advanced biotechnology. Operationally, a hybrid is made, and this hybrid is se...

Automatic estimation of elasticity parameters in breast tissue

NASA Astrophysics Data System (ADS)

Skerl, Katrin; Cochran, Sandy; Evans, Andrew

2014-03-01

Shear wave elastography (SWE), a novel ultrasound imaging technique, can provide unique information about cancerous tissue. To estimate elasticity parameters, a region of interest (ROI) is manually positioned over the stiffest part of the shear wave image (SWI). The aim of this work is to estimate the elasticity parameters i.e. mean elasticity, maximal elasticity and standard deviation, fully automatically. Ultrasonic SWI of a breast elastography phantom and breast tissue in vivo were acquired using the Aixplorer system (SuperSonic Imagine, Aix-en-Provence, France). First, the SWI within the ultrasonic B-mode image was detected using MATLAB then the elasticity values were extracted. The ROI was automatically positioned over the stiffest part of the SWI and the elasticity parameters were calculated. Finally all values were saved in a spreadsheet which also contains the patient's study ID. This spreadsheet is easily available for physicians and clinical staff for further evaluation and so increase efficiency. Therewith the efficiency is increased. This algorithm simplifies the handling, especially for the performance and evaluation of clinical trials. The SWE processing method allows physicians easy access to the elasticity parameters of the examinations from their own and other institutions. This reduces clinical time and effort and simplifies evaluation of data in clinical trials. Furthermore, reproducibility will be improved.

Identification of reference genes and validation for gene expression studies in diverse axolotl (Ambystoma mexicanum) tissues.

PubMed

Guelke, Eileen; Bucan, Vesna; Liebsch, Christina; Lazaridis, Andrea; Radtke, Christine; Vogt, Peter M; Reimers, Kerstin

2015-04-10

For the precise quantitative RT-PCR normalization a set of valid reference genes is obligatory. Moreover have to be taken into concern the experimental conditions as they bias the regulation of reference genes. Up till now, no reference targets have been described for the axolotl (Ambystoma mexicanum). In a search in the public database SalSite for genetic information of the axolotl we identified fourteen presumptive reference genes, eleven of which were further tested for their gene expression stability. This study characterizes the expressional patterns of 11 putative endogenous control genes during axolotl limb regeneration and in an axolotl tissue panel. All 11 reference genes showed variable expression. Strikingly, ACTB was to be found most stable expressed in all comparative tissue groups, so we reason it to be suitable for all different kinds of axolotl tissue-type investigations. Moreover do we suggest GAPDH and RPLP0 as suitable for certain axolotl tissue analysis. When it comes to axolotl limb regeneration, a validated pair of reference genes is ODC and RPLP0. With these findings, new insights into axolotl gene expression profiling might be gained. Copyright © 2015 Elsevier B.V. All rights reserved.

Magneto-acousto-electrical Measurement Based Electrical Conductivity Reconstruction for Tissues.

PubMed

Zhou, Yan; Ma, Qingyu; Guo, Gepu; Tu, Juan; Zhang, Dong

2018-05-01

Based on the interaction of ultrasonic excitation and magnetoelectrical induction, magneto-acousto-electrical (MAE) technology was demonstrated to have the capability of differentiating conductivity variations along the acoustic transmission. By applying the characteristics of the MAE voltage, a simplified algorithm of MAE measurement based conductivity reconstruction was developed. With the analyses of acoustic vibration, ultrasound propagation, Hall effect, and magnetoelectrical induction, theoretical and experimental studies of MAE measurement and conductivity reconstruction were performed. The formula of MAE voltage was derived and simplified for the transducer with strong directivity. MAE voltage was simulated for a three-layer gel phantom and the conductivity distribution was reconstructed using the modified Wiener inverse filter and Hilbert transform, which was also verified by experimental measurements. The experimental results are basically consistent with the simulations, and demonstrate that the wave packets of MAE voltage are generated at tissue interfaces with the amplitudes and vibration polarities representing the values and directions of conductivity variations. With the proposed algorithm, the amplitude and polarity of conductivity gradient can be restored and the conductivity distribution can also be reconstructed accurately. The favorable results demonstrate the feasibility of accurate conductivity reconstruction with improved spatial resolution using MAE measurement for tissues with conductivity variations, especially suitable for nondispersive tissues with abrupt conductivity changes. This study demonstrates that the MAE measurement based conductivity reconstruction algorithm can be applied as a new strategy for nondestructive real-time monitoring of conductivity variations in biomedical engineering.

Chemical Probes for Visualizing Intact Animal and Human Brain Tissue.

PubMed

Lai, Hei Ming; Ng, Wai-Lung; Gentleman, Steve M; Wu, Wutian

2017-06-22

Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain. Copyright © 2017 Elsevier Ltd. All rights reserved.

Steady State Fluorescence Spectroscopy for Medical Diagnosis

NASA Astrophysics Data System (ADS)

Mahadevan-Jansen, Anita; Gebhart, Steven C.

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

Teaching Differential Diagnosis by Computer: A Pathophysiological Approach

ERIC Educational Resources Information Center

Goroll, Allan H.; And Others

1977-01-01

An interactive, computer-based teaching exercise in diagnosis that emphasizes pathophysiology in the analysis of clinical data is described. Called the Jaundice Program, its objective is to simplify the pattern recognition problem by relating clinical findings to diagnosis via reference to disease mechanisms. (LBH)

Further Studies of the Response of Single Rotor Helicopters to Vortex Encounters

DOT National Transportation Integrated Search

1985-09-01

This report is a continuation of the studies described in Reference where a simplified approach to the problem of predicting the uncontrolled response of a single rotor helicopter to an encounter with the wing tip vortex of a large transport aircraft...

Spatial accuracy of a simplified disaggregation method for traffic emissions applied in seven mid-sized Chilean cities

NASA Astrophysics Data System (ADS)

Ossés de Eicker, Margarita; Zah, Rainer; Triviño, Rubén; Hurni, Hans

The spatial accuracy of top-down traffic emission inventory maps obtained with a simplified disaggregation method based on street density was assessed in seven mid-sized Chilean cities. Each top-down emission inventory map was compared against a reference, namely a more accurate bottom-up emission inventory map from the same study area. The comparison was carried out using a combination of numerical indicators and visual interpretation. Statistically significant differences were found between the seven cities with regard to the spatial accuracy of their top-down emission inventory maps. In compact cities with a simple street network and a single center, a good accuracy of the spatial distribution of emissions was achieved with correlation values>0.8 with respect to the bottom-up emission inventory of reference. In contrast, the simplified disaggregation method is not suitable for complex cities consisting of interconnected nuclei, resulting in correlation values<0.5. Although top-down disaggregation of traffic emissions generally exhibits low accuracy, the accuracy is significantly higher in compact cities and might be further improved by applying a correction factor for the city center. Therefore, the method can be used by local environmental authorities in cities with limited resources and with little knowledge on the pollution situation to get an overview on the spatial distribution of the emissions generated by traffic activities.

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

PubMed

Grayson, Phil; Sin, Simon Y W; Sackton, Timothy B; Edwards, Scott V

2017-01-01

Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

Growth patterns for shape-shifting elastic bilayers.

PubMed

van Rees, Wim M; Vouga, Etienne; Mahadevan, L

2017-10-31

Inspired by the differential-growth-driven morphogenesis of leaves, flowers, and other tissues, there is increasing interest in artificial analogs of these shape-shifting thin sheets made of active materials that respond to environmental stimuli such as heat, light, and humidity. But how can we determine the growth patterns to achieve a given shape from another shape? We solve this geometric inverse problem of determining the growth factors and directions (the metric tensors) for a given isotropic elastic bilayer to grow into a target shape by posing and solving an elastic energy minimization problem. A mathematical equivalence between bilayers and curved monolayers simplifies the inverse problem considerably by providing algebraic expressions for the growth metric tensors in terms of those of the final shape. This approach also allows us to prove that we can grow any target surface from any reference surface using orthotropically growing bilayers. We demonstrate this by numerically simulating the growth of a flat sheet into a face, a cylindrical sheet into a flower, and a flat sheet into a complex canyon-like structure.

Growth patterns for shape-shifting elastic bilayers

PubMed Central

van Rees, Wim M.; Vouga, Etienne; Mahadevan, L.

2017-01-01

Inspired by the differential-growth-driven morphogenesis of leaves, flowers, and other tissues, there is increasing interest in artificial analogs of these shape-shifting thin sheets made of active materials that respond to environmental stimuli such as heat, light, and humidity. But how can we determine the growth patterns to achieve a given shape from another shape? We solve this geometric inverse problem of determining the growth factors and directions (the metric tensors) for a given isotropic elastic bilayer to grow into a target shape by posing and solving an elastic energy minimization problem. A mathematical equivalence between bilayers and curved monolayers simplifies the inverse problem considerably by providing algebraic expressions for the growth metric tensors in terms of those of the final shape. This approach also allows us to prove that we can grow any target surface from any reference surface using orthotropically growing bilayers. We demonstrate this by numerically simulating the growth of a flat sheet into a face, a cylindrical sheet into a flower, and a flat sheet into a complex canyon-like structure. PMID:29078336

Reagent Precoated Targets for Rapid In-Tissue Derivatization of the Anti-Tuberculosis Drug Isoniazid Followed by MALDI Imaging Mass Spectrometry

NASA Astrophysics Data System (ADS)

Manier, M. Lisa; Reyzer, Michelle L.; Goh, Anne; Dartois, Veronique; Via, Laura E.; Barry, Clifton E.; Caprioli, Richard M.

2011-08-01

Isoniazid (INH) is an important component of front-line anti-tuberculosis therapy with good serum pharmacokinetics but unknown ability to penetrate tuberculous lesions. However, endogenous background interferences hinder our ability to directly analyze INH in tissues. Chemical derivatization has been successfully used to measure isoniazid directly from tissue samples using matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). MALDI targets were pretreated with trans-cinnamaldehyde (CA) prior to mounting tissue slices. Isoniazid present in the tissues was efficiently derivatized and the INH-CA product measured by MS/MS. Precoating of MALDI targets allows the tissues to be directly thaw-mounted and derivatized, thus simplifying the preparation. A time-course series of tissues from tuberculosis infected/INH dosed animals were assayed and the MALDI MS/MS response correlates well with the amount of INH determined to be in the tissues by high-performance liquid chromatography (HPLC)-MS/MS.

Mass Media and Socialization: A Selected Bibliography.

ERIC Educational Resources Information Center

Gordon, Thomas F.; Verna, Mary Ellen

Given the growing interest in the area of socialization and mass media, this bibliography of articles and books is intended to simplify reference to the literature and to stimulate research. Three primary sources are used: "Psychological Abstracts (1950-1972),""Sociological Abstracts (1953-1972)," and the "Cumulative Book…

A reversibly sealed, easy access, modular (SEAM) microfluidic architecture to establish in vitro tissue interfaces

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

Abhyankar, Vinay V.; Wu, Meiye; Koh, Chung -Yan

Microfluidic barrier tissue models have emerged as advanced in vitro tools to explore interactions with external stimuli such as drug candidates, pathogens, or toxins. However, the procedures required to establish and maintain these systems can be challenging to implement for end users, particularly those without significant in-house engineering expertise. Here we present a module-based approach that provides an easy-to-use workflow to establish, maintain, and analyze microscale tissue constructs. Our approach begins with a removable culture insert that is magnetically coupled, decoupled, and transferred between standalone, prefabricated microfluidic modules for simplified cell seeding, culture, and downstream analysis. The modular approach allowsmore » several options for perfusion including standard syringe pumps or integration with a self-contained gravity-fed module for simple cell maintenance. As proof of concept, we establish a culture of primary human microvascular endothelial cells (HMVEC) and report combined surface protein imaging and gene expression after controlled apical stimulation with the bacterial endotoxin lipopolysaccharide (LPS). We also demonstrate the feasibility of incorporating hydrated biomaterial interfaces into the microfluidic architecture by integrating an ultra-thin (< 1 μm), self-assembled hyaluronic acid/peptide amphiphile culture membrane with brain-specific Young’s modulus (~ 1kPa). To highlight the importance of including biomimetic interfaces into microscale models we report multi-tiered readouts from primary rat cortical cells cultured on the self-assembled membrane and compare a panel of mRNA targets with primary brain tissue signatures. As a result, we anticipate that the modular approach and simplified operational workflows presented here will enable a wide range of research groups to incorporate microfluidic barrier tissue models into their work.« less

A reversibly sealed, easy access, modular (SEAM) microfluidic architecture to establish in vitro tissue interfaces

DOE PAGES

Abhyankar, Vinay V.; Wu, Meiye; Koh, Chung -Yan; ...

2016-05-26

Microfluidic barrier tissue models have emerged as advanced in vitro tools to explore interactions with external stimuli such as drug candidates, pathogens, or toxins. However, the procedures required to establish and maintain these systems can be challenging to implement for end users, particularly those without significant in-house engineering expertise. Here we present a module-based approach that provides an easy-to-use workflow to establish, maintain, and analyze microscale tissue constructs. Our approach begins with a removable culture insert that is magnetically coupled, decoupled, and transferred between standalone, prefabricated microfluidic modules for simplified cell seeding, culture, and downstream analysis. The modular approach allowsmore » several options for perfusion including standard syringe pumps or integration with a self-contained gravity-fed module for simple cell maintenance. As proof of concept, we establish a culture of primary human microvascular endothelial cells (HMVEC) and report combined surface protein imaging and gene expression after controlled apical stimulation with the bacterial endotoxin lipopolysaccharide (LPS). We also demonstrate the feasibility of incorporating hydrated biomaterial interfaces into the microfluidic architecture by integrating an ultra-thin (< 1 μm), self-assembled hyaluronic acid/peptide amphiphile culture membrane with brain-specific Young’s modulus (~ 1kPa). To highlight the importance of including biomimetic interfaces into microscale models we report multi-tiered readouts from primary rat cortical cells cultured on the self-assembled membrane and compare a panel of mRNA targets with primary brain tissue signatures. As a result, we anticipate that the modular approach and simplified operational workflows presented here will enable a wide range of research groups to incorporate microfluidic barrier tissue models into their work.« less

Selection of reference genes for tissue/organ samples on day 3 fifth-instar larvae in silkworm, Bombyx mori.

PubMed

Wang, Genhong; Chen, Yanfei; Zhang, Xiaoying; Bai, Bingchuan; Yan, Hao; Qin, Daoyuan; Xia, Qingyou

2018-06-01

The silkworm, Bombyx mori, is one of the world's most economically important insect. Surveying variations in gene expression among multiple tissue/organ samples will provide clues for gene function assignments and will be helpful for identifying genes related to economic traits or specific cellular processes. To ensure their accuracy, commonly used gene expression quantification methods require a set of stable reference genes for data normalization. In this study, 24 candidate reference genes were assessed in 10 tissue/organ samples of day 3 fifth-instar B. mori larvae using geNorm and NormFinder. The results revealed that, using the combination of the expression of BGIBMGA003186 and BGIBMGA008209 was the optimum choice for normalizing the expression data of the B. mori tissue/organ samples. The most stable gene, BGIBMGA003186, is recommended if just one reference gene is used. Moreover, the commonly used reference gene encoding cytoplasmic actin was the least appropriate reference gene of the samples investigated. The reliability of the selected reference genes was further confirmed by evaluating the expression profiles of two cathepsin genes. Our results may be useful for future studies involving the quantification of relative gene expression levels of different tissue/organ samples in B. mori. © 2018 Wiley Periodicals, Inc.

Expediting the transition from replacement medicine to tissue engineering.

PubMed

Coury, Arthur J

2016-06-01

In this article, an expansive interpretation of "Tissue Engineering" is proposed which is in congruence with classical and recent published definitions. I further simplify the definition of tissue engineering as: "Exerting systematic control of the body's cells, matrices and fluids." As a consequence, many medical therapies not commonly considered tissue engineering are placed in this category because of their effect on the body's responses. While the progress of tissue engineering strategies is inexorable and generally positive, it has been subject to setbacks as have many important medical therapies. Medical practice is currently undergoing a transition on several fronts (academics, start-up companies, going concerns) from the era of "replacement medicine" where body parts and functions are replaced by mechanical, electrical or chemical therapies to the era of tissue engineering where health is restored by regeneration generation or limitation of the body's tissues and functions by exploiting our expanding knowledge of the body's biological processes to produce natural, healthy outcomes.

Hyperspectral microscope for in vivo imaging of microstructures and cells in tissues

DOEpatents

Demos,; Stavros, G [Livermore, CA

2011-05-17

An optical hyperspectral/multimodal imaging method and apparatus is utilized to provide high signal sensitivity for implementation of various optical imaging approaches. Such a system utilizes long working distance microscope objectives so as to enable off-axis illumination of predetermined tissue thereby allowing for excitation at any optical wavelength, simplifies design, reduces required optical elements, significantly reduces spectral noise from the optical elements and allows for fast image acquisition enabling high quality imaging in-vivo. Such a technology provides a means of detecting disease at the single cell level such as cancer, precancer, ischemic, traumatic or other type of injury, infection, or other diseases or conditions causing alterations in cells and tissue micro structures.

A simplified PBPK modeling approach for prediction of pharmacokinetics of four primarily renally excreted and CYP3A metabolized compounds during pregnancy.

PubMed

Xia, Binfeng; Heimbach, Tycho; Gollen, Rakesh; Nanavati, Charvi; He, Handan

2013-10-01

During pregnancy, a drug's pharmacokinetics may be altered and hence anticipation of potential systemic exposure changes is highly desirable. Physiologically based pharmacokinetics (PBPK) models have recently been used to influence clinical trial design or to facilitate regulatory interactions. Ideally, whole-body PBPK models can be used to predict a drug's systemic exposure in pregnant women based on major physiological changes which can impact drug clearance (i.e., in the kidney and liver) and distribution (i.e., adipose and fetoplacental unit). We described a simple and readily implementable multitissue/organ whole-body PBPK model with key pregnancy-related physiological parameters to characterize the PK of reference drugs (metformin, digoxin, midazolam, and emtricitabine) in pregnant women compared with the PK in nonpregnant or postpartum (PP) women. Physiological data related to changes in maternal body weight, tissue volume, cardiac output, renal function, blood flows, and cytochrome P450 activity were collected from the literature and incorporated into the structural PBPK model that describes HV or PP women PK data. Subsequently, the changes in exposure (area under the curve (AUC) and maximum concentration (C max)) in pregnant women were simulated. Model-simulated PK profiles were overall in agreement with observed data. The prediction fold error for C max and AUC ratio (pregnant vs. nonpregnant) was less than 1.3-fold, indicating that the pregnant PBPK model is useful. The utilization of this simplified model in drug development may aid in designing clinical studies to identify potential exposure changes in pregnant women a priori for compounds which are mainly eliminated renally or metabolized by CYP3A4.

Two-Dimensional Distributed Velocity Collision Avoidance

DTIC Science & Technology

2014-02-11

place (i.e., in the global problem space) as much as possible in an effort to simplify the process/description. Additionally, to make some of the...guide agents without collision in the vast majority of cases. NAWCWD TP 8786 31 7.0 REFERENCES 1. P. L. Franchi . “Near Misses Between

Introducing Analysis of Conflict Theory Into the Social Science Classroom.

ERIC Educational Resources Information Center

Harris, Thomas E.

The paper provides a simplified introduction to conflict theory through a series of in-class exercises. Conflict resolution, defined as negotiated settlement, can occur through three forms of communication: tacit, implicit, and explicit. Tacit communication, taking place without face-to-face or written interaction, refers to inferences made and…

Simplified Laboratory Procedures for Wastewater Examination. Second Edition.

ERIC Educational Resources Information Center

Water Pollution Control Federation, Washington, DC.

This booklet is for wastewater treatment plant operators who find it difficult to follow the detailed discussions and procedures found in "Standard Methods for the Examination of Water and Wastewater." It is intended to be used with "Standard Methods" available for reference. Included in this publication are chapters on…

Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

PubMed Central

Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

2002-01-01

Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops. PMID:12023882

Optimisation and evaluation of pre-design models for offshore wind turbines with jacket support structures and their influence on integrated load simulations

NASA Astrophysics Data System (ADS)

Schafhirt, S.; Kaufer, D.; Cheng, P. W.

2014-12-01

In recent years many advanced load simulation tools, allowing an aero-servo-hydroelastic analyses of an entire offshore wind turbine, have been developed and verified. Nowadays, even an offshore wind turbine with a complex support structure such as a jacket can be analysed. However, the computational effort rises significantly with an increasing level of details. This counts especially for offshore wind turbines with lattice support structures, since those models do naturally have a higher number of nodes and elements than simpler monopile structures. During the design process multiple load simulations are demanded to obtain an optimal solution. In the view of pre-design tasks it is crucial to apply load simulations which keep the simulation quality and the computational effort in balance. The paper will introduce a reference wind turbine model consisting of the REpower5M wind turbine and a jacket support structure with a high level of detail. In total twelve variations of this reference model are derived and presented. Main focus is to simplify the models of the support structure and the foundation. The reference model and the simplified models are simulated with the coupled simulation tool Flex5-Poseidon and analysed regarding frequencies, fatigue loads, and ultimate loads. A model has been found which reaches an adequate increase of simulation speed while holding the results in an acceptable range compared to the reference results.

Validation and quantification of [18F]altanserin binding in the rat brain using blood input and reference tissue modeling

PubMed Central

Riss, Patrick J; Hong, Young T; Williamson, David; Caprioli, Daniele; Sitnikov, Sergey; Ferrari, Valentina; Sawiak, Steve J; Baron, Jean-Claude; Dalley, Jeffrey W; Fryer, Tim D; Aigbirhio, Franklin I

2011-01-01

The 5-hydroxytryptamine type 2a (5-HT2A) selective radiotracer [18F]altanserin has been subjected to a quantitative micro-positron emission tomography study in Lister Hooded rats. Metabolite-corrected plasma input modeling was compared with reference tissue modeling using the cerebellum as reference tissue. [18F]altanserin showed sufficient brain uptake in a distribution pattern consistent with the known distribution of 5-HT2A receptors. Full binding saturation and displacement was documented, and no significant uptake of radioactive metabolites was detected in the brain. Blood input as well as reference tissue models were equally appropriate to describe the radiotracer kinetics. [18F]altanserin is suitable for quantification of 5-HT2A receptor availability in rats. PMID:21750562

Optical probe with reference fiber

DOEpatents

Da Silva, Luiz B [Danville, CA; Chase, Charles L [Dublin, CA

2006-03-14

A system for characterizing tissue includes the steps of generating an emission signal, generating a reference signal, directing the emission signal to and from the tissue, directing the reference signal in a predetermined manner relative to the emission signal, and using the reference signal to compensate the emission signal. In one embodiment compensation is provided for fluctuations in light delivery to the tip of the probe due to cable motion.

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

Frederick, P.R.

The purpose of this research was to provide a handbook on Project PETROL RAM and its ideas for enhancing the base-level fuels operations. This handbook is to serve as an introduction and reference guide to the components, characteristics, and capabilities of the proposed initiative. In preparing this handbook, available information on the structure, operations, and procedures of a typical base Fuels Management Branch was gathered, then condensed and simplified. For added depth and understanding, personal interviews with personnel involved in the design and development of this project were conducted. The research resulted in a handbook that describes, in simplified terminology,more » the different systems which are being developed under the Project PETROL RAM initiative.« less

Shielding analyses of an AB-BNCT facility using Monte Carlo simulations and simplified methods

NASA Astrophysics Data System (ADS)

Lai, Bo-Lun; Sheu, Rong-Jiun

2017-09-01

Accurate Monte Carlo simulations and simplified methods were used to investigate the shielding requirements of a hypothetical accelerator-based boron neutron capture therapy (AB-BNCT) facility that included an accelerator room and a patient treatment room. The epithermal neutron beam for BNCT purpose was generated by coupling a neutron production target with a specially designed beam shaping assembly (BSA), which was embedded in the partition wall between the two rooms. Neutrons were produced from a beryllium target bombarded by 1-mA 30-MeV protons. The MCNP6-generated surface sources around all the exterior surfaces of the BSA were established to facilitate repeated Monte Carlo shielding calculations. In addition, three simplified models based on a point-source line-of-sight approximation were developed and their predictions were compared with the reference Monte Carlo results. The comparison determined which model resulted in better dose estimation, forming the basis of future design activities for the first ABBNCT facility in Taiwan.

Simplified Calculation Model and Experimental Study of Latticed Concrete-Gypsum Composite Panels

PubMed Central

Jiang, Nan; Ma, Shaochun

2015-01-01

In order to address the performance complexity of the various constituent materials of (dense-column) latticed concrete-gypsum composite panels and the difficulty in the determination of the various elastic constants, this paper presented a detailed structural analysis of the (dense-column) latticed concrete-gypsum composite panel and proposed a feasible technical solution to simplified calculation. In conformity with mechanical rules, a typical panel element was selected and divided into two homogenous composite sub-elements and a secondary homogenous element, respectively for solution, thus establishing an equivalence of the composite panel to a simple homogenous panel and obtaining the effective formulas for calculating the various elastic constants. Finally, the calculation results and the experimental results were compared, which revealed that the calculation method was correct and reliable and could meet the calculation needs of practical engineering and provide a theoretical basis for simplified calculation for studies on composite panel elements and structures as well as a reference for calculations of other panels. PMID:28793631

A simplified digital lock-in amplifier for the scanning grating spectrometer.

PubMed

Wang, Jingru; Wang, Zhihong; Ji, Xufei; Liu, Jie; Liu, Guangda

2017-02-01

For the common measurement and control system of a scanning grating spectrometer, the use of an analog lock-in amplifier requires complex circuitry and sophisticated debugging, whereas the use of a digital lock-in amplifier places a high demand on the calculation capability and storage space. In this paper, a simplified digital lock-in amplifier based on averaging the absolute values within a complete period is presented and applied to a scanning grating spectrometer. The simplified digital lock-in amplifier was implemented on a low-cost microcontroller without multipliers, and got rid of the reference signal and specific configuration of the sampling frequency. Two positive zero-crossing detections were used to lock the phase of the measured signal. However, measurement method errors were introduced by the following factors: frequency fluctuation, sampling interval, and integer restriction of the sampling number. The theoretical calculation and experimental results of the signal-to-noise ratio of the proposed measurement method were 2055 and 2403, respectively.

On equivalent parameter learning in simplified feature space based on Bayesian asymptotic analysis.

PubMed

Yamazaki, Keisuke

2012-07-01

Parametric models for sequential data, such as hidden Markov models, stochastic context-free grammars, and linear dynamical systems, are widely used in time-series analysis and structural data analysis. Computation of the likelihood function is one of primary considerations in many learning methods. Iterative calculation of the likelihood such as the model selection is still time-consuming though there are effective algorithms based on dynamic programming. The present paper studies parameter learning in a simplified feature space to reduce the computational cost. Simplifying data is a common technique seen in feature selection and dimension reduction though an oversimplified space causes adverse learning results. Therefore, we mathematically investigate a condition of the feature map to have an asymptotically equivalent convergence point of estimated parameters, referred to as the vicarious map. As a demonstration to find vicarious maps, we consider the feature space, which limits the length of data, and derive a necessary length for parameter learning in hidden Markov models. Copyright © 2012 Elsevier Ltd. All rights reserved.

Simplified Calculation Model and Experimental Study of Latticed Concrete-Gypsum Composite Panels.

PubMed

Jiang, Nan; Ma, Shaochun

2015-10-27

In order to address the performance complexity of the various constituent materials of (dense-column) latticed concrete-gypsum composite panels and the difficulty in the determination of the various elastic constants, this paper presented a detailed structural analysis of the (dense-column) latticed concrete-gypsum composite panel and proposed a feasible technical solution to simplified calculation. In conformity with mechanical rules, a typical panel element was selected and divided into two homogenous composite sub-elements and a secondary homogenous element, respectively for solution, thus establishing an equivalence of the composite panel to a simple homogenous panel and obtaining the effective formulas for calculating the various elastic constants. Finally, the calculation results and the experimental results were compared, which revealed that the calculation method was correct and reliable and could meet the calculation needs of practical engineering and provide a theoretical basis for simplified calculation for studies on composite panel elements and structures as well as a reference for calculations of other panels.

Computerized Dental Comparison: A Critical Review of Dental Coding and Ranking Algorithms Used in Victim Identification.

PubMed

Adams, Bradley J; Aschheim, Kenneth W

2016-01-01

Comparison of antemortem and postmortem dental records is a leading method of victim identification, especially for incidents involving a large number of decedents. This process may be expedited with computer software that provides a ranked list of best possible matches. This study provides a comparison of the most commonly used conventional coding and sorting algorithms used in the United States (WinID3) with a simplified coding format that utilizes an optimized sorting algorithm. The simplified system consists of seven basic codes and utilizes an optimized algorithm based largely on the percentage of matches. To perform this research, a large reference database of approximately 50,000 antemortem and postmortem records was created. For most disaster scenarios, the proposed simplified codes, paired with the optimized algorithm, performed better than WinID3 which uses more complex codes. The detailed coding system does show better performance with extremely large numbers of records and/or significant body fragmentation. © 2015 American Academy of Forensic Sciences.

A simplified technique for in situ excision of cornea and evisceration of retinal tissue from human ocular globe.

PubMed

Parekh, Mohit; Ferrari, Stefano; Di Iorio, Enzo; Barbaro, Vanessa; Camposampiero, Davide; Karali, Marianthi; Ponzin, Diego; Salvalaio, Gianni

2012-06-12

Enucleation is the process of retrieving the ocular globe from a cadaveric donor leaving the rest of the globe undisturbed. Excision refers to the retrieval of ocular tissues, especially cornea, by cutting it separate from the ocular globe. Evisceration is the process of removing the internal organs referred here as retina. The ocular globe consists of the cornea, the sclera, the vitreous body, the lens, the iris, the retina, the choroid, muscles etc (Suppl. Figure 1). When a patient is suffering from corneal damage, the cornea needs to be removed and a healthy one must be transplanted by keratoplastic surgeries. Genetic disorders or defects in retinal function can compromise vision. Human ocular globes can be used for various surgical procedures such as eye banking, transplantation of human cornea or sclera and research on ocular tissues. However, there is little information available on human corneal and retinal excision, probably due to the limited accessibility to human tissues. Most of the studies describing similar procedures are performed on animal models. Research scientists rely on the availability of properly dissected and well-conserved ocular tissues in order to extend the knowledge on human eye development, homeostasis and function. As we receive high amount of ocular globes out of which approximately 40% (Table 1) of them are used for research purposes, we are able to perform huge amount of experiments on these tissues, defining techniques to excise and preserve them regularly. The cornea is an avascular tissue which enables the transmission of light onto the retina and for this purpose should always maintain a good degree of transparency. Within the cornea, the limbus region, which is a reservoir of the stem cells, helps the reconstruction of epithelial cells and restricts the overgrowth of the conjunctiva maintaining corneal transparency and clarity. The size and thickness of the cornea are critical for clear vision, as changes in either of them could lead to distracted, unclear vision. The cornea comprises of 5 layers; a) epithelium, b) Bowman's layer, c) stroma, d) Descemet's membrane and e) endothelium. All layers should function properly to ensure clear vision(4,5,6). The choroid is the intermediate tunic between the sclera and retina, bounded on the interior by the Bruch's membrane and is responsible for blood flow in the eye. The choroid also helps to regulate the temperature and supplies nourishment to the outer layers of the retina(5,6). The retina is a layer of nervous tissue that covers the back of the ocular globe (Suppl. Figure 1) and consists of two parts: a photoreceptive part and a non-receptive part. The retina helps to receive the light from the cornea and lens and converts it into the chemical energy eventually transmitted to the brain with help of the optic nerve(5,6). The aim of this paper is to provide a protocol for the dissection of corneal and retinal tissues from human ocular globes. Avoiding cross-contamination with adjacent tissues and preserving RNA integrity is of fundamental importance as such tissues are indispensable for research purposes aimed at (i) characterizing the transcriptome of the ocular tissues, (ii) isolating stem cells for regenerative medicine projects, and (iii) evaluating histological differences between tissues from normal/affected subjects. In this paper we describe the technique we currently use to remove the cornea, the choroid and retinal tissues from an ocular globe. Here we provide a detailed protocol for the dissection of the human ocular globe and the excision of corneal and retinal tissues. The accompanying video will help researchers to learn an appropriate technique for the retrieval of precious human tissues which are difficult to find regularly.

Using Program Theory-Driven Evaluation Science to Crack the Da Vinci Code

ERIC Educational Resources Information Center

Donaldson, Stewart I.

2005-01-01

Program theory-driven evaluation science uses substantive knowledge, as opposed to method proclivities, to guide program evaluations. It aspires to update, clarify, simplify, and make more accessible the evolving theory of evaluation practice commonly referred to as theory-driven or theory-based evaluation. The evaluator in this chapter provides a…

Motion video analysis using planar parallax

NASA Astrophysics Data System (ADS)

Sawhney, Harpreet S.

1994-04-01

Motion and structure analysis in video sequences can lead to efficient descriptions of objects and their motions. Interesting events in videos can be detected using such an analysis--for instance independent object motion when the camera itself is moving, figure-ground segregation based on the saliency of a structure compared to its surroundings. In this paper we present a method for 3D motion and structure analysis that uses a planar surface in the environment as a reference coordinate system to describe a video sequence. The motion in the video sequence is described as the motion of the reference plane, and the parallax motion of all the non-planar components of the scene. It is shown how this method simplifies the otherwise hard general 3D motion analysis problem. In addition, a natural coordinate system in the environment is used to describe the scene which can simplify motion based segmentation. This work is a part of an ongoing effort in our group towards video annotation and analysis for indexing and retrieval. Results from a demonstration system being developed are presented.

Testing of a simplified LED based vis/NIR system for rapid ripeness evaluation of white grape (Vitis vinifera L.) for Franciacorta wine.

PubMed

Giovenzana, Valentina; Civelli, Raffaele; Beghi, Roberto; Oberti, Roberto; Guidetti, Riccardo

2015-11-01

The aim of this work was to test a simplified optical prototype for a rapid estimation of the ripening parameters of white grape for Franciacorta wine directly in field. Spectral acquisition based on reflectance at four wavelengths (630, 690, 750 and 850 nm) was proposed. The integration of a simple processing algorithm in the microcontroller software would allow to visualize real time values of spectral reflectance. Non-destructive analyses were carried out on 95 grape bunches for a total of 475 berries. Samplings were performed weekly during the last ripening stages. Optical measurements were carried out both using the simplified system and a portable commercial vis/NIR spectrophotometer, as reference instrument for performance comparison. Chemometric analyses were performed in order to extract the maximum useful information from optical data. Principal component analysis (PCA) was performed for a preliminary evaluation of the data. Correlations between the optical data matrix and ripening parameters (total soluble solids content, SSC; titratable acidity, TA) were carried out using partial least square (PLS) regression for spectra and using multiple linear regression (MLR) for data from the simplified device. Classification analysis were also performed with the aim of discriminate ripe and unripe samples. PCA, MLR and classification analyses show the effectiveness of the simplified system in separating samples among different sampling dates and in discriminating ripe from unripe samples. Finally, simple equations for SSC and TA prediction were calculated. Copyright © 2015 Elsevier B.V. All rights reserved.

Next-Generation NATO Reference Mobility Model (NRMM) Development (Developpement de la nouvella generation du modele de mobilite de reference de l’OTAN (NRMM))

DTIC Science & Technology

2018-01-01

Profile Database E-17 Attachment 2: NRMM Data Input Requirements E-25 Attachment 3: General Physics -Based Model Data Input Requirements E-28...E-15 Figure E-11 Examples of Unique Surface Types E-20 Figure E-12 Correlating Physical Testing with Simulation E-21 Figure E-13 Simplified Tire...Table 10-8 Scoring Values 10-19 Table 10-9 Accuracy – Physics -Based 10-20 Table 10-10 Accuracy – Validation Through Measurement 10-22 Table 10-11

Evaluation of different methods to estimate daily reference evapotranspiration in ungauged basins in Southern Brazil

NASA Astrophysics Data System (ADS)

Ribeiro Fontoura, Jessica; Allasia, Daniel; Herbstrith Froemming, Gabriel; Freitas Ferreira, Pedro; Tassi, Rutineia

2016-04-01

Evapotranspiration is a key process of hydrological cycle and a sole term that links land surface water balance and land surface energy balance. Due to the higher information requirements of the Penman-Monteith method and the existing data uncertainty, simplified empirical methods for calculating potential and actual evapotranspiration are widely used in hydrological models. This is especially important in Brazil, where the monitoring of meteorological data is precarious. In this study were compared different methods for estimating evapotranspiration for Rio Grande do Sul, the Southernmost State of Brazil, aiming to suggest alternatives to the recommended method (Penman-Monteith-FAO 56) for estimate daily reference evapotranspiration (ETo) when meteorological data is missing or not available. The input dataset included daily and hourly-observed data from conventional and automatic weather stations respectively maintained by the National Weather Institute of Brazil (INMET) from the period of 1 January 2007 to 31 January 2010. Dataset included maximum temperature (Tmax, °C), minimum temperature (Tmin, °C), mean relative humidity (%), wind speed at 2 m height (u2, m s-1), daily solar radiation (Rs, MJ m- 2) and atmospheric pressure (kPa) that were grouped at daily time-step. Was tested the Food and Agriculture Organization of the United Nations (FAO) Penman-Monteith method (PM) at its full form, against PM assuming missing several variables not normally available in Brazil in order to calculate daily reference ETo. Missing variables were estimated as suggested in FAO56 publication or from climatological means. Furthermore, PM was also compared against the following simplified empirical methods: Hargreaves-Samani, Priestley-Taylor, Mccloud, McGuiness-Bordne, Romanenko, Radiation-Temperature, Tanner-Pelton. The statistical analysis indicates that even if just Tmin and Tmax are available, it is better to use PM estimating missing variables from syntetic data than simplified empirical methods evaluated except for Tanner-Pelton and Priestley-Taylor.

Spatial disaggregation of POWER-NASA air temperatures and effects on grass reference evapotranspiration in Sicily, Italy

NASA Astrophysics Data System (ADS)

Negm, Amro; Minacapilli, Mario; Provenzano, Giuseppe

2017-04-01

The accurate estimation of grass reference evapotranspiration (ET0) is important for many fields, including hydrology and irrigation water management. Being direct measure of ET0 difficult, expensive and time consuming, application of simplified approaches and web-based meteorological information are often preferred. The Prediction of Worldwide Energy Resource project developed by the American National Aeronautics and Space Administration (POWER-NASA) provides meteorological observations and surface energy fluxes on 1° latitude by 1° longitude grid, with a continuous daily coverage and for the entire globe. However, the broad spatial resolution of these data represents a limiting factor, for example when they have to be used for local estimations of reference ET0. In this work, a procedure for the spatial disaggregation of POWER-NASA daily average air temperature was proposed. In particular, a daily scaling factor was initially defined as the ratio between disaggregated average air temperature and the corresponding native value. This ratio was then modeled with a cosine function, characterized by three parameters depending on elevation, so to account for seasonal and regional variability. The proposed model was calibrated with three years of ground measurements (2006-2008) and then validated over six years (2009-2014). The suitability of the procedure was finally assessed by applying two simplified empirical models to estimate ET0 (Turc, 1961; Hargreaves, 1975). When compared to ET0 values obtained with FAO-56 PM equation, both simplified equations associated to downscaled meteorological observations, were characterized by RMSE ranging between 0.44 and 1.08 mm (average of 0.72-0.74 mm), and average MBE of -0.06 (Turc equation) and 0.13 mm (Hargreaves equation). These results indicated the strength of the proposed procedure to estimate ET0, even for regions characterized by the lack of detailed meteorological information.

Reference genes for quantitative PCR in the adipose tissue of mice with metabolic disease.

PubMed

Almeida-Oliveira, Fernanda; Leandro, João G B; Ausina, Priscila; Sola-Penna, Mauro; Majerowicz, David

2017-04-01

Obesity and diabetes are metabolic diseases and they are increasing in prevalence. The dynamics of gene expression associated with these diseases is fundamental to identifying genes involved in related biological processes. qPCR is a sensitive technique for mRNA quantification and the most commonly used method in gene-expression studies. However, the reliability of these results is directly influenced by data normalization. As reference genes are the major normalization method used, this work aims to identify reference genes for qPCR in adipose tissues of mice with type-I diabetes or obesity. We selected 12 genes that are commonly used as reference genes. The expression of these genes in the adipose tissues of mice was analyzed in the context of three different experimental protocols: 1) untreated animals; 2) high-fat-diet animals; and 3) streptozotocin-treated animals. Gene-expression stability was analyzed using four different algorithms. Our data indicate that TATA-binding protein is stably expressed across adipose tissues in control animals. This gene was also a useful reference when the brown adipose tissues of control and obese mice were analyzed. The mitochondrial ATP synthase F1 complex gene exhibits stable expression in subcutaneous and perigonadal adipose tissue from control and obese mice. Moreover, this gene is the best reference for qPCR normalization in adipose tissue from streptozotocin-treated animals. These results show that there is no perfect stable gene suited for use under all experimental conditions. In conclusion, the selection of appropriate genes is a prerequisite to ensure qPCR reliability and must be performed separately for different experimental protocols. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Aerodynamic Design of Axial-flow Compressors. Volume 2

NASA Technical Reports Server (NTRS)

1956-01-01

Available experimental two-dimensional-cascade data for conventional compressor blade sections are correlated. The two-dimensional cascade and some of the principal aerodynamic factors involved in its operation are first briefly described. Then the data are analyzed by examining the variation of cascade performance at a reference incidence angle in the region of minimum loss. Variations of reference incidence angle, total-pressure loss, and deviation angle with cascade geometry, inlet Mach number, and Reynolds number are investigated. From the analysis and the correlations of the available data, rules and relations are evolved for the prediction of the magnitude of the reference total-pressure loss and the reference deviation and incidence angles for conventional blade profiles. These relations are developed in simplified forms readily applicable to compressor design procedures.

Analysis of Different Cost Functions in the Geosect Airspace Partitioning Tool

NASA Technical Reports Server (NTRS)

Wong, Gregory L.

2010-01-01

A new cost function representing air traffic controller workload is implemented in the Geosect airspace partitioning tool. Geosect currently uses a combination of aircraft count and dwell time to select optimal airspace partitions that balance controller workload. This is referred to as the aircraft count/dwell time hybrid cost function. The new cost function is based on Simplified Dynamic Density, a measure of different aspects of air traffic controller workload. Three sectorizations are compared. These are the current sectorization, Geosect's sectorization based on the aircraft count/dwell time hybrid cost function, and Geosect s sectorization based on the Simplified Dynamic Density cost function. Each sectorization is evaluated for maximum and average workload along with workload balance using the Simplified Dynamic Density as the workload measure. In addition, the Airspace Concept Evaluation System, a nationwide air traffic simulator, is used to determine the capacity and delay incurred by each sectorization. The sectorization resulting from the Simplified Dynamic Density cost function had a lower maximum workload measure than the other sectorizations, and the sectorization based on the combination of aircraft count and dwell time did a better job of balancing workload and balancing capacity. However, the current sectorization had the lowest average workload, highest sector capacity, and the least system delay.

Levels of detail analysis of microwave scattering from human head models for brain stroke detection

PubMed Central

2017-01-01

In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model. After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to find out the solution of subject microwave scattering problem in a minimum computational time along with memory resources requirement. It is seen from this study that the microwave imaging may effectively be utilized for the detection, localization and differentiation of different types of brain stroke. The simulation results verified that the microwave imaging can be efficiently exploited to study the significant contrast between electric field values of the normal and abnormal brain tissues for the investigation of brain anomalies. In the end, a specific absorption rate analysis was carried out to compare the ionizing effects of microwave signals to different types of head model using a factor of safety for brain tissues. It is also suggested after careful study of various inversion methods in practice for microwave head imaging, that the contrast source inversion method may be more suitable and computationally efficient for such problems. PMID:29177115

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.

A Simplified and Systematic Method to Isolate, Culture, and Characterize Multiple Types of Human Dental Stem Cells from a Single Tooth.

PubMed

Bakkar, Mohammed; Liu, Younan; Fang, Dongdong; Stegen, Camille; Su, Xinyun; Ramamoorthi, Murali; Lin, Li-Chieh; Kawasaki, Takako; Makhoul, Nicholas; Pham, Huan; Sumita, Yoshinori; Tran, Simon D

2017-01-01

This chapter describes a simplified method that allows the systematic isolation of multiple types of dental stem cells such as dental pulp stem cells (DPSC), periodontal ligament stem cells (PDLSC), and stem cells of the apical papilla (SCAP) from a single tooth. Of specific interest is the modified laboratory approach to harvest/retrieve the dental pulp tissue by minimizing trauma to DPSC by continuous irrigation, reduction of frictional heat from the bur rotation, and reduction of the bur contact time with the dentin. Also, the use of a chisel and a mallet will maximize the number of live DPSC for culture. Steps demonstrating the potential for multiple cell differentiation lineages of each type of dental stem cell into either osteocytes, adipocytes, or chondrocytes are described. Flow cytometry, with a detailed strategy for cell gating and analysis, is described to verify characteristic markers of human mesenchymal multipotent stromal cells (MSC) from DPSC, PDLSC, or SCAP for subsequent experiments in cell therapy and in tissue engineering. Overall, this method can be adapted to any laboratory with a general setup for cell culture experiments.

A simplified method for identification of human cardiac myosin heavy-chain isoforms.

PubMed

Piao, Shengfu; Yu, Fushun; Mihm, Michael J; Reiser, Peter J; McCarthy, Patrick M; Van Wagoner, David R; Bauer, John Anthony

2003-02-01

Cardiac myosin is a central participant in the cross-bridge cycling that mediates myocyte contraction and consists of multiple subunits that mediate both hydrolysis of ATP and mechanical production of contractile force Two isoforms of myosin heavy chain (MHC- alpha and MHC- beta ) are known to exist in mammalian cardiac tissue, and it is within this myosin subunit that ATPase activity resides. These isoforms differ by less than 0.2% in total molecular mass and amino acid sequence, but, strikingly, influence the rate and efficiency of energy utilization for generation of contractile force. Changes in the MHC- alpha /MHC- beta ratio has been classically viewed as an adaptation of a failing myocyte in both animal models and humans; however, their measurement has traditionally required specialized preparations and materials for sufficient resolution. Here we describe a greatly simplified method for routine assessments of myosin isoform composition in human cardiac tissues. The primary advantages of our approach include higher throughput and reduced supply costs with no apparent loss of statistical power, reproducibility or achieved results. Use of this more convenient method may provide enhanced access to an otherwise specialized technique and could provide additional opportunity for investigation of cardiac myocyte adaptive changes.

Selection of internal reference genes for normalization of quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis in the canine brain and other organs.

PubMed

Park, Sang-Je; Huh, Jae-Won; Kim, Young-Hyun; Lee, Sang-Rae; Kim, Sang-Hyun; Kim, Sun-Uk; Kim, Heui-Soo; Kim, Min Kyu; Chang, Kyu-Tae

2013-05-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive technique for quantifying gene expression. To analyze qRT-PCR data accurately, suitable reference genes that show consistent expression patterns across different tissues and experimental conditions should be selected. The objective of this study was to obtain the most stable reference genes in dogs, using samples from 13 different brain tissues and 10 other organs. 16 well-known candidate reference genes were analyzed by the geNorm, NormFinder, and BestKeeper programs. Brain tissues were derived from several different anatomical regions, including the forebrain, cerebrum, diencephalon, hindbrain, and metencephalon, and grouped accordingly. Combination of the three different analyses clearly indicated that the ideal reference genes are ribosomal protien S5 (RPS5) in whole brain, RPL8 and RPS5 in whole body tissues, RPS5 and RPS19 in the forebrain and cerebrum, RPL32 and RPS19 in the diencephalon, GAPDH and RPS19 in the hindbrain, and MRPS7 and RPL13A in the metencephalon. These genes were identified as ideal for the normalization of qRT-PCR results in the respective tissues. These findings indicate more suitable and stable reference genes for future studies of canine gene expression.

Multiple-wavelength spectroscopic quantitation of light-absorbing species in scattering media

DOEpatents

Nathel, Howard; Cartland, Harry E.; Colston, Jr., Billy W.; Everett, Matthew J.; Roe, Jeffery N.

2000-01-01

An oxygen concentration measurement system for blood hemoglobin comprises a multiple-wavelength low-coherence optical light source that is coupled by single mode fibers through a splitter and combiner and focused on both a target tissue sample and a reference mirror. Reflections from both the reference mirror and from the depths of the target tissue sample are carried back and mixed to produce interference fringes in the splitter and combiner. The reference mirror is set such that the distance traversed in the reference path is the same as the distance traversed into and back from the target tissue sample at some depth in the sample that will provide light attenuation information that is dependent on the oxygen in blood hemoglobin in the target tissue sample. Two wavelengths of light are used to obtain concentrations. The method can be used to measure total hemoglobin concentration [Hb.sub.deoxy +Hb.sub.oxy ] or total blood volume in tissue and in conjunction with oxygen saturation measurements from pulse oximetry can be used to absolutely quantify oxyhemoglobin [HbO.sub.2 ] in tissue. The apparatus and method provide a general means for absolute quantitation of an absorber dispersed in a highly scattering medium.

Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture.

PubMed

Chan, Pek-Lan; Rose, Ray J; Abdul Murad, Abdul Munir; Zainal, Zamri; Low, Eng-Ti Leslie; Ooi, Leslie Cheng-Li; Ooi, Siew-Eng; Yahya, Suzaini; Singh, Rajinder

2014-01-01

The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels. In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization. Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses.

Testing the effectiveness of simplified search strategies for updating systematic reviews.

PubMed

Rice, Maureen; Ali, Muhammad Usman; Fitzpatrick-Lewis, Donna; Kenny, Meghan; Raina, Parminder; Sherifali, Diana

2017-08-01

The objective of the study was to test the overall effectiveness of a simplified search strategy (SSS) for updating systematic reviews. We identified nine systematic reviews undertaken by our research group for which both comprehensive and SSS updates were performed. Three relevant performance measures were estimated, that is, sensitivity, precision, and number needed to read (NNR). The update reference searches for all nine included systematic reviews identified a total of 55,099 citations that were screened resulting in final inclusion of 163 randomized controlled trials. As compared with reference search, the SSS resulted in 8,239 hits and had a median sensitivity of 83.3%, while precision and NNR were 4.5 times better. During analysis, we found that the SSS performed better for clinically focused topics, with a median sensitivity of 100% and precision and NNR 6 times better than for the reference searches. For broader topics, the sensitivity of the SSS was 80% while precision and NNR were 5.4 times better compared with reference search. SSS performed well for clinically focused topics and, with a median sensitivity of 100%, could be a viable alternative to a conventional comprehensive search strategy for updating this type of systematic reviews particularly considering the budget constraints and the volume of new literature being published. For broader topics, 80% sensitivity is likely to be considered too low for a systematic review update in most cases, although it might be acceptable if updating a scoping or rapid review. Copyright © 2017 Elsevier Inc. All rights reserved.

The Emerging Role of School Leadership in Israel: From External to Internal Locus of Control.

ERIC Educational Resources Information Center

Volansky, Ami; Habinski, Avi

1998-01-01

In 1997, all elementary schools in Jerusalem were transferred to a self-managing program over a three-year period. Research undertaken in schools entering the program in 1995 reveals high satisfaction among principals and teachers, enhanced school relations with local authorities, and simplified financial-reporting mechanisms. (10 references) (MLH)

Transition to a Unified System: Using Perl To Drive Library Databases and Enhance Web Site Functionality.

ERIC Educational Resources Information Center

Fagan, Judy Condit

2001-01-01

Discusses the need for libraries to routinely redesign their Web sites, and presents a case study that describes how a Perl-driven database at Southern Illinois University's library improved Web site organization and patron access, simplified revisions, and allowed staff unfamiliar with HTML to update content. (Contains 56 references.) (Author/LRW)

Soft-tissue facial characteristics of attractive Chinese men compared to normal men.

PubMed

Wu, Feng; Li, Junfang; He, Hong; Huang, Na; Tang, Youchao; Wang, Yuanqing

2015-01-01

To compare the facial characteristics of attractive Chinese men with those of reference men. The three-dimensional coordinates of 50 facial landmarks were collected in 40 healthy reference men and in 40 "attractive" men, soft tissue facial angles, distances, areas, and volumes were computed and compared using analysis of variance. When compared with reference men, attractive men shared several similar facial characteristics: relatively large forehead, reduced mandible, and rounded face. They had a more acute soft tissue profile, an increased upper facial width and middle facial depth, larger mouth, and more voluminous lips than reference men. Attractive men had several facial characteristics suggesting babyness. Nonetheless, each group of men was characterized by a different development of these features. Esthetic reference values can be a useful tool for clinicians, but should always consider the characteristics of individual faces.

Selection and validation of reference genes for gene expression analysis in apomictic and sexual Cenchrus ciliaris

PubMed Central

2013-01-01

Background Apomixis is a naturally occurring asexual mode of seed reproduction resulting in offspring genetically identical to the maternal plant. Identifying differential gene expression patterns between apomictic and sexual plants is valuable to help deconstruct the trait. Quantitative RT-PCR (qRT-PCR) is a popular method for analyzing gene expression. Normalizing gene expression data using proper reference genes which show stable expression under investigated conditions is critical in qRT-PCR analysis. We used qRT-PCR to validate expression and stability of six potential reference genes (EF1alpha, EIF4A, UBCE, GAPDH, ACT2 and TUBA) in vegetative and reproductive tissues of B-2S and B-12-9 accessions of C. ciliaris. Findings Among tissue types evaluated, EF1alpha showed the highest level of expression while TUBA showed the lowest. When all tissue types were evaluated and compared between genotypes, EIF4A was the most stable reference gene. Gene expression stability for specific ovary stages of B-2S and B-12-9 was also determined. Except for TUBA, all other tested reference genes could be used for any stage-specific ovary tissue normalization, irrespective of the mode of reproduction. Conclusion Our gene expression stability assay using six reference genes, in sexual and apomictic accessions of C. ciliaris, suggests that EIF4A is the most stable gene across all tissue types analyzed. All other tested reference genes, with the exception of TUBA, could be used for gene expression comparison studies between sexual and apomictic ovaries over multiple developmental stages. This reference gene validation data in C. ciliaris will serve as an important base for future apomixis-related transcriptome data validation. PMID:24083672

Elasmobranch qPCR reference genes: a case study of hypoxia preconditioned epaulette sharks

PubMed Central

2010-01-01

Background Elasmobranch fishes are an ancient group of vertebrates which have high potential as model species for research into evolutionary physiology and genomics. However, no comparative studies have established suitable reference genes for quantitative PCR (qPCR) in elasmobranchs for any physiological conditions. Oxygen availability has been a major force shaping the physiological evolution of vertebrates, especially fishes. Here we examined the suitability of 9 reference candidates from various functional categories after a single hypoxic insult or after hypoxia preconditioning in epaulette shark (Hemiscyllium ocellatum). Results Epaulette sharks were caught and exposed to hypoxia. Tissues were collected from 10 controls, 10 individuals with single hypoxic insult and 10 individuals with hypoxia preconditioning (8 hypoxic insults, 12 hours apart). We produced sequence information for reference gene candidates and monitored mRNA expression levels in four tissues: cerebellum, heart, gill and eye. The stability of the genes was examined with analysis of variance, geNorm and NormFinder. The best ranking genes in our study were eukaryotic translation elongation factor 1 beta (eef1b), ubiquitin (ubq) and polymerase (RNA) II (DNA directed) polypeptide F (polr2f). The performance of the ribosomal protein L6 (rpl6) was tissue-dependent. Notably, in one tissue the analysis of variance indicated statistically significant differences between treatments for genes that were ranked as the most stable candidates by reference gene software. Conclusions Our results indicate that eef1b and ubq are generally the most suitable reference genes for the conditions and tissues in the present epaulette shark studies. These genes could also be potential reference gene candidates for other physiological studies examining stress in elasmobranchs. The results emphasise the importance of inter-group variation in reference gene evaluation. PMID:20416043

Role of temperature dependence of optical properties in laser irradiation of biological tissue

NASA Astrophysics Data System (ADS)

Rastegar, Sohi; Kim, Beop-Min; Jacques, Steven L.

1992-08-01

Optical properties of biological tissue can change as a result of thermal denaturation due to temperature rise; a familiar example is whitening observed in cooking egg-white. Changes in optical properties with temperature have been reported in the literature. Temperature rise due to laser irradiation is a function of the optical properties of tissue which themselves are a function of temperature of the tissue. This creates a coupling between light and temperature fields for biological tissue under laser irradiation. The effects of this coupling on the temperature response and light distribution may play an important role in dosimetry consideration for therapeutic as well as diagnostic application of lasers in medicine. In a previous study this problem was addressed in one dimension, for short irradiation exposures, using certain simplifying assumptions. The purpose of this research was to develop a mathematical model for dynamic optical changes with thermal denaturation and a computer program for simulation of these effects for a multi-dimensional geometry.

Numerical Simulation of Thawing Process of Biological Tissue

NASA Astrophysics Data System (ADS)

Momose, Noboru; Tada, Yukio; Hayashi, Yujiro

Heat transfer and simplified physicochemical model for thawing of the frozen biological cell element consisting of cell and extracellular region was proposed. The melting of intra-and extra-cellular ice, the water transport through cell membrane and other microscale behavior during thawing process were discussed as a function of temperature. Recovery of the cell volume and change of osmotic pressure difference during thawing were clarified theortically in connection with heating velocity, initial cell volume and membrane permeability. Extending this model, the thawing of cellular tissue consisted of numerous cell elements was also simulated. There was a position where osmotic pressure difference became maximum during thawing. Summarizing these results, the thawing damage due to osmotic stress was discussed in relation with the heating operation and the size effect of tissue.

MicroRNA Expression in Formalin-fixed Paraffin-embedded Cancer Tissue: Identifying Reference MicroRNAs and Variability.

PubMed

Boisen, Mogens Karsbøl; Dehlendorff, Christian; Linnemann, Dorte; Schultz, Nicolai Aagaard; Jensen, Benny Vittrup; Høgdall, Estrid Vilma Solyom; Johansen, Julia Sidenius

2015-12-29

Archival formalin-fixed paraffin-embedded (FFPE) cancer tissue samples are a readily available resource for microRNA (miRNA) biomarker identification. No established standard for reference miRNAs in FFPE tissue exists. We sought to identify stable reference miRNAs for normalization of miRNA expression in FFPE tissue samples from patients with colorectal (CRC) and pancreatic (PC) cancer and to quantify the variability associated with sample age and fixation. High-throughput miRNA profiling results from 203 CRC and 256 PC FFPE samples as well as from 37 paired frozen/FFPE samples from nine other CRC tumors (methodological samples) were used. Candidate reference miRNAs were identified by their correlation with global mean expression. The stability of reference genes was analyzed according to published methods. The association between sample age and global mean miRNA expression was tested using linear regression. Variability was described using correlation coefficients and linear mixed effects models. Normalization effects were determined by changes in standard deviation and by hierarchical clustering. We created lists of 20 miRNAs with the best correlation to global mean expression in each cancer type. Nine of these miRNAs were present in both lists, and miR-103a-3p was the most stable reference miRNA for both CRC and PC FFPE tissue. The optimal number of reference miRNAs was 4 in CRC and 10 in PC. Sample age had a significant effect on global miRNA expression in PC (50% reduction over 20 years) but not in CRC. Formalin fixation for 2-6 days decreased miRNA expression 30-65%. Normalization using global mean expression reduced variability for technical and biological replicates while normalization using the expression of the identified reference miRNAs reduced variability only for biological replicates. Normalization only had a minor impact on clustering results. We identified suitable reference miRNAs for future miRNA expression experiments using CRC- and PC FFPE tissue samples. Formalin fixation decreased miRNA expression considerably, while the effect of increasing sample age was estimated to be negligible in a clinical setting.

A tissue engineered human endometrial stroma that responds to cues for secretory differentiation, decidualization and menstruation

PubMed Central

Schutte, Stacey C.; Taylor, Robert N.

2012-01-01

Objective To show the responsiveness of a tissue engineered human endometrial stroma to combinations of hormones mimicking the secretory and menstrual phases of the cycle. Design In vitro experimental study Setting University uterine biology research laboratory Cells Telomerase immortalized human endometrial stromal cells Interventions The stromal cells were cultured in monolayers (2D) or encapsulated in a collagen I hydrogel (3D) to create a simplified tissue engineered stroma. The cells and tissues were exposed to hormone treatments mimicking early and late secretory phases, decidualization and steroid withdrawal conditions to recapitulate menstruation. Main Outcome Measure(s) Morphological and biochemical markers of decidualization and collagenase activity Result(s) The 3D tissue is capable of manifesting changes in morphology and biochemical markers of decidualization similar to 2D culture and characteristic of endometrial stroma in vivo. Unlike 2D culture, the 3D tissue responded to steroid withdrawal by increased collagenase activity and tissue breakdown. Conclusion(s) 3D tissue engineered endometrial stroma can mimic secretory and menstrual phases of the cycle and may be useful for studying uterine receptivity and menstruation in a physiological endocrine environment. PMID:22306710

Peptide- and Amine-Modified Glucan Particles for the Delivery of Therapeutic siRNA

PubMed Central

Aouadi, Myriam; Vangala, Pranitha; Tencerova, Michaela; Amano, Shinya U.; Nicoloro, Sarah M.; Yawe, Joseph C.; Czech, Michael P.

2016-01-01

Translation of siRNA technology into the clinic is limited by the need for improved delivery systems that target specific cell types. Macrophages are particularly attractive targets for RNAi therapy because they promote pathogenic inflammatory responses in a number of important human diseases. We previously demonstrated that a multi-component formulation of β-1,3-D-glucan-encapsulated siRNA particles (GeRPs) can specifically and potently silence genes in mouse macrophages. A major advance would be to simplify the GeRP system by reducing the number of delivery components, thus enabling more facile manufacturing and future commercialization. Here we report the synthesis and evaluation of a simplified glucan-based particle (GP) capable of delivering siRNA in vivo to selectively silence macrophage genes. Covalent attachment of small-molecule amines and short peptides containing weak bases to GPs facilitated electrostatic interaction of the particles with siRNA and aided in the endosomal release of siRNA by the proton-sponge effect. Modified GPs were non-toxic and were efficiently internalized by macrophages in vitro. When injected intraperitoneally (i.p.), several of the new peptide-modified GPs were found to efficiently deliver siRNA to peritoneal macrophages in lean, healthy mice. In an animal model of obesity-induced inflammation, i.p. administration of one of the peptide-modified GPs (GP-EP14) bound to siRNA selectively reduced the expression of target inflammatory cytokines in the visceral adipose tissue macrophages. Decreasing adipose tissue inflammation resulted in an improvement of glucose metabolism in these metabolically challenged animals. Thus, modified GPs represent a promising new simplified system for the efficient delivery of therapeutic siRNAs specifically to phagocytic cells in vivo for modulation of inflammation responses. PMID:26815386

Motion of a Point Mass in a Rotating Disc: A Quantitative Analysis of the Coriolis and Centrifugal Force

NASA Astrophysics Data System (ADS)

Haddout, Soufiane

2016-06-01

In Newtonian mechanics, the non-inertial reference frames is a generalization of Newton's laws to any reference frames. While this approach simplifies some problems, there is often little physical insight into the motion, in particular into the effects of the Coriolis force. The fictitious Coriolis force can be used by anyone in that frame of reference to explain why objects follow curved paths. In this paper, a mathematical solution based on differential equations in non-inertial reference is used to study different types of motion in rotating system. In addition, the experimental data measured on a turntable device, using a video camera in a mechanics laboratory was conducted to compare with mathematical solution in case of parabolically curved, solving non-linear least-squares problems, based on Levenberg-Marquardt's and Gauss-Newton algorithms.

Weather data for simplified energy calculation methods. Volume II. Middle United States: TRY data

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

Olsen, A.R.; Moreno, S.; Deringer, J.

1984-08-01

The objective of this report is to provide a source of weather data for direct use with a number of simplified energy calculation methods available today. Complete weather data for a number of cities in the United States are provided for use in the following methods: degree hour, modified degree hour, bin, modified bin, and variable degree day. This report contains sets of weather data for 22 cities in the continental United States using Test Reference Year (TRY) source weather data. The weather data at each city has been summarized in a number of ways to provide differing levels ofmore » detail necessary for alternative simplified energy calculation methods. Weather variables summarized include dry bulb and wet bulb temperature, percent relative humidity, humidity ratio, wind speed, percent possible sunshine, percent diffuse solar radiation, total solar radiation on horizontal and vertical surfaces, and solar heat gain through standard DSA glass. Monthly and annual summaries, in some cases by time of day, are available. These summaries are produced in a series of nine computer generated tables.« less

Validity for the simplified water displacement instrument to measure arm lymphedema as a result of breast cancer surgery.

PubMed

Sagen, Ase; Kåresen, Rolf; Skaane, Per; Risberg, May Arna

2009-05-01

To evaluate concurrent and construct validity for the Simplified Water Displacement Instrument (SWDI), an instrument for measuring arm volumes and arm lymphedema as a result of breast cancer surgery. Validity design. Hospital setting. Women (N=23; mean age, 64+/-11y) were examined 6 years after breast cancer surgery with axillary node dissection. Not applicable. The SWDI was included for measuring arm volumes to estimate arm lymphedema as a result of breast cancer surgery. A computed tomography (CT) scan was included to examine the cross-sectional areas (CSAs) in square millimeters for the subcutaneous tissue, for the muscle tissue, and for measuring tissue density in Hounsfield units. Magnetic resonance imaging (MRI) with T2-weighted sequences was included to show increased signal intensity in subcutaneous and muscle tissue areas. The affected arm volume measured by the SWDI was significantly correlated to the total CSA of the affected upper limb (R=.904) and also to the CSA of the subcutaneous tissue and muscles tissue (R=.867 and R=.725), respectively (P<.001). The CSA of the subcutaneous tissue for the upper limb was significantly larger compared with the control limb (11%). Tissue density measured in Hounsfield units did not correlate significantly with arm volume (P>.05). The affected arm volume was significantly larger (5%) than the control arm volume (P<.05). Five (22%) women had arm lymphedema defined as a 10% increase in the affected arm volume compared with the control arm volume, and an increased signal intensity was identified in all 5 women on MRI (T2-weighted, kappa=.777, P<.001). The SWDI showed high concurrent and construct validity as shown with significant correlations between the CSA (CT) of the subcutaneous and muscle areas of the affected limb and the affected arm volume (P>.001). There was a high agreement between those subjects who were diagnosed with arm lymphedema by using the SWDI and the increased signal intensity on MRI, with a kappa value of .777 (P<.001). High construct validity for the SWDI was confirmed for arm lymphedema as a volume increase, but it was not confirmed for lymphedema without an increase in arm volume (swelling). The SWDI is a simple and valid tool for estimating arm volume and arm lymphedema after breast cancer surgery.

Multiplicative Versus Additive Filtering for Spacecraft Attitude Determination

NASA Technical Reports Server (NTRS)

Markley, F. Landis

2003-01-01

The absence of a globally nonsingular three-parameter representation of rotations forces attitude Kalman filters to estimate either a singular or a redundant attitude representation. We compare two filtering strategies using simplified kinematics and measurement models. Our favored strategy estimates a three-parameter representation of attitude deviations from a reference attitude specified by a higher- dimensional nonsingular parameterization. The deviations from the reference are assumed to be small enough to avoid any singularity or discontinuity of the three-dimensional parameterization. We point out some disadvantages of the other strategy, which directly estimates the four-parameter quaternion representation.

Reference Materials: Significance, General Requirements, and Demand.

PubMed

Kiełbasa, Anna; Gadzała-Kopciuch, Renata; Buszewski, Bogusław

2016-05-03

Reference materials play an important part in the quality control of measurements. Rapid development of such new scientific disciplines as proteomics, metabolomics, and genomics also necessitates development of new reference materials. This is a great challenge due to the complexity of the production of new reference materials and difficulties associated with achieving their homogeneity and stability. CRMs of tissue are of particular importance. They can be counted among the matrices that are most complex and time consuming in preparation. Tissue is the place of transformation and accumulation of many substances (e.g., metabolites, which are intermediate or end products resulting from metabolic processes). Trace amounts of many substances in tissues must be determined with adequate precision and accuracy. To meet the needs stemming from research and from problems and challenges faced by chemists, analysts, and toxicologists, the number of certified reference materials should be continuously increased.

Soft-tissue facial characteristics of attractive Chinese men compared to normal men

PubMed Central

Wu, Feng; Li, Junfang; He, Hong; Huang, Na; Tang, Youchao; Wang, Yuanqing

2015-01-01

Objective: To compare the facial characteristics of attractive Chinese men with those of reference men. Materials and Methods: The three-dimensional coordinates of 50 facial landmarks were collected in 40 healthy reference men and in 40 “attractive” men, soft tissue facial angles, distances, areas, and volumes were computed and compared using analysis of variance. Results: When compared with reference men, attractive men shared several similar facial characteristics: relatively large forehead, reduced mandible, and rounded face. They had a more acute soft tissue profile, an increased upper facial width and middle facial depth, larger mouth, and more voluminous lips than reference men. Conclusions: Attractive men had several facial characteristics suggesting babyness. Nonetheless, each group of men was characterized by a different development of these features. Esthetic reference values can be a useful tool for clinicians, but should always consider the characteristics of individual faces. PMID:26221357

Integrating Analysis Goals for EOP, CRF and TRF

NASA Technical Reports Server (NTRS)

Ma, Chopo; MacMillan, Daniel; Petrov, Leonid

2002-01-01

In a simplified, idealized way the TRF (Terrestrial Reference Frame) can be considered a set of positions at epoch and corresponding linear rates of change while the CRF (Celestial Reference Frame) is a set of fixed directions in space. VLBI analysis can be optimized for CRF and TRF separately while handling some of the complexity of geodetic and astrometric reality. For EOP (Earth Orientation Parameter) time series both CRF and TRF should be accurate at the epoch of interest and well defined over time. The optimal integration of EOP, TRF and CRF in a single VLBI solution configuration requires a detailed consideration of the data set and the possibly conflicting nature of the reference frames. A possible approach for an integrated analysis is described.

Soft Tissue Strain Rates in Side-Blast Incidents

DTIC Science & Technology

2014-11-02

improve models’ representativeness. This paper introduces a simplified finite element model of a human neck to study the reaction of armour vehicle...light armour vehicles (LAV). The establishment of meaningful injury criteria is, however, a challenging task that is still under extensive studies...Advanced shock absorption product already exists in the market but each design/material has its limitation. For example, the widespread use of foams in

Photoactivated methods for enabling cartilage-to-cartilage tissue fixation

NASA Astrophysics Data System (ADS)

Sitterle, Valerie B.; Roberts, David W.

2003-06-01

The present study investigates whether photoactivated attachment of cartilage can provide a viable method for more effective repair of damaged articular surfaces by providing an alternative to sutures, barbs, or fibrin glues for initial fixation. Unlike artificial materials, biological constructs do not possess the initial strength for press-fitting and are instead sutured or pinned in place, typically inducing even more tissue trauma. A possible alternative involves the application of a photosensitive material, which is then photoactivated with a laser source to attach the implant and host tissues together in either a photothermal or photochemical process. The photothermal version of this method shows potential, but has been almost entirely applied to vascularized tissues. Cartilage, however, exhibits several characteristics that produce appreciable differences between applying and refining these techniques when compared to previous efforts involving vascularized tissues. Preliminary investigations involving photochemical photosensitizers based on singlet oxygen and electron transfer mechanisms are discussed, and characterization of the photodynamic effects on bulk collagen gels as a simplified model system using FTIR is performed. Previous efforts using photothermal welding applied to cartilaginous tissues are reviewed.

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 of expression stability across three different olive cultivars, Barnea, Frantoio and Picual, however the combination of the three most stable reference genes do vary amongst individual cultivars. This study will provide guidance to other researchers to select reference genes for normalization against target genes by qPCR across tissues obtained from the mesocarp region of the olive fruit in the cultivars, Barnea, Frantoio and Picual. PMID:24884716

Teaching the English Active and Passive Voice with the Help of Cognitive Grammar: An Empirical Study

ERIC Educational Resources Information Center

Bielak, Jakub; Pawlak, Mirosuaw; Mystkowska-Wiertelak, Anna

2013-01-01

Functionally-oriented linguistic theories, such as cognitive grammar (CG), offer nuanced descriptions of the meanings and uses of grammatical features. A simplified characterization of the semantics of the English active and passive voice grounded in CG terms and based on the reference point model is presented, as it is the basis of the…

Geoseq: a tool for dissecting deep-sequencing datasets.

PubMed

Gurtowski, James; Cancio, Anthony; Shah, Hardik; Levovitz, Chaya; George, Ajish; Homann, Robert; Sachidanandam, Ravi

2010-10-12

Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a) identify differential isoform expression in mRNA-seq datasets, b) identify miRNAs (microRNAs) in libraries, and identify mature and star sequences in miRNAS and c) to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

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 challenging Raman endoscopic applications.

A Simplified GCS-DCSK Modulation and Its Performance Optimization

NASA Astrophysics Data System (ADS)

Xu, Weikai; Wang, Lin; Chi, Chong-Yung

2016-12-01

In this paper, a simplified Generalized Code-Shifted Differential Chaos Shift Keying (GCS-DCSK) whose transmitter never needs any delay circuits, is proposed. However, its performance is deteriorated because the orthogonality between substreams cannot be guaranteed. In order to optimize its performance, the system model of the proposed GCS-DCSK with power allocations on substreams is presented. An approximate bit error rate (BER) expression of the proposed model, which is a function of substreams’ power, is derived using Gaussian Approximation. Based on the BER expression, an optimal power allocation strategy between information substreams and reference substream is obtained. Simulation results show that the BER performance of the proposed GCS-DCSK with the optimal power allocation can be significantly improved when the number of substreams M is large.

Navigation system and method

NASA Technical Reports Server (NTRS)

Taylor, R. E.; Sennott, J. W. (Inventor)

1984-01-01

In a global positioning system (GPS), such as the NAVSTAR/GPS system, wherein the position coordinates of user terminals are obtained by processing multiple signals transmitted by a constellation of orbiting satellites, an acquisition-aiding signal generated by an earth-based control station is relayed to user terminals via a geostationary satellite to simplify user equipment. The aiding signal is FSK modulated on a reference channel slightly offset from the standard GPS channel. The aiding signal identifies satellites in view having best geometry and includes Doppler prediction data as well as GPS satellite coordinates and identification data associated with user terminals within an area being served by the control station and relay satellite. The aiding signal significantly reduces user equipment by simplifying spread spectrum signal demodulation and reducing data processing functions previously carried out at the user terminals.

Reflector and Protections in a Sodium-cooled Fast Reactor: Modelling and Optimization

NASA Astrophysics Data System (ADS)

Blanchet, David; Fontaine, Bruno

2017-09-01

The ASTRID project (Advanced Sodium Technological Reactor for Industrial Demonstration) is a Generation IV nuclear reactor concept under development in France [1]. In this frame, studies are underway to optimize radial reflectors and protections. Considering radial protections made in natural boron carbide, this study is conducted to assess the neutronic performances of the MgO as the reference choice for reflector material, in comparison with other possible materials including a more conventional stainless steel. The analysis is based upon a simplified 1-D and 2-D deterministic modelling of the reactor, providing simplified interfaces between core, reflector and protections. Such models allow examining detailed reaction rate distributions; they also provide physical insights into local spectral effects occurring at the Core-Reflector and at the Reflector-Protection interfaces.

Determination of polychlorinated biphenyl congeners and chlorinated pesticides in a fish tissue standard reference material.

PubMed

Poster, Dianne L; Kucklick, John R; Schantz, Michele M; Porter, Barbara J; Leigh, Stefan D; Wise, Stephen A

2003-01-01

The concentrations of a wide range of polychlorinated biphenyl congeners (PCBs) and chlorinated pesticides in a fish tissue Standard Reference Material (SRM) have been determined using multiple methods of analysis. This material, SRM 1946, Lake Superior Fish Tissue, was recently issued by the National Institute of Standards and Technology (NIST) and complements a suite of marine environmental natural-matrix SRMs that are currently available from NIST for the determination of organic contaminants such as aliphatic hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), PCBs, and chlorinated pesticides. SRM 1946 is a fresh tissue homogenate (frozen) prepared from filleted adult lake trout (Salvelinus namaycush namaycush) collected from the Apostle Islands region of Lake Superior. SRM 1946 has certified and reference concentrations for PCB congeners, including the three non- ortho PCB congeners, and chlorinated pesticides. Certified concentrations are available for 30 PCB congeners and 15 chlorinated pesticides. Reference concentrations are available for 12 PCB congeners and 2 chlorinated pesticides. In addition, SRM 1946 is characterized for additional chemical constituents and properties: fatty acids, extractable fat, methylmercury, total mercury, selected trace elements, proximates, and caloric content. The characterization of chlorinated compounds is described in this paper with an emphasis on the approach used for the certification of the concentrations of PCB congeners and chlorinated pesticides. The PCB congener and chlorinated pesticide data are also compared to concentrations in other marine natural-matrix reference materials available from NIST (fish oil, mussel tissue, whale blubber, and a second fresh frozen fish tissue homogenate prepared from filleted adult lake trout collected from Lake Michigan) and from other organizations such as the National Research Council Canada (ground whole carp), the International Atomic Energy Agency (fish homogenate), and the European Commission Joint Research Centre [fish oils (cod and mackerel) and mussel tissue].

Improved selenium recovery from tissue with modified sample decomposition

USGS Publications Warehouse

Brumbaugh, W. G.; Walther, M.J.

1991-01-01

The present paper describes a simple modification of a recently reported decomposition method for determination of selenium in biological tissue by hydride generation atomic absorption. The modified method yielded slightly higher selenium recoveries (3-4%) for selected reference tissues and fish tissue spiked with selenomethionine. Radiotracer experiments indicated that the addition of a small volume of hydrochloric acid to the wet digestate mixture reduced slight losses of selenium as the sample initially went to dryness before ashing. With the modified method, selenium spiked as selenomethionine behaved more like the selenium in reference tissues than did the inorganic spike forms when this digestion modification was used.

The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

PubMed

Cai, Jing; Li, Tao; Huang, Bangxing; Cheng, Henghui; Ding, Hui; Dong, Weihong; Xiao, Man; Liu, Ling; Wang, Zehua

2014-01-01

Quantitative real-time PCR (qPCR) is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M) were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD), an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA) and nonparametric (Kruskal-Wallis) tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP) and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.

Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

PubMed Central

Chan, Pek-Lan; Rose, Ray J.; Abdul Murad, Abdul Munir; Zainal, Zamri; Leslie Low, Eng-Ti; Ooi, Leslie Cheng-Li; Ooi, Siew-Eng; Yahya, Suzaini; Singh, Rajinder

2014-01-01

Background The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels. Results In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization. Conclusions Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses. PMID:24927412

Effects of osmotic pressure in the extracellular matrix on tissue deformation.

PubMed

Lu, Y; Parker, K H; Wang, W

2006-06-15

In soft tissues, large molecules such as proteoglycans trapped in the extracellular matrix (ECM) generate high levels of osmotic pressure to counter-balance external pressures. The semi-permeable matrix and fixed negative charges on these molecules serve to promote the swelling of tissues when there is an imbalance of molecular concentrations. Structural molecules, such as collagen fibres, form a network of stretch-resistant matrix, which prevents tissue from over-swelling and keeps tissue integrity. However, collagen makes little contribution to load bearing; the osmotic pressure in the ECM is the main contributor balancing external pressures. Although there have been a number of studies on tissue deformation, there is no rigorous analysis focusing on the contribution of the osmotic pressure in the ECM on the viscoelastic behaviour of soft tissues. Furthermore, most previous works were carried out based on the assumption of infinitesimal deformation, whereas tissue deformation is finite under physiological conditions. In the current study, a simplified mathematical model is proposed. Analytic solutions for solute distribution in the ECM and the free-moving boundary were derived by solving integro-differential equations under constant and dynamic loading conditions. Osmotic pressure in the ECM is found to contribute significantly to the viscoelastic characteristics of soft tissues during their deformation.

Selection and validation of reference genes for miRNA expression studies during porcine pregnancy.

PubMed

Wessels, Jocelyn M; Edwards, Andrew K; Zettler, Candace; Tayade, Chandrakant

2011-01-01

MicroRNAs comprise a family of small non-coding RNAs that modulate several developmental and physiological processes including pregnancy. Their ubiquitous presence is confirmed in mammals, worms, flies and plants. Although rapid advances have been made in microRNA research, information on stable reference genes for validation of microRNA expression is still lacking. Real time PCR is a widely used tool to quantify gene transcripts. An appropriate reference gene must be chosen to minimize experimental error in this system. A small difference in miRNA levels between experimental samples can be biologically meaningful as these entities can affect multiple targets in a pathway. This study examined the suitability of six commercially available reference genes (RNU1A, RNU5A, RNU6B, SNORD25, SCARNA17, and SNORA73A) in maternal-fetal tissues from healthy and spontaneously arresting/dying conceptuses from sows were separately analyzed at gestation day 20. Comparisons were also made with non-pregnant endometrial tissues from sows. Spontaneous fetal loss is a prime concern to the commercial pork industry. Our laboratory has previously identified deficits in vasculature development at maternal-fetal interface as one of the major participating causes of fetal loss. Using this well-established model, we have extended our studies to identify suitable microRNA reference genes. A methodical approach to assessing suitability was adopted using standard curve and melting curve analysis, PCR product sequencing, real time PCR expression in a panel of gestational tissues, and geNorm and NormFinder analysis. Our quantitative real time PCR analysis confirmed expression of all 6 reference genes in maternal and fetal tissues. All genes were uniformly expressed in tissues from healthy and spontaneously arresting conceptus attachment sites. Comparisons between tissue types (maternal/fetal/non-pregnant) revealed significant differences for RNU5A, RNU6B, SCARNA17, and SNORA73A expression. Based on our methodical assessment of all 6 reference genes, results suggest that RNU1A is the most stable reference gene for porcine pregnancy studies.

Identification of normalization factors for quantitative real-time RT-PCR analysis of gene expression in Pacific abalone Haliotis discus hannai

NASA Astrophysics Data System (ADS)

Qiu, Reng; Sun, Boguang; Fang, Shasha; Sun, Li; Liu, Xiao

2013-03-01

Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is widely used in studies of gene expression. In most of these studies, housekeeping genes are used as internal references without validation. To identify appropriate reference genes for qRT-PCR in Pacific abalone Haliotis discus hannai, we examined the transcription stability of six housekeeping genes in abalone tissues in the presence and absence of bacterial infection. For this purpose, abalone were infected with the bacterial pathogen Vibrio anguillarum for 12 h and 48 h. The mRNA levels of the housekeeping genes in five tissues (digestive glands, foot muscle, gill, hemocyte, and mantle) were determined by qRT-PCR. The PCR data was subsequently analyzed with the geNorm and NormFinder algorithms. The results show that in the absence of bacterial infection, elongation factor-1-alpha and beta-actin were the most stably expressed genes in all tissues, and thus are suitable as cross-tissue type normalization factors. However, we did not identify any universal reference genes post infection because the most stable genes varied between tissue types. Furthermore, for most tissues, the optimal reference genes identified by both algorithms at 12 h and 48 h post-infection differed. These results indicate that bacterial infection induced significant changes in the expression of abalone housekeeping genes in a manner that is dependent on tissue type and duration of infection. As a result, different normalization factors must be used for different tissues at different infection points.

Validation of a T1 and T2* leakage correction method based on multi-echo DSC-MRI using MION as a reference standard

PubMed Central

Stokes, Ashley M.; Semmineh, Natenael; Quarles, C. Chad

2015-01-01

Purpose A combined biophysical- and pharmacokinetic-based method is proposed to separate, quantify, and correct for both T1 and T2* leakage effects using dual-echo DSC acquisitions to provide more accurate hemodynamic measures, as validated by a reference intravascular contrast agent (CA). Methods Dual-echo DSC-MRI data were acquired in two rodent glioma models. The T1 leakage effects were removed and also quantified in order to subsequently correct for the remaining T2* leakage effects. Pharmacokinetic, biophysical, and combined biophysical and pharmacokinetic models were used to obtain corrected cerebral blood volume (CBV) and cerebral blood flow (CBF), and these were compared with CBV and CBF from an intravascular CA. Results T1-corrected CBV was significantly overestimated compared to MION CBV, while T1+T2*-correction yielded CBV values closer to the reference values. The pharmacokinetic and simplified biophysical methods showed similar results and underestimated CBV in tumors exhibiting strong T2* leakage effects. The combined method was effective for correcting T1 and T2* leakage effects across tumor types. Conclusions Correcting for both T1 and T2* leakage effects yielded more accurate measures of CBV. The combined correction method yields more reliable CBV measures than either correction method alone, but for certain brain tumor types (e.g., gliomas) the simplified biophysical method may provide a robust and computationally efficient alternative. PMID:26362714

Ultrasound Imaging Using Diffraction Tomography in a Cylindrical Geometry

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

Chambers, D H; Littrup, P

2002-01-24

Tomographic images of tissue phantoms and a sample of breast tissue have been produced from an acoustic synthetic array system for frequencies near 500 kHz. The images for sound speed and attenuation show millimeter resolution and demonstrate the feasibility of obtaining high-resolution tomographic images with frequencies that can deeply penetrate tissue. The image reconstruction method is based on the Born approximation to acoustic scattering and is a simplified version of a method previously used by Andre (Andre, et. al., Int. J. Imaging Systems and Technology, Vol 8, No. 1, 1997) for a circular acoustic array system. The images have comparablemore » resolution to conventional ultrasound images at much higher frequencies (3-5 MHz) but with lower speckle noise. This shows the potential of low frequency, deeply penetrating, ultrasound for high-resolution quantitative imaging.« less

Exome copy number variation detection: Use of a pool of unrelated healthy tissue as reference sample.

PubMed

Wenric, Stephane; Sticca, Tiberio; Caberg, Jean-Hubert; Josse, Claire; Fasquelle, Corinne; Herens, Christian; Jamar, Mauricette; Max, Stéphanie; Gothot, André; Caers, Jo; Bours, Vincent

2017-01-01

An increasing number of bioinformatic tools designed to detect CNVs (copy number variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been published in the recent years. The idea of using a pool of unrelated healthy DNA as reference has previously been formulated but not thoroughly validated. As of today, the gold standard for CNV calling is still aCGH but there is an increasing interest in detecting CNVs by exome sequencing. We propose to design a metric allowing the comparison of two CNV profiles, independently of the technique used and assessed the validity of using a pool of unrelated healthy DNA instead of a matched healthy tissue as reference in exome-based CNV detection. We compared the CNV profiles obtained with three different approaches (aCGH, exome sequencing with a matched healthy tissue as reference, exome sequencing with a pool of eight unrelated healthy tissue as reference) on three multiple myeloma samples. We show that the usual analyses performed to compare CNV profiles (deletion/amplification ratios and CNV size distribution) lack in precision when confronted with low LRR values, as they only consider the binary status of each CNV. We show that the metric-based distance constitutes a more accurate comparison of two CNV profiles. Based on these analyses, we conclude that a reliable picture of CNV alterations in multiple myeloma samples can be obtained from whole-exome sequencing in the absence of a matched healthy sample. © 2016 WILEY PERIODICALS, INC.

Highly Simplified Reddish Orange Phosphorescent Organic Light-Emitting Diodes Incorporating a Novel Carrier- and Exciton-Confining Spiro-Exciplex-Forming Host for Reduced Efficiency Roll-off.

PubMed

Xu, Ting; Zhang, Ye-Xin; Wang, Bo; Huang, Chen-Chao; Murtaza, Imran; Meng, Hong; Liao, Liang-Sheng

2017-01-25

A novel exciplex-forming host is applied so as to design highly simplified reddish orange light-emitting diodes (OLEDs) with low driving voltage, high efficiency, and an extraordinarily low efficiency roll-off, by combining N,N-10-triphenyl-10H-spiro [acridine-9,9'-fluoren]-3'-amine (SAFDPA) with 4,7-diphenyl-1,10-phenanthroline (Bphen) doped with trivalent iridium complex bis(2-methyldibenzo[f,h]quinoxaline) (acetylacetonate)iridium(III) (Ir(MDQ) 2 (acac)). The reddish orange OLEDs achieve a strikingly high power efficiency (PE) of 31.80 lm/W with an ultralow threshold voltage of 2.24 V which is almost equal to the triplet energy level of the phosphorescent reddish orange emitting dopant. The power efficiency of the device with the exciplex-forming host is enhanced, achieving 36.2% mainly owing to the lower operating voltage by the novel exciplex forming cohost, compared with the reference device (23.54 lm/W). Moreover, the OLEDs show extraordinarily low current efficiency (CE) roll-off to 1.41% at the brightness from 500 to 5000 cd/m 2 with a maximal CE of 32.87 cd/A (EQE max = 11.01%). The devices display a good reddish orange color (CIE of (0.628, 0.372) at 500 cd/m 2 ) nearly without color shift with increasing brightness. Co-host architecture phosphorescent OLEDs show a simpler device structure, lower working voltage, and a better efficiency and stability than those of the reference devices without the cohost architecture, which helps to simplify the OLED structure, lower the cost, and popularize OLED technology.

International Conference on Environmental Ergonomics (4th) Held in Austin, Texas on 1-5 October 1990

DTIC Science & Technology

1991-01-15

measurement error in relation 94 Ducharme, Michel B. to clothing and tissue insulation -- a simplified view 5 Reischl, Uwe Breathability measurements...PROTECTIVE CLOTHING Uwe Reischl, Francis N. Dukes-Dobos, Thomas E. Bernard and Kai Buller Department of Environmental and Occupational Health 0 College of...understood. 117 BREATHING APPARATUS AND VENTILATION William P. Morgan Biodynamics Laboratory University of Wisconsin- Madison 0 Madison , Wisconsin USA

Toxic Hazards Research Unit Annual Technical Report: 1974

DTIC Science & Technology

1974-07-01

Deuterium Fluoride 130 iv TABLE OF CONTENTS (CONT’D) Section Page Use of Ion Selective Electrodes in Inhalation Toxicology 135 Analysis of Coal Tar...Chamber Atmospheres 144 Tissue Coal Tar Analysis 145 Fractionation of Crude Coal Tar 146 Blood Cyanide (CN - ) Analysis 155 Engineering Programs 162...flask temperature 134 21 System for analysis of chamber contaminant concentration by specific ion electrode 137 22 Simplified scheme of coal tar

Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism

PubMed Central

Abehsera, Shai; Glazer, Lilah; Tynyakov, Jenny; Plaschkes, Inbar; Chalifa-Caspi, Vered; Khalaila, Isam; Aflalo, Eliahu D.; Sagi, Amir

2015-01-01

In crustaceans, like all arthropods, growth is accompanied by a molting cycle. This cycle comprises major physiological events in which mineralized chitinous structures are built and degraded. These events are in turn governed by genes whose patterns of expression are presumably linked to the molting cycle. To study these genes we performed next generation sequencing and constructed a molt-related transcriptomic library from two exoskeletal-forming tissues of the crayfish Cherax quadricarinatus, namely the gastrolith and the mandible cuticle-forming epithelium. To simplify the study of such a complex process as molting, a novel approach, binary patterning of gene expression, was employed. This approach revealed that key genes involved in the synthesis and breakdown of chitin exhibit a molt-related pattern in the gastrolith-forming epithelium. On the other hand, the same genes in the mandible cuticle-forming epithelium showed a molt-independent pattern of expression. Genes related to the metabolism of glucosamine-6-phosphate, a chitin precursor synthesized from simple sugars, showed a molt-related pattern of expression in both tissues. The binary patterning approach unfolds typical patterns of gene expression during the molt cycle of a crustacean. The use of such a simplifying integrative tool for assessing gene patterning seems appropriate for the study of complex biological processes. PMID:25919476

Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi.

PubMed

Huang, Xuena; Gao, Yangchun; Jiang, Bei; Zhou, Zunchun; Zhan, Aibin

2016-01-15

As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species. Copyright © 2015 Elsevier B.V. All rights reserved.

A general model for the absorption of ultrasound by biological tissues and experimental verification.

PubMed

Jongen, H A; Thijssen, J M; van den Aarssen, M; Verhoef, W A

1986-02-01

In this paper, a closed-form expression is derived for the absorption of ultrasound by biological tissues. In this expression, the viscothermal and viscoelastic theories of relaxation processes are combined. Three relaxation time distribution functions are introduced, and it is assumed that each of these distributions can be described by an identical and simple hyperbolic function. Several simplifying assumptions had to be made to enable the experimental verification of the derived closed-form expression of the absorption coefficient. The simplified expression leaves two degrees of freedom and it was fitted to the experimental data obtained from homogenized beef liver. The model produced a considerably better fit to the data than other, more pragmatic models for the absorption coefficient as a function of frequency that could be found in the literature. Scattering in beef liver was estimated indirectly from the difference between attenuation in in vitro liver tissue as compared to absorption in a homogenate. The frequency dependence of the scattering coefficient could be described by a power law with a power of the order of 2. A comparable figure was found in direct backscattering measurements, performed at our laboratory with the same liver samples [Van den Aarssen et al., J. Acoust. Soc. Am. (to be published)]. A model for scattering recently proposed by Sehgal and Greenleaf [Ultrason. Imag. 6, 60-80 (1984)] was fitted to the scattering data as well. This latter model enabled the estimation of a maximum scatterer distance, which appeared to be of the order of 25 micron.

Measurements of the Exerted Pressure by Pelvic Circumferential Compression Devices

PubMed Central

Knops, Simon P; van Riel, Marcel P.J.M; Goossens, Richard H.M; van Lieshout, Esther M.M; Patka, Peter; Schipper, Inger B

2010-01-01

Background: Data on the efficacy and safety of non-invasive Pelvic Circumferential Compression Devices (PCCDs) is limited. Tissue damage may occur if a continuous pressure on the skin exceeding 9.3 kPa is sustained for more than two or three hours. The aim of this study was to gain insight into the pressure build-up at the interface, by measuring the PCCD-induced pressure when applying pulling forces to three different PCCDs (Pelvic Binder® , SAM-Sling ® and T-POD® ) in a simplified model. Methods: The resulting exerted pressures were measured at four ‘anatomical’ locations (right, left, posterior and anterior) in a model using a pressure measurement system consisting of pressure cuffs. Results: The exerted pressure varied substantially between the locations as well as between the PCCDs. Maximum pressures ranged from 18.9-23.3 kPa and from 19.2-27.5 kPa at the right location and left location, respectively. Pressures at the posterior location stayed below 18 kPa. At the anterior location pressures varied markedly between the different PCCDs. Conclusion: The circumferential compression by the different PCCDs showed high pressures measured at the four locations using a simplified model. Difference in design and functional characteristics of the PCCDs resulted in different pressure build-up at the four locations. When following the manufacturer’s instructions, the exerted pressure of all three PCCDs tested exceeded the tissue damaging level (9.3 kPa). In case of prolonged use in a clinical situation this might put patients at risk for developing tissue damage. PMID:20361001

High-resolution confocal imaging of wall ingrowth deposition in plant transfer cells: Semi-quantitative analysis of phloem parenchyma transfer cell development in leaf minor veins of Arabidopsis.

PubMed

Nguyen, Suong T T; McCurdy, David W

2015-04-23

Transfer cells (TCs) are trans-differentiated versions of existing cell types designed to facilitate enhanced membrane transport of nutrients at symplasmic/apoplasmic interfaces. This transport capacity is conferred by intricate wall ingrowths deposited secondarily on the inner face of the primary cell wall, hence promoting the potential trans-membrane flux of solutes and consequently assigning TCs as having key roles in plant growth and productivity. However, TCs are typically positioned deep within tissues and have been studied mostly by electron microscopy. Recent advances in fluorophore labelling of plant cell walls using a modified pseudo-Schiff-propidium iodide (mPS-PI) staining procedure in combination with high-resolution confocal microscopy have allowed visualization of cellular details of individual tissue layers in whole mounts, hence enabling study of tissue and cellular architecture without the need for tissue sectioning. Here we apply a simplified version of the mPS-PI procedure for confocal imaging of cellulose-enriched wall ingrowths in vascular TCs at the whole tissue level. The simplified mPS-PI staining procedure produced high-resolution three-dimensional images of individual cell types in vascular bundles and, importantly, wall ingrowths in phloem parenchyma (PP) TCs in minor veins of Arabidopsis leaves and companion cell TCs in pea. More efficient staining of tissues was obtained by replacing complex clearing procedures with a simple post-fixation bleaching step. We used this modified procedure to survey the presence of PP TCs in other tissues of Arabidopsis including cotyledons, cauline leaves and sepals. This high-resolution imaging enabled us to classify different stages of wall ingrowth development in Arabidopsis leaves, hence enabling semi-quantitative assessment of the extent of wall ingrowth deposition in PP TCs at the whole leaf level. Finally, we conducted a defoliation experiment as an example of using this approach to statistically analyze responses of PP TC development to leaf ablation. Use of a modified mPS-PI staining technique resulted in high-resolution confocal imaging of polarized wall ingrowth deposition in TCs. This technique can be used in place of conventional electron microscopy and opens new possibilities to study mechanisms determining polarized deposition of wall ingrowths and use reverse genetics to identify regulatory genes controlling TC trans-differentiation.

Certification of the methylmercury content in SRM 2977 mussel tissue (organic contaminants and trace elements) and SRM 1566b oyster tissue.

PubMed

Tutschku, S; Schantz, M M; Horvat, M; Logar, M; Akagi, H; Emons, H; Levenson, M; Wise, S A

2001-02-01

The methylmercury content in two new marine bivalve mollusk tissue Standard Reference Materials (SRMs) has been certified using results of analyses from the National Institute of Standards and Technology (NIST) and two other laboratories. The certified concentrations of methylmercury were established based on the results from four and six different (independent) analytical methods, respectively, for SRM 1566b Oyster Tissue (13.2 +/- 0.7 microg/kg) and SRM 2977 Mussel Tissue (organic contaminants and trace elements) (36.2 +/- 1.7 microg/kg). The certified concentration of methylmercury in SRM 1566b is among the lowest in any certified reference material (CRM).

Catheter Insertion Reference Trajectory Construction Method Using Photoelastic Stress Analysis for Quantification of Respect for Tissue During Endovascular Surgery Simulation

NASA Astrophysics Data System (ADS)

Tercero, Carlos; Ikeda, Seiichi; Fukuda, Toshio; Arai, Fumihito; Negoro, Makoto; Takahashi, Ikuo

2011-10-01

There is a need to develop quantitative evaluation for simulator based training in medicine. Photoelastic stress analysis can be used in human tissue modeling materials; this enables the development of simulators that measure respect for tissue. For applying this to endovascular surgery, first we present a model of saccular aneurism where stress variation during micro-coils deployment is measured, and then relying on a bi-planar vision system we measure a catheter trajectory and compare it to a reference trajectory considering respect for tissue. New photoelastic tissue modeling materials will expand the applications of this technology to other medical training domains.

Origin of the subepidermal tissue in Piper L. leaves.

PubMed

Nakamura, A T; Simão, E; Silva, L; Torres, G A

2015-05-01

Studies on the anatomy of Piper leaves demonstrate the presence of a subepidermal tissue distinct from the adjacent epidermis, which cells show thin walls and hyaline contents. Some authors consider such cells a hypodermal tissue, while others refer to them as components of a multiple epidermis. In this study, the nature of this subepidermal tissue was investigated through the analysis of leaf ontogeny in three Piper species. The analysis showed that the referred tissue originates from the ground meristem and, thus, should be considered a hypodermis. The studied species suggests that the role of the hypodermis would be to protect the photosynthetic apparatus from excess light, regulating the intensity of light reaching the chlorophyll parenchyma.

[Review on community herbal monographs for traditional herbal medicinal products].

PubMed

Zou, Wenjun; Qu, Liping; Ye, Zuguang; Ji, Jianxin; Li, Bogang

2011-12-01

This article discusses the characteristics of cmmunity herbal monographs for traditional herbal medicinal products and its establishment procedure. It also reviews the new development of cmmunity traditional herbal monographs. The purpose is to clarify the relationship between cmmunity herbal monographs and simplified registration for traditional herbal medicinal product in European Union and provide reference to the registration of taditional Chinese mdicinal products in Europe.

Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs.

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.

Bioprinting of Cartilage and Skin Tissue Analogs Utilizing a Novel Passive Mixing Unit Technique for Bioink Precellularization

PubMed Central

Thayer, Patrick Scott; Orrhult, Linnea Stridh; Martínez, Héctor

2018-01-01

Bioprinting is a powerful technique for the rapid and reproducible fabrication of constructs for tissue engineering applications. In this study, both cartilage and skin analogs were fabricated after bioink pre-cellularization utilizing a novel passive mixing unit technique. This technique was developed with the aim to simplify the steps involved in the mixing of a cell suspension into a highly viscous bioink. The resolution of filaments deposited through bioprinting necessitates the assurance of uniformity in cell distribution prior to printing to avoid the deposition of regions without cells or retention of large cell clumps that can clog the needle. We demonstrate the ability to rapidly blend a cell suspension with a bioink prior to bioprinting of both cartilage and skin analogs. Both tissue analogs could be cultured for up to 4 weeks. Histological analysis demonstrated both cell viability and deposition of tissue specific extracellular matrix (ECM) markers such as glycosaminoglycans (GAGs) and collagen I respectively. PMID:29364216

Advantages of a dual-tracer model over reference tissue models for binding potential measurement in tumors

PubMed Central

Tichauer, K M; Samkoe, K S; Klubben, W S; Hasan, T; Pogue, B W

2012-01-01

The quantification of tumor molecular expression in vivo could have a significant impact for informing and monitoring immerging targeted therapies in oncology. Molecular imaging of targeted tracers can be used to quantify receptor expression in the form of a binding potential (BP) if the arterial input curve or a surrogate of it is also measured. However, the assumptions of the most common approaches (reference tissue models) may not be valid for use in tumors. In this study, the validity of reference tissue models is investigated for use in tumors experimentally and in simulations. Three different tumor lines were grown subcutaneously in athymic mice and the mice were injected with a mixture of an epidermal growth factor receptor- (EGFR-) targeted fluorescent tracer and an untargeted fluorescent tracer. A one-compartment plasma input model demonstrated that the transport kinetics of both tracers were significantly different between tumors and all potential reference tissues, and using the reference tissue model resulted in a theoretical underestimation in BP of 50 ± 37%. On the other hand, the targeted and untargeted tracers demonstrated similar transport kinetics, allowing a dual-tracer approach to be employed to accurately estimate binding potential (with a theoretical error of 0.23 ± 9.07%). These findings highlight the potential for using a dual-tracer approach to quantify receptor expression in tumors with abnormal hemodynamics, possibly to inform the choice or progress of molecular cancer therapies. PMID:23022732

Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues.

PubMed

Mangeot-Peter, Lauralie; Legay, Sylvain; Hausman, Jean-Francois; Esposito, Sergio; Guerriero, Gea

2016-09-15

Gene expression profiling via quantitative real-time PCR is a robust technique widely used in the life sciences to compare gene expression patterns in, e.g., different tissues, growth conditions, or after specific treatments. In the field of plant science, real-time PCR is the gold standard to study the dynamics of gene expression and is used to validate the results generated with high throughput techniques, e.g., RNA-Seq. An accurate relative quantification of gene expression relies on the identification of appropriate reference genes, that need to be determined for each experimental set-up used and plant tissue studied. Here, we identify suitable reference genes for expression profiling in stems of textile hemp (Cannabis sativa L.), whose tissues (isolated bast fibres and core) are characterized by remarkable differences in cell wall composition. We additionally validate the reference genes by analysing the expression of putative candidates involved in the non-oxidative phase of the pentose phosphate pathway and in the first step of the shikimate pathway. The goal is to describe the possible regulation pattern of some genes involved in the provision of the precursors needed for lignin biosynthesis in the different hemp stem tissues. The results here shown are useful to design future studies focused on gene expression analyses in hemp.

Lysimetric evaluation of simplified surface energy balance approach in the Texas high plains

USGS Publications Warehouse

Gowda, P.H.; Senay, G.B.; Howell, T.A.; Marek, T.H.

2009-01-01

Numerous energy balance (EB) algorithms have been developed to make use of remote sensing data to estimate evapotranspiration (ET) regionally. However, most EB models are complex to use and efforts are being made to simplify procedures mainly through the scaling of reference ET. The Simplified Surface Energy Balance (SSEB) is one such method. This approach has never been evaluated using measured ET data. In this study, the SSEB approach was applied to 14 Landsat TM images covering a major portion of the Southern High Plains that were acquired during 2006 and 2007 cropping seasons. Performance of the SSEB was evaluated by comparing estimated ET with measured daily ET from four large monolithic lysimeters at the USDA-ARS Conservation and Production Research Laboratory, Bushland, Texas. Statistical evaluation of results indicated that the SSEB accounted for 84% of the variability in the measured ET values with a slope and intercept of 0.75 and 1.1 mm d-1, respectively. Considering the minimal amount of ancillary data required and excellent performance in predicting daily ET, the SSEB approach is a promising tool for mapping ET in the semiarid Texas High Plains and in other parts of the world with similar hydro-climatic conditions.

Lysimetric Evaluation of Simplified Surface Energy Balance Approach in the Texas High Plains

USGS Publications Warehouse

Senay, Gabriel B.; Gowda, P.H.; Howell, T.A.; Marek, T.H.

2009-01-01

Numerous energy balance (EB) algorithms have been developed to make use of remote sensing data to estimate evapotranspiration (ET) regionally. However, most EB models are complex to use and efforts are being made to simplify procedures mainly through the scaling of reference ET. The Simplified Surface Energy Balance (SSEB) is one such method. This approach has never been evaluated using measured ET data. In this study, the SSEB approach was applied to fourteen Landsat TM images covering a major portion of the Southern High Plains that were acquired during 2006 and 2007 cropping seasons. Performance of the SSEB was evaluated by comparing estimated ET with measured daily ET from four large monolithic lysimeters at the USDA-ARS Conservation and Production Research Laboratory, Bushland, Texas. Statistical evaluation of results indicated that the SSEB accounted for 84% of the variability in the measured ET values with a slope and intercept of 0.75 and 1.1 mm d-1, respectively. Considering the minimal amount of ancillary data required and excellent performance in predicting daily ET, the SSEB approach is a promising tool for mapping ET in the semiarid Texas High Plains and in other parts of the world with similar hydro-climatic conditions.

Using Heavy Metal Content and Lipid Peroxidation Indicators in the Tissues of the Mussel Crenomytilus grayanus for Pollution Assessment After Marine Environmental Remediation.

PubMed

Belcheva, Nina; Istomina, Alexandra; Dovzhenko, Nadezhda; Lishavskaya, Tatiana; Chelomin, Victor

2015-10-01

We examined the effects of environmental remediation on the heavy metal concentration and lipid peroxidation activity in the digestive gland and gills of the marine mussel Crenomytilus grayanus. Changes in heavy metal concentrations and lipid peroxidation biomarkers in the tissues of mussels collected at a contaminated site were compared with those obtained from a reference site. Prior to remediation the concentration of Pb, Cu, Cd, Fe and Zn and the levels of malondialdehyde, conjugated dienes and lipofuscin in mussels collected from the contaminated site were significantly increased compared with those obtained from the reference site. Three years after remediation, these parameters did not significantly exceed the reference site parameters, except Pb, whose concentration, though markedly decreased, yet was much higher than in tissues of mussels from the reference site.

SPM analysis of parametric (R)-[11C]PK11195 binding images: plasma input versus reference tissue parametric methods.

PubMed

Schuitemaker, Alie; van Berckel, Bart N M; Kropholler, Marc A; Veltman, Dick J; Scheltens, Philip; Jonker, Cees; Lammertsma, Adriaan A; Boellaard, Ronald

2007-05-01

(R)-[11C]PK11195 has been used for quantifying cerebral microglial activation in vivo. In previous studies, both plasma input and reference tissue methods have been used, usually in combination with a region of interest (ROI) approach. Definition of ROIs, however, can be labourious and prone to interobserver variation. In addition, results are only obtained for predefined areas and (unexpected) signals in undefined areas may be missed. On the other hand, standard pharmacokinetic models are too sensitive to noise to calculate (R)-[11C]PK11195 binding on a voxel-by-voxel basis. Linearised versions of both plasma input and reference tissue models have been described, and these are more suitable for parametric imaging. The purpose of this study was to compare the performance of these plasma input and reference tissue parametric methods on the outcome of statistical parametric mapping (SPM) analysis of (R)-[11C]PK11195 binding. Dynamic (R)-[11C]PK11195 PET scans with arterial blood sampling were performed in 7 younger and 11 elderly healthy subjects. Parametric images of volume of distribution (Vd) and binding potential (BP) were generated using linearised versions of plasma input (Logan) and reference tissue (Reference Parametric Mapping) models. Images were compared at the group level using SPM with a two-sample t-test per voxel, both with and without proportional scaling. Parametric BP images without scaling provided the most sensitive framework for determining differences in (R)-[11C]PK11195 binding between younger and elderly subjects. Vd images could only demonstrate differences in (R)-[11C]PK11195 binding when analysed with proportional scaling due to intersubject variation in K1/k2 (blood-brain barrier transport and non-specific binding).

[Consideration about chemistry, manufacture and control (CMC) key problems in simplified registration of classical traditional Chinese medicine excellent prescriptions].

PubMed

Wang, Zhi-Min; Liu, Ju-Yan; Liu, Xiao-Qian; Wang, De-Qin; Yan, Li-Hua; Zhu, Jin-Jin; Gao, Hui-Min; Li, Chun; Wang, Jin-Yu; Li, Chu-Yuan; Ni, Qing-Chun; Huang, Ji-Sheng; Lin, Juan

2017-05-01

As an outstanding representative of traditional Chinese medicine(TCM) prescriptions accumulated from famous TCM doctors' clinical experiences in past dynasties, classical TCM excellent prescriptions (cTCMeP) are the most valuable part of TCM system. To support the research and development of cTCMeP, a series of regulations and measures were issued to encourage its simplified registration. There is still a long-way to go because many key problems and puzzles about technology, registration and administration in cTCMeP R&D process are not resolved. Based on the analysis of registration and management regulations of botanical drug products in FDA of USA and Japan, and EMA of Europe, the possible key problems and countermeasures in chemistry, manufacture and control (CMC) of simplified registration of cTCMeP were analyzed on the consideration of its actual situation. The method of "reference decoction extract by traditional prescription" (RDETP) was firstly proposed as standard to evaluate the quality and preparation uniformity between the new developing product under simplified registration and traditional original usages of cTCMeP, instead of Standard Decoction method in Japan. "Totality of the evidence" approach, mass balance and bioassay/biological assay of cTCMeP were emphatically suggested to introduce to the quality uniformity evaluation system in the raw drug material, drug substance and final product between the modern product and traditional decoction. Copyright© by the Chinese Pharmaceutical Association.

Breast Cancer Tissue Bioreactor for Direct Interrogation and Observation of Response to Antitumor Therapies

DTIC Science & Technology

2012-07-01

regulate microfluidic flow rates within the TTB, including flow channel height variation and incorporation of valves (see Figure 2 and Supplemental...cartridge. As an alternative to individual channel TURN valve -adjusted flow regulators, we investigated use of pre-fabricated microfluidic flow resistance...Small Parts, Inc. and B) Microfluidic manifolds with built-in TURN valves . Supplemental Figure S3. Simplified 2D and 3D diffusional model

Experimental verification of stopping-power prediction from single- and dual-energy computed tomography in biological tissues

NASA Astrophysics Data System (ADS)

Möhler, Christian; Russ, Tom; Wohlfahrt, Patrick; Elter, Alina; Runz, Armin; Richter, Christian; Greilich, Steffen

2018-01-01

An experimental setup for consecutive measurement of ion and x-ray absorption in tissue or other materials is introduced. With this setup using a 3D-printed sample container, the reference stopping-power ratio (SPR) of materials can be measured with an uncertainty of below 0.1%. A total of 65 porcine and bovine tissue samples were prepared for measurement, comprising five samples each of 13 tissue types representing about 80% of the total body mass (three different muscle and fatty tissues, liver, kidney, brain, heart, blood, lung and bone). Using a standard stoichiometric calibration for single-energy CT (SECT) as well as a state-of-the-art dual-energy CT (DECT) approach, SPR was predicted for all tissues and then compared to the measured reference. With the SECT approach, the SPRs of all tissues were predicted with a mean error of (-0.84  ±  0.12)% and a mean absolute error of (1.27  ±  0.12)%. In contrast, the DECT-based SPR predictions were overall consistent with the measured reference with a mean error of (-0.02  ±  0.15)% and a mean absolute error of (0.10  ±  0.15)%. Thus, in this study, the potential of DECT to decrease range uncertainty could be confirmed in biological tissue.

Generation of branching ureteric bud tissues from human pluripotent stem cells.

PubMed

Mae, Shin-Ichi; Ryosaka, Makoto; Toyoda, Taro; Matsuse, Kyoko; Oshima, Yoichi; Tsujimoto, Hiraku; Okumura, Shiori; Shibasaki, Aya; Osafune, Kenji

2018-01-01

Recent progress in kidney regeneration research is noteworthy. However, the selective and robust differentiation of the ureteric bud (UB), an embryonic renal progenitor, from human pluripotent stem cells (hPSCs) remains to be established. The present study aimed to establish a robust induction method for branching UB tissue from hPSCs towards the creation of renal disease models. Here, we found that anterior intermediate mesoderm (IM) differentiates from anterior primitive streak, which allowed us to successfully develop an efficient two-dimensional differentiation method of hPSCs into Wolffian duct (WD) cells. We also established a simplified procedure to generate three-dimensional WD epithelial structures that can form branching UB tissues. This system may contribute to hPSC-based regenerative therapies and disease models for intractable disorders arising in the kidney and lower urinary tract. Copyright © 2017 Elsevier Inc. All rights reserved.

Detection of toxoplasmosis in experimentally infected goats by PCR.

PubMed

Sreekumar, C; Rao, J R; Mishra, A K; Ray, D; Joshi, P; Singh, R K

2004-05-15

PCR was used to diagnose toxoplasmosis in two pairs of Barbari goats infected by oral administration of doses of either 10(4) or 10(5) oocysts of Toxoplasma gondii. Blood and lymph node aspirates were collected from the infected goats and control goat at intervals, and tissues were also collected from a fetus that was aborted and a doe that died during the trial. Both processed and unprocessed samples were used for the PCR, using primers directed to the multicopy B1 gene. None of the blood samples was positive, but a specific signal was obtained from the lymph node aspirates after partial DNA extraction. Direct PCR of the lung, muscle and mesenteric lymph node of the doe and lung tissue of the aborted fetus yielded the target fragment. The simplified PCR protocols, including partial DNA extraction and direct assay of lung tissue, were effective for the diagnosis of toxoplasmosis.

Enhancing Aesthetic Outcomes of Soft Tissue Coverage of the Hand

PubMed Central

Rehim, Shady A.; Kowalski, Evan; Chung, Kevin C.

2016-01-01

Hand aesthetics in general and aesthetic refinements of soft-tissue coverage of the hand in particular have been increasingly considered over the past few years. Advancements of microsurgery together with the traditional methods of tissue transfer have expanded the armamentarium of the reconstructive surgeon, thus shifting the reconstructive paradigm from simply ‘filling the defect’ to reconstructive refinement to provide the best functional and aesthetic results. However, drawing the boundary between what does and what does not constitute ‘aesthetic’ reconstruction of the hand is not straightforward. The selection amongst the vast amount of currently available reconstructive methods and the difficulties in objectively measuring or quantifying aesthetics has made this task complex and rather arbitrary. In this article we divide the hand into several units and subunits to simplify our understanding of the basic functional and aesthetic requirements of these regions that may ultimately bring order to complexity. PMID:25626826

Spectral imaging perspective on cytomics.

PubMed

Levenson, Richard M

2006-07-01

Cytomics involves the analysis of cellular morphology and molecular phenotypes, with reference to tissue architecture and to additional metadata. To this end, a variety of imaging and nonimaging technologies need to be integrated. Spectral imaging is proposed as a tool that can simplify and enrich the extraction of morphological and molecular information. Simple-to-use instrumentation is available that mounts on standard microscopes and can generate spectral image datasets with excellent spatial and spectral resolution; these can be exploited by sophisticated analysis tools. This report focuses on brightfield microscopy-based approaches. Cytological and histological samples were stained using nonspecific standard stains (Giemsa; hematoxylin and eosin (H&E)) or immunohistochemical (IHC) techniques employing three chromogens plus a hematoxylin counterstain. The samples were imaged using the Nuance system, a commercially available, liquid-crystal tunable-filter-based multispectral imaging platform. The resulting data sets were analyzed using spectral unmixing algorithms and/or learn-by-example classification tools. Spectral unmixing of Giemsa-stained guinea-pig blood films readily classified the major blood elements. Machine-learning classifiers were also successful at the same task, as well in distinguishing normal from malignant regions in a colon-cancer example, and in delineating regions of inflammation in an H&E-stained kidney sample. In an example of a multiplexed ICH sample, brown, red, and blue chromogens were isolated into separate images without crosstalk or interference from the (also blue) hematoxylin counterstain. Cytomics requires both accurate architectural segmentation as well as multiplexed molecular imaging to associate molecular phenotypes with relevant cellular and tissue compartments. Multispectral imaging can assist in both these tasks, and conveys new utility to brightfield-based microscopy approaches. Copyright 2006 International Society for Analytical Cytology.

Efficient Adaptive FIR and IIR Filters.

DTIC Science & Technology

1979-12-01

Squared) algorithm. -An analysis of the simplified gradient approach is presented and confirmed experimentally for the specific example of an adaptive line...APPENDIX A - SIMULATION 130 A.1 - THE SIMULATION METHOD 130 A.2 - FIR SIMULATION PRO)GRAM 133 A.3 - IIR SIMULATION PROGRAM 136 APPENDIX B - RANDOM...surface. The generation of the reference signal is a key consi- deration in adaptive filter implementation. There are various practical methods as

Multidisciplinary Thermal Analysis of Hot Aerospace Structures

DTIC Science & Technology

2010-05-02

Seidel iteration. Such a strategy simplifies explicit/implicit treatment , subcycling, load balancing, software modularity, and replacements as better... Stefan -Boltzmann constant , E is the emissivity of the surface, f is the form factor from the surface to the reference surface, Br is the temperature of...Stokes equations using Gauss- Seidel line Relaxation, Computers and Fluids, 17, pp.l35-150, 1989. [22] Hung C.M. and MacCormack R.W., Numerical

A Methodology for Benchmarking Relational Database Machines,

DTIC Science & Technology

1984-01-01

user benchmarks is to compare the multiple users to the best-case performance The data for each query classification coll and the performance...called a benchmark. The term benchmark originates from the markers used by sur - veyors in establishing common reference points for their measure...formatted databases. In order to further simplify the problem, we restrict our study to those DBMs which support the relational model. A sur - vey

A pediatric brain structure atlas from T1-weighted MR images

NASA Astrophysics Data System (ADS)

Shan, Zuyao Y.; Parra, Carlos; Ji, Qing; Ogg, Robert J.; Zhang, Yong; Laningham, Fred H.; Reddick, Wilburn E.

2006-03-01

In this paper, we have developed a digital atlas of the pediatric human brain. Human brain atlases, used to visualize spatially complex structures of the brain, are indispensable tools in model-based segmentation and quantitative analysis of brain structures. However, adult brain atlases do not adequately represent the normal maturational patterns of the pediatric brain, and the use of an adult model in pediatric studies may introduce substantial bias. Therefore, we proposed to develop a digital atlas of the pediatric human brain in this study. The atlas was constructed from T1 weighted MR data set of a 9 year old, right-handed girl. Furthermore, we extracted and simplified boundary surfaces of 25 manually defined brain structures (cortical and subcortical) based on surface curvature. Higher curvature surfaces were simplified with more reference points; lower curvature surfaces, with fewer. We constructed a 3D triangular mesh model for each structure by triangulation of the structure's reference points. Kappa statistics (cortical, 0.97; subcortical, 0.91) indicated substantial similarities between the mesh-defined and the original volumes. Our brain atlas and structural mesh models (www.stjude.org/BrainAtlas) can be used to plan treatment, to conduct knowledge and modeldriven segmentation, and to analyze the shapes of brain structures in pediatric patients.

Multireference second order perturbation theory with a simplified treatment of dynamical correlation.

PubMed

Xu, Enhua; Zhao, Dongbo; Li, Shuhua

2015-10-13

A multireference second order perturbation theory based on a complete active space configuration interaction (CASCI) function or density matrix renormalized group (DMRG) function has been proposed. This method may be considered as an approximation to the CAS/A approach with the same reference, in which the dynamical correlation is simplified with blocked correlated second order perturbation theory based on the generalized valence bond (GVB) reference (GVB-BCPT2). This method, denoted as CASCI-BCPT2/GVB or DMRG-BCPT2/GVB, is size consistent and has a similar computational cost as the conventional second order perturbation theory (MP2). We have applied it to investigate a number of problems of chemical interest. These problems include bond-breaking potential energy surfaces in four molecules, the spectroscopic constants of six diatomic molecules, the reaction barrier for the automerization of cyclobutadiene, and the energy difference between the monocyclic and bicyclic forms of 2,6-pyridyne. Our test applications demonstrate that CASCI-BCPT2/GVB can provide comparable results with CASPT2 (second order perturbation theory based on the complete active space self-consistent-field wave function) for systems under study. Furthermore, the DMRG-BCPT2/GVB method is applicable to treat strongly correlated systems with large active spaces, which are beyond the capability of CASPT2.

Use of internal references for assessing CT density measurements of the pelvis as replacement for use of an external phantom.

PubMed

Boomsma, Martijn F; Slouwerhof, Inge; van Dalen, Jorn A; Edens, Mireille A; Mueller, Dirk; Milles, Julien; Maas, Mario

2015-11-01

The purpose of this research is to study the use of an internal reference standard for fat- and muscle as a replacement for an external reference standard with a phantom. By using a phantomless internal reference standard, Hounsfield unit (HU) measurements of various tissues can potentially be assessed in patients with a CT scan of the pelvis without an added phantom at time of CT acquisition. This paves the way for development of a tool for quantification of the change in tissue density in one patient over time and between patients. This could make every CT scan made without contrast available for research purposes. Fifty patients with unilateral metal-on-metal total hip replacements, scanned together with a calibration reference phantom used in bone mineral density measurements, were included in this study. On computed tomography scans of the pelvis without the use of intravenous iodine contrast, reference values for fat and muscle were measured in the phantom as well as within the patient's body. The conformity between the references was examined with the intra-class correlation coefficient. The mean HU (± SD) of reference values for fat for the internal- and phantom references were -91.5 (±7.0) and -90.9 (±7.8), respectively. For muscle, the mean HU (± SD) for the internal- and phantom references were 59.2 (±6.2) and 60.0 (±7.2), respectively. The intra-class correlation coefficients for fat and muscle were 0.90 and 0.84 respectively and show excellent agreement between the phantom and internal references. Internal references can be used with similar accuracy as references from an external phantom. There is no need to use an external phantom to asses CT density measurements of body tissue.

Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation.

PubMed

Masè, Michela; Grasso, Margherita; Avogaro, Laura; D'Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

2017-01-24

MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-C q , GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions.

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.

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

Refer prior to biopsy of suspected appendicular soft tissue sarcoma.

PubMed

Elliott, Robert S J; Flint, Michael; French, Gary

2012-11-23

Appendicular soft tissue tumours are rare and inappropriate investigation can result in unnecessary loss of limb or life. We reviewed the investigation and referrals of patients to our institution. This is a review of prospectively collected data stored in a tumour registry database. We included all patients (126) referred to the service for investigation and management with a primary soft tissue tumour in 2006 and 2007. There was a highly significant association (RR=6.2) between pre referral procedures (PRPs) and suffering a complication (P<0.0001) in comparison to non-biopsied referrals (NBRs). Those referred by general surgeons were more likely (RR=2.6) to have undergone PRP (p<0.0017). The median interval between referral and senior author review was 8 days for the PRP group and 10 days for the NBR group (P=0.2574). Biopsy of suspected appendicular soft tissue sarcoma should be performed by a tumour specialist or in prior consultation with, to minimise adverse outcomes. There was minimal delay till review by an orthopaedic tumour specialist at Middlemore Hospital and achieving a tissue diagnosis does not expedite this.

Application of a Simplified Method for Estimating Perfusion Derived from Diffusion-Weighted MR Imaging in Glioma Grading.

PubMed

Cao, Mengqiu; Suo, Shiteng; Han, Xu; Jin, Ke; Sun, Yawen; Wang, Yao; Ding, Weina; Qu, Jianxun; Zhang, Xiaohua; Zhou, Yan

2017-01-01

Purpose : To evaluate the feasibility of a simplified method based on diffusion-weighted imaging (DWI) acquired with three b -values to measure tissue perfusion linked to microcirculation, to validate it against from perfusion-related parameters derived from intravoxel incoherent motion (IVIM) and dynamic contrast-enhanced (DCE) magnetic resonance (MR) imaging, and to investigate its utility to differentiate low- from high-grade gliomas. Materials and Methods : The prospective study was approved by the local institutional review board and written informed consent was obtained from all patients. From May 2016 and May 2017, 50 patients confirmed with glioma were assessed with multi- b -value DWI and DCE MR imaging at 3.0 T. Besides conventional apparent diffusion coefficient (ADC 0,1000 ) map, perfusion-related parametric maps for IVIM-derived perfusion fraction ( f ) and pseudodiffusion coefficient (D*), DCE MR imaging-derived pharmacokinetic metrics, including K trans , v e and v p , as well as a metric named simplified perfusion fraction (SPF), were generated. Correlation between perfusion-related parameters was analyzed by using the Spearman rank correlation. All imaging parameters were compared between the low-grade ( n = 19) and high-grade ( n = 31) groups by using the Mann-Whitney U test. The diagnostic performance for tumor grading was evaluated with receiver operating characteristic (ROC) analysis. Results : SPF showed strong correlation with IVIM-derived f and D* ( ρ = 0.732 and 0.716, respectively; both P < 0.001). Compared with f , SPF was more correlated with DCE MR imaging-derived K trans ( ρ = 0.607; P < 0.001) and v p ( ρ = 0.397; P = 0.004). Among all parameters, SPF achieved the highest accuracy for differentiating low- from high-grade gliomas, with an area under the ROC curve value of 0.942, which was significantly higher than that of ADC 0,1000 ( P = 0.004). By using SPF as a discriminative index, the diagnostic sensitivity and specificity were 87.1% and 94.7%, respectively, at the optimal cut-off value of 19.26%. Conclusion : The simplified method to measure tissue perfusion based on DWI by using three b -values may be helpful to differentiate low- from high-grade gliomas. SPF may serve as a valuable alternative to measure tumor perfusion in gliomas in a noninvasive, convenient and efficient way.

[Muscles and connective tissue: histology].

PubMed

Delage, J-P

2012-10-01

Here, we give some comments about the DVD movies "Muscle Attitudes" from Endovivo productions, the movies up lighting some loss in the attention given to studies on the connective tissue, and especially them into muscles. The main characteristics of the different components in the intra-muscular connective tissue (perimysium, endomysium, epimysium) are shown here with special references to their ordered architecture and special references to their spatial distributions. This connective tissue is abundant into the muscles and is in continuity with the muscles in vicinity, with their tendons and their sheath, sticking the whole on skin. This connective tissue has also very abundant connections on the muscles fibres. It is then assumed that the connective tissue sticks every organs or cells of the locomotion system. Considering the elastic properties of the collagen fibres which are the most abundant component of connective tissue, it is possible to up light a panel of connective tissue associated functions such as the transmission of muscle contractions or the regulation of protein and energetic muscles metabolism. Copyright © 2012. Published by Elsevier SAS.

Recent advances in QM/MM free energy calculations using reference potentials.

PubMed

Duarte, Fernanda; Amrein, Beat A; Blaha-Nelson, David; Kamerlin, Shina C L

2015-05-01

Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Etiology of Syncope and Unexplained Falls in Elderly Adults with Dementia: Syncope and Dementia (SYD) Study.

PubMed

Ungar, Andrea; Mussi, Chiara; Ceccofiglio, Alice; Bellelli, Giuseppe; Nicosia, Franco; Bo, Mario; Riccio, Daniela; Martone, Anna Maria; Guadagno, Livia; Noro, Gabriele; Ghidoni, Giulia; Rafanelli, Martina; Marchionni, Niccolò; Abete, Pasquale

2016-08-01

To investigate the etiology of transient loss of consciousness (T-LOC) suspected to be syncope and unexplained falls in elderly adults with dementia. Prospective, observational, multicenter study. Acute care wards, syncope units or centers for the diagnosis of dementia. Individuals aged 65 and older with a diagnosis of dementia and one or more episodes of T-LOC of a suspected syncopal nature or unexplained falls during the previous 3 months were enrolled. The causes of T-LOC suspected to be syncope and unexplained falls were evaluated using a simplified protocol based on European Society of Cardiology guidelines. Of 357 individuals enrolled, 181 (50.7%) had been referred for T-LOC suspected to be syncope, 166 (46.5%) for unexplained falls, and 10 (2.8%) for both. An initially suspected diagnosis of syncope was confirmed in 158 (87.3%), and syncope was identified as the cause of the event in 75 (45.2%) of those referred for unexplained falls. Orthostatic hypotension was the cause of the event in 117 of 242 (48.3%) participants with a final diagnosis of syncope. The simplified syncope diagnostic protocol can be used in elderly people with dementia referred for suspected syncope or unexplained falls. Unexplained falls may mask a diagnosis of syncope or pseudosyncope in almost 50% of cases. Given the high prevalence of orthostatic syncope in participants (~50%), a systematic reappraisal of drugs potentially responsible for orthostatic hypotension is warranted. © 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.

Histopathological Diagnostic Discrepancies in Soft Tissue Tumours Referred to a Specialist Centre: Reassessment in the Era of Ancillary Molecular Diagnosis

PubMed Central

Thway, Khin; Mubako, Taka

2014-01-01

Introduction. Soft tissue tumour pathology is a highly specialised area of surgical pathology, but soft tissue neoplasms can occur at virtually all sites and are therefore encountered by a wide population of surgical pathologists. Potential sarcomas require referral to specialist centres for review by pathologists who see a large number of soft tissue lesions and where appropriate ancillary investigations can be performed. We have previously assessed the types of diagnostic discrepancies between referring and final diagnosis for soft tissue lesions referred to our tertiary centre. We now reaudit this 6 years later, assessing changes in discrepancy patterns, particularly in relation to the now widespread use of ancillary molecular diagnostic techniques which were not prevalent in our original study. Materials and Methods. We compared the sarcoma unit's histopathology reports with referring reports on 348 specimens from 286 patients with suspected or proven soft tissue tumours in a one-year period. Results. Diagnostic agreement was seen in 250 cases (71.8%), with 57 (16.4%) major and 41 (11.8%) minor discrepancies. There were 23 cases of benign/malignant discrepancies (23.5% of all discrepancies). 50 ancillary molecular tests were performed, 33 for aiding diagnosis and 17 mutational analyses for gastrointestinal stromal tumour to guide therapy. Findings from ancillary techniques contributed to 3 major and 4 minor discrepancies. While the results were broadly similar to those of the previous study, there was an increase in frequency of major discrepancies. Conclusion. Six years following our previous study and notably now in an era of widespread ancillary molecular diagnosis, the overall discrepancy rate between referral and tertiary centre diagnosis remains similar, but there is an increase in frequency of major discrepancies likely to alter patient management. A possible reason for the increase in major discrepancies is the increasing lack of exposure to soft tissue cases in nonspecialist centres in a time of subspecialisation. The findings support the national guidelines in which all suspected soft tissue tumour pathology specimens should be referred to a specialist sarcoma unit. PMID:25165418

Histopathological diagnostic discrepancies in soft tissue tumours referred to a specialist centre: reassessment in the era of ancillary molecular diagnosis.

PubMed

Thway, Khin; Wang, Jayson; Mubako, Taka; Fisher, Cyril

2014-01-01

Introduction. Soft tissue tumour pathology is a highly specialised area of surgical pathology, but soft tissue neoplasms can occur at virtually all sites and are therefore encountered by a wide population of surgical pathologists. Potential sarcomas require referral to specialist centres for review by pathologists who see a large number of soft tissue lesions and where appropriate ancillary investigations can be performed. We have previously assessed the types of diagnostic discrepancies between referring and final diagnosis for soft tissue lesions referred to our tertiary centre. We now reaudit this 6 years later, assessing changes in discrepancy patterns, particularly in relation to the now widespread use of ancillary molecular diagnostic techniques which were not prevalent in our original study. Materials and Methods. We compared the sarcoma unit's histopathology reports with referring reports on 348 specimens from 286 patients with suspected or proven soft tissue tumours in a one-year period. Results. Diagnostic agreement was seen in 250 cases (71.8%), with 57 (16.4%) major and 41 (11.8%) minor discrepancies. There were 23 cases of benign/malignant discrepancies (23.5% of all discrepancies). 50 ancillary molecular tests were performed, 33 for aiding diagnosis and 17 mutational analyses for gastrointestinal stromal tumour to guide therapy. Findings from ancillary techniques contributed to 3 major and 4 minor discrepancies. While the results were broadly similar to those of the previous study, there was an increase in frequency of major discrepancies. Conclusion. Six years following our previous study and notably now in an era of widespread ancillary molecular diagnosis, the overall discrepancy rate between referral and tertiary centre diagnosis remains similar, but there is an increase in frequency of major discrepancies likely to alter patient management. A possible reason for the increase in major discrepancies is the increasing lack of exposure to soft tissue cases in nonspecialist centres in a time of subspecialisation. The findings support the national guidelines in which all suspected soft tissue tumour pathology specimens should be referred to a specialist sarcoma unit.

Adenosine 2A receptor occupancy by tozadenant and preladenant in rhesus monkeys.

PubMed

Barret, Olivier; Hannestad, Jonas; Alagille, David; Vala, Christine; Tavares, Adriana; Papin, Caroline; Morley, Thomas; Fowles, Krista; Lee, Hsiaoju; Seibyl, John; Tytgat, Dominique; Laruelle, Marc; Tamagnan, Gilles

2014-10-01

Motor symptoms in Parkinson disease (PD) are caused by a loss of dopamine input from the substantia nigra to the striatum. Blockade of adenosine 2A (A(2A)) receptors facilitates dopamine D(2) receptor function. In phase 2 clinical trials, A(2A) antagonists (istradefylline, preladenant, and tozadenant) improved motor function in PD. We developed a new A(2A) PET radiotracer, (18)F-MNI-444, and used it to investigate the relationship between plasma levels and A(2A) occupancy by preladenant and tozadenant in nonhuman primates (NHP). A series of 20 PET experiments was conducted in 5 adult rhesus macaques. PET data were analyzed with both plasma-input (Logan graphical analysis) and reference-region-based (simplified reference tissue model and noninvasive Logan graphical analysis) methods. Whole-body PET images were acquired for radiation dosimetry estimates. Human pharmacokinetic parameters for tozadenant and preladenant were used to predict A(2A) occupancy in humans, based on median effective concentration (EC(50)) values estimated from the NHP PET measurements. (18)F-MNI-444 regional uptake was consistent with A(2A) receptor distribution in the brain. Selectivity was demonstrated by dose-dependent blocking by tozadenant and preladenant. The specific-to-nonspecific ratio was superior to that of other A(2A) PET radiotracers. Pharmacokinetic modeling predicted that tozadenant and preladenant may have different profiles of A(2A) receptor occupancy in humans. (18)F-MNI-444 appears to be a better PET radiotracer for A(2A) imaging than currently available radiotracers. Assuming that EC(50) in humans is similar to that in NHP, it appears that tozadenant will provide a more sustained A(2A) receptor occupancy than preladenant in humans at clinically tested doses. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Characterization of age/sex and the regional distribution of mGluR5 availability in the healthy human brain measured by high-resolution [(11)C]ABP688 PET.

PubMed

DuBois, Jonathan M; Rousset, Olivier G; Rowley, Jared; Porras-Betancourt, Manuel; Reader, Andrew J; Labbe, Aurelie; Massarweh, Gassan; Soucy, Jean-Paul; Rosa-Neto, Pedro; Kobayashi, Eliane

2016-01-01

Metabotropic glutamate receptor type 5 (mGluR5) is a G protein-coupled receptor that has been implicated in several psychiatric and neurological diseases. The radiopharmaceutical [(11)C]ABP688 allows for in vivo quantification of mGluR5 availability using positron emission tomography (PET). In this study, we aimed to detail the regional distribution of [(11)C]ABP688 binding potential (BPND) and the existence of age/sex effects in healthy individuals. Thirty-one healthy individuals aged 20 to 77 years (men, n = 18, 45.3 ± 18.2 years; females, n = 13, 41.5 ± 19.6 years) underwent imaging with [(11)C]ABP688 using the high-resolution research tomograph (HRRT). We developed an advanced partial volume correction (PVC) method using surface-based analysis in order to accurately estimate the regional variation of radioactivity. BPND was calculated using the simplified reference tissue model, with the cerebellum as the reference region. Surface-based and volume-based analyses were performed for 39 cortical and subcortical regions of interest per hemisphere. We found the highest [(11)C]ABP688 BPND in the lateral prefrontal and anterior cingulate cortices. The lowest [(11)C]ABP688 BPND was observed in the pre- and post-central gyri as well as the occipital lobes and the thalami. No sex effect was observed. Associations between age and [(11)C]ABP688 BPND without PVC were observed in the right amygdala and left putamen, but were not significant after multiple comparisons correction. The present results highlight complexities underlying brain adaptations during the aging process, and support the notion that certain aspects of neurotransmission remain stable during the adult life span.

PET imaging of putative microglial activation in individuals at ultra-high risk for psychosis, recently diagnosed and chronically ill with schizophrenia.

PubMed

Di Biase, M A; Zalesky, A; O'keefe, G; Laskaris, L; Baune, B T; Weickert, C S; Olver, J; McGorry, P D; Amminger, G P; Nelson, B; Scott, A M; Hickie, I; Banati, R; Turkheimer, F; Yaqub, M; Everall, I P; Pantelis, C; Cropley, V

2017-08-29

We examined putative microglial activation as a function of illness course in schizophrenia. Microglial activity was quantified using [ 11 C](R)-(1-[2-chrorophynyl]-N-methyl-N-[1-methylpropyl]-3 isoquinoline carboxamide ( 11 C-(R)-PK11195) positron emission tomography (PET) in: (i) 10 individuals at ultra-high risk (UHR) of psychosis; (ii) 18 patients recently diagnosed with schizophrenia; (iii) 15 patients chronically ill with schizophrenia; and, (iv) 27 age-matched healthy controls. Regional-binding potential (BP ND ) was calculated using the simplified reference-tissue model with four alternative reference inputs. The UHR, recent-onset and chronic patient groups were compared to age-matched healthy control groups to examine between-group BP ND differences in 6 regions: dorsal frontal, orbital frontal, anterior cingulate, medial temporal, thalamus and insula. Correlation analysis tested for BP ND associations with gray matter volume, peripheral cytokines and clinical variables. The null hypothesis of equality in BP ND between patients (UHR, recent-onset and chronic) and respective healthy control groups (younger and older) was not rejected for any group comparison or region. Across all subjects, BP ND was positively correlated to age in the thalamus (r=0.43, P=0.008, false discovery rate). No correlations with regional gray matter, peripheral cytokine levels or clinical symptoms were detected. We therefore found no evidence of microglial activation in groups of individuals at high risk, recently diagnosed or chronically ill with schizophrenia. While the possibility of 11 C-(R)-PK11195-binding differences in certain patient subgroups remains, the patient cohorts in our study, who also displayed normal peripheral cytokine profiles, do not substantiate the assumption of microglial activation in schizophrenia as a regular and defining feature, as measured by 11 C-(R)-PK11195 BP ND .

Dual-wavelength excitation to reduce background fluorescence for fluorescence spectroscopic quantitation of erythrocyte zinc protoporphyrin-IX and protoporphyrin-IX from whole blood and oral mucosa

NASA Astrophysics Data System (ADS)

Hennig, Georg; Vogeser, Michael; Holdt, Lesca M.; Homann, Christian; Großmann, Michael; Stepp, Herbert; Gruber, Christian; Erdogan, Ilknur; Hasmüller, Stephan; Hasbargen, Uwe; Brittenham, Gary M.

2014-02-01

Erythrocyte zinc protoporphyrin-IX (ZnPP) and protoporphyrin-IX (PPIX) accumulate in a variety of disorders that restrict or disrupt the biosynthesis of heme, including iron deficiency and various porphyrias. We describe a reagent-free spectroscopic method based on dual-wavelength excitation that can measure simultaneously both ZnPP and PPIX fluorescence from unwashed whole blood while virtually eliminating background fluorescence. We further aim to quantify ZnPP and PPIX non-invasively from the intact oral mucosa using dual-wavelength excitation to reduce the strong tissue background fluorescence while retaining the faint porphyrin fluorescence signal originating from erythrocytes. Fluorescence spectroscopic measurements were made on 35 diluted EDTA blood samples using a custom front-face fluorometer. The difference spectrum between fluorescence at 425 nm and 407 nm excitation effectively eliminated background autofluorescence while retaining the characteristic porphyrin peaks. These peaks were evaluated quantitatively and the results compared to a reference HPLC-kit method. A modified instrument using a single 1000 μm fiber for light delivery and detection was used to record fluorescence spectra from oral mucosa. For blood measurements, the ZnPP and PPIX fluorescence intensities from the difference spectra correlated well with the reference method (ZnPP: Spearman's rho rs = 0.943, p < 0.0001; PPIX: rs = 0.959, p < 0.0001). In difference spectra from oral mucosa, background fluorescence was reduced significantly, while porphyrin signals remained observable. The dual-wavelength excitation method evaluates quantitatively the ZnPP/heme and PPIX/heme ratios from unwashed whole blood, simplifying clinical laboratory measurements. The difference technique reduces the background fluorescence from measurements on oral mucosa, allowing for future non-invasive quantitation of erythrocyte ZnPP and PPIX.

Genetics Home Reference: arterial tortuosity syndrome

MedlinePlus

... tortuosity syndrome is a disorder that affects connective tissue. Connective tissue provides strength and flexibility to structures throughout the ... outside the circulatory system are caused by abnormal connective tissue in other parts of the body. These features ...

Cross-cultural Adaptation and Validation of the Simplified Chinese Version of the Knee Outcome Survey Activities of Daily Living Scale.

PubMed

Jia, Zhen-Yu; Wang, Wei; Nian, Xin-Wen; Zhang, Xiao-Xi; Huang, Zhi-Ping; Cui, Jin; Xu, Wei-Dong

2016-10-01

To perform a cross-cultural adaptation and translation of the original version of the Activities of Daily Living Scale of the Knee Outcome Survey into Simplified Chinese and validate of the Simplified Chinese version. The original version was translated and cross-culturally adapted into Simplified Chinese according to the guidelines and the recommendations of the American Academy of Orthopaedic Surgeons Outcome Committee. A total of 213 patients (96 male, 117 female) were selected to participate in our investigation. The inclusion criteria were as follows: 18 years of age and older, able to speak Chinese Mandarin and read Simplified Chinese, and referred to physical therapy for evaluation and treatment for a knee disorder. The exclusion criteria were as follows: patients who had disorders or impairments involving both knees, patients who had other conditions that could affect lower extremity function, patients with physical therapy related to the knee in the previous 1 month, and patients with psychological problems. Each participant was asked to complete the Knee Outcome Survey Activities of Daily Living Scale (KOS-ADLS), International Knee Documentation Committee Subjective Knee Form, Western Ontario and McMaster Universities Osteoarthritis Index, and Short Form 36 forms and to provide baseline demographic data. Each participant completed the KOS-ADLS twice on 2 nonconsecutive days for reliability evaluation. A portion of the participants (n = 161) finished the KOS-ADLS a third time 4 weeks after physical treatment to test responsiveness. The original version of the KOS-ADLS was well adapted and translated into Simplified Chinese. Simplified Chinese of KOS-ADLS was shown to have good internal consistency (Cronbach's alpha = 0.855 to 0.929), great test-retest reliability (intraclass correlation coefficient = 0.935 to 0.961), high construct validity as we hypothesized (significant correlations with Short Form 36 subscales, Western Ontario and McMaster Universities Osteoarthritis Index, and International Knee Documentation Committee Subjective Knee Form), and high responsiveness (standard response means = 0.97 to 1.23, standard effect size = 0.81 to 0.91). Simplified Chinese of KOS-ADLS was shown to have good reliability, validity, and responsiveness for use in patients with knee disorders in China. Level II, testing of previously developed diagnostic criteria in a series of consecutive patients with universally applied gold standard. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments

PubMed Central

Niu, Xiaoping; Qi, Jianmin; Zhang, Gaoyang; Xu, Jiantang; Tao, Aifen; Fang, Pingping; Su, Jianguang

2015-01-01

To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. Corchorus capsularis, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, ACT7 and RAN were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, UBC, and DnaJ were sufficient for accurate normalization. For the tissues subset, four reference genes TUBβ, UBI, EF1α, and RAN were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of WRKY15 in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in C. capsularis, and will facilitate gene expression study under these conditions. PMID:26528312

SU-F-T-409: Modelling of the Magnetic Port in Temporary Breast Tissue Expanders for a Treatment Planning System

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

Yoon, J; Heins, D; Zhang, R

Purpose: To model the magnetic port in the temporary breast tissue expanders and to improve accuracy of dose calculation in Pinnacle, a commercial treatment planning system (TPS). Methods: A magnetic port in the tissue expander was modeled with a radiological measurement-basis; we have determined the dimension and the density of the model by film images and ion chamber measurement under the magnetic port, respectively. The model was then evaluated for various field sizes and photon energies by comparing depth dose values calculated by TPS (using our new model) and ion chamber measurement in a water tank. Also, the model wasmore » further evaluated by using a simplified anthropomorphic phantom with realistic geometry by placing thermoluminescent dosimeters (TLD)s around the magnetic port. Dose perturbations in a real patient’s treatment plan from the new model and a current clinical model, which is based on the subjective contouring created by the dosimetrist, were also compared. Results: Dose calculations based on our model showed less than 1% difference from ion chamber measurements for various field sizes and energies under the magnetic port when the magnetic port was placed parallel to the phantom surface. When it was placed perpendicular to the phantom surface, the maximum difference was 3.5%, while average differences were less than 3.1% for all cases. For the simplified anthropomorphic phantom, the calculated point doses agreed with TLD measurements within 5.2%. By comparing with the current model which is being used in clinic by TPS, it was found that current clinical model overestimates the effect from the magnetic port. Conclusion: Our new model showed good agreement with measurement for all cases. It could potentially improve the accuracy of dose delivery to the breast cancer patients.« less

Numerical Modeling of Interstitial Fluid Flow Coupled with Blood Flow through a Remodeled Solid Tumor Microvascular Network

PubMed Central

Soltani, M.; Chen, P.

2013-01-01

Modeling of interstitial fluid flow involves processes such as fluid diffusion, convective transport in extracellular matrix, and extravasation from blood vessels. To date, majority of microvascular flow modeling has been done at different levels and scales mostly on simple tumor shapes with their capillaries. However, with our proposed numerical model, more complex and realistic tumor shapes and capillary networks can be studied. Both blood flow through a capillary network, which is induced by a solid tumor, and fluid flow in tumor’s surrounding tissue are formulated. First, governing equations of angiogenesis are implemented to specify the different domains for the network and interstitium. Then, governing equations for flow modeling are introduced for different domains. The conservation laws for mass and momentum (including continuity equation, Darcy’s law for tissue, and simplified Navier–Stokes equation for blood flow through capillaries) are used for simulating interstitial and intravascular flows and Starling’s law is used for closing this system of equations and coupling the intravascular and extravascular flows. This is the first study of flow modeling in solid tumors to naturalistically couple intravascular and extravascular flow through a network. This network is generated by sprouting angiogenesis and consisting of one parent vessel connected to the network while taking into account the non-continuous behavior of blood, adaptability of capillary diameter to hemodynamics and metabolic stimuli, non-Newtonian blood flow, and phase separation of blood flow in capillary bifurcation. The incorporation of the outlined components beyond the previous models provides a more realistic prediction of interstitial fluid flow pattern in solid tumors and surrounding tissues. Results predict higher interstitial pressure, almost two times, for realistic model compared to the simplified model. PMID:23840579

High-fidelity meshes from tissue samples for diffusion MRI simulations.

PubMed

Panagiotaki, Eleftheria; Hall, Matt G; Zhang, Hui; Siow, Bernard; Lythgoe, Mark F; Alexander, Daniel C

2010-01-01

This paper presents a method for constructing detailed geometric models of tissue microstructure for synthesizing realistic diffusion MRI data. We construct three-dimensional mesh models from confocal microscopy image stacks using the marching cubes algorithm. Random-walk simulations within the resulting meshes provide synthetic diffusion MRI measurements. Experiments optimise simulation parameters and complexity of the meshes to achieve accuracy and reproducibility while minimizing computation time. Finally we assess the quality of the synthesized data from the mesh models by comparison with scanner data as well as synthetic data from simple geometric models and simplified meshes that vary only in two dimensions. The results support the extra complexity of the three-dimensional mesh compared to simpler models although sensitivity to the mesh resolution is quite robust.

Hills and Valleys: Understanding the Under-Eye

PubMed Central

Naik, Milind N

2016-01-01

Soft tissue deflation and descent have long been implicated in the pathogenesis of facial aging. In the periorbital area, the upper orbital region is thought to change by descent of the eyebrow, as well as deflation of brow fat. While the understanding of the aging changes in the upper eyelid region are relatively simple, the lower eyelid poses a myriad of aging changes, each demanding a specific management plan. These can be best described in terms of elevations, or ‘Hills’ and hollows, or ‘Valleys’. This article simplifies the understanding of the lower eyelid in the light of anatomical knowledge, and available literature. It forms a basis of easy diagnosis and treatment of the soft tissue changes in the lower eyelid and malar region. PMID:27398004

Oscillating water column structural model

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

Copeland, Guild; Bull, Diana L; Jepsen, Richard Alan

2014-09-01

An oscillating water column (OWC) wave energy converter is a structure with an opening to the ocean below the free surface, i.e. a structure with a moonpool. Two structural models for a non-axisymmetric terminator design OWC, the Backward Bent Duct Buoy (BBDB) are discussed in this report. The results of this structural model design study are intended to inform experiments and modeling underway in support of the U.S. Department of Energy (DOE) initiated Reference Model Project (RMP). A detailed design developed by Re Vision Consulting used stiffeners and girders to stabilize the structure against the hydrostatic loads experienced by amore » BBDB device. Additional support plates were added to this structure to account for loads arising from the mooring line attachment points. A simplified structure was designed in a modular fashion. This simplified design allows easy alterations to the buoyancy chambers and uncomplicated analysis of resulting changes in buoyancy.« less

A simplified scheme for computing radiation transfer in the troposphere

NASA Technical Reports Server (NTRS)

Katayama, A.

1973-01-01

A scheme is presented, for the heating of clear and cloudy air by solar and infrared radiation transfer, designed for use in tropospheric general circulation models with coarse vertical resolution. A bulk transmission function is defined for the infrared transfer. The interpolation factors, required for computing the bulk transmission function, are parameterized as functions of such physical parameters as the thickness of the layer, the pressure, and the mixing ratio at a reference level. The computation procedure for solar radiation is significantly simplified by the introduction of two basic concepts. The first is that the solar radiation spectrum can be divided into a scattered part, for which Rayleigh scattering is significant but absorption by water vapor is negligible, and an absorbed part for which absorption by water vapor is significant but Rayleigh scattering is negligible. The second concept is that of an equivalent cloud water vapor amount which absorbs the same amount of radiation as the cloud.

RefPrimeCouch—a reference gene primer CouchApp

PubMed Central

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html PMID:24368831

RefPrimeCouch--a reference gene primer CouchApp.

PubMed

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html.

Optical properties of light absorbing carbon aggregates mixed with sulfate: assessment of different model geometries for climate forcing calculations.

PubMed

Kahnert, Michael; Nousiainen, Timo; Lindqvist, Hannakaisa; Ebert, Martin

2012-04-23

Light scattering by light absorbing carbon (LAC) aggregates encapsulated into sulfate shells is computed by use of the discrete dipole method. Computations are performed for a UV, visible, and IR wavelength, different particle sizes, and volume fractions. Reference computations are compared to three classes of simplified model particles that have been proposed for climate modeling purposes. Neither model matches the reference results sufficiently well. Remarkably, more realistic core-shell geometries fall behind homogeneous mixture models. An extended model based on a core-shell-shell geometry is proposed and tested. Good agreement is found for total optical cross sections and the asymmetry parameter. © 2012 Optical Society of America

Strong enhancement of dispersion forces from microwave radiation

NASA Astrophysics Data System (ADS)

Sernelius, B. E.

2002-11-01

We have studied non-thermal effects of microwave radiation on the forces between objects. This is the first step in a study of possible effects of microwave radiation from cellular phones on biological tissue. We have used a simplified model for human blood cells in blood. We find for the normal radiation level of cellular phones an enhancement of the attractive force with ten orders of magnitude as compared to the corresponding effect at thermal radiation.

Endogenous synchronous fluorescence spectroscopy (SFS) of basal cell carcinoma-initial study

NASA Astrophysics Data System (ADS)

Borisova, E.; Zhelyazkova, Al.; Keremedchiev, M.; Penkov, N.; Semyachkina-Glushkovskaya, O.; Avramov, L.

2016-01-01

The human skin is a complex, multilayered and inhomogeneous organ with spatially varying optical properties. Analysis of cutaneous fluorescence spectra could be a very complicated task; therefore researchers apply complex mathematical tools for data evaluation, or try to find some specific approaches, that would simplify the spectral analysis. Synchronous fluorescence spectroscopy (SFS) allows improving the spectral resolution, which could be useful for the biological tissue fluorescence characterization and could increase the tumour detection diagnostic accuracy.

Simplified one-pot synthesis of [.sup.18F]SFB for radiolabeling

DOEpatents

Olma, Sebastian; Shen, Clifton Kwang-Fu

2015-08-04

A non-aqueous single pot synthesis of [.sup.18F]SFB is set forth. The [.sup.18F]SFB produced with this method is then used, for example, to label a peptide or an engineered antibody fragment (diabody) targeting human epidermal growth factor receptor 2 (HER2) as representative examples of labeled compounds for use as an injectable composition to locate abnormal tissue, specifically tumors within an animal or human using a PET scan.

Simplified one-pot synthesis of [.sup.18F]SFB for radiolabeling

DOEpatents

Olma, Sebastian; Shen, Clifton Kwang-Fu

2013-07-16

A non-aqueous single pot synthesis of [.sup.18F]SFB is set forth. The [.sup.18F]SFB produced with this method is then used, for example, to label a peptide or an engineered antibody fragment (diabody) targeting human epidermal growth factor receptor 2 (HER2) as representative examples of labeled compounds for use as an injectable composition to locate abnormal tissue, specifically tumors within an animal or human using a PET scan.

Computational studies of transthoracic and transvenous defibrillation in a detailed 3-D human thorax model.

PubMed

Jorgenson, D B; Haynor, D R; Bardy, G H; Kim, Y

1995-02-01

A method for constructing and solving detailed patient-specific 3-D finite element models of the human thorax is presented for use in defibrillation studies. The method utilizes the patient's own X-ray CT scan and a simplified meshing scheme to quickly and efficiently generate a model typically composed of approximately 400,000 elements. A parameter sensitivity study on one human thorax model to examine the effects of variation in assigned tissue resistivity values, level of anatomical detail included in the model, and number of CT slices used to produce the model is presented. Of the seven tissue types examined, the average left ventricular (LV) myocardial voltage gradient was most sensitive to the values of myocardial and blood resistivity. Incorrectly simplifying the model, for example modeling the heart as a homogeneous structure by ignoring the blood in the chambers, caused the average LV myocardial voltage gradient to increase by 12%. The sensitivity of the model to variations in electrode size and position was also examined. Small changes (< 2.0 cm) in electrode position caused average LV myocardial voltage gradient values to increase by up to 12%. We conclude that patient-specific 3-D finite element modeling of human thoracic electric fields is feasible and may reduce the empiric approach to insertion of implantable defibrillators and improve transthoracic defibrillation techniques.

A simplified, low power system for effective vessel sealing

NASA Astrophysics Data System (ADS)

Lyle, Allison B.; Kennedy, Jenifer S.; Schmaltz, Dale F.; Kennedy, Aaron S.

2015-03-01

The first bipolar vessel sealing system was developed nearly 15 years ago and has since become standard of care in surgery. These systems make use of radio frequency current that is delivered between bipolar graspers to permanently seal arteries, veins and tissue bundles. Conventional vessel sealing generators are based off traditional electrosurgery generator architecture and deliver high power (150-300 Watts) and high current using complex control and sense algorithms to adjust the output for vessel sealing applications. In recent years, a need for small-scale surgical vessel sealers has developed as surgeons strive to further reduce their footprint on patients. There are many technical challenges associated with miniaturization of vessel sealing devices including maintaining electrical isolation while delivering high current in a saline environment. Research into creating a small, 3mm diameter vessel sealer revealed that a highly simplified generator system could be used to achieve excellent results and subsequently a low power vessel sealing system was developed. This system delivers 25 Watts constant power while limiting voltage (<= Vrms) and current (<= Amps) until an impedance endpoint is achieved, eliminating the use of complicated control and sensing software. The result is optimized tissue effect, where high seal strength is maintained (> 360mmHg), but seal times (1.7 +/- 0.7s versus 4.1 +/- 0.7s), thermal spread (<1mm vs <=2mm) and total energy delivery are reduced, when compared to an existing high power system.

Fundamental period of Italian reinforced concrete buildings: comparison between numerical, experimental and Italian code simplified values

NASA Astrophysics Data System (ADS)

Ditommaso, Rocco; Carlo Ponzo, Felice; Auletta, Gianluca; Iacovino, Chiara; Nigro, Antonella

2015-04-01

Aim of this study is a comparison among the fundamental period of reinforced concrete buildings evaluated using the simplified approach proposed by the Italian Seismic code (NTC 2008), numerical models and real values retrieved from an experimental campaign performed on several buildings located in Basilicata region (Italy). With the intention of proposing simplified relationships to evaluate the fundamental period of reinforced concrete buildings, scientists and engineers performed several numerical and experimental campaigns, on different structures all around the world, to calibrate different kind of formulas. Most of formulas retrieved from both numerical and experimental analyses provides vibration periods smaller than those suggested by the Italian seismic code. However, it is well known that the fundamental period of a structure play a key role in the correct evaluation of the spectral acceleration for seismic static analyses. Generally, simplified approaches impose the use of safety factors greater than those related to in depth nonlinear analyses with the aim to cover possible unexpected uncertainties. Using the simplified formula proposed by the Italian seismic code the fundamental period is quite higher than fundamental periods experimentally evaluated on real structures, with the consequence that the spectral acceleration adopted in the seismic static analysis may be significantly different than real spectral acceleration. This approach could produces a decreasing in safety factors obtained using linear and nonlinear seismic static analyses. Finally, the authors suggest a possible update of the Italian seismic code formula for the simplified estimation of the fundamental period of vibration of existing RC buildings, taking into account both elastic and inelastic structural behaviour and the interaction between structural and non-structural elements. Acknowledgements This study was partially funded by the Italian Civil Protection Department within the project DPC-RELUIS 2014 - RS4 ''Seismic observatory of structures and health monitoring''. References R. Ditommaso, M. Vona, M. R. Gallipoli and M. Mucciarelli (2013). Evaluation and considerations about fundamental periods of damaged reinforced concrete buildings. Nat. Hazards Earth Syst. Sci., 13, 1903-1912, 2013. www.nat-hazards-earth-syst-sci.net/13/1903/2013. doi:10.5194/nhess-13-1903-2013

Astronomical Instruments with Two Scales Drawn on Their Common Circumference of Rings in the Joseon Dynasty

NASA Astrophysics Data System (ADS)

Mihn, Byeong-Hee; Choi, Goeun; Lee, Yong Sam

2017-03-01

This study examines the scale unique instruments used for astronomical observation during the Joseon dynasty. The Small Simplified Armillary Sphere (小簡儀, So-ganui) and the Sun-and-Stars Time-Determining Instrument (日星定時儀, Ilseong-jeongsi-ui) are minimized astronomical instruments, which can be characterized, respectively, as an observational instrument and a clock, and were influenced by the Simplified Armilla (簡儀, Jianyi) of the Yuan dynasty. These two instruments were equipped with several rings, and the rings of one were similar both in size and in scale to those of the other. Using the classic method of drawing the scale on the circumference of a ring, we analyze the scales of the Small Simplified Armillary Sphere and the Sun-and-Stars Time-Determining Instrument. Like the scale feature of the Simplified Armilla, we find that these two instruments selected the specific circumference which can be drawn by two kinds of scales. If Joseon`s astronomical instruments is applied by the dual scale drawing on one circumference, we suggest that 3.14 was used as the ratio of the circumference of circle, not 3 like China, when the ring`s size was calculated in that time. From the size of Hundred-interval disk of the extant Simplified Sundial in Korea, we make a conclusion that the three rings` diameter of the Sun-and-Stars Time-Determining Instrument described in the Sejiong Sillok (世宗實錄, Veritable Records of the King Sejong) refers to that of the middle circle of every ring, not the outer circle. As analyzing the degree of 28 lunar lodges (lunar mansions) in the equator written by Chiljeongsan-naepyeon (七政算內篇, the Inner Volume of Calculation of the Motions of the Seven Celestial Determinants), we also obtain the result that the scale of the Celestial-circumference-degree in the Small Simplified Armillary Sphere was made with a scale error about 0.1 du in root mean square (RMS).

An Exposition on the Nonlinear Kinematics of Shells, Including Transverse Shearing Deformations

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

2013-01-01

An in-depth exposition on the nonlinear deformations of shells with "small" initial geometric imperfections, is presented without the use of tensors. First, the mathematical descriptions of an undeformed-shell reference surface, and its deformed image, are given in general nonorthogonal coordinates. The two-dimensional Green-Lagrange strains of the reference surface derived and simplified for the case of "small" strains. Linearized reference-surface strains, rotations, curvatures, and torsions are then derived and used to obtain the "small" Green-Lagrange strains in terms of linear deformation measures. Next, the geometry of the deformed shell is described mathematically and the "small" three-dimensional Green-Lagrange strains are given. The deformations of the shell and its reference surface are related by introducing a kinematic hypothesis that includes transverse shearing deformations and contains the classical Love-Kirchhoff kinematic hypothesis as a proper, explicit subset. Lastly, summaries of the essential equations are given for general nonorthogonal and orthogonal coordinates, and the basis for further simplification of the equations is discussed.

The embodiment of beauty: Evidence from viewing Chinese concrete words and pictographs.

PubMed

Zhang, Wei; He, Xianyou; Zhao, Xueru; Lai, Siyan; Lai, Shuxian; Situ, Suiyan

2018-02-01

How is beauty embodied? According to the viewpoint of embodied cognition, the aesthetic processing of words or pictographs has roots in their referential archetypes. Four experiments tested whether the beauty of referential archetypes was routinely activated during the explicit and implicit aesthetic evaluations of the font structures of concrete Chinese words and pictographs in congruent or incongruent font colour. Results showed font structures of simplified Chinese words and pictographs were judged to be more beautiful when they referred to beautiful archetypes; and this pattern was reversed when they referred to ugly archetypes. Moreover, judgement was facilitated when font colour was congruent for Chinese words and pictographs referred to beautiful archetypes. For those referred to ugly archetypes, judgement was inhibited in congruent font colour but facilitated in incongruent font colour, suggesting aesthetic perceptions of the font structures of Chinese words and pictographs were derived from their referential natural objects. The spontaneous generation hypothesis of beauty is proposed to account for these findings. © 2016 International Union of Psychological Science.

Design and implementation of magnetically maneuverable capsule endoscope system with direction reference for image navigation.

PubMed

Sun, Zhen-Jun; Ye, Bo; Sun, Yi; Zhang, Hong-Hai; Liu, Sheng

2014-07-01

This article describes a novel magnetically maneuverable capsule endoscope system with direction reference for image navigation. This direction reference was employed by utilizing a specific magnet configuration between a pair of external permanent magnets and a magnetic shell coated on the external capsule endoscope surface. A pair of customized Cartesian robots, each with only 4 degrees of freedom, was built to hold the external permanent magnets as their end-effectors. These robots, together with their external permanent magnets, were placed on two opposite sides of a "patient bed." Because of the optimized configuration based on magnetic analysis between the external permanent magnets and the magnetic shell, a simplified control strategy was proposed, and only two parameters, yaw step angle and moving step, were necessary for the employed robotic system. Step-by-step experiments demonstrated that the proposed system is capable of magnetically maneuvering the capsule endoscope while providing direction reference for image navigation. © IMechE 2014.

Exposure and effects of perfluoroalkyl compounds on tree swallows nesting at Lake Johanna in east central Minnesota, USA

USGS Publications Warehouse

Custer, Christine M.; Custer, Thomas W.; Schoenfuss, Heiko L.; Poganski, Beth H.; Solem, Laura

2012-01-01

Tree swallow (Tachycineta bicolor) samples were collected at a reference lake and a nearby lake (Lake Johanna) in east central Minnesota, USA contaminated with perfluorinated carboxylic and sulfonic acids. Tissues were analyzed for a suite of 13 perfluoroalkyl compounds (PFCs) to quantify exposure and to determine if there was an association between egg concentrations of PFCs and reproductive success of tree swallows. Concentrations of perfluoroocatane sulfonate (PFOS) were elevated in all tree swallow tissues from Lake Johanna compared to tissues collected at the reference lake. Other PFCs, except for two, were elevated in blood plasma at Lake Johanna compared to the reference lake. PFOS was the dominant PFC (>75%) at Lake Johanna, but accounted for <50% of total PFCs at the reference lake. There was a negative association between concentrations of PFOS in eggs and hatching success. Reduced hatching success was associated with PFOS levels as low as 150 ng/g wet weight.

Fracture on Curved Surfaces

NASA Astrophysics Data System (ADS)

Mitchell, Noah; Koning, Vinzenz; Vitelli, Vincenzo; Irvine, William T. M.

2014-03-01

When an elastic film conforms to a surface with Gaussian curvature, stresses arise in the film. As a result, cracks--typically studied in flat materials--interact with curvature when propagating through the system. Using silicone elastomer sheets that conform to the surface of a Gaussian bump, we find experimental evidence for the deflection of a crack propagating through the material. We interpret our experiments with reference to analytical modeling and simulations of a simplified model system.

Vibrational Energy Transfer within the B 3Pi (0(+) sub u) State of 79BR2 Upon Collision with N2, O2, NO, and SF6

DTIC Science & Technology

1993-12-01

molecular radii derived for a (6,12) Lennard - Jones potential from viscosity data tabulated in reference (7). 49 Table A. 1. Gas Kinetic Collision...transfer rates and electronic quenching rates of the diatomic interhalogens in determining potential candidates for visible chemical lasers. This thesis...configuration ..................... 4 2. B2 potential energy curves ................................................................... 5 3. Simplified

Preliminary Evaluation of Altitude Scaling for Turbofan Engine Ice Crystal Icing

NASA Technical Reports Server (NTRS)

Tsao, Jen-Ching

2017-01-01

Preliminary evaluation of altitude scaling for turbofan engine ice crystal icing simulation was conducted during the 2015 LF11 engine icing test campaign in PSL.The results showed that a simplified approach for altitude scaling to simulate the key reference engine ice growth feature and associated icing effects to the engine is possible. But special considerations are needed to address the facility operation limitation for lower altitude engine icing simulation.

A ground based phase control system for the solar power satellite, volume 4

NASA Technical Reports Server (NTRS)

Chie, C. M.

1980-01-01

A ground phase control system is studied as an alternative approach to the current reference retrodirective phase control system in order to simplify the spaceborne hardware requirement. Based on waveform selections, functional subsystems to implement the ground-based phase control concept are identified and functionally represented. It was concluded that the feasibility of the concept becomes unclear if the conditions of the ionosphere and satellite motion are not met.

Work performed on velocity profiles in a hot jet by simplified RELIEF

NASA Technical Reports Server (NTRS)

Miles, Richard B.; Lempert, Walter R.

1991-01-01

The Raman Excitation + Laser Induced Electronic Fluorescence (RELIEF) velocity measurement method is based on vibrationally tagging oxygen molecules and observing their displacement after a short period of time. Two papers that discuss the use and implementation of the RELIEF technique are presented in this final report. Additionally, the end of the report contains a listing of the personnel involved and the reference documents used in the production of this final report.

Evaluation of reference genes for quantitative real-time RT-PCR analysis of gene expression in Nile tilapia (Oreochromis niloticus).

PubMed

Yang, Chang Geng; Wang, Xian Li; Tian, Juan; Liu, Wei; Wu, Fan; Jiang, Ming; Wen, Hua

2013-09-15

Quantitative real-time reverse-transcriptase polymerase chain reaction (RT-qPCR) has been used frequently to study gene expression related to fish immunology. In such studies, a stable reference gene should be selected to correct the expression of the target gene. In this study, seven candidate reference genes (glyceraldehyde-3-phosphate dehydrogenase (GADPH), ubiquitin-conjugating enzyme (UBCE), 18S ribosomal RNA (18S rRNA), beta-2-microglobulin (B2M), elongation factor 1 alpha (EF1A), tubulin alpha chain-like (TUBA) and beta actin (ACTB)), were selected to analyze their stability and normalization in seven tissues (liver, spleen, kidney, brain, heart, muscle and intestine) of Nile tilapia (Oreochromis niloticus) challenged with Streptococcus agalactiae or Streptococcus iniae, respectively. The results showed that all the candidate reference genes exhibited tissue-dependent transcriptional variations. With PBS injection as a control, UBCE was the most stable and suitable single reference gene in the intestine, liver, brain, kidney, and spleen after S. iniae infection, and in the liver, kidney, and spleen after S. agalactiae infection. EF1A was the most suitable in heart and muscle after S. iniae or S. agalactiae infection. GADPH was the most suitable gene in intestine and brain after S. agalactiae infection. In normal conditions, UBCE and 18S rRNA were the most stably expressed genes across the various tissues. These results showed that for RT-qPCR analysis of tilapia, selecting two or more reference genes may be more suitable for cross-tissue analysis of gene expression. Copyright © 2013 Elsevier B.V. All rights reserved.

Selection of Reference Genes for Quantitative Real Time PCR (qPCR) Assays in Tissue from Human Ascending Aorta

PubMed Central

Rueda-Martínez, Carmen; Lamas, Oscar; Mataró, María José; Robledo-Carmona, Juan; Sánchez-Espín, Gemma; Jiménez-Navarro, Manuel; Such-Martínez, Miguel; Fernández, Borja

2014-01-01

Dilatation of the ascending aorta (AAD) is a prevalent aortopathy that occurs frequently associated with bicuspid aortic valve (BAV), the most common human congenital cardiac malformation. The molecular mechanisms leading to AAD associated with BAV are still poorly understood. The search for differentially expressed genes in diseased tissue by quantitative real-time PCR (qPCR) is an invaluable tool to fill this gap. However, studies dedicated to identify reference genes necessary for normalization of mRNA expression in aortic tissue are scarce. In this report, we evaluate the qPCR expression of six candidate reference genes in tissue from the ascending aorta of 52 patients with a variety of clinical and demographic characteristics, normal and dilated aortas, and different morphologies of the aortic valve (normal aorta and normal valve n = 30; dilated aorta and normal valve n = 10; normal aorta and BAV n = 4; dilated aorta and BAV n = 8). The expression stability of the candidate reference genes was determined with three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable genes for the three algorithms employed were CDKN1β, POLR2A and CASC3, independently of the structure of the aorta and the valve morphology. In conclusion, we propose the use of these three genes as reference genes for mRNA expression analysis in human ascending aorta. However, we suggest searching for specific reference genes when conducting qPCR experiments with new cohort of samples. PMID:24841551

Reference Models for Multi-Layer Tissue Structures

DTIC Science & Technology

2016-09-01

simulation,  finite   element  analysis 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON USAMRMC...Physiologically realistic, fully specimen-specific, nonlinear reference models. Tasks. Finite element analysis of non-linear mechanics of cadaver...models. Tasks. Finite element analysis of non-linear mechanics of multi-layer tissue regions of human subjects. Deliverables. Partially subject- and

Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence

PubMed Central

2017-01-01

Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies. PMID:28591185

Mapping absolute tissue endogenous fluorophore concentrations with chemometric wide-field fluorescence microscopy

NASA Astrophysics Data System (ADS)

Xu, Zhang; Reilley, Michael; Li, Run; Xu, Min

2017-06-01

We report chemometric wide-field fluorescence microscopy for imaging the spatial distribution and concentration of endogenous fluorophores in thin tissue sections. Nonnegative factorization aided by spatial diversity is used to learn both the spectral signature and the spatial distribution of endogenous fluorophores from microscopic fluorescence color images obtained under broadband excitation and detection. The absolute concentration map of individual fluorophores is derived by comparing the fluorescence from "pure" fluorophores under the identical imaging condition following the identification of the fluorescence species by its spectral signature. This method is then demonstrated by characterizing the concentration map of endogenous fluorophores (including tryptophan, elastin, nicotinamide adenine dinucleotide, and flavin adenine dinucleotide) for lung tissue specimens. The absolute concentrations of these fluorophores are all found to decrease significantly from normal, perilesional, to cancerous (squamous cell carcinoma) tissue. Discriminating tissue types using the absolute fluorophore concentration is found to be significantly more accurate than that achievable with the relative fluorescence strength. Quantification of fluorophores in terms of the absolute concentration map is also advantageous in eliminating the uncertainties due to system responses or measurement details, yielding more biologically relevant data, and simplifying the assessment of competing imaging approaches.

Evaluation and selection of reliable reference genes for gene expression under abiotic stress in cotton (Gossypium hirsutum L.).

PubMed

Wang, Min; Wang, Qinglian; Zhang, Baohong

2013-11-01

Reference genes are critical for normalization of the gene expression level of target genes. The widely used housekeeping genes may change their expression levels at different tissue under different treatment or stress conditions. Therefore, systematical evaluation on the housekeeping genes is required for gene expression analysis. Up to date, no work was performed to evaluate the housekeeping genes in cotton under stress treatment. In this study, we chose 10 housekeeping genes to systematically assess their expression levels at two different tissues (leaves and roots) under two different abiotic stresses (salt and drought) with three different concentrations. Our results show that there is no best reference gene for all tissues at all stress conditions. The reliable reference gene should be selected based on a specific condition. For example, under salt stress, UBQ7, GAPDH and EF1A8 are better reference genes in leaves; TUA10, UBQ7, CYP1, GAPDH and EF1A8 were better in roots. Under drought stress, UBQ7, EF1A8, TUA10, and GAPDH showed less variety of expression level in leaves and roots. Thus, it is better to identify reliable reference genes first before performing any gene expression analysis. However, using a combination of housekeeping genes as reference gene may provide a new strategy for normalization of gene expression. In this study, we found that combination of four housekeeping genes worked well as reference genes under all the stress conditions. © 2013.

Reference Gene Selection for Quantitative Real-Time Reverse-Transcriptase PCR in Annual Ryegrass (Lolium multiflorum) Subjected to Various Abiotic Stresses.

PubMed

Liu, Qiuxu; Qi, Xiao; Yan, Haidong; Huang, Linkai; Nie, Gang; Zhang, Xinquan

2018-01-16

To select the most stable reference genes in annual ryegrass ( Lolium multiflorum ), we studied annual ryegrass leaf tissues exposed to various abiotic stresses by qRT-PCR and selected 11 candidate reference genes, i.e., 18S rRNA, E2, GAPDH, eIF4A, HIS3, SAMDC, TBP-1, Unigene71, Unigene77, Unigene755, and Unigene14912. We then used GeNorm, NormFinder, and BestKeeper to analyze the expression stability of these 11 genes, and used RefFinder to comprehensively rank genes according to stability. Under different stress conditions, the most suitable reference genes for studies of leaf tissues of annual ryegrass were different. The expression of the eIF4A gene was the most stable under drought stress. Under saline-alkali stress, Unigene14912 has the highest expression stability. Under acidic aluminum stress, SAMDC expression stability was highest. Under heavy metal stress, Unigene71 expression had the highest stability. According to the software analyses, Unigene14912, HIS3, and eIF4A were the most suitable for analyses of abiotic stress in tissues of annual ryegrass. GAPDH was the least suitable reference gene. In conclusion, selecting appropriate reference genes under abiotic stress not only improves the accuracy of annual ryegrass gene expression analyses, but also provides a theoretical reference for the development of reference genes in plants of the genus Lolium .

Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation

PubMed Central

Masè, Michela; Grasso, Margherita; Avogaro, Laura; D’Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

2017-01-01

MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions. PMID:28117343

Finite-element simulation of blood perfusion in muscle tissue during compression and sustained contraction.

PubMed

Vankan, W J; Huyghe, J M; Slaaf, D W; van Donkelaar, C C; Drost, M R; Janssen, J D; Huson, A

1997-09-01

Mechanical interaction between tissue stress and blood perfusion in skeletal muscles plays an important role in blood flow impediment during sustained contraction. The exact mechanism of this interaction is not clear, and experimental investigation of this mechanism is difficult. We developed a finite-element model of the mechanical behavior of blood-perfused muscle tissue, which accounts for mechanical blood-tissue interaction in maximally vasodilated vasculature. Verification of the model was performed by comparing finite-element results of blood pressure and flow with experimental measurements in a muscle that is subject to well-controlled mechanical loading conditions. In addition, we performed simulations of blood perfusion during tetanic, isometric contraction and maximal vasodilation in a simplified, two-dimensional finite-element model of a rat calf muscle. A vascular waterfall in the venous compartment was identified as the main cause for blood flow impediment both in the experiment and in the finite-element simulations. The validated finite-element model offers possibilities for detailed analysis of blood perfusion in three-dimensional muscle models under complicated loading conditions.

Modeling the heat transfer problem for the novel combined cryosurgery and hyperthermia system.

PubMed

Zhao, Gang; Bai, Xue-Fei; Luo, Da-Wei; Gao, Da-Yong

2006-01-01

A multidimensional, finite element analysis (FEA) for the freezing, holding, rewarming and heating processes of biological tissues during the cryosurgery process of the new Combined Cryosurgery/Hyperthermia System is presented to theoretically test its validity. The tissues are treated as nonideal materials freezing over a temperature range, and the thermophysical properties of which are temperature dependent. The enthalpy method is applied to solve the highly nonlinear problem. It was found that when the same boundary condition and the same target tissue presented, the novel Cryosurgery/Hyperthermia System could supply the target tissue an approximative cooling rate, a much lower minimal temperature, a much greater warming rate, and a much greater thermal gradients compared with that of the simplified Endocare system. The numerical simulation indicates that the novel combined cryosurgery and hyperthermia system can provide an excellent curative effect in the corresponding cryotherapy. And the most attractive feature of this FEA framework is that it can be easily mastered by the surgeon without in-depth theory of heat transfer to analyze the cryosurgery process beforehand due to the friendly GUI (graphical user interface) of Ansys software.

Virtual wall-based haptic-guided teleoperated surgical robotic system for single-port brain tumor removal surgery.

PubMed

Seung, Sungmin; Choi, Hongseok; Jang, Jongseong; Kim, Young Soo; Park, Jong-Oh; Park, Sukho; Ko, Seong Young

2017-01-01

This article presents a haptic-guided teleoperation for a tumor removal surgical robotic system, so-called a SIROMAN system. The system was developed in our previous work to make it possible to access tumor tissue, even those that seat deeply inside the brain, and to remove the tissue with full maneuverability. For a safe and accurate operation to remove only tumor tissue completely while minimizing damage to the normal tissue, a virtual wall-based haptic guidance together with a medical image-guided control is proposed and developed. The virtual wall is extracted from preoperative medical images, and the robot is controlled to restrict its motion within the virtual wall using haptic feedback. Coordinate transformation between sub-systems, a collision detection algorithm, and a haptic-guided teleoperation using a virtual wall are described in the context of using SIROMAN. A series of experiments using a simplified virtual wall are performed to evaluate the performance of virtual wall-based haptic-guided teleoperation. With haptic guidance, the accuracy of the robotic manipulator's trajectory is improved by 57% compared to one without. The tissue removal performance is also improved by 21% ( p < 0.05). The experiments show that virtual wall-based haptic guidance provides safer and more accurate tissue removal for single-port brain surgery.

Solvent Separating Secondary Metabolites Directly from Biosynthetic Tissue for Surface-Assisted Laser Desorption Ionisation Mass Spectrometry

PubMed Central

Rudd, David; Benkendorff, Kirsten; Voelcker, Nicolas H.

2015-01-01

Marine bioactive metabolites are often heterogeneously expressed in tissues both spatially and over time. Therefore, traditional solvent extraction methods benefit from an understanding of the in situ sites of biosynthesis and storage to deal with heterogeneity and maximize yield. Recently, surface-assisted mass spectrometry (MS) methods namely nanostructure-assisted laser desorption ionisation (NALDI) and desorption ionisation on porous silicon (DIOS) surfaces have been developed to enable the direct detection of low molecular weight metabolites. Since direct tissue NALDI-MS or DIOS-MS produce complex spectra due to the wide variety of other metabolites and fragments present in the low mass range, we report here the use of “on surface” solvent separation directly from mollusc tissue onto nanostructured surfaces for MS analysis, as a mechanism for simplifying data annotation and detecting possible artefacts from compound delocalization during the preparative steps. Water, ethanol, chloroform and hexane selectively extracted a range of choline esters, brominated indoles and lipids from Dicathais orbita hypobranchial tissue imprints. These compounds could be quantified on the nanostructured surfaces by comparison to standard curves generated from the pure compounds. Surface-assisted MS could have broad utility for detecting a broad range of secondary metabolites in complex marine tissue samples. PMID:25786067

Simplified methods for screening cowpea cultivars for manganese leaf-tissue tolerance. [Vigna unguiculata

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

Wissemeier, A.H.; Horst, W.J.

In cowpea (Vigna unguiculata (L.) Walp.) dark brown speckles on old leaves are typical symptoms of Mn toxicity and indicate Mn sensitivity of leaf tissue. Induction and subsequent quantification of brown Mn speckles in leaf tissues were used to screen cowpea cultivars for Mn leaf-tissue tolerance using three different techniques: (i) leaf cuttings cultured for 22 days in solution culture with 20 {mu}M MnSO{sub 4}, (ii) leaf rings mounted on leaves of intact plants and filled with 500 {mu}M MnSO{sub 4} for 5 days, and (iii) leaf disks floated for 3 days on 500 {mu}M MnSO{sub 4}. Density of brownmore » speckles differed considerably among the six cultivars tested, and was not related to the Mn concentrations of the leaf tissues. There were close relationships between genotypic Mn-toxicity symptom expression and depression of dry matter production of the cultivars at high Mn supply in a long-term sand culture experiment. The floating leaf-disk method is particularly suited for screening large numbers of cowpea cultivars for Mn leaf-tissue tolerance because it requires only 3 days. The ranking of the cultivars for Mn tolerance was highly correlated to Mn tolerance of intact plants.« less

A 'Global Reference' Comparator for Biosimilar Development.

PubMed

Webster, Christopher J; Woollett, Gillian R

2017-08-01

Major drug regulators have indicated in guidance their flexibility to accept some development data for biosimilars generated with reference product versions licensed outside their own jurisdictions, but most authorities require new bridging studies between these versions and the versions of them licensed locally. The costs of these studies are not trivial in absolute terms and, due to the multiplier effect of required repetition by each biosimilar sponsor, their collective costs are substantial. Yet versions of biologics licensed in different jurisdictions usually share the same development data, and any manufacturing changes between versions have been justified by a rigorous comparability process. The fact that a biosimilar is usually expected to be licensed in multiple jurisdictions, in each case as similar to the local reference product, confirms that minor analytical differences between versions of reference biologics are typically inconsequential for clinical outcomes and licensing. A greatly simplified basis for selecting a reference comparator, that does not require conducting new bridging studies, is proposed and justified based on the shared data of the reference product versions as well as the proof offered where biosimilars have already been approved. The relevance of this proposal to the interchangeability designation available in the US is discussed.

The Effect of Simplifying Dental Implant Drilling Sequence on Osseointegration: An Experimental Study in Dogs

PubMed Central

Giro, Gabriela; Tovar, Nick; Marin, Charles; Bonfante, Estevam A.; Jimbo, Ryo; Suzuki, Marcelo; Janal, Malvin N.; Coelho, Paulo G.

2013-01-01

Objectives. To test the hypothesis that there would be no differences in osseointegration by reducing the number of drills for site preparation relative to conventional drilling sequence. Methods. Seventy-two implants were bilaterally placed in the tibia of 18 beagle dogs and remained for 1, 3, and 5 weeks. Thirty-six implants were 3.75 mm in diameter and the other 36 were 4.2 mm. Half of the implants of each diameter were placed under a simplified technique (pilot drill + final diameter drill) and the other half were placed under conventional drilling where multiple drills of increasing diameter were utilized. After euthanisation, the bone-implant samples were processed and referred to histological analysis. Bone-to-implant contact (BIC) and bone-area-fraction occupancy (BAFO) were assessed. Statistical analyses were performed by GLM ANOVA at 95% level of significance considering implant diameter, time in vivo, and drilling procedure as independent variables and BIC and BAFO as the dependent variables. Results. Both techniques led to implant integration. No differences in BIC and BAFO were observed between drilling procedures as time elapsed in vivo. Conclusions. The simplified drilling protocol presented comparable osseointegration outcomes to the conventional protocol, which proved the initial hypothesis. PMID:23431303

Simplified three-dimensional model provides anatomical insights in lizards' caudal autotomy as printed illustration.

PubMed

De Amorim, Joana D C G; Travnik, Isadora; De Sousa, Bernadete M

2015-03-01

Lizards' caudal autotomy is a complex and vastly employed antipredator mechanism, with thorough anatomic adaptations involved. Due to its diminished size and intricate structures, vertebral anatomy is hard to be clearly conveyed to students and researchers of other areas. Three-dimensional models are prodigious tools in unveiling anatomical nuances. Some of the techniques used to create them can produce irregular and complicated forms, which despite being very accurate, lack didactical uniformity and simplicity. Since both are considered fundamental characteristics for comprehension, a simplified model could be the key to improve learning. The model here presented depicts the caudal osteology of Tropidurus itambere, and was designed to be concise, in order to be easily assimilated, yet complete, not to compromise the informative aspect. The creation process requires only basic skills in manipulating polygons in 3D modeling softwares, in addition to the appropriate knowledge of the structure to be modeled. As reference for the modeling, we used microscopic observation and a photograph database of the caudal structures. This way, no advanced laboratory equipment was needed and all biological materials were preserved for future research. Therefore, we propose a wider usage of simplified 3D models both in the classroom and as illustrations for scientific publications.

Effect of picric acid and enzymatic creatinine on the efficiency of the glomerular filtration rate predicator formula.

PubMed

Qiu, Ling; Guo, Xiuzhi; Zhu, Yan; Shou, Weilin; Gong, Mengchun; Zhang, Lin; Han, Huijuan; Quan, Guoqiang; Xu, Tao; Li, Hang; Li, Xuewang

2013-01-01

To investigate the impact of serum creatinine measurement on the applicability of glomerular filtration rate (GFR) evaluation equations. 99mTc-DTPA plasma clearance rate was used as GFR reference (rGFR) in patients with chronic kidney disease (CKD). Serum creatinine was measureded using enzymatic or picric acid creatinine reagent. The GFR of the patients were estimated using the Cockcroft-Gault equation corrected for body surface area, simplified Modification of Diet in Renal Disease (MDRD) equation, simplified MDRD equation corrected to isotopes dilution mass spectrometry, the CKD epidemiology collaborative research equation, and two Chinese simplified MDRD equations. Significant differences in the eGFR results estimated through enzymatic and picric acid methods were observed for the same evaluation equation. The intraclass correlation coefficient (ICC) of eGFR when the creatinine was measured by the picric acid method was significantly lower than that of the enzymatic method. The assessment accuracy of every equation using the enzymatic method to measure creatinine was significantly higher than that measured by the picric acid method when rGFR was > or = 60 mL/min/1.73m2. A significant difference was demonstrated in the same GFR evaluation equation using the picric acid and enzymatic methods. The enzymatic creatinine method was better than the picric acid method.

Test-retest reproducibility of quantitative binding measures of [11C]Ro15-4513, a PET ligand for GABAA receptors containing alpha5 subunits.

PubMed

McGinnity, Colm J; Riaño Barros, Daniela A; Rosso, Lula; Veronese, Mattia; Rizzo, Gaia; Bertoldo, Alessandra; Hinz, Rainer; Turkheimer, Federico E; Koepp, Matthias J; Hammers, Alexander

2017-05-15

Alteration of γ-aminobutyric acid "A" (GABA A ) receptor-mediated neurotransmission has been associated with various neurological and psychiatric disorders. [ 11 C]Ro15-4513 is a PET ligand with high affinity for α5-subunit-containing GABA A receptors, which are highly expressed in limbic regions of the human brain (Sur et al., 1998). We quantified the test-retest reproducibility of measures of [ 11 C]Ro15-4513 binding derived from six different quantification methods (12 variants). Five healthy males (median age 40 years, range 38-49 years) had a 90-min PET scan on two occasions (median interval 12 days, range 11-30 days), after injection of a median dose of 441 MegaBequerels of [ 11 C]Ro15-4513. Metabolite-corrected arterial plasma input functions (parent plasma input functions, ppIFs) were generated for all scans. We quantified regional binding using six methods (12 variants), some of which were region-based (applied to the average time-activity curve within a region) and others were voxel-based: 1) Models requiring arterial ppIFs - regional reversible compartmental models with one and two tissue compartments (2kbv and 4kbv); 2) Regional and voxelwise Logan's graphical analyses (Logan et al., 1990), which required arterial ppIFs; 3) Model-free regional and voxelwise (exponential) spectral analyses (SA; (Cunningham and Jones, 1993)), which also required arterial ppIFs; 4) methods not requiring arterial ppIFs - voxelwise standardised uptake values (Kenney et al., 1941), and regional and voxelwise simplified reference tissue models (SRTM/SRTM2) using brainstem or alternatively cerebellum as pseudo-reference regions (Lammertsma and Hume, 1996; Gunn et al., 1997). To compare the variants, we sampled the mean values of the outcome parameters within six bilateral, non-reference grey matter regions-of-interest. Reliability was quantified in terms of median absolute percentage test-retest differences (MA-TDs; preferentially low) and between-subject coefficient of variation (BS-CV, preferentially high), both compounded by the intraclass correlation coefficient (ICC). These measures were compared between variants, with particular interest in the hippocampus. Two of the six methods (5/12 variants) yielded reproducible data (i.e. MA-TD <10%): regional SRTMs and voxelwise SRTM2s, both using either the brainstem or the cerebellum; and voxelwise SA. However, the SRTMs using the brainstem yielded a lower median BS-CV (7% for regional, 7% voxelwise) than the other variants (8-11%), resulting in lower ICCs. The median ICCs across six regions were 0.89 (interquartile range 0.75-0.90) for voxelwise SA, 0.71 (0.64-0.84) for regional SRTM-cerebellum and 0.83 (0.70-0.86) for voxelwise SRTM-cerebellum. The ICCs for the hippocampus were 0.89 for voxelwise SA, 0.95 for regional SRTM-cerebellum and 0.93 for voxelwise SRTM-cerebellum. Quantification of [ 11 C]Ro15-4513 binding shows very good to excellent reproducibility with SRTM and with voxelwise SA which, however, requires an arterial ppIF. Quantification in the α5 subunit-rich hippocampus is particularly reliable. The very low expression of the α5 in the cerebellum (Fritschy and Mohler, 1995; Veronese et al., 2016) and the substantial α1 subunit density in this region may hamper the application of reference tissue methods. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Equilibrium Passive Sampling of POP in Lipid-Rich and Lean Fish Tissue: Quality Control Using Performance Reference Compounds.

PubMed

Rusina, Tatsiana P; Carlsson, Pernilla; Vrana, Branislav; Smedes, Foppe

2017-10-03

Passive sampling is widely used to measure levels of contaminants in various environmental matrices, including fish tissue. Equilibrium passive sampling (EPS) of persistent organic pollutants (POP) in fish tissue has been hitherto limited to application in lipid-rich tissue. We tested several exposure methods to extend EPS applicability to lean tissue. Thin-film polydimethylsiloxane (PDMS) passive samplers were exposed statically to intact fillet and fish homogenate and dynamically by rolling with cut fillet cubes. The release of performance reference compounds (PRC) dosed to passive samplers prior to exposure was used to monitor the exchange process. The sampler-tissue exchange was isotropic, and PRC were shown to be good indicators of sampler-tissue equilibration status. The dynamic exposures demonstrated equilibrium attainment in less than 2 days for all three tested fish species, including lean fish containing 1% lipid. Lipid-based concentrations derived from EPS were in good agreement with lipid-normalized concentrations obtained using conventional solvent extraction. The developed in-tissue EPS method is robust and has potential for application in chemical monitoring of biota and bioaccumulation studies.

A study of the high-precision displacement laser probe

NASA Astrophysics Data System (ADS)

Fan, Yuming; Zhang, Guoxiong

2006-06-01

On the basis of the measuring principle of the dynamic active optical confocal probe based on time difference measurement that has a reference path, a dynamic active optical confocal probe based on time difference measurement but has no reference path is developed. In this paper, the working principle of this optical confocal probe is dissertated. A large-scale integrated measuring system is designed to simplify the structure of the probe and to enhance the stability of the probe. Single-chip microcomputer system with a high-speed ADC is selected in the measurement and control system of the probe. At the end of the paper, experiments on the performance of the optical confocal probe based on time difference measurement with no reference path are carried out. Experiment results show that the probe has a measuring resolution of 0.05μm, a measuring range of 0.2mm and a linearity of 0.4μm.

An image-based skeletal tissue model for the ICRP reference newborn

NASA Astrophysics Data System (ADS)

Pafundi, Deanna; Lee, Choonsik; Watchman, Christopher; Bourke, Vincent; Aris, John; Shagina, Natalia; Harrison, John; Fell, Tim; Bolch, Wesley

2009-07-01

Hybrid phantoms represent a third generation of computational models of human anatomy needed for dose assessment in both external and internal radiation exposures. Recently, we presented the first whole-body hybrid phantom of the ICRP reference newborn with a skeleton constructed from both non-uniform rational B-spline and polygon-mesh surfaces (Lee et al 2007 Phys. Med. Biol. 52 3309-33). The skeleton in that model included regions of cartilage and fibrous connective tissue, with the remainder given as a homogenous mixture of cortical and trabecular bone, active marrow and miscellaneous skeletal tissues. In the present study, we present a comprehensive skeletal tissue model of the ICRP reference newborn to permit a heterogeneous representation of the skeleton in that hybrid phantom set—both male and female—that explicitly includes a delineation of cortical bone so that marrow shielding effects are correctly modeled for low-energy photons incident upon the newborn skeleton. Data sources for the tissue model were threefold. First, skeletal site-dependent volumes of homogeneous bone were obtained from whole-cadaver CT image analyses. Second, selected newborn bone specimens were acquired at autopsy and subjected to micro-CT image analysis to derive model parameters of the marrow cavity and bone trabecular 3D microarchitecture. Third, data given in ICRP Publications 70 and 89 were selected to match reference values on total skeletal tissue mass. Active marrow distributions were found to be in reasonable agreement with those given previously by the ICRP. However, significant differences were seen in total skeletal and site-specific masses of trabecular and cortical bone between the current and ICRP newborn skeletal tissue models. The latter utilizes an age-independent ratio of 80%/20% cortical and trabecular bone for the reference newborn. In the current study, a ratio closer to 40%/60% is used based upon newborn CT and micro-CT skeletal image analyses. These changes in mineral bone composition may have significant dosimetric implications when considering localized marrow dosimetry for radionuclides that target mineral bone in the newborn child.

Growing Three-Dimensional Cartilage-Cell Cultures

NASA Technical Reports Server (NTRS)

Spaulding, Glenn F.; Prewett, Tacey L.; Goodwin, Thomas J.

1995-01-01

Process for growing three-dimensional cultures of mammalian cartilage from normal mammalian cells devised. Effected using horizontal rotating bioreactor described in companion article, "Simplified Bioreactor for Growing Mammalian Cells" (MSC-22060). Bioreactor provides quiescent environment with generous supplies of nutrient and oxygen. Initiated with noncartilage cells. Artificially grown tissue resembles that in mammalian cartilage. Potential use in developing therapies for damage to cartilage by joint and back injuries and by such inflammatory diseases as arthritis and temporal-mandibular joint disease. Also used to test nonsteroid anti-inflammation medicines.

Trace element reference values in tissues from inhabitants of the EU. XII. Development of BioReVa program for statistical treatment.

PubMed

Iversen, B S; Sabbioni, E; Fortaner, S; Pietra, R; Nicolotti, A

2003-01-20

Statistical data treatment is a key point in the assessment of trace element reference values being the conclusive stage of a comprehensive and organized evaluation process of metal concentration in human body fluids. The EURO TERVIHT project (Trace Elements Reference Values in Human Tissues) was started for evaluating, checking and suggesting harmonized procedures for the establishment of trace element reference intervals in body fluids and tissues. Unfortunately, different statistical approaches are being used in this research field making data comparison difficult and in some cases impossible. Although international organizations such as International Federation of Clinical Chemistry (IFCC) or International Union of Pure and Applied Chemistry (IUPAC) have issued recommended guidelines for reference values assessment, including the statistical data treatment, a unique format and a standardized data layout is still missing. The aim of the present study is to present a software (BioReVa) running under Microsoft Windows platform suitable for calculating the reference intervals of trace elements in body matrices. The main scope for creating an ease-of-use application was to control the data distribution, to establish the reference intervals according to the accepted recommendation, on the base of the simple statistic, to get a standard presentation of experimental data and to have an application to which further need could be integrated in future. BioReVa calculates the IFCC reference intervals as well as the coverage intervals recommended by IUPAC as a supplement to the IFCC intervals. Examples of reference values and reference intervals calculated with BioReVa software concern Pb and Se in blood; Cd, In and Cr in urine, Hg and Mo in hair of different general European populations. University of Michigan

A simplified and cost-effective enrichment protocol for the isolation of Campylobacter spp. from retail broiler meat without microaerobic incubation

PubMed Central

2011-01-01

Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat. PMID:21812946

Assessment of nerve involvement in the lumbar spine: agreement between magnetic resonance imaging, physical examination and pain drawing findings.

PubMed

Bertilson, Bo C; Brosjö, Eva; Billing, Hans; Strender, Lars-Erik

2010-09-10

Detection of nerve involvement originating in the spine is a primary concern in the assessment of spine symptoms. Magnetic resonance imaging (MRI) has become the diagnostic method of choice for this detection. However, the agreement between MRI and other diagnostic methods for detecting nerve involvement has not been fully evaluated. The aim of this diagnostic study was to evaluate the agreement between nerve involvement visible in MRI and findings of nerve involvement detected in a structured physical examination and a simplified pain drawing. Sixty-one consecutive patients referred for MRI of the lumbar spine were - without knowledge of MRI findings - assessed for nerve involvement with a simplified pain drawing and a structured physical examination. Agreement between findings was calculated as overall agreement, the p value for McNemar's exact test, specificity, sensitivity, and positive and negative predictive values. MRI-visible nerve involvement was significantly less common than, and showed weak agreement with, physical examination and pain drawing findings of nerve involvement in corresponding body segments. In spine segment L4-5, where most findings of nerve involvement were detected, the mean sensitivity of MRI-visible nerve involvement to a positive neurological test in the physical examination ranged from 16-37%. The mean specificity of MRI-visible nerve involvement in the same segment ranged from 61-77%. Positive and negative predictive values of MRI-visible nerve involvement in segment L4-5 ranged from 22-78% and 28-56% respectively. In patients with long-standing nerve root symptoms referred for lumbar MRI, MRI-visible nerve involvement significantly underestimates the presence of nerve involvement detected by a physical examination and a pain drawing. A structured physical examination and a simplified pain drawing may reveal that many patients with "MRI-invisible" lumbar symptoms need treatment aimed at nerve involvement. Factors other than present MRI-visible nerve involvement may be responsible for findings of nerve involvement in the physical examination and the pain drawing.

A Simplified Approach for Simultaneous Measurements of Wavefront Velocity and Curvature in the Heart Using Activation Times.

PubMed

Mazeh, Nachaat; Haines, David E; Kay, Matthew W; Roth, Bradley J

2013-12-01

The velocity and curvature of a wave front are important factors governing the propagation of electrical activity through cardiac tissue, particularly during heart arrhythmias of clinical importance such as fibrillation. Presently, no simple computational model exists to determine these values simultaneously. The proposed model uses the arrival times at four or five sites to determine the wave front speed ( v ), direction (θ), and radius of curvature (ROC) ( r 0 ). If the arrival times are measured, then v , θ, and r 0 can be found from differences in arrival times and the distance between these sites. During isotropic conduction, we found good correlation between measured values of the ROC r 0 and the distance from the unipolar stimulus ( r = 0.9043 and p < 0.0001). The conduction velocity (m/s) was correlated ( r = 0.998, p < 0.0001) using our method (mean = 0.2403, SD = 0.0533) and an empirical method (mean = 0.2352, SD = 0.0560). The model was applied to a condition of anisotropy and a complex case of reentry with a high voltage extra stimulus. Again, results show good correlation between our simplified approach and established methods for multiple wavefront morphologies. In conclusion, insignificant measurement errors were observed between this simplified approach and an approach that was more computationally demanding. Accuracy was maintained when the requirement that ε (ε = b/r 0 , ratio of recording site spacing over wave fronts ROC) was between 0.001 and 0.5. The present simplified model can be applied to a variety of clinical conditions to predict behavior of planar, elliptical, and reentrant wave fronts. It may be used to study the genesis and propagation of rotors in human arrhythmias and could lead to rotor mapping using low density endocardial recording electrodes.

Recent advances in QM/MM free energy calculations using reference potentials☆

PubMed Central

Duarte, Fernanda; Amrein, Beat A.; Blaha-Nelson, David; Kamerlin, Shina C.L.

2015-01-01

Background Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. PMID:25038480

Impacts and pathways of mine contaminants to bull trout (Salvelinus confluentus) in an Idaho watershed.

PubMed

Kiser, Tim; Hansen, James; Kennedy, Brian

2010-08-01

Metals contamination from mining activities is a persistent problem affecting aquatic ecosystems throughout mining districts in the western USA. The Gold Creek drainage in northern Idaho has a history of mining within its headwaters and contains elevated sediment concentrations of As, Cd, Cu, Pb, and Zn. To determine system-wide impacts of increased metals, we measured concentrations of metals in water, sediment, and benthic macroinvertebrate tissues and related them to whole-body fish tissues and histopathological alterations in native salmonids. Water concentrations were higher than those in reference areas, but were below water quality criteria for protection of aquatic biota for most of the study area. Sediment and benthic macroinvertebrate tissue concentrations for all metals were significantly higher at all sites compared with the reference site. Fish tissues were significantly higher for all metals below mine sites compared with the reference site, but only Cd and Pb were higher in fish tissues in the furthest downstream reach in the Gold Creek Delta. Metals concentrations in benthic macroinvertebrate tissues and fish tissues were strongly correlated, suggesting a transfer of metals through a dietary pathway. The concentrations within sediments and biota were similar to those reported in other studies in which adverse effects to salmonids occurred. We observed histopathological changes in livers of bull trout, including inflammation, necrosis, and pleomorphism. Our study is consistent with other work in which sediment-driven exposure can transfer up the food chain and may cause adverse impacts to higher organisms.

Understanding young stars - A history

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

Stahler, S.W.

1988-12-01

The history of pre-main-sequence theory is briefly reviewed. The paper of Henyey et al. (1955) is seen as an important transitional work, one which abandoned previous simplifying assumptions yet failed to incorporate newer insights into the surface structure of late-type stars. The subsequent work of Hayashi and his contemporaries is outlined, with an emphasis on the underlying physical principles. Finally, the recent impact of protostar theory is discussed, and speculations are offered on future developments. 56 references.

Aligning HST Images to Gaia: A Faster Mosaicking Workflow

NASA Astrophysics Data System (ADS)

Bajaj, V.

2017-11-01

We present a fully programmatic workflow for aligning HST images using the high-quality astrometry provided by Gaia Data Release 1. Code provided in a Jupyter Notebook works through this procedure, including parsing the data to determine the query area parameters, querying Gaia for the coordinate catalog, and using the catalog with TweakReg as reference catalog. This workflow greatly simplifies the normally time-consuming process of aligning HST images, especially those taken as part of mosaics.

Predictions of GPS X-Set Performance during the Places Experiment

DTIC Science & Technology

1979-07-01

previously existing GPS X-set receiver simulation was modified to include the received signal spectrum and the receiver code correlation operation... CORRELATION OPERATION The X-set receiver simulation documented in Reference 3-1 is a direct sampled -data digital implementation of the GPS X-set...ul(t) -sin w2t From Carrier and Code Loops (wit +0 1 (t)) Figure 3-6. Simplified block diagram of code correlator operation and I-Q sampling . 6 I

Techno-Economic Analysis of Magnesium Extraction from Seawater via a Catalyzed Organo-Metathetical Process

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

Liu, Jian; Bearden, Mark D.; Fernandez, Carlos A.

Magnesium (Mg) has many useful applications especially in various Mg alloys which can decrease weight while increasing strength. To increase the affordability and minimize environment consequence, a novel catalyzed organo-metathetical (COMET) process was proposed to extract Mg from seawater aiming to achieve significant reduction in total energy and production cost comparing with the melting salt electrolysis method currently adopted by US Mg LLC. A process flowsheet for a reference COMET process was set-up using Aspen Plus which included five key steps, anhydrous MgCl2 production, transmetallation, dibutyl Mg decomposition, n-BuLi regeneration, and LiCL electrolysis. The energy and production cost and CO2more » emission were estimated based on the Aspen modeling using Aspen economic analyzer. Our results showed that it is possible to produce Mg from seawater with a production cost of $2.0/kg-Mg while consuming about 35.3 kWh/kg-Mg and releasing 7.0 kg CO2/kg-Mg. A simplified US Mg manufacturing process was also generated using Aspen and the cost and emission results were estimated for comparison purpose. Under our simulation conditions, the reference COMET process maintain a comparable CO2 emission rate and can save about 40% in production cost and save about 15% energy compared to the simplified US Mg process.« less

A simplified interventional mapping system (SIMS) for the selection of combinations of targeted treatments in non-small cell lung cancer

PubMed Central

Lazar, Vladimir; Martini, Jean-François; Gomez-Navarro, Jesus; Yver, Antoine; Kan, Zhengyin; Dry, Jonathan R.; Kehren, Jeanne; Validire, Pierre; Rodon, Jordi; Vielh, Philippe; Ducreux, Michel; Galbraith, Susan; Lehnert, Manfred; Onn, Amir; Berger, Raanan; Pierotti, Marco A.; Porgador, Angel; Pramesh, CS; Ye, Ding-wei; Carvalho, Andre L.; Batist, Gerald; Le Chevalier, Thierry; Morice, Philippe; Besse, Benjamin; Vassal, Gilles; Mortlock, Andrew; Hansson, Johan; Berindan-Neagoe, Ioana; Dann, Robert; Haspel, Joel; Irimie, Alexandru; Laderman, Steve; Nechushtan, Hovav; Al Omari, Amal S.; Haywood, Trent; Bresson, Catherine; Soo, Khee Chee; Osman, Iman; Mata, Hilario; Lee, Jack J.; Jhaveri, Komal; Meurice, Guillaume; Palmer, Gary; Lacroix, Ludovic; Koscielny, Serge; Eterovic, Karina Agda; Blay, Jean-Yves; Buller, Richard; Eggermont, Alexander; Schilsky, Richard L.; Mendelsohn, John; Soria, Jean-Charles; Rothenberg, Mace

2015-01-01

Non-small cell lung cancer (NSCLC) is a leading cause of death worldwide. Targeted monotherapies produce high regression rates, albeit for limited patient subgroups, who inevitably succumb. We present a novel strategy for identifying customized combinations of triplets of targeted agents, utilizing a simplified interventional mapping system (SIMS) that merges knowledge about existent drugs and their impact on the hallmarks of cancer. Based on interrogation of matched lung tumor and normal tissue using targeted genomic sequencing, copy number variation, transcriptomics, and miRNA expression, the activation status of 24 interventional nodes was elucidated. An algorithm was developed to create a scoring system that enables ranking of the activated interventional nodes for each patient. Based on the trends of co-activation at interventional points, combinations of drug triplets were defined in order to overcome resistance. This methodology will inform a prospective trial to be conducted by the WIN consortium, aiming to significantly impact survival in metastatic NSCLC and other malignancies. PMID:25944621

Validation of reference genes aiming accurate normalization of qRT-PCR data in Dendrocalamus latiflorus Munro.

PubMed

Liu, Mingying; Jiang, Jing; Han, Xiaojiao; Qiao, Guirong; Zhuo, Renying

2014-01-01

Dendrocalamus latiflorus Munro distributes widely in subtropical areas and plays vital roles as valuable natural resources. The transcriptome sequencing for D. latiflorus Munro has been performed and numerous genes especially those predicted to be unique to D. latiflorus Munro were revealed. qRT-PCR has become a feasible approach to uncover gene expression profiling, and the accuracy and reliability of the results obtained depends upon the proper selection of stable reference genes for accurate normalization. Therefore, a set of suitable internal controls should be validated for D. latiflorus Munro. In this report, twelve candidate reference genes were selected and the assessment of gene expression stability was performed in ten tissue samples and four leaf samples from seedlings and anther-regenerated plants of different ploidy. The PCR amplification efficiency was estimated, and the candidate genes were ranked according to their expression stability using three software packages: geNorm, NormFinder and Bestkeeper. GAPDH and EF1α were characterized to be the most stable genes among different tissues or in all the sample pools, while CYP showed low expression stability. RPL3 had the optimal performance among four leaf samples. The application of verified reference genes was illustrated by analyzing ferritin and laccase expression profiles among different experimental sets. The analysis revealed the biological variation in ferritin and laccase transcript expression among the tissues studied and the individual plants. geNorm, NormFinder, and BestKeeper analyses recommended different suitable reference gene(s) for normalization according to the experimental sets. GAPDH and EF1α had the highest expression stability across different tissues and RPL3 for the other sample set. This study emphasizes the importance of validating superior reference genes for qRT-PCR analysis to accurately normalize gene expression of D. latiflorus Munro.

Reference tissue normalization in longitudinal (18)F-florbetapir positron emission tomography of late mild cognitive impairment.

PubMed

Shokouhi, Sepideh; Mckay, John W; Baker, Suzanne L; Kang, Hakmook; Brill, Aaron B; Gwirtsman, Harry E; Riddle, William R; Claassen, Daniel O; Rogers, Baxter P

2016-01-15

Semiquantitative methods such as the standardized uptake value ratio (SUVR) require normalization of the radiotracer activity to a reference tissue to monitor changes in the accumulation of amyloid-β (Aβ) plaques measured with positron emission tomography (PET). The objective of this study was to evaluate the effect of reference tissue normalization in a test-retest (18)F-florbetapir SUVR study using cerebellar gray matter, white matter (two different segmentation masks), brainstem, and corpus callosum as reference regions. We calculated the correlation between (18)F-florbetapir PET and concurrent cerebrospinal fluid (CSF) Aβ1-42 levels in a late mild cognitive impairment cohort with longitudinal PET and CSF data over the course of 2 years. In addition to conventional SUVR analysis using mean and median values of normalized brain radiotracer activity, we investigated a new image analysis technique-the weighted two-point correlation function (wS2)-to capture potentially more subtle changes in Aβ-PET data. Compared with the SUVRs normalized to cerebellar gray matter, all cerebral-to-white matter normalization schemes resulted in a higher inverse correlation between PET and CSF Aβ1-42, while the brainstem normalization gave the best results (high and most stable correlation). Compared with the SUVR mean and median values, the wS2 values were associated with the lowest coefficient of variation and highest inverse correlation to CSF Aβ1-42 levels across all time points and reference regions, including the cerebellar gray matter. The selection of reference tissue for normalization and the choice of image analysis method can affect changes in cortical (18)F-florbetapir uptake in longitudinal studies.

Diagnosis of retrodiscal tissue in painful temporomandibular joint (TMJ) by fluid-attenuated inversion recovery (FLAIR) signal intensity.

PubMed

Kuroda, Migiwa; Otonari-Yamamoto, Mika; Sano, Tsukasa; Fujikura, Mamiko; Wakoh, Mamoru

2014-09-09

Aims: The purpose of the present study is to analyze the fluid-attenuated inversion recovery (FLAIR) signal intensity of the retrodiscal tissue in a painful temporomandibular joint (TMJ), and to develop a diagnostic system based on FLAIR data. Methodology: The study was based on 33 joints of 17 patients referred for MR imaging of the TMJ. Regions of interest were placed over retrodiscal tissue and gray matter (GM) on FLAIR images. Using signal intensities of GM as reference points, signal intensity ratios (SIR) of retrodiscal tissue were calculated. SIRs in painful TMJ were compared with those in painless TMJ. Wilcoxon's Rank Sum Test was used to analyze the difference in SIRs between the painful and painless groups (P<0·05). Results: The SIRs of retrodiscal tissue were significantly higher in painful joints than in painless joints. Conclusion: FLAIR sequences provide a high signal in patients having painful TMJ, and it suggests that retrodiscal tissue in painful TMJ contains elements such as protein.

Diagnosis of retrodiscal tissue in painful temporomandibular joint (TMJ) by fluid-attenuated inversion recovery (FLAIR) signal intensity.

PubMed

Kuroda, Migiwa; Otonari-Yamamoto, Mika; Sano, Tsukasa; Fujikura, Mamiko; Wakoh, Mamoru

2015-10-01

The purpose of the present study is to analyze the fluid-attenuated inversion recovery (FLAIR) signal intensity of the retrodiscal tissue in a painful temporomandibular joint (TMJ), and to develop a diagnostic system based on FLAIR data. The study was based on 33 joints of 17 patients referred for MR imaging of the TMJ. Regions of interest were placed over retrodiscal tissue and gray matter (GM) on FLAIR images. Using signal intensities of GM as reference points, signal intensity ratios (SIR) of retrodiscal tissue were calculated. SIRs in painful TMJ were compared with those in painless TMJ. Wilcoxon's Rank Sum Test was used to analyze the difference in SIRs between the painful and painless groups (P<0·05). The SIRs of retrodiscal tissue were significantly higher in painful joints than in painless joints. FLAIR sequences provide a high signal in patients having painful TMJ, and it suggests that retrodiscal tissue in painful TMJ contains elements such as protein.

Using RNA-seq data to select reference genes for normalizing gene expression in apple roots.

PubMed

Zhou, Zhe; Cong, Peihua; Tian, Yi; Zhu, Yanmin

2017-01-01

Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization.

Using RNA-seq data to select reference genes for normalizing gene expression in apple roots

PubMed Central

Zhou, Zhe; Cong, Peihua; Tian, Yi

2017-01-01

Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization. PMID:28934340

Study on photon transport problem based on the platform of molecular optical simulation environment.

PubMed

Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

2010-01-01

As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

PubMed Central

Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

2010-01-01

As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

Radiosynthesis and initial characterization of a PDE10A specific PET tracer [18F]AMG 580 in non-human primates.

PubMed

Hwang, Dah-Ren; Hu, Essa; Allen, Jennifer R; Davis, Carl; Treanor, James; Miller, Silke; Chen, Hang; Shi, Bingzhi; Narayanan, Tanjorie K; Barret, Olivier; Alagille, David; Yu, Zhigang; Slifstein, Mark

2015-08-01

Phosphodiesterase 10A (PDE10A) is an intracellular enzyme responsible for the breakdown of cyclic nucleotides which are important second messengers for neurotransmission. Inhibition of PDE10A has been identified as a potential target for treatment of various neuropsychiatric disorders. To assist drug development, we have identified a selective PDE10A positron emission tomography (PET) tracer, AMG 580. We describe here the radiosynthesis of [(18)F]AMG 580 and in vitro and in vivo characterization results. The potency and selectivity were determined by in vitro assay using [(3)H]AMG 580 and baboon brain tissues. [(18)F]AMG 580 was prepared by a 1-step [(18)F]fluorination procedure. Dynamic brain PET scans were performed in non-human primates. Regions-of-interest were defined on individuals' MRIs and transferred to the co-registered PET images. Data were analyzed using two tissue compartment analysis (2TC), Logan graphical (Logan) analysis with metabolite-corrected input function and the simplified reference tissue model (SRTM) method. A PDE10A inhibitor and unlabeled AMG 580 were used to demonstrate the PDE10A specificity. KD was estimated by Scatchard analysis of high and low affinity PET scans. AMG 580 has an in vitro KD of 71.9 pM. Autoradiography showed specific uptake in striatum. Mean activity of 121 ± 18 MBq was used in PET studies. In Rhesus, the baseline BPND for putamen and caudate was 3.38 and 2.34, respectively, via 2TC, and 3.16, 2.34 via Logan, and 2.92, and 2.01 via SRTM. A dose dependent decrease of BPND was observed by the pre-treatment with a PDE10A inhibitor. In baboons, 0.24 mg/kg dose of AMG 580 resulted in about 70% decrease of BPND. The in vivo KD of [(18)F]AMG 580 was estimated to be around 0.44 nM in baboons. [(18)F]AMG 580 is a selective and potent PDE10A PET tracer with excellent specific striatal binding in non-human primates. It warrants further evaluation in humans. Copyright © 2015 Elsevier Inc. All rights reserved.

PET Imaging of D2/3 agonist binding in healthy human subjects with the radiotracer [11C]-N-propyl-nor-apomorphine (NPA): preliminary evaluation and reproducibility studies

PubMed Central

Narendran, Rajesh; Frankle, W. Gordon; Mason, N. Scott; Laymon, Charles M.; Lopresti, Brian J; Price, Julie C.; Kendro, Steve; Vora, Shivangi; Litschge, Maralee; Mountz, James M.; Mathis, Chester A.

2009-01-01

Objective (-)-N-[11C]-Propyl-norapomorphine (NPA) is a full dopamine D2/3 receptor agonist radiotracer suitable for imaging D2/3 receptors configured in a state of high affinity for agonists using Positron Emission Tomography (PET). The aim of the present study was to define the optimal analytic method to derive accurate and reliable D2/3 receptor parameters with [11C]NPA. Methods Six healthy subjects (4 females/2 males) underwent two [11C]NPA scans in the same day. D2/3 receptor binding parameters were estimated using kinetic analysis (using 1- and 2- tissue compartment models) as well as simplified reference tissue method in the three functional subdivisions of the striatum (associative striatum, AST; limbic striatum LST and sensorimotor striatum SMST). The test-retest variability and intraclass correlation coefficient were assessed for distribution volume (VT), binding potential relative to plasma concentration (BPP), and binding potential relative to nondisplaceable uptake (BPND) Results A two-tissue compartment kinetic model adequately described the functional subdivisions of the striatum as well as cerebellum time-activity data. The reproducibility of VT was excellent (≤ 10%) in all regions, for this approach. The reproducibility of both BPP (≤ 12%) and BPND (≤ 10%) was also excellent. The intraclass correlation coefficient of BPP and BPND were acceptable as well (> 0.75) in the three functional subdivisions of the striatum. Although SRTM led to an underestimation of BPND values relative to that estimated by kinetic analysis by 8 to 13%, the values derived using both the methods were reasonably well correlated (r2 = 0.89, n = 84). Both methods were similarly effective at detecting the differences in [11C]NPA BPND between subjects. Conclusion The results of this study indicate that [11C]NPA can be used to measure D2/3 receptors configured in a state of high affinity for the agonists with high reliability and reproducibility in the functional subdivisions of the human striatum. PMID:19301416

TU-AB-BRC-03: Accurate Tissue Characterization for Monte Carlo Dose Calculation Using Dual-and Multi-Energy CT Data

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

Lalonde, A; Bouchard, H

Purpose: To develop a general method for human tissue characterization with dual-and multi-energy CT and evaluate its performance in determining elemental compositions and the associated proton stopping power relative to water (SPR) and photon mass absorption coefficients (EAC). Methods: Principal component analysis is used to extract an optimal basis of virtual materials from a reference dataset of tissues. These principal components (PC) are used to perform two-material decomposition using simulated DECT data. The elemental mass fraction and the electron density in each tissue is retrieved by measuring the fraction of each PC. A stoichiometric calibration method is adapted to themore » technique to make it suitable for clinical use. The present approach is compared with two others: parametrization and three-material decomposition using the water-lipid-protein (WLP) triplet. Results: Monte Carlo simulations using TOPAS for four reference tissues shows that characterizing them with only two PC is enough to get a submillimetric precision on proton range prediction. Based on the simulated DECT data of 43 references tissues, the proposed method is in agreement with theoretical values of protons SPR and low-kV EAC with a RMS error of 0.11% and 0.35%, respectively. In comparison, parametrization and WLP respectively yield RMS errors of 0.13% and 0.29% on SPR, and 2.72% and 2.19% on EAC. Furthermore, the proposed approach shows potential applications for spectral CT. Using five PC and five energy bins reduces the SPR RMS error to 0.03%. Conclusion: The proposed method shows good performance in determining elemental compositions from DECT data and physical quantities relevant to radiotherapy dose calculation and generally shows better accuracy and unbiased results compared to reference methods. The proposed method is particularly suitable for Monte Carlo calculations and shows promise in using more than two energies to characterize human tissue with CT.« less

Establishing references for gene expression analyses by RT-qPCR in Theobroma cacao tissues.

PubMed

Pinheiro, T T; Litholdo, C G; Sereno, M L; Leal, G A; Albuquerque, P S B; Figueira, A

2011-11-17

Lack of continuous progress in Theobroma cacao (Malvaceae) breeding, especially associated with seed quality traits, requires more efficient selection methods based on genomic information. Reverse transcript quantitative PCR (RT-qPCR) has become the method of choice for gene expression analysis, but relative expression analysis requires various reference genes, which must be stable across various biological conditions. We sought suitable reference genes for various tissues of cacao, especially developing seeds. Ten potential reference genes were analyzed for stability at various stages of embryo development, leaves, stems, roots, flowers, and pod epicarp; seven of them were also evaluated in shoot tips treated either with hormones (salicylate; ethefon; methyl-jasmonate) or after inoculation with the fungus Moniliophthora perniciosa (Marasmiaceae sensu lato). For developing embryos, the three most stable genes were actin (ACT), polyubiquitin (PUB), and ribosomal protein L35 (Rpl35). In the analyses of various tissues, the most stable genes were malate dehydrogenase (MDH), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and acyl-carrier protein B (ACP B). GAPDH, MDH and tubulin (TUB) were the most appropriate for normalization when shoot apexes were treated with hormones, while ACT, TUB and Rpl35 were the most appropriate after inoculation with M. perniciosa. We conclude that for each plant system and biological or ontogenetical condition, there is a need to define suitable reference genes. This is the first report to define reference genes for expression studies in cacao.

Validation of reference genes for real-time quantitative PCR normalization in soybean developmental and germinating seeds.

PubMed

Li, Qing; Fan, Cheng-Ming; Zhang, Xiao-Mei; Fu, Yong-Fu

2012-10-01

Most of traditional reference genes chosen for real-time quantitative PCR normalization were assumed to be ubiquitously and constitutively expressed in vegetative tissues. However, seeds show distinct transcriptomes compared with the vegetative tissues. Therefore, there is a need for re-validation of reference genes in samples of seed development and germination, especially for soybean seeds. In this study, we aimed at identifying reference genes suitable for the quantification of gene expression level in soybean seeds. In order to identify the best reference genes for soybean seeds, 18 putative reference genes were tested with various methods in different seed samples. We combined the outputs of both geNorm and NormFinder to assess the expression stability of these genes. The reference genes identified as optimums for seed development were TUA5 and UKN2, whereas for seed germination they were novel reference genes Glyma05g37470 and Glyma08g28550. Furthermore, for total seed samples it was necessary to combine four genes of Glyma05g37470, Glyma08g28550, Glyma18g04130 and UKN2 [corrected] for normalization. Key message We identified several reference genes that stably expressed in soybean seed developmental and germinating processes.

Impact of indoor environment on path loss in body area networks.

PubMed

Hausman, Sławomir; Januszkiewicz, Łukasz

2014-10-20

In this paper the influence of an example indoor environment on narrowband radio channel path loss for body area networks operating around 2.4 GHz is investigated using computer simulations and on-site measurements. In contrast to other similar studies, the simulation model included both a numerical human body phantom and its environment-room walls, floor and ceiling. As an example, radio signal attenuation between two different configurations of transceivers with dipole antennas placed in a direct vicinity of a human body (on-body scenario) is analyzed by computer simulations for several types of reflecting environments. In the analyzed case the propagation environments comprised a human body and office room walls. As a reference environment for comparison, free space with only a conducting ground plane, modelling a steel mesh reinforced concrete floor, was chosen. The transmitting and receiving antennas were placed in two on-body configurations chest-back and chest-arm. Path loss vs. frequency simulation results obtained using Finite Difference Time Domain (FDTD) method and a multi-tissue anthropomorphic phantom were compared to results of measurements taken with a vector network analyzer with a human subject located in an average-size empty cuboidal office room. A comparison of path loss values in different environments variants gives some qualitative and quantitative insight into the adequacy of simplified indoor environment model for the indoor body area network channel representation.

Impact of Indoor Environment on Path Loss in Body Area Networks

PubMed Central

Hausman, Sławomir; Januszkiewicz, Łukasz

2014-01-01

In this paper the influence of an example indoor environment on narrowband radio channel path loss for body area networks operating around 2.4 GHz is investigated using computer simulations and on-site measurements. In contrast to other similar studies, the simulation model included both a numerical human body phantom and its environment—room walls, floor and ceiling. As an example, radio signal attenuation between two different configurations of transceivers with dipole antennas placed in a direct vicinity of a human body (on-body scenario) is analyzed by computer simulations for several types of reflecting environments. In the analyzed case the propagation environments comprised a human body and office room walls. As a reference environment for comparison, free space with only a conducting ground plane, modelling a steel mesh reinforced concrete floor, was chosen. The transmitting and receiving antennas were placed in two on-body configurations chest–back and chest–arm. Path loss vs. frequency simulation results obtained using Finite Difference Time Domain (FDTD) method and a multi-tissue anthropomorphic phantom were compared to results of measurements taken with a vector network analyzer with a human subject located in an average-size empty cuboidal office room. A comparison of path loss values in different environments variants gives some qualitative and quantitative insight into the adequacy of simplified indoor environment model for the indoor body area network channel representation. PMID:25333289

Measurement of susceptibility artifacts with histogram-based reference value on magnetic resonance images according to standard ASTM F2119.

PubMed

Heinrich, Andreas; Teichgräber, Ulf K; Güttler, Felix V

2015-12-01

The standard ASTM F2119 describes a test method for measuring the size of a susceptibility artifact based on the example of a passive implant. A pixel in an image is considered to be a part of an image artifact if the intensity is changed by at least 30% in the presence of a test object, compared to a reference image in which the test object is absent (reference value). The aim of this paper is to simplify and accelerate the test method using a histogram-based reference value. Four test objects were scanned parallel and perpendicular to the main magnetic field, and the largest susceptibility artifacts were measured using two methods of reference value determination (reference image-based and histogram-based reference value). The results between both methods were compared using the Mann-Whitney U-test. The difference between both reference values was 42.35 ± 23.66. The difference of artifact size was 0.64 ± 0.69 mm. The artifact sizes of both methods did not show significant differences; the p-value of the Mann-Whitney U-test was between 0.710 and 0.521. A standard-conform method for a rapid, objective, and reproducible evaluation of susceptibility artifacts could be implemented. The result of the histogram-based method does not significantly differ from the ASTM-conform method.

A study of a tissue equivalent gelatine based tissue substitute

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

Spence, J.L.

1992-11-01

A study of several tissue substitutes for use as volumetric dosimeters was performed. The tissue substitutes studied included tissue substitutes from previous studies and from ICRU 44. The substitutes were evaluated for an overall match to Reference Man which was used as a basis for this study. The evaluation was based on the electron stopping power, the mass attenuation coefficient, the electron density, and the specific gravity. The tissue substitute chosen also had to be capable of changing from a liquid into a solid form to maintain an even distribution of thermoluminesent dosimetry (TLD) powder and then back to amore » liquid for recovery of the TLD powder without adversely effecting the TLD powder. The gelatine mixture provided the closest match to the data from Reference Man tissue. The gelatine mixture was put through a series of test to determine it's usefulness as a reliable tissue substitute. The TLD powder was cast in the gelatine mixture and recovered to determine if the TLD powder was adversely effected. The distribution of the TLD powder after being cast into the gelatin mixture was tested in insure an even was maintained.« less

A study of a tissue equivalent gelatine based tissue substitute

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

Spence, Jody L.

1992-11-01

A study of several tissue substitutes for use as volumetric dosimeters was performed. The tissue substitutes studied included tissue substitutes from previous studies and from ICRU 44. The substitutes were evaluated for an overall match to Reference Man which was used as a basis for this study. The evaluation was based on the electron stopping power, the mass attenuation coefficient, the electron density, and the specific gravity. The tissue substitute chosen also had to be capable of changing from a liquid into a solid form to maintain an even distribution of thermoluminesent dosimetry (TLD) powder and then back to amore » liquid for recovery of the TLD powder without adversely effecting the TLD powder. The gelatine mixture provided the closest match to the data from Reference Man tissue. The gelatine mixture was put through a series of test to determine it`s usefulness as a reliable tissue substitute. The TLD powder was cast in the gelatine mixture and recovered to determine if the TLD powder was adversely effected. The distribution of the TLD powder after being cast into the gelatin mixture was tested in insure an even was maintained.« less

Development and myogenesis of the vermiform Buddenbrockia (Myxozoa) and implications for cnidarian body plan evolution

PubMed Central

2012-01-01

Background The enigmatic wormlike parasite Buddenbrockia plumatellae has recently been shown to belong to the Myxozoa, which are now supported as a clade within Cnidaria. Most myxozoans are morphologically extremely simplified, lacking major metazoan features such as epithelial tissue layers, gut, nervous system, body axes and gonads. This hinders comparisons to free-living cnidarians and thus an understanding of myxozoan evolution and identification of their cnidarian sister group. However, B. plumatellae is less simplified than other myxozoans and therefore is of specific significance for such evolutionary considerations. Methods We analyse and describe the development of major body plan features in Buddenbrockia worms using a combination of histology, electron microscopy and confocal microscopy. Results Early developmental stages develop a primary body axis that shows a polarity, which is manifested as a gradient of tissue development, enabling distinction between the two worm tips. This polarity is maintained in adult worms, which, in addition, often develop a pore at the distal tip. The musculature comprises tetraradially arranged longitudinal muscle blocks consisting of independent myocytes embedded in the extracellular matrix between inner and outer epithelial tissue layers. The muscle fibres are obliquely oriented and in fully grown worms consistently form an angle of 12° with respect to the longitudinal axis of the worm in each muscle block and hence confer chirality. Connecting cells form a link between each muscle block and constitute four rows of cells that run in single file along the length of the worm. These connecting cells are remnants of the inner epithelial tissue layer and are anchored to the extracellular matrix. They are likely to have a biomechanical function. Conclusions The polarised primary body axis represents an ancient feature present in the last common ancestor of Cnidaria and Bilateria. The tetraradial arrangement of musculature is consistent with a medusozoan affinity for Myxozoa. However, the chiral pattern of muscle fibre orientation is apparently novel within Cnidaria and could thus be a specific adaptation. The presence of independent myocytes instead of Cnidaria-like epitheliomuscular cells can be interpreted as further support for the presence of mesoderm in cnidarians, or it may represent convergent evolution to a bilaterian condition. PMID:22594622

Three new mussel tissue standard reference materials (SRMs) for the determination of organic contaminants.

PubMed

Poster, Dianne L; Schantz, Michele M; Kucklick, John R; Lopez de Alda, Maria J; Porter, Barbara J; Pugh, Rebecca; Wise, Stephen A

2004-03-01

Three new mussel tissue standard reference materials (SRMs) have been developed by the National Institute of Standards and Technology (NIST) for the determination of the concentrations of organic contaminants. The most recently prepared material, SRM 1974b, is a fresh frozen tissue homogenate prepared from mussels ( Mytilus edulis) collected in Boston Harbor, Massachusetts. The other two materials, SRMs 2977 and 2978, are freeze-dried tissue homogenates prepared from mussels collected in Guanabara Bay, Brazil and Raritan Bay, New Jersey, respectively. All three new mussel tissue SRMs complement the current suite of marine natural-matrix SRMs available from NIST that are characterized for a wide range of contaminants (organic and inorganic). SRM 1974b has been developed to replace its predecessor SRM 1974a, Organics in Mussel Tissue, for which the supply is depleted. Similarly, SRMs 2977 and 2978 were developed to replace a previously available (supply depleted) freeze-dried version of SRM 1974a, SRM 2974, Organics in Freeze-Dried Mussel Tissue. SRM 1974b is the third in a series of fresh frozen mussel tissue homogenate SRMs prepared from mussels collected in Boston Harbor starting in 1988. SRM 1974b has certified concentration values for 22 polycyclic aromatic hydrocarbons (PAHs), 31 polychlorinated biphenyl congeners (PCBs), and 7 chlorinated pesticides. Reference values are provided for additional constituents: 16 PAHs, 8 PCBs plus total PCBs, 6 pesticides, total extractable organics, methylmercury, and 11 trace elements. PAH concentrations range from about 2 ng g(-1 )dry mass (cyclopenta[ cd]pyrene) to 180 ng g(-1 )dry mass (pyrene). PCB concentrations range from about 2 ng g(-1 )dry mass (PCB 157) to 120 ng g(-1 )dry mass (PCB 153). The reference value for total PCBs in SRM 1974b is (2020 +/- 420) ng g(-1 )dry mass. Pesticide concentrations range from about 4 ng g(-1 )dry mass (4,4'-DDT) to 40 ng g(-1 )dry mass (4,4'-DDE). SRM 2977 has certified values for 14 PAHs, 25 PCB congeners, 7 pesticides, 6 trace elements, and methylmercury. Reference values for 16 additional PAHs and 9 inorganic constituents are provided, and information values are given for 23 additional trace elements. SRM 2978 has certified and reference concentrations for 41 and 22 organic compounds, respectively, and contains contaminant levels similar to those of SRM 1974b. Organic contaminant levels in SRM 2977 (mussels from Guanabara Bay, Brazil) are typically a factor of 2 to 4 lower than those in SRM 1974b and SRM 2978. The organic contaminant concentrations in each new mussel tissue SRM are presented and compared in this paper. In addition, a chronological review of contaminant concentrations associated with mussels collected in Boston Harbor is discussed as well as a stability assessment of SRM 1974a.

How accurately can the peak skin dose in fluoroscopy be determined using indirect dose metrics?

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

Jones, A. Kyle, E-mail: kyle.jones@mdanderson.org; Ensor, Joe E.; Pasciak, Alexander S.

Purpose: Skin dosimetry is important for fluoroscopically-guided interventions, as peak skin doses (PSD) that result in skin reactions can be reached during these procedures. There is no consensus as to whether or not indirect skin dosimetry is sufficiently accurate for fluoroscopically-guided interventions. However, measuring PSD with film is difficult and the decision to do so must be madea priori. The purpose of this study was to assess the accuracy of different types of indirect dose estimates and to determine if PSD can be calculated within ±50% using indirect dose metrics for embolization procedures. Methods: PSD were measured directly using radiochromicmore » film for 41 consecutive embolization procedures at two sites. Indirect dose metrics from the procedures were collected, including reference air kerma. Four different estimates of PSD were calculated from the indirect dose metrics and compared along with reference air kerma to the measured PSD for each case. The four indirect estimates included a standard calculation method, the use of detailed information from the radiation dose structured report, and two simplified calculation methods based on the standard method. Indirect dosimetry results were compared with direct measurements, including an analysis of uncertainty associated with film dosimetry. Factors affecting the accuracy of the different indirect estimates were examined. Results: When using the standard calculation method, calculated PSD were within ±35% for all 41 procedures studied. Calculated PSD were within ±50% for a simplified method using a single source-to-patient distance for all calculations. Reference air kerma was within ±50% for all but one procedure. Cases for which reference air kerma or calculated PSD exhibited large (±35%) differences from the measured PSD were analyzed, and two main causative factors were identified: unusually small or large source-to-patient distances and large contributions to reference air kerma from cone beam computed tomography or acquisition runs acquired at large primary gantry angles. When calculated uncertainty limits [−12.8%, 10%] were applied to directly measured PSD, most indirect PSD estimates remained within ±50% of the measured PSD. Conclusions: Using indirect dose metrics, PSD can be determined within ±35% for embolization procedures. Reference air kerma can be used without modification to set notification limits and substantial radiation dose levels, provided the displayed reference air kerma is accurate. These results can reasonably be extended to similar procedures, including vascular and interventional oncology. Considering these results, film dosimetry is likely an unnecessary effort for these types of procedures when indirect dose metrics are available.« less

3D on-chip microscopy of optically cleared tissue

NASA Astrophysics Data System (ADS)

Zhang, Yibo; Shin, Yoonjung; Sung, Kevin; Yang, Sam; Chen, Harrison; Wang, Hongda; Teng, Da; Rivenson, Yair; Kulkarni, Rajan P.; Ozcan, Aydogan

2018-02-01

Traditional pathology relies on tissue biopsy, micro-sectioning, immunohistochemistry and microscopic imaging, which are relatively expensive and labor-intensive, and therefore are less accessible in resource-limited areas. Low-cost tissue clearing techniques, such as the simplified CLARITY method (SCM), are promising to potentially reduce the cost of disease diagnosis by providing 3D imaging and phenotyping of thicker tissue samples with simpler preparation steps. However, the mainstream imaging approach for cleared tissue, fluorescence microscopy, suffers from high-cost, photobleaching and signal fading. As an alternative approach to fluorescence, here we demonstrate 3D imaging of SCMcleared tissue using on-chip holography, which is based on pixel-super-resolution and multi-height phase recovery algorithms to digitally compute the sample's amplitude and phase images at various z-slices/depths through the sample. The tissue clearing procedures and the lens-free imaging system were jointly optimized to find the best illumination wavelength, tissue thickness, staining solution pH, and the number of hologram heights to maximize the imaged tissue volume, minimize the amount of acquired data, while maintaining a high contrast-to-noise ratio for the imaged cells. After this optimization, we achieved 3D imaging of a 200-μm thick cleared mouse brain tissue over a field-of-view of <20mm2 , and the resulting 3D z-stack agrees well with the images acquired with a scanning lens-based microscope (20× 0.75NA). Moreover, the lens-free microscope achieves an order-of-magnitude better data efficiency compared to its lens-based counterparts for volumetric imaging of samples. The presented low-cost and high-throughput lens-free tissue imaging technique enabled by CLARITY can be used in various biomedical applications in low-resource-settings.

Selection of reference genes for qRT-PCR analysis of gene expression in sea cucumber Apostichopus japonicus during aestivation

NASA Astrophysics Data System (ADS)

Zhao, Ye; Chen, Muyan; Wang, Tianming; Sun, Lina; Xu, Dongxue; Yang, Hongsheng

2014-11-01

Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a technique that is widely used for gene expression analysis, and its accuracy depends on the expression stability of the internal reference genes used as normalization factors. However, many applications of qRT-PCR used housekeeping genes as internal controls without validation. In this study, the expression stability of eight candidate reference genes in three tissues (intestine, respiratory tree, and muscle) of the sea cucumber Apostichopus japonicus was assessed during normal growth and aestivation using the geNorm, NormFinder, delta CT, and RefFinder algorithms. The results indicate that the reference genes exhibited significantly different expression patterns among the three tissues during aestivation. In general, the β-tubulin (TUBB) gene was relatively stable in the intestine and respiratory tree tissues. The optimal reference gene combination for intestine was 40S ribosomal protein S18 (RPS18), TUBB, and NADH dehydrogenase (NADH); for respiratory tree, it was β-actin (ACTB), TUBB, and succinate dehydrogenase cytochrome B small subunit (SDHC); and for muscle it was α-tubulin (TUBA) and NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 (NDUFA13). These combinations of internal control genes should be considered for use in further studies of gene expression in A. japonicus during aestivation.

Geomagnetic field models for satellite angular motion studies

NASA Astrophysics Data System (ADS)

Ovchinnikov, M. Yu.; Penkov, V. I.; Roldugin, D. S.; Pichuzhkina, A. V.

2018-03-01

Four geomagnetic field models are discussed: IGRF, inclined, direct and simplified dipoles. Geomagnetic induction vector expressions are provided in different reference frames. Induction vector behavior is compared for different models. Models applicability for the analysis of satellite motion is studied from theoretical and engineering perspectives. Relevant satellite dynamics analysis cases using analytical and numerical techniques are provided. These cases demonstrate the benefit of a certain model for a specific dynamics study. Recommendations for models usage are summarized in the end.

Logic Design of a Shared Disk System in a Multi-Micro Computer Environment.

DTIC Science & Technology

1983-06-01

overall system, is given. An exnaustive description of eacn device can De found in tne cited references. A. INTEL 80S5 Tne INTEL Be86 is a nign...eitner could De accomplished, it was necessary to understand ootn tne existing system arcnitecture ani software. Tne last cnapter addressed tnat...to De adapted: tne loader program and tne Doot ROP program. Tne loader program is a simplified version of CP/M-Bö and contains cniy encu^n file

A Projectile for a Rectangular Barreled Rail Gun

DTIC Science & Technology

1999-12-01

fins Cfb ’ skin friction drag coefficient for nose/body combination modified for equations of motion Cff’ skin friction drag coefficient for fins...occasionally referred to as the last point method, uses a loop , shown in simplified form in Figure (2) as a flow chart. The program loop takes the final... Cfb ’ = CfofCf(Sno/s+Sbs)/ScsS (4.11) Cff = CfffcfSw/Scss (4.12) 2. Form Drag The form drag coefficients are determined by the methods from

Advanced propulsion for LEO-Moon transport. 3: Transportation model. M.S. Thesis - California Univ.

NASA Technical Reports Server (NTRS)

Henley, Mark W.

1992-01-01

A simplified computational model of low Earth orbit-Moon transportation system has been developed to provide insight into the benefits of new transportation technologies. A reference transportation infrastructure, based upon near-term technology developments, is used as a departure point for assessing other, more advanced alternatives. Comparison of the benefits of technology application, measured in terms of a mass payback ratio, suggests that several of the advanced technology alternatives could substantially improve the efficiency of low Earth orbit-Moon transportation.

Demonstration of Simplified Field Test Methods for the Measurement of Diesel Particulate Matter (PM) from Military Diesel Engines

DTIC Science & Technology

2008-07-01

EPA emission standards, the EPA has also specified the measurement methods . According to EPA, the most accurate and precise method of determining ...function of particle size and refractive index . If particle size distributions and refractive indices in diesel exhaust strongly depend on the...to correct the bias of the raw SFTM data and align the data with the values determined by the federal reference method . Thus, to use these methods a

Methodology Investigation of AI(Artificial Intelligence) Test Officer Support Tool. Volume 2

DTIC Science & Technology

1989-03-01

a mathematical representation of a PE and its connections. This representation describes the " neurodynamics " of a PE. A sigmoid transfer function is...Element(i) Neurodynamics : Summation Function: Wo*XO + W,*X + W*X "X 0 0 1 1 2 W~fn Transfer Function: F(k) = (1 + e k) Output: x. - F(I) Figure 2-4...simplifies the description of the network operations. Thus, one or more PEs grouped together, with the same neurodynamics , is a layer [reference 5]. A

Numerical Solutions for Laminar Boundary Layer Behind Blast Waves.

DTIC Science & Technology

1980-05-01

DISTRIBUTION STATEMENT (of thle Report) Approved for public release; distribution unlimited. 17 . DISTRIBUTION STATEMENT (of the abstract entered in Block 20...Reference I ............. 41 5. Boundary-Layer Functions for Case A, B, C, and D ......... 98 3 NOMENCLATURE A constant, Eqs. (10) and ( 17 ) B...the constant A was chosen as follows to simplify the coefficients of f and g1 A = 2mF CZ(a+i) OPO/pCO ( The ( 17 ) The explicit dependence of the flow

Comparison of [11C]TZ1964B and [18F]MNI659 for PET imaging brain PDE10A in nonhuman primates.

PubMed

Liu, Hui; Jin, Hongjun; Yue, Xuyi; Han, Junbin; Yang, Hao; Flores, Hubert; Su, Yi; Alagille, David; Perlmutter, Joel S; Tamagnan, Gilles; Tu, Zhude

2016-10-01

Phosphodiesterase 10A (PDE10A) inhibitors show therapeutic effects for diseases with striatal pathology. PET radiotracers have been developed to quantify in vivo PDE10A levels and target engagement for therapeutic interventions. The aim of this study was to compare two potent and selective PDE10A radiotracers, [ 11 C]TZ1964B and [ 18 F]MNI659 in the nonhuman primate (NHP) brain. Double scans in the same cynomolgus monkey on the same day were performed after injection of [ 11 C]TZ1964B and [ 18 F]MNI659. Specific uptake was determined in two ways: nondisplaceable binding potential (BP ND ) was calculated using cerebellum as the reference region and the PDE-10A enriched striatum as the target region of interest (ROI); the area under the time-activity curve (AUC) for the striatum to cerebellum ratio was also calculated. High-performance liquid chromatography (HPLC) analysis of solvent-extracted NHP plasma identified the percentage of intact tracer versus radiolabeled metabolites samples post injection of each radiotracer. Both radiotracers showed high specific accumulation in NHP striatum. [ 11 C]TZ1964B has higher striatal retention and lower specific striatal uptake than [ 18 F]MNI659. The BP ND estimates of [ 11 C]TZ1964B were 3.72 by Logan Reference model (LoganREF) and 4.39 by simplified reference tissue model (SRTM); the BP ND estimates for [ 18 F]MNI659 were 5.08 (LoganREF) and 5.33 (SRTM). AUC ratios were 5.87 for [ 11 C]TZ1964B and 7.60 for [ 18 F]MNI659. Based on BP ND values in NHP striatum, coefficients of variation were ~10% for [ 11 C]TZ1964B and ~30% for [ 18 F]MNI659. Moreover, the metabolism study showed the percentage of parent compounds were ~70% for [ 11 C]TZ1964B and ~50% for [ 18 F]MNI659 60 min post injection. These data indicate that either [ 11 C]TZ1964B or [ 18 F]MNI659 could serve as suitable PDE10A PET radiotracers with distinguishing features for particular clinical application.

Decoupling feedforward and feedback structures in hybrid active noise control systems for uncorrelated narrowband disturbances

NASA Astrophysics Data System (ADS)

Wu, Lifu; Qiu, Xiaojun; Burnett, Ian S.; Guo, Yecai

2015-08-01

Hybrid feedforward and feedback structures are useful for active noise control (ANC) applications where the noise can only be partially obtained with reference sensors. The traditional method uses the secondary signals of both the feedforward and feedback structures to synthesize a reference signal for the feedback structure in the hybrid structure. However, this approach introduces coupling between the feedforward and feedback structures and parameter changes in one structure affect the other during adaptation such that the feedforward and feedback structures must be optimized simultaneously in practical ANC system design. Two methods are investigated in this paper to remove such coupling effects. One is a simplified method, which uses the error signal directly as the reference signal in the feedback structure, and the second method generates the reference signal for the feedback structure by using only the secondary signal from the feedback structure and utilizes the generated reference signal as the error signal of the feedforward structure. Because the two decoupling methods can optimize the feedforward and feedback structures separately, they provide more flexibility in the design and optimization of the adaptive filters in practical ANC applications.

Alveolar Ridge Contouring with Free Connective Tissue Graft at Implant Placement: A 5-Year Consecutive Clinical Study.

PubMed

Hanser, Thomas; Khoury, Fouad

2016-01-01

This study evaluated volume stability after alveolar ridge contouring with free connective tissue grafts at implant placement in single-tooth gaps. A total of 52 single-tooth gaps with labial volume deficiencies in the maxilla (incisors, canines, and premolars) were consecutively treated with implants and concomitant free palatal connective tissue grafts in 46 patients between 2006 and 2009. Implants had to be covered with at least 2 mm peri-implant local bone after insertion. At implant placement, a free connective tissue graft from the palate was fixed inside a labial split-thickness flap to form an existing concave buccal alveolar ridge contour due to tissue volume deficiency into a convex shape. Standardized volumetric measurements of the labial alveolar contour using a template were evaluated before connective tissue grafting and at 2 weeks, 1 year, and 5 years after implantprosthetic incorporation. Tissue volume had increased significantly (P < .05) in all six reference points representing the outer alveolar soft tissue contour of the implant before connective tissue grafting to baseline (2 weeks after implant-prosthetic incorporation). Statistically, 50% of the reference points (P > .05) kept their volume from baseline to 1 year after prosthetic incorporation and from baseline to 5 years after prosthetic incorporation, respectively, whereas reference points located within the area of the implant sulcus showed a significant (P < .05) decrease in volume. Clinically, 5 years after prosthetic incorporation the originally concave buccal alveolar contour was still convex in all implants, leading to a continuous favorable anatomical shape and improved esthetic situation. Intraoral radiographs confirmed osseointegration and stable peri-implant parameters with a survival rate of 100% after a follow-up of approximately 5 years. Implant placement with concomitant free connective tissue grafting appears to be an appropriate long-term means to contour preexisting buccal alveolar volume deficiencies in single implants.

Quantitative real time RT-PCR study of pathogen-induced gene expression in rock bream (Oplegnathus fasciatus): internal controls for data normalization.

PubMed

Zhang, Bao-cun; Sun, Li; Xiao, Zhi-zhong; Hu, Yong-hua

2014-06-01

Rock bream Oplegnathus fasciatus is an important economic fish species. In this study, we evaluated the appropriateness of six housekeeping genes as internal controls for quantitative real-time PCR (RT-qPCR) analysis of gene expression in rock bream before and after pathogen infection. The expression of the selected genes in eight tissues infected with Vibrio alginolyticus or megalocytivirus was determined by RT-qPCR, and the PCR data were analyzed with geNorm and NormFinder algorithms. The results showed that before pathogen infection, mediator of RNA polymerase II transcription subunit 8 and β-actin were ranked as the most stable genes across the examined tissues. After bacterial or viral infection, the stabilities of the housekeeping genes varied to significant extents in tissue-dependent manners, and no single pair of genes was identified as suitable references for all tissues for either of the pathogen stimuli. In addition, for the majority of tissues, the most stable genes during bacterial infection differed from those during viral infection. Nevertheless, optimum reference genes were identified for each tissue under different conditions. Taken together, these results indicate that tissue type and the nature of the infectious agent used in the study can all influence the choice of normalization factors, and that the optimum reference genes identified in this study will provide a useful guidance for the selection of internal controls in future RT-PCR study of gene expression in rock bream. Copyright © 2014 Elsevier B.V. All rights reserved.

Engineered Three-Dimensional Cardiac Fibrotic Tissue to Study Fibrotic Remodeling

PubMed Central

Sadeghi, Amir Hossein; Shin, Su Ryon; Deddens, Janine C.; Fratta, Giuseppe; Mandla, Serena; Yazdi, Iman K.; Prakash, Gyan; Antona, Silvia; Demarchi, Danilo; Buijsrogge, Marc P.; Sluijter, Joost P.G.; Hjortnaes, Jesper

2017-01-01

Activation of cardiac fibroblasts (CF) into myofibroblasts is considered to play an essential role in cardiac remodeling and fibrosis. A limiting factor in studying this process is the spontaneous activation of CFs when cultured on two-dimensional (2D) culture plates. Here, a simplified 3D hydrogel platform of contractile cardiac tissue, stimulated by transforming growth factor-β1 (TGF-β1), is presented to recapitulate a fibrogenic micro-environment. It was hypothesized that the quiescent state of CFs can be maintained by mimicking the mechanical stiffness of native heart tissue. To test this hypothesis, a 3D cell culture model consisting of cardiomyocytes and CFs encapsulated within mechanically engineered gelatin methacryloyl (GelMA) hydrogel, was developed. The study shows that CFs maintain their quiescent phenotype in mechanically tuned hydrogels. Additionally, treatment with a beta-adrenergic agonist increased beating frequency, demonstrating physiologic-like behavior of the heart constructs. Subsequently, quiescent CFs within the constructs were activated by the exogenous addition of TGF-β1. The expression of fibrotic protein markers (and the functional changes in mechanical stiffness) in the fibrotic-like tissues were analyzed to validate the model. Overall, this 3D engineered culture model of contractile cardiac tissue enabled controlled activation of CFs, demonstrating the usability of this platform to study fibrotic remodeling. PMID:28498548

A simplified analytical dose calculation algorithm accounting for tissue heterogeneity for low-energy brachytherapy sources.

PubMed

Mashouf, Shahram; Lechtman, Eli; Beaulieu, Luc; Verhaegen, Frank; Keller, Brian M; Ravi, Ananth; Pignol, Jean-Philippe

2013-09-21

The American Association of Physicists in Medicine Task Group No. 43 (AAPM TG-43) formalism is the standard for seeds brachytherapy dose calculation. But for breast seed implants, Monte Carlo simulations reveal large errors due to tissue heterogeneity. Since TG-43 includes several factors to account for source geometry, anisotropy and strength, we propose an additional correction factor, called the inhomogeneity correction factor (ICF), accounting for tissue heterogeneity for Pd-103 brachytherapy. This correction factor is calculated as a function of the media linear attenuation coefficient and mass energy absorption coefficient, and it is independent of the source internal structure. Ultimately the dose in heterogeneous media can be calculated as a product of dose in water as calculated by TG-43 protocol times the ICF. To validate the ICF methodology, dose absorbed in spherical phantoms with large tissue heterogeneities was compared using the TG-43 formalism corrected for heterogeneity versus Monte Carlo simulations. The agreement between Monte Carlo simulations and the ICF method remained within 5% in soft tissues up to several centimeters from a Pd-103 source. Compared to Monte Carlo, the ICF methods can easily be integrated into a clinical treatment planning system and it does not require the detailed internal structure of the source or the photon phase-space.

Simulation of Ectopic Pacemakers in the Heart: Multiple Ectopic Beats Generated by Reentry inside Fibrotic Regions

PubMed Central

Gouvêa de Barros, Bruno; Weber dos Santos, Rodrigo; Alonso, Sergio

2015-01-01

The inclusion of nonconducting media, mimicking cardiac fibrosis, in two models of cardiac tissue produces the formation of ectopic beats. The fraction of nonconducting media in comparison with the fraction of healthy myocytes and the topological distribution of cells determines the probability of ectopic beat generation. First, a detailed subcellular microscopic model that accounts for the microstructure of the cardiac tissue is constructed and employed for the numerical simulation of action potential propagation. Next, an equivalent discrete model is implemented, which permits a faster integration of the equations. This discrete model is a simplified version of the microscopic model that maintains the distribution of connections between cells. Both models produce similar results when describing action potential propagation in homogeneous tissue; however, they slightly differ in the generation of ectopic beats in heterogeneous tissue. Nevertheless, both models present the generation of reentry inside fibrotic tissues. This kind of reentry restricted to microfibrosis regions can result in the formation of ectopic pacemakers, that is, regions that will generate a series of ectopic stimulus at a fast pacing rate. In turn, such activity has been related to trigger fibrillation in the atria and in the ventricles in clinical and animal studies. PMID:26583127

In vitro studies evaluating the effects of biofilms on wound-healing cells: a review.

PubMed

Kirker, Kelly R; James, Garth A

2017-04-01

Chronic wounds are characterized as wounds that have failed to proceed through the well-orchestrated healing process and have remained open for months to years. Open wounds are at risk for colonization by opportunistic pathogens. Bacteria that colonize the open wound bed form surface-attached, multicellular communities called biofilms, and chronic wound biofilms can contain a diverse microbiota. Investigators are just beginning to elucidate the role of biofilms in chronic wound pathogenesis, and have simplified the complex wound environment using in vitro models to obtain a fundamental understanding of the impact of biofilms on wound-healing cell types. The intent of this review is to describe current in vitro methodologies and their results. Investigations started with one host cell-type and single species biofilms and demonstrated that biofilms, or their secretions, had deleterious effects on wound-healing cells. More complex systems involved the use of multiple host cell/tissue types and single species biofilms. Using human skin-equivalent tissues, investigators demonstrated that a number of different species can grow on the tissue and elicit an inflammatory response from the tissue. A full understanding of how biofilms impact wound-healing cells and host tissues will have a profound effect on how chronic wounds are treated. © 2017 APMIS. Published by John Wiley & Sons Ltd.

The effects of capillary transit time heterogeneity (CTH) on brain oxygenation

PubMed Central

Angleys, Hugo; Østergaard, Leif; Jespersen, Sune N

2015-01-01

We recently extended the classic flow–diffusion equation, which relates blood flow to tissue oxygenation, to take capillary transit time heterogeneity (CTH) into account. Realizing that cerebral oxygen availability depends on both cerebral blood flow (CBF) and capillary flow patterns, we have speculated that CTH may be actively regulated and that changes in the capillary morphology and function, as well as in blood rheology, may be involved in the pathogenesis of conditions such as dementia and ischemia-reperfusion injury. The first extended flow–diffusion equation involved simplifying assumptions which may not hold in tissue. Here, we explicitly incorporate the effects of oxygen metabolism on tissue oxygen tension and extraction efficacy, and assess the extent to which the type of capillary transit time distribution affects the overall effects of CTH on flow–metabolism coupling reported earlier. After incorporating tissue oxygen metabolism, our model predicts changes in oxygen consumption and tissue oxygen tension during functional activation in accordance with literature reports. We find that, for large CTH values, a blood flow increase fails to cause significant improvements in oxygen delivery, and can even decrease it; a condition of malignant CTH. These results are found to be largely insensitive to the choice of the transit time distribution. PMID:25669911

Comparison of temporal and spectral scattering methods using acoustically large breast models derived from magnetic resonance images.

PubMed

Hesford, Andrew J; Tillett, Jason C; Astheimer, Jeffrey P; Waag, Robert C

2014-08-01

Accurate and efficient modeling of ultrasound propagation through realistic tissue models is important to many aspects of clinical ultrasound imaging. Simplified problems with known solutions are often used to study and validate numerical methods. Greater confidence in a time-domain k-space method and a frequency-domain fast multipole method is established in this paper by analyzing results for realistic models of the human breast. Models of breast tissue were produced by segmenting magnetic resonance images of ex vivo specimens into seven distinct tissue types. After confirming with histologic analysis by pathologists that the model structures mimicked in vivo breast, the tissue types were mapped to variations in sound speed and acoustic absorption. Calculations of acoustic scattering by the resulting model were performed on massively parallel supercomputer clusters using parallel implementations of the k-space method and the fast multipole method. The efficient use of these resources was confirmed by parallel efficiency and scalability studies using large-scale, realistic tissue models. Comparisons between the temporal and spectral results were performed in representative planes by Fourier transforming the temporal results. An RMS field error less than 3% throughout the model volume confirms the accuracy of the methods for modeling ultrasound propagation through human breast.

Simplified Computation for Nonparametric Windows Method of Probability Density Function Estimation.

PubMed

Joshi, Niranjan; Kadir, Timor; Brady, Michael

2011-08-01

Recently, Kadir and Brady proposed a method for estimating probability density functions (PDFs) for digital signals which they call the Nonparametric (NP) Windows method. The method involves constructing a continuous space representation of the discrete space and sampled signal by using a suitable interpolation method. NP Windows requires only a small number of observed signal samples to estimate the PDF and is completely data driven. In this short paper, we first develop analytical formulae to obtain the NP Windows PDF estimates for 1D, 2D, and 3D signals, for different interpolation methods. We then show that the original procedure to calculate the PDF estimate can be significantly simplified and made computationally more efficient by a judicious choice of the frame of reference. We have also outlined specific algorithmic details of the procedures enabling quick implementation. Our reformulation of the original concept has directly demonstrated a close link between the NP Windows method and the Kernel Density Estimator.

Attitude Determination Algorithm based on Relative Quaternion Geometry of Velocity Incremental Vectors for Cost Efficient AHRS Design

NASA Astrophysics Data System (ADS)

Lee, Byungjin; Lee, Young Jae; Sung, Sangkyung

2018-05-01

A novel attitude determination method is investigated that is computationally efficient and implementable in low cost sensor and embedded platform. Recent result on attitude reference system design is adapted to further develop a three-dimensional attitude determination algorithm through the relative velocity incremental measurements. For this, velocity incremental vectors, computed respectively from INS and GPS with different update rate, are compared to generate filter measurement for attitude estimation. In the quaternion-based Kalman filter configuration, an Euler-like attitude perturbation angle is uniquely introduced for reducing filter states and simplifying propagation processes. Furthermore, assuming a small angle approximation between attitude update periods, it is shown that the reduced order filter greatly simplifies the propagation processes. For performance verification, both simulation and experimental studies are completed. A low cost MEMS IMU and GPS receiver are employed for system integration, and comparison with the true trajectory or a high-grade navigation system demonstrates the performance of the proposed algorithm.

Quantum theory of the structure and bonding in proteins. Part 11. A simplified method and its application to the α-amino-isobutyric acid residue

NASA Astrophysics Data System (ADS)

Peters, David; Peters, Jane

Information about the preferred conformation of the α-amino-isobutyric acid residue (α-AIB) is obtained without explicit computation of its wave function. The conformation of lowest energy of this residue is close to the usual helical conformation and so the residue may occur at the 2 position of a type I or I' bend or in either position of a type III or III' bend. The available experimental information refers to a β bend formed from α-AIB-PRO and then the theory and experiment agree that the only possibility is a type III bend. It is predicted that a β sheet structure may be formed at rather higher energy and in the planar and not the pleated form. There is no apparent reason why this residue should not form an α helix. The simplified method used here is closely related to the partitioned potential energy methods which are widely used in this subject.

Assessment of railway wagon suspension characteristics

NASA Astrophysics Data System (ADS)

Soukup, Josef; Skočilas, Jan; Skočilasová, Blanka

2017-05-01

The article deals with assessment of railway wagon suspension characteristics. The essential characteristics of a suspension are represented by the stiffness constants of the equivalent springs and the eigen frequencies of the oscillating movements in reference to the main central inertia axes of a vehicle. The premise of the experimental determination of these characteristic is the knowledge of the gravity center position and the knowledge of the main central inertia moments of the vehicle frame. The vehicle frame performs the general spatial movement when the vehicle moves. An analysis of the frame movement generally arises from Euler's equations which are commonly used for the description of the spherical movement. This solution is difficult and it can be simplified by applying the specific assumptions. The eigen frequencies solutions and solutions of the suspension stiffness are presented in the article. The solutions are applied on the railway and road vehicles with the simplifying conditions. A new method which assessed the characteristics is described in the article.

[Equivalent Lever Principle of Ossicular Chain and Amplitude Reduction Effect of Internal Ear Lymph].

PubMed

Zhao, Xiaoyan; Qin, Renjia

2015-04-01

This paper makes persuasive demonstrations on some problems about the human ear sound transmission principle in existing physiological textbooks and reference books, and puts forward the authors' view to make up for its literature. Exerting the knowledge of lever in physics and the acoustics theory, we come up with an equivalent simplified model of manubrium mallei which is to meet the requirements as the long arm of the lever. We also set up an equivalent simplified model of ossicular chain--a combination of levers of ossicular chain. We disassemble the model into two simple levers, and make full analysis and demonstration on them. Through the calculation and comparison of displacement amplitudes in both external auditory canal air and internal ear lymph, we may draw a conclusion that the key reason, which the sound displacement amplitude is to be decreased to adapt to the endurance limit of the basement membrane, is that the density and sound speed in lymph is much higher than those in the air.

A New Dual-purpose Quality Control Dosimetry Protocol for Diagnostic Reference-level Determination in Computed Tomography.

PubMed

Sohrabi, Mehdi; Parsi, Masoumeh; Sina, Sedigheh

2018-05-17

A diagnostic reference level is an advisory dose level set by a regulatory authority in a country as an efficient criterion for protection of patients from unwanted medical exposure. In computed tomography, the direct dose measurement and data collection methods are commonly applied for determination of diagnostic reference levels. Recently, a new quality-control-based dose survey method was proposed by the authors to simplify the diagnostic reference-level determination using a retrospective quality control database usually available at a regulatory authority in a country. In line with such a development, a prospective dual-purpose quality control dosimetry protocol is proposed for determination of diagnostic reference levels in a country, which can be simply applied by quality control service providers. This new proposed method was applied to five computed tomography scanners in Shiraz, Iran, and diagnostic reference levels for head, abdomen/pelvis, sinus, chest, and lumbar spine examinations were determined. The results were compared to those obtained by the data collection and quality-control-based dose survey methods, carried out in parallel in this study, and were found to agree well within approximately 6%. This is highly acceptable for quality-control-based methods according to International Atomic Energy Agency tolerance levels (±20%).

A constitutive law for continuous fiber reinforced brittle matrix composites with fiber fragmentation and stress recovery

NASA Astrophysics Data System (ADS)

Neumeister, Jonas M.

1993-08-01

THE TENSILE BEHAVIOR of a brittle matrix composite is studied for post matrix crack saturation conditions. Scatter of fiber strength following the Weibull distribution as well as the influence of the major microstructural variables is considered. The stress in a fiber is assumed to recover linearly around a failure due to a fiber-matrix interface behavior mainly ruled by friction. The constitutive behavior for such a composite is analysed. Results are given for a simplified and a refined approximate description and compared with an analysis resulting from the exact analytical theory of fiber fragmentation. It is shown that the stress-strain relation for the refined model excellently follows the exact solution and gives the location of the maximum to within 1% in both stress and strain; for most materials the agreement is even better. Also it is shown that all relations can be normalized to depend on only two variables; a stress reference and the Weibull exponent. For systems with low scatter in fiber strength the simplified model is sufficient to determine the stress maximum but not the postcritical behavior. In addition, the simplified model gives explicit analytical expressions for the maximum stress and corresponding strain. None of the models contain any volume dependence or statistical scatter, but the maximum stress given by the stress-strain relation constitutes an upper bound for the ultimate tensile strength of the composite.

Simplified MPN method for enumeration of soil naphthalene degraders using gaseous substrate.

PubMed

Wallenius, Kaisa; Lappi, Kaisa; Mikkonen, Anu; Wickström, Annika; Vaalama, Anu; Lehtinen, Taru; Suominen, Leena

2012-02-01

We describe a simplified microplate most-probable-number (MPN) procedure to quantify the bacterial naphthalene degrader population in soil samples. In this method, the sole substrate naphthalene is dosed passively via gaseous phase to liquid medium and the detection of growth is based on the automated measurement of turbidity using an absorbance reader. The performance of the new method was evaluated by comparison with a recently introduced method in which the substrate is dissolved in inert silicone oil and added individually to each well, and the results are scored visually using a respiration indicator dye. Oil-contaminated industrial soil showed slightly but significantly higher MPN estimate with our method than with the reference method. This suggests that gaseous naphthalene was dissolved in an adequate concentration to support the growth of naphthalene degraders without being too toxic. The dosing of substrate via gaseous phase notably reduced the work load and risk of contamination. The result scoring by absorbance measurement was objective and more reliable than measurement with indicator dye, and it also enabled further analysis of cultures. Several bacterial genera were identified by cloning and sequencing of 16S rRNA genes from the MPN wells incubated in the presence of gaseous naphthalene. In addition, the applicability of the simplified MPN method was demonstrated by a significant positive correlation between the level of oil contamination and the number of naphthalene degraders detected in soil.

Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don.

PubMed

Xiao, Zheng; Sun, Xiaobo; Liu, Xiaoqing; Li, Chang; He, Lisi; Chen, Shangping; Su, Jiale

2016-01-01

The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper. The results showed that EF1- α (elongation factor 1-alpha), 18S (18s ribosomal RNA), and RPL3 (ribosomal protein L3) were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin ( TUB ) was the least stable. ACT5 (actin), RPL3 , 18S , and EF1- α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle . Furthermore, the expression profiles of RmPSY (phytoene synthase) and RmPDS (phytoene dehydrogenase) were assessed using EF1- α, 18S , ACT5 , RPL3 , and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle .

Selection of suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using quantitative real-time polymerase chain reaction.

PubMed

Zornhagen, K W; Kristensen, A T; Hansen, A E; Oxboel, J; Kjaer, A

2015-12-01

Quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive technique for quantifying gene expression. Stably expressed reference genes are necessary for normalization of RT-qPCR data. Only a few articles have been published on reference genes in canine tumours. The objective of this study was to demonstrate how to identify suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using RT-qPCR. Primer pairs for 17 potential reference genes were designed and tested in archival tumour biopsies from six dogs. The geNorm algorithm was used to analyse the most suitable reference genes. Eight potential reference genes were excluded from this final analysis because of their dissociation curves. β-Glucuronidase (GUSB) and proteasome subunit, beta type, 6 (PSMB6) were most stably expressed with an M value of 0.154 and a CV of 0.053 describing their average stability. We suggest that choice of reference genes should be based on specific testing in every new experimental set-up. © 2014 John Wiley & Sons Ltd.

[Transplant coordination and logistics of intra and extra-hospital cadaver donor tissue. "The Pamplona Model". Sequence of tasks performed from 1992-2006].

PubMed

Maraví-Poma, E; Martín, A; Maraví-Aznar, A; Iturralde, O; Compains, E; Álvarez, J; Cabal, S; Maraví-Aznar, E; Teijeira, R; Unzué, J J; González, R

2006-01-01

Tissue and organ donations are the only option for many patients. Cerebral death (CD) facilitates this approach. However, hospitals that do not provide CD donors have to adapt in order to obtain donors, referred to as tissue donors (TD), who have died from cardiac arrest. Is this paper it descripte the model for coordination and donation of intra and extra-hospital TD in the Autonomous Community of Navarra. It creats a program for detection, donation and extractions called the Pamplona Model, from 1992-2006. In 1990, a transplant team was created by an Intensive Medicine Physician of HVC, INML and SOS-Navarra. In 1996, VCH Transplant Coordination is defined as a reference centre for the Tissue Transplant Programme in the Autonomous Community of Navarra. Consensus protocols for "intra and extra-hospital detection" of persons having died from cardiac arrest are developed: - Alerts from NHS-O hospitals, SOS-Navarra; judges and INML forensic pathologists. - Criteria for selection, search and contacts with relatives. - Alert serology, extraction and transport teams. - Logistics and distribution of tissue. - Agreed incentives: Economic, administrative and relevant regulations. The Pamplona Model, with the Virgen Del Camino hospital has made important contributions and is unique in the world. Intra and extra-hospital coordination of cadaver donor from a referred hospital, it is a scientific and organizational advance to have in it counts for the creation of extraction and transplant tissues teams.

Uncovering Suitable Reference Proteins for Expression Studies in Human Adipose Tissue with Relevance to Obesity

PubMed Central

Pérez-Pérez, Rafael; López, Juan A.; García-Santos, Eva; Camafeita, Emilio; Gómez-Serrano, María; Ortega-Delgado, Francisco J.; Ricart, Wifredo; Fernández-Real, José M.; Peral, Belén

2012-01-01

Background Protein expression studies based on the two major intra-abdominal human fat depots, the subcutaneous and the omental fat, can shed light into the mechanisms involved in obesity and its co-morbidities. Here we address, for the first time, the identification and validation of reference proteins for data standardization, which are essential for accurate comparison of protein levels in expression studies based on fat from obese and non-obese individuals. Methodology and Findings To uncover adipose tissue proteins equally expressed either in omental and subcutaneous fat depots (study 1) or in omental fat from non-obese and obese individuals (study 2), we have reanalyzed our previously published data based on two-dimensional fluorescence difference gel electrophoresis. Twenty-four proteins (12 in study 1 and 12 in study 2) with similar expression levels in all conditions tested were selected and identified by mass spectrometry. Immunoblotting analysis was used to confirm in adipose tissue the expression pattern of the potential reference proteins and three proteins were validated: PARK7, ENOA and FAA. Western Blot analysis was also used to test customary loading control proteins. ENOA, PARK7 and the customary loading control protein Beta-actin showed steady expression profiles in fat from non-obese and obese individuals, whilst FAA maintained steady expression levels across paired omental and subcutaneous fat samples. Conclusions ENOA, PARK7 and Beta-actin are proper reference standards in obesity studies based on omental fat, whilst FAA is the best loading control for the comparative analysis of omental and subcutaneous adipose tissues either in obese and non-obese subjects. Neither customary loading control proteins GAPDH and TBB5 nor CALX are adequate standards in differential expression studies on adipose tissue. The use of the proposed reference proteins will facilitate the adequate analysis of proteins differentially expressed in the context of obesity, an aim difficult to achieve before this study. PMID:22272336

Cryopreservation and hypothermic storage of lacrimal gland: towards enabling delivery of regenerative medicine therapies for treatment of dry eye syndrome.

PubMed

Massie, I; Spaniol, K; Geerling, G; Schrader, S

2017-12-01

Severe dry eye syndrome (DES) can cause painful loss of vision and may result from lacrimal gland dysfunction. Current treatments are palliative, so a causative therapy is desirable. The ability to (cryo)preserve lacrimal gland tissue or epithelial cells would simplify this. Here, lacrimal gland tissue was cryopreserved in 10% dimethylsulphoxide in liquid nitrogen, or stored at 4 °C in culture medium for up to 7 days, and compared with fresh tissue using immunohistochemistry. Cultures were initiated from fresh and stored tissue, and cells characterised in P1 for proliferation (WST-1), colony-forming efficiency (CFE) and secretory capacity (immunocytochemistry and β-hexosaminidase activity assay). Tissue stored for > 3 days at 4 °C displayed grossly altered tissue architecture when compared with fresh tissue, decreased acinus density and increased caspase-3 activity. Cryopreserved tissue showed less obvious signs of damage without caspase-3 activation. Storage at 4 °C and cryopreservation delayed epithelial outgrowth compared with that from fresh tissue initially (p  <  0.05) but, by day 9, all explants showed comparable outgrowth (~90%), except tissue stored at 4 °C for 3 or 7 days (p  <  0.05 compared with fresh tissue). Epithelial cell yields per explant were similar from fresh and stored tissue, apart from tissue stored at 4 °C for 7 days (p  <  0.01). In P1, epithelial cells from fresh and stored tissue were largely equivalent in terms of: proliferation; CFE (~21%); Rab3D, HexA and lysozyme expression; mucin production; and β-hexosaminidase activity. These data demonstrate that cryo(preservation) of lacrimal gland tissue and cells is possible, which may enable use of autologous cells in regenerative medicine approaches to treating DES. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Debriding effect of bromelain on firearm wounds in pigs.

PubMed

Hu, Wei; Wang, Ai-Min; Wu, Si-Yu; Zhang, Bo; Liu, Shuai; Gou, Yuan-Bin; Wang, Jian-Min

2011-10-01

Wound excision is the standard treatment for firearm wounds. However, achieving a satisfactory curative effect is difficult because of the traumatic mechanism of high-velocity projectiles. We propose a new therapy by using topical bromelain as a supplement to wound incision for the debridement of firearm wounds. We clarified the debriding effect of bromelain on firearm wounds in pigs. In vitro, muscle tissues around the wound track and normal muscle were incubated in bromelain solutions of different concentrations. Tissue hydrolization was estimated by measuring tissue weight and the release of total amino acids. In vivo, the hind limbs of 15 pigs were wounded with high-velocity projectiles. Five groups were classified as follows: wound excision (E), wound incision (I), bromelain (B), incision + bromelain (IB), and control (C). Debriding effectiveness was estimated using bacterial content, histopathologic examination, and wound healing time. In vitro, hydrolization of wound tissue was significantly more intensive than that of normal tissue. Bromelain solution (10 mg/mL) hydrolyzed wound tissue rapidly with minimal proteolysis of normal tissue. In vivo, the wound-track bacterial content of group IB was similar to that of group E and was significantly lower than that of groups I, B, and C. The wound healing time of group IB was also shorter. Bromelain is effective in the debridement of uncomplicated firearm wounds if used as a supplement to simple wound incision. This new therapy shows notable advantages over conventional surgical debridement as it greatly simplifies the procedures.

Soft tissue modelling with conical springs.

PubMed

Omar, Nadzeri; Zhong, Yongmin; Jazar, Reza N; Subic, Aleksandar; Smith, Julian; Shirinzadeh, Bijan

2015-01-01

This paper presents a new method for real-time modelling soft tissue deformation. It improves the traditional mass-spring model with conical springs to deal with nonlinear mechanical behaviours of soft tissues. A conical spring model is developed to predict soft tissue deformation with reference to deformation patterns. The model parameters are formulated according to tissue deformation patterns and the nonlinear behaviours of soft tissues are modelled with the stiffness variation of conical spring. Experimental results show that the proposed method can describe different tissue deformation patterns using one single equation and also exhibit the typical mechanical behaviours of soft tissues.

The reference frame for encoding and retention of motion depends on stimulus set size.

PubMed

Huynh, Duong; Tripathy, Srimant P; Bedell, Harold E; Öğmen, Haluk

2017-04-01

The goal of this study was to investigate the reference frames used in perceptual encoding and storage of visual motion information. In our experiments, observers viewed multiple moving objects and reported the direction of motion of a randomly selected item. Using a vector-decomposition technique, we computed performance during smooth pursuit with respect to a spatiotopic (nonretinotopic) and to a retinotopic component and compared them with performance during fixation, which served as the baseline. For the stimulus encoding stage, which precedes memory, we found that the reference frame depends on the stimulus set size. For a single moving target, the spatiotopic reference frame had the most significant contribution with some additional contribution from the retinotopic reference frame. When the number of items increased (Set Sizes 3 to 7), the spatiotopic reference frame was able to account for the performance. Finally, when the number of items became larger than 7, the distinction between reference frames vanished. We interpret this finding as a switch to a more abstract nonmetric encoding of motion direction. We found that the retinotopic reference frame was not used in memory. Taken together with other studies, our results suggest that, whereas a retinotopic reference frame may be employed for controlling eye movements, perception and memory use primarily nonretinotopic reference frames. Furthermore, the use of nonretinotopic reference frames appears to be capacity limited. In the case of complex stimuli, the visual system may use perceptual grouping in order to simplify the complexity of stimuli or resort to a nonmetric abstract coding of motion information.

Interstitial hyperthermia treatment of countercurrent vascular tissue: a comparison of Pennes, WJ and porous media bioheat models.

PubMed

Hassanpour, Saied; Saboonchi, Ahmad

2014-12-01

Development of appropriate heat transfer models to investigate the thermal behavior of living tissues has become increasingly important in simulations of cancer hyperthermia. In this paper, a review is initially presented of the more important general models developed for heat transfer description of perfused tissues. Comparisons are then made between Pennes' simplified Weinbaum and Jiji "WJ" and the more recent porous media "PM" bioheat models. For this purpose, a mathematical model is developed for the heat transfer in a cylindrical medium containing parallel counter-current pairs of small vessels with characteristics as much as possible similar to those of living tissues. The validity of the models is examined and confirmed using the Pennes in vivo experiments and one-dimensional analytical solutions. For consideration of interstitial hyperthermia treatment the smaller cylindrical zone with typical heat generation, is assumed in the center of the main cylinder. The numerical simulation results revealed that, despite difference in temperature distributions calculated by these three models at normal condition, the heat affected zone at hyperthermic condition predicted by all three models are similar. Copyright © 2014 Elsevier Ltd. All rights reserved.

Selection of novel reference genes for use in the human central nervous system: a BrainNet Europe Study.

PubMed

Durrenberger, Pascal F; Fernando, Francisca S; Magliozzi, Roberta; Kashefi, Samira N; Bonnert, Timothy P; Ferrer, Isidro; Seilhean, Danielle; Nait-Oumesmar, Brahim; Schmitt, Andrea; Gebicke-Haerter, Peter J; Falkai, Peter; Grünblatt, Edna; Palkovits, Miklos; Parchi, Piero; Capellari, Sabina; Arzberger, Thomas; Kretzschmar, Hans; Roncaroli, Federico; Dexter, David T; Reynolds, Richard

2012-12-01

The use of an appropriate reference gene to ensure accurate normalisation is crucial for the correct quantification of gene expression using qPCR assays and RNA arrays. The main criterion for a gene to qualify as a reference gene is a stable expression across various cell types and experimental settings. Several reference genes are commonly in use but more and more evidence reveals variations in their expression due to the presence of on-going neuropathological disease processes, raising doubts concerning their use. We conducted an analysis of genome-wide changes of gene expression in the human central nervous system (CNS) covering several neurological disorders and regions, including the spinal cord, and were able to identify a number of novel stable reference genes. We tested the stability of expression of eight novel (ATP5E, AARS, GAPVD1, CSNK2B, XPNPEP1, OSBP, NAT5 and DCTN2) and four more commonly used (BECN1, GAPDH, QARS and TUBB) reference genes in a smaller cohort using RT-qPCR. The most stable genes out of the 12 reference genes were tested as normaliser to validate increased levels of a target gene in CNS disease. We found that in human post-mortem tissue the novel reference genes, XPNPEP1 and AARS, were efficient in replicating microarray target gene expression levels and that XPNPEP1 was more efficient as a normaliser than BECN1, which has been shown to change in expression as a consequence of neuronal cell loss. We provide herein one more suitable novel reference gene, XPNPEP1, with no current neuroinflammatory or neurodegenerative associations that can be used for gene quantitative gene expression studies with human CNS post-mortem tissue and also suggest a list of potential other candidates. These data also emphasise the importance of organ/tissue-specific stably expressed genes as reference genes for RNA studies.

Estimation of the minimum permeability coefficient in rats for perfusion-limited tissue distribution in whole-body physiologically-based pharmacokinetics.

PubMed

Jeong, Yoo-Seong; Yim, Chang-Soon; Ryu, Heon-Min; Noh, Chi-Kyoung; Song, Yoo-Kyung; Chung, Suk-Jae

2017-06-01

The objective of the current study was to determine the minimum permeability coefficient, P, needed for perfusion-limited distribution in PBPK. Two expanded kinetic models, containing both permeability and perfusion terms for the rate of tissue distribution, were considered: The resulting equations could be simplified to perfusion-limited distribution depending on tissue permeability. Integration plot analyses were carried out with theophylline in 11 typical tissues to determine their apparent distributional clearances and the model-dependent permeabilities of the tissues. Effective surface areas were calculated for 11 tissues from the tissue permeabilities of theophylline and its PAMPA P. Tissue permeabilities of other drugs were then estimated from their PAMPA P and the effective surface area of the tissues. The differences between the observed and predicted concentrations, as expressed by the sum of squared log differences with the present models were at least comparable to or less than the values obtained using the traditional perfusion-limited distribution model for 24 compounds with diverse PAMPA P values. These observations suggest that the use of a combination of the proposed models, PAMPA P and the effective surface area can be used to reasonably predict the pharmacokinetics of 22 out of 24 model compounds, and is potentially applicable to calculating the kinetics for other drugs. Assuming that the fractional distribution parameter of 80% of the perfusion rate is a reasonable threshold for perfusion-limited distribution in PBPK, our theoretical prediction indicates that the pharmacokinetics of drugs having an apparent PAMPA P of 1×10 -6 cm/s or more will follow the traditional perfusion-limited distribution in PBPK for major tissues in the body. Copyright © 2017 Elsevier B.V. All rights reserved.

Simulation of wave propagation inside a human eye: acoustic eye model (AEM)

NASA Astrophysics Data System (ADS)

Požar, T.; Halilovič, M.; Horvat, D.; Petkovšek, R.

2018-02-01

The design and development of the acoustic eye model (AEM) is reported. The model consists of a computer-based simulation that describes the propagation of mechanical disturbance inside a simplified model of a human eye. The capabilities of the model are illustrated with examples, using different laser-induced initial loading conditions in different geometrical configurations typically occurring in ophthalmic medical procedures. The potential of the AEM is to predict the mechanical response of the treated eye tissue in advance, thus complementing other preliminary procedures preceding medical treatments.

Artificial testing targets with controllable blur for adaptive optics microscopes

NASA Astrophysics Data System (ADS)

Hattori, Masayuki; Tamada, Yosuke; Murata, Takashi; Oya, Shin; Hasebe, Mitsuyasu; Hayano, Yutaka; Kamei, Yasuhiro

2017-08-01

This letter proposes a method of configuring a testing target to evaluate the performance of adaptive optics microscopes. In this method, a testing slide with fluorescent beads is used to simultaneously determine the point spread function and the field of view. The point spread function is reproduced to simulate actual biological samples by etching a microstructure on the cover glass. The fabrication process is simplified to facilitate an onsite preparation. The artificial tissue consists of solid materials and silicone oil and is stable for use in repetitive experiments.

Space proton transport in one dimension

NASA Technical Reports Server (NTRS)

Lamkin, S. L.; Khandelwal, G. S.; Shinn, J. L.; Wilson, J. W.

1994-01-01

An approximate evaluation procedure is derived for a second-order theory of coupled nucleon transport in one dimension. An analytical solution with a simplified interaction model is used to determine quadrature parameters to minimize truncation error. Effects of the improved method on transport solutions with the BRYNTRN data base are evaluated. Comparisons with Monte Carlo benchmarks are given. Using different shield materials, the computational procedure is used to study the physics of space protons. A transition effect occurs in tissue near the shield interface and is most important in shields of high atomic number.

SIMPLIFIED PRACTICAL TEST METHOD FOR PORTABLE DOSE METERS USING SEVERAL SEALED RADIOACTIVE SOURCES.

PubMed

Mikamoto, Takahiro; Yamada, Takahiro; Kurosawa, Tadahiro

2016-09-01

Sealed radioactive sources which have small activity were employed for the determination of response and tests for non-linearity and energy dependence of detector responses. Close source-to-detector geometry (at 0.3 m or less) was employed to practical tests for portable dose meters to accumulate statistically sufficient ionizing currents. Difference between response in the present experimentally studied field and in the reference field complied with ISO 4037 due to non-uniformity of radiation fluence at close geometry was corrected by use of Monte Carlo simulation. As a consequence, corrected results were consistent with the results obtained in the ISO 4037 reference field within their uncertainties. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A case of poor substructure diagnostics

NASA Technical Reports Server (NTRS)

Butler, Thomas G.

1992-01-01

The NASTRAN Manuals in the substructuring area are all geared toward instant success, but the solution paths are fraught with many traps for human error. Thus, the probability of suffering a fatal abort is high. In such circumstances, the necessity for diagnostics that are user friendly is paramount. This paper is written in the spirit of improving the diagnostics as well as the documentation in one area where the author felt he was backed into a blind corner as a result of his having committed a data oversight. This topic is aired by referring to an analysis of a particular structure. The structure, under discussion, used a number of local coordinate systems that simplified the preparation of input data. The principle features of this problem are introduced by reference to a series of figures.

VIEWCACHE: An incremental pointer-base access method for distributed databases. Part 1: The universal index system design document. Part 2: The universal index system low-level design document. Part 3: User's guide. Part 4: Reference manual. Part 5: UIMS test suite

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos

1992-01-01

The goal of the Universal Index System (UIS), is to provide an easy-to-use and reliable interface to many different kinds of database systems. The impetus for this system was to simplify database index management for users, thus encouraging the use of indexes. As the idea grew into an actual system design, the concept of increasing database performance by facilitating the use of time-saving techniques at the user level became a theme for the project. This Final Report describes the Design, the Implementation of UIS, and its Language Interfaces. It also includes the User's Guide and the Reference Manual.

Second-order Compton-Getting effect on arbitrary intensity distribution

NASA Technical Reports Server (NTRS)

Ng, C. K.

1985-01-01

Theoretical studies of energetic particles in space are often referred to a special frame of reference. To compare theory with experiment, one has to transform the particle distribution from the special frame to the observer's frame, or vice versa. Various methods have been derived to obtain the directional distribution in the comoving frame from the directional fluxes measured on a spacecraft. These methods have become progressively complicated as increasingly detailed directional particle data become available. A set of 2nd order correct formulae for the transformation of an arbitrary differential intensity distribution, expressed as a series of spherical harmonics, between any two frames in constant relative motion is presented. These formulae greatly simplify the complicated procedures currently in use for the determination of the differential intensity distribution in a comoving frame.

Nonlinear Dynamic Inversion Baseline Control Law: Architecture and Performance Predictions

NASA Technical Reports Server (NTRS)

Miller, Christopher J.

2011-01-01

A model reference dynamic inversion control law has been developed to provide a baseline control law for research into adaptive elements and other advanced flight control law components. This controller has been implemented and tested in a hardware-in-the-loop simulation; the simulation results show excellent handling qualities throughout the limited flight envelope. A simple angular momentum formulation was chosen because it can be included in the stability proofs for many basic adaptive theories, such as model reference adaptive control. Many design choices and implementation details reflect the requirements placed on the system by the nonlinear flight environment and the desire to keep the system as basic as possible to simplify the addition of the adaptive elements. Those design choices are explained, along with their predicted impact on the handling qualities.

Birefringence imaging in biological tissue using polarization sensitive optical coherent tomography

DOEpatents

De Boer, Johannes F.; Milner, Thomas E.; Nelson, J. Stuart

2001-01-01

Employing a low coherence Michelson interferometer, two dimensional images of optical birefringence in turbid samples as a function of depth are measured. Polarization sensitive detection of the signal formed by interference of backscattered light from the sample and a mirror or reference plane in the reference arm which defines a reference optical path length, give the optical phase delay between light propagating along the fast and slow axes of the birefringence sample. Images showing the change in birefringence in response to irradiation of the sample are produced as an example of the detection apparatus and methodology. The technique allow rapid, noncontact investigation of tissue or sample diagnostic imaging for various medical or materials procedures.

Method for detection of dental caries and periodontal disease using optical imaging

DOEpatents

Nathel, Howard; Kinney, John H.; Otis, Linda L.

1996-01-01

A method for detecting the presence of active and inactive caries in teeth and diagnosing periodontal disease uses non-ionizing radiation with techniques for reducing interference from scattered light. A beam of non-ionizing radiation is divided into sample and reference beams. The region to be examined is illuminated by the sample beam, and reflected or transmitted radiation from the sample is recombined with the reference beam to form an interference pattern on a detector. The length of the reference beam path is adjustable, allowing the operator to select the reflected or transmitted sample photons that recombine with the reference photons. Thus radiation scattered by the dental or periodontal tissue can be prevented from obscuring the interference pattern. A series of interference patterns may be generated and interpreted to locate dental caries and periodontal tissue interfaces.

Modeling of the metallic port in breast tissue expanders for photon radiotherapy.

PubMed

Yoon, Jihyung; Xie, Yibo; Heins, David; Zhang, Rui

2018-03-30

The purpose of this study was to model the metallic port in breast tissue expanders and to improve the accuracy of dose calculations in a commercial photon treatment planning system (TPS). The density of the model was determined by comparing TPS calculations and ion chamber (IC) measurements. The model was further validated and compared with two widely used clinical models by using a simplified anthropomorphic phantom and thermoluminescent dosimeters (TLD) measurements. Dose perturbations and target coverage for a single postmastectomy radiotherapy (PMRT) patient were also evaluated. The dimensions of the metallic port model were determined to be 1.75 cm in diameter and 5 mm in thickness. The density of the port was adjusted to be 7.5 g/cm 3 which minimized the differences between IC measurements and TPS calculations. Using the simplified anthropomorphic phantom, we found the TPS calculated point doses based on the new model were in agreement with TLD measurements within 5.0% and were more accurate than doses calculated based on the clinical models. Based on the photon treatment plans for a real patient, we found that the metallic port has a negligible dosimetric impact on chest wall, while the port introduced significant dose shadow in skin area. The current clinical port models either overestimate or underestimate the attenuation from the metallic port, and the dose perturbation depends on the plan and the model in a complex way. TPS calculations based on our model of the metallic port showed good agreement with measurements for all cases. This new model could improve the accuracy of dose calculations for PMRT patients who have temporary tissue expanders implanted during radiotherapy and could potentially reduce the risk of complications after the treatment. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions

PubMed Central

Barsalobres-Cavallari, Carla F; Severino, Fábio E; Maluf, Mirian P; Maia, Ivan G

2009-01-01

Background Quantitative data from gene expression experiments are often normalized by transcription levels of reference or housekeeping genes. An inherent assumption for their use is that the expression of these genes is highly uniform in living organisms during various phases of development, in different cell types and under diverse environmental conditions. To date, the validation of reference genes in plants has received very little attention and suitable reference genes have not been defined for a great number of crop species including Coffea arabica. The aim of the research reported herein was to compare the relative expression of a set of potential reference genes across different types of tissue/organ samples of coffee. We also validated the expression profiles of the selected reference genes at various stages of development and under a specific biotic stress. Results The expression levels of five frequently used housekeeping genes (reference genes), namely alcohol dehydrogenase (adh), 14-3-3, polyubiquitin (poly), β-actin (actin) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) was assessed by quantitative real-time RT-PCR over a set of five tissue/organ samples (root, stem, leaf, flower, and fruits) of Coffea arabica plants. In addition to these commonly used internal controls, three other genes encoding a cysteine proteinase (cys), a caffeine synthase (ccs) and the 60S ribosomal protein L7 (rpl7) were also tested. Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. The obtained results revealed significantly variable expression levels of all reference genes analyzed, with the exception of gapdh, which showed no significant changes in expression among the investigated experimental conditions. Conclusion Our data suggests that the expression of housekeeping genes is not completely stable in coffee. Based on our results, gapdh, followed by 14-3-3 and rpl7 were found to be homogeneously expressed and are therefore adequate for normalization purposes, showing equivalent transcript levels in different tissue/organ samples. Gapdh is therefore the recommended reference gene for measuring gene expression in Coffea arabica. Its use will enable more accurate and reliable normalization of tissue/organ-specific gene expression studies in this important cherry crop plant. PMID:19126214

Equivalence testing using existing reference data: An example with genetically modified and conventional crops in animal feeding studies.

PubMed

van der Voet, Hilko; Goedhart, Paul W; Schmidt, Kerstin

2017-11-01

An equivalence testing method is described to assess the safety of regulated products using relevant data obtained in historical studies with assumedly safe reference products. The method is illustrated using data from a series of animal feeding studies with genetically modified and reference maize varieties. Several criteria for quantifying equivalence are discussed, and study-corrected distribution-wise equivalence is selected as being appropriate for the example case study. An equivalence test is proposed based on a high probability of declaring equivalence in a simplified situation, where there is no between-group variation, where the historical and current studies have the same residual variance, and where the current study is assumed to have a sample size as set by a regulator. The method makes use of generalized fiducial inference methods to integrate uncertainties from both the historical and the current data. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Modifications to the NIST reference measurement procedure (RMP) for the determination of serum glucose by isotope dilution gas chromatography/mass spectrometry.

PubMed

Prendergast, Jocelyn L; Sniegoski, Lorna T; Welch, Michael J; Phinney, Karen W

2010-07-01

The definitive method (DM), now known as the reference measurement procedure (RMP), for the analysis of glucose in serum was originally published in 1982 by the National Institute of Standards and Technology (NIST). Over the years the method has been subject to a number of modifications to adapt to newer technologies and simplify sample preparation. We discuss here an adaptation of the method associated with serum glucose measurements using a modified isotope dilution gas chromatography/mass spectrometry (ID-GC/MS) method. NIST has used this modified method to certify the concentrations of glucose in SRM 965b, Glucose in Frozen Human Serum, and SRM 1950, Metabolites in Human Plasma. Comparison of results from the revised method with certified values for existing Standard Reference Materials (SRMs) demonstrated that these modifications have not affected the quality of the measurements, giving both good precision and accuracy, while reducing the sample preparation time by a day and a half.

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.

PubMed

Caracausi, Maria; Piovesan, Allison; Antonaros, Francesca; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara

2017-09-01

The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross‑ and within‑tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra‑ and inter‑sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross‑tissue width of expression for more than 31,000 transcripts. The present study conducted a meta‑analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue‑ and organ‑specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative, quantitative portrait of the relative, typical gene‑expression profile in the form of searchable database tables.

Study of Biological Pigments by Single Specimen Derivative Spectrophotometry

PubMed Central

Goldstein, Jack M.

1970-01-01

The single specimen derivative (SSD) method provides an absolute absorption spectrum of a substance in the absence of a suitable reference. Both a reference and a measuring monochromatic beam pass through a single sample, and the specimen itself acts as its own reference. The two monochromatic beams maintain a fixed wavelength difference upon scanning, and the difference in absorbance of the two beams is determined. Thus, the resulting spectrum represents the first derivative of the conventional type absorption spectrum. Tissues and cell fractions have been examined at room and liquid N2 temperature and chromophoric molecules such as the mitochondrial cytochromes and blood pigments have been detectable in low concentrations. In the case of isolated cellular components, the observed effects of substrates and inhibitors confirm similar studies by conventional spectrophotometry. The extension of the SSD concept to the microscopic level has permitted the study of the tissue compartmentalization and function of cytochromes and other pigments within layered tissue. PMID:4392452

Simplified 4-item criteria for polycystic ovary syndrome: A bridge too far?

PubMed

Indran, Inthrani R; Huang, Zhongwei; Khin, Lay Wai; Chan, Jerry K Y; Viardot-Foucault, Veronique; Yong, Eu Leong

2018-05-30

Although the Rotterdam 2003 polycystic ovarian syndrome (PCOS) diagnostic criteria is widely used, the need to consider multiple variables makes it unwieldy in clinical practice. We propose a simplified PCOS criteria wherein diagnosis is made if two of the following three items were present: (i) oligomenorrhoea, (ii) anti-mullerian hormone (AMH) above threshold and/or (iii) hyperandrogenism defined as either testosterone above threshold and/or the presence of hirsutism. This prospective cross-sectional study consists of healthy women (n = 157) recruited at an annual hospital health screen for staff and volunteers from the university community, and a patient cohort (n = 174) comprising women referred for suspected PCOS. We used the healthy cohort to establish threshold values for serum testosterone, antral follicle counts (AFC), ovarian volume (OV) and AMH. Women from the patient cohort, classified as PCOS by simplified PCOS criteria, AMH alone and Rotterdam 2003, were compared with respect to prevalence of oligomenorrhoea, hyperandrogenism and metabolic indices. In healthy women, testosterone ≥1.89 nmol/L, AFC ≥22 follicles and OV ≥8.44 mL, best predicted oligomenorrhoea and were used as threshold values for PCOS criteria. An AMH level ≥37.0 pmol/L best predicted polycystic ovarian morphology. AMH alone as a single biomarker demonstrated poor specificity (58.9%) for PCOS compared to Rotterdam 2003. In contrast, there was a 94% overlap in women selected as PCOS by the simplified PCOS criteria and Rotterdam 2003. The population characteristics of these two groups of PCOS women showed no significant mean differences in androgenic, ovarian, AMH and metabolic (BMI, HOMA-IR) variables. Our data recommend the simplified PCOS criteria with population-specific thresholds for diagnosis of PCOS. Its ability to replace ovarian ultrasound biometry with the highly correlated variable AMH, and use of testosterone as a single marker for hyperandrogenaemia alongside the key symptoms of oligomenorrhoea and hirsutism confers significant clinical potential for the diagnosis of PCOS. © 2018 John Wiley & Sons Ltd.

Handheld echocardiographic screening for rheumatic heart disease by non-experts.

PubMed

Ploutz, Michelle; Lu, Jimmy C; Scheel, Janet; Webb, Catherine; Ensing, Greg J; Aliku, Twalib; Lwabi, Peter; Sable, Craig; Beaton, Andrea

2016-01-01

Handheld echocardiography (HAND) has good sensitivity and specificity for rheumatic heart disease (RHD) when performed by cardiologists. However, physician shortages in RHD-endemic areas demand less-skilled users to make RHD screening practical. We examine nurse performance and interpretation of HAND using a simplified approach for RHD screening. Two nurses received training on HAND and a simplified screening approach. Consented students at two schools in Uganda were eligible for participation. A simplified approach (HAND performed and interpreted by a non-expert) was compared with the reference standard (standard portable echocardiography, performed and interpreted by experts according to the 2012 World Heart Federation guidelines). Reasons for false-positive and false-negative HAND studies were identified. A total of 1002 children were consented, with 956 (11.1 years, 41.8% male) having complete data for review. Diagnoses included: 913 (95.5%) children were classified normal, 32 (3.3%) borderline RHD and 11 (1.2%) definite RHD. The simplified approach had a sensitivity of 74.4% (58.8% to 86.5%) and a specificity of 78.8% (76.0% to 81.4%) for any RHD (borderline and definite). Sensitivity improved to 90.9% (58.7% to 98.5%) for definite RHD. Identification and measurement of erroneous colour jets was the most common reason for false-positive studies (n=164/194), while missed mitral regurgitation and shorter regurgitant jet lengths with HAND were the most common reasons for false-negative studies (n=10/11). Non-expert-led HAND screening programmes offer a potential solution to financial and workforce barriers that limit widespread RHD screening. Nurses trained on HAND using a simplified approach had reasonable sensitivity and specificity for RHD screening. Information on reasons for false-negative and false-positive screening studies should be used to inform future training protocols, which could lead to improved screening performance. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

MicroCT-Based Skeletal Models for Use in Tomographic Voxel Phantoms for Radiological Protection

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

Bolch, Wesley

The University of Florida (UF) proposes to develop two high-resolution image-based skeletal dosimetry models for direct use by ICRP Committee 2’s Task Group on Dose Calculation in their forthcoming Reference Voxel Male (RVM) and Reference Voxel Female (RVF) whole-body dosimetry phantoms. These two phantoms are CT-based, and thus do not have the image resolution to delineate and perform radiation transport modeling of the individual marrow cavities and bone trabeculae throughout their skeletal structures. Furthermore, new and innovative 3D microimaging techniques will now be required for the skeletal tissues following Committee 2’s revision of the target tissues of relevance for radiogenicmore » bone cancer induction. This target tissue had been defined in ICRP Publication 30 as a 10-μm cell layer on all bone surfaces of trabecular and cortical bone. The revised target tissue is now a 50-μm layer within the marrow cavities of trabecular bone only and is exclusive of the marrow adipocytes. Clearly, this new definition requires the use of 3D microimages of the trabecular architecture not available from past 2D optical studies of the adult skeleton. With our recent acquisition of two relatively young cadavers (males of age 18-years and 40-years), we will develop a series of reference skeletal models that can be directly applied to (1) the new ICRP reference voxel man and female phantoms developed for the ICRP, and (2) pediatric phantoms developed to target the ICRP reference children. Dosimetry data to be developed will include absorbed fractions for internal beta and alpha-particle sources, as well as photon and neutron fluence-to-dose response functions for direct use in external dosimetry studies of the ICRP reference workers and members of the general public« less

Selection of suitable soybean EF1α genes as internal controls for real-time PCR analyses of tissues during plant development and under stress conditions.

PubMed

Saraiva, Kátia D C; Fernandes de Melo, Dirce; Morais, Vanessa D; Vasconcelos, Ilka M; Costa, José H

2014-09-01

The EF1α genes were stable in the large majority of soybean tissues during development and in specific tissues/conditions under stress. Quantitative real-time PCR (qPCR) analysis strongly depends on transcript normalization using stable reference genes. Reference genes are generally encoded by multigene families and are used in qPCR normalization; however, little effort has been made to verify the stability of different gene members within a family. Here, the expression stability of members of the soybean EF1α gene family (named EF1α 1a1, 1a2, 1b, 2a, 2b and 3) was evaluated in different tissues during plant development and stress exposure (SA and PEG). Four genes (UKN1, SKIP 16, EF1β and MTP) already established as stably expressed were also used in the comparative analysis. GeNorm analyses revealed different combinations of reference genes as stable in soybean tissues during development. The EF1α genes were the most stable in cotyledons (EF1α 3 and EF1α 1b), epicotyls (EF1α 1a2, EF1α 2b and EF1α 1a1), hypocotyls (EF1α 1a1 and EF1β), pods (EF1α 2a and EF1α 2b) and roots (EF1α 2a and UKN1) and less stable in tissues such as trifoliate and unifoliate leaves and germinating seeds. Under stress conditions, no suitable combination including only EF1α genes was found; however, some genes were relatively stable in leaves (EF1α 1a2) and roots (EF1α 1a1) treated with SA as well as in roots treated with PEG (EF1α 2b). EF1α 2a was the most stably expressed EF1α gene in all soybean tissues under stress. Taken together, our data provide guidelines for the selection of EF1α genes for use as reference genes in qPCR expression analyses during plant development and under stress conditions.

Validity of the semi-infinite tumor model in diffuse reflectance spectroscopy for epithelial cancer diagnosis: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Zhu, Caigang; Liu, Quan

2011-08-01

The accurate understanding of optical properties of human tissues plays an important role in the optical diagnosis of early epithelial cancer. Many inverse models used to determine the optical properties of a tumor have assumed that the tumor was semi-infinite, which infers infinite width and length but finite thickness. However, this simplified assumption could lead to large errors for small tumor, especially at the early stages. We used a modified Monte Carlo code, which is able to simulate light transport in a layered tissue model with buried tumor-like targets, to investigate the validity of the semi-infinite tumor assumption in two common epithelial tissue models: a squamous cell carcinoma (SCC) tissue model and a basal cell carcinoma (BCC) tissue model. The SCC tissue model consisted of three layers, i.e. the top epithelium, the middle tumor and the bottom stroma. The BCC tissue model also consisted of three layers, i.e. the top epidermis, the middle tumor and the bottom dermis. Diffuse reflectance was simulated for two common fiber-optic probes. In one probe, both source and detector fibers were perpendicular to the tissue surface; while in the other, both fibers were tilted at 45 degrees relative to the normal axis of the tissue surface. It was demonstrated that the validity of the semi-infinite tumor model depends on both the fiber-optic probe configuration and the tumor dimensions. Two look-up tables, which relate the validity of the semi-infinite tumor model to the tumor width in terms of the source-detector separation, were derived to guide the selection of appropriate tumor models and fiber optic probe configuration for the optical diagnosis of early epithelial cancers.

Evaluation in Monkey of Two Candidate PET Radioligands, [11C]RX-1 and [18F]RX-2, for Imaging Brain 5-HT4 Receptors

PubMed Central

LOHITH, TALAKAD G.; XU, RONG; TSUJIKAWA, TETSUYA; MORSE, CHERYL L.; ANDERSON, KACEY B.; GLADDING, ROBERT L.; ZOGHBI, SAMI S.; FUJITA, MASAHIRO; INNIS, ROBERT B.; PIKE, VICTOR W.

2014-01-01

The serotonin subtype-4 (5-HT4) receptor, which is known to be involved physiologically in learning and memory, and pathologically in Alzheimer’s disease, anxiety and other neuropsychiatric disorders – has few radioligands readily available for imaging in vivo. We have previously reported two novel 5-HT4 receptor radioligands, namely [methoxy-11C](1-butylpiperidin-4-yl)methyl 4-amino-3-methoxybenzoate; [11C]RX-1) and the [18F]3-fluoromethoxy analog ([18F]RX-2), and in this study we evaluated them by PET in rhesus monkey. Brain scans were performed at baseline, receptor preblock or displacement conditions using SB 207710, a 5-HT4 receptor antagonist, on the same day for [11C]RX-1 and on different days for [18F]RX-2. Specific-to-nondisplaceable ratio (BPND) was measured with the simplified reference tissue model from all baseline scans. To determine specific binding, total distribution volume (VT) was also measured in some monkeys by radiometabolite-corrected arterial input function after ex vivo inhibition of esterases from baseline and blocked scans. Both radioligands showed moderate to high peak brain uptake of radioactivity (2–6 SUV). Regional BPND values were in the rank order of known 5-HT4 receptor distribution with a trend for higher BPND values from [18F]RX-2. One-tissue compartmental model provided good fits with well identified VT values for both radioligands. In the highest 5-HT4 receptor density region, striatum, 50–60% of total binding was specific. The VT in receptor-poor cerebellum reached stable values by about 60 min for both radioligands indicating little influence of radiometabolites on brain signal. In conclusion, both [11C]RX-1 and [18F]RX-2 showed positive attributes for PET imaging of brain 5-HT4 receptors, validating the radioligand design strategy. PMID:25088028

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species

PubMed Central

Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses. PMID:26863232

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species.

PubMed

Reddy, Dumbala Srinivas; Bhatnagar-Mathur, Pooja; Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses.

Integrative analysis of 111 reference human epigenomes

PubMed Central

Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Kheradpour, Pouya; Zhang, Zhizhuo; Heravi-Moussavi, Alireza; Liu, Yaping; Amin, Viren; Ziller, Michael J; Whitaker, John W; Schultz, Matthew D; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Wang, Jianrong; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Pfenning, Andreas; Wang, Xinchen; Claussnitzer, Melina; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven; Li, Wei; Marra, Marco; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, Manolis

2015-01-01

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but a similar reference has lacked for epigenomic studies. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection to-date of human epigenomes for primary cells and tissues. Here, we describe the integrative analysis of 111 reference human epigenomes generated as part of the program, profiled for histone modification patterns, DNA accessibility, DNA methylation, and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically-relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation, and human disease. PMID:25693563

Method for detection of dental caries and periodontal disease using optical imaging

DOEpatents

Nathel, H.; Kinney, J.H.; Otis, L.L.

1996-10-29

A method is disclosed for detecting the presence of active and inactive caries in teeth and diagnosing periodontal disease uses non-ionizing radiation with techniques for reducing interference from scattered light. A beam of non-ionizing radiation is divided into sample and reference beams. The region to be examined is illuminated by the sample beam, and reflected or transmitted radiation from the sample is recombined with the reference beam to form an interference pattern on a detector. The length of the reference beam path is adjustable, allowing the operator to select the reflected or transmitted sample photons that recombine with the reference photons. Thus radiation scattered by the dental or periodontal tissue can be prevented from obscuring the interference pattern. A series of interference patterns may be generated and interpreted to locate dental caries and periodontal tissue interfaces. 7 figs.

Integrative analysis of 111 reference human epigenomes.

PubMed

Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J; Amin, Viren; Whitaker, John W; Schultz, Matthew D; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Pfenning, Andreas R; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas A; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip L; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven J M; Li, Wei; Marra, Marco A; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael Q; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, Manolis

2015-02-19

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Large Osteoarthritic Cyst Presenting as Soft Tissue Tumour – A Case Report

PubMed Central

Kosuge, DD; Park, DH; Cannon, SR; Briggs, TW; Pollock, RC; Skinner, JA

2007-01-01

Large osteoarthritic cysts can sometimes be difficult to distinguish from primary osseous and soft tissue tumours. We present such a case involving a cyst arising from the hip joint and eroding the acetabulum which presented as a soft tissue malignancy referred to a tertiary bone and soft tissue tumour centre. We discuss the diagnostic problems it may pose, and present a literature review of the subject. PMID:17535605

Trends in the use of tissue culture in forest improvement

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

Haissig, B.E.; Nelson, N.D.; Kidd, G.H.

1987-01-01

We have analyzed and described the problems and potentials of using tissue culture in micropropagation and biotechnologies related to forest improvement. Trends in forest management concepts, commerical micropropagation, and tissue culture biotechnologies are discussed. Our analysis suggests that tissue culture will contribute significantly to the improvement of forests through exploitation of existing genotypes and production of new, commercially valuble genotypes. Such changes may significantly influence worldwide management decisions in forestry. 97 references.

Genetics Home Reference: medium-chain acyl-CoA dehydrogenase deficiency

MedlinePlus

... body's fat tissues. Fatty acids are a major source of energy for the heart and muscles. During periods of fasting, fatty acids are also an important energy source for the liver and other tissues. Mutations in ...

Measurement of stable isotopic enrichment and concentration of long-chain fatty acyl-carnitines in tissue by HPLC-MS.

PubMed

Sun, Dayong; Cree, Melanie G; Zhang, Xiao-Jun; Bøersheim, Elisabet; Wolfe, Robert R

2006-02-01

We have developed a new method for the simultaneous measurements of stable isotopic tracer enrichments and concentrations of individual long-chain fatty acyl-carnitines in muscle tissue using ion-pairing high-performance liquid chromatography-electrospray ionization quadrupole mass spectrometry in the selected ion monitoring (SIM) mode. Long-chain fatty acyl-carnitines were extracted from frozen muscle tissue samples by acetonitrile/methanol. Baseline separation was achieved by reverse-phase HPLC in the presence of the volatile ion-pairing reagent heptafluorobutyric acid. The SIM capability of a single quadrupole mass analyzer allows further separation of the ions of interest from the sample matrixes, providing very clean total and selected ion chromatograms that can be used to calculate the stable isotopic tracer enrichment and concentration of long-chain fatty acyl-carnitines in a single analysis. The combination of these two separation techniques greatly simplifies the sample preparation procedure and increases the detection sensitivity. Applying this protocol to biological muscle samples proves it to be a very sensitive, accurate, and precise analytical tool.

Micromechanical modeling of elastic properties of cortical bone accounting for anisotropy of dense tissue.

PubMed

Salguero, Laura; Saadat, Fatemeh; Sevostianov, Igor

2014-10-17

The paper analyzes the connection between microstructure of the osteonal cortical bone and its overall elastic properties. The existing models either neglect anisotropy of the dense tissue or simplify cortical bone microstructure (accounting for Haversian canals only). These simplifications (related mostly to insufficient mathematical apparatus) complicate quantitative analysis of the effect of microstructural changes - produced by age, microgravity, or some diseases - on the overall mechanical performance of cortical bone. The present analysis fills this gap; it accounts for anisotropy of the dense tissue and uses realistic model of the porous microstructure. The approach is based on recent results of Sevostianov et al. (2005) and Saadat et al. (2012) on inhomogeneities in a transversely-isotropic material. Bone's microstructure is modeled according to books of Martin and Burr (1989), Currey (2002), and Fung (1993) and includes four main families of pores. The calculated elastic constants for porous cortical bone are in agreement with available experimental data. The influence of each of the pore types on the overall moduli is examined. Copyright © 2014 Elsevier Ltd. All rights reserved.

Photon migration in non-scattering tissue and the effects on image reconstruction

NASA Astrophysics Data System (ADS)

Dehghani, H.; Delpy, D. T.; Arridge, S. R.

1999-12-01

Photon propagation in tissue can be calculated using the relationship described by the transport equation. For scattering tissue this relationship is often simplified and expressed in terms of the diffusion approximation. This approximation, however, is not valid for non-scattering regions, for example cerebrospinal fluid (CSF) below the skull. This study looks at the effects of a thin clear layer in a simple model representing the head and examines its effect on image reconstruction. Specifically, boundary photon intensities (total number of photons exiting at a point on the boundary due to a source input at another point on the boundary) are calculated using the transport equation and compared with data calculated using the diffusion approximation for both non-scattering and scattering regions. The effect of non-scattering regions on the calculated boundary photon intensities is presented together with the advantages and restrictions of the transport code used. Reconstructed images are then presented where the forward problem is solved using the transport equation for a simple two-dimensional system containing a non-scattering ring and the inverse problem is solved using the diffusion approximation to the transport equation.

Assessment of nerve involvement in the lumbar spine: agreement between magnetic resonance imaging, physical examination and pain drawing findings

PubMed Central

2010-01-01

Background Detection of nerve involvement originating in the spine is a primary concern in the assessment of spine symptoms. Magnetic resonance imaging (MRI) has become the diagnostic method of choice for this detection. However, the agreement between MRI and other diagnostic methods for detecting nerve involvement has not been fully evaluated. The aim of this diagnostic study was to evaluate the agreement between nerve involvement visible in MRI and findings of nerve involvement detected in a structured physical examination and a simplified pain drawing. Methods Sixty-one consecutive patients referred for MRI of the lumbar spine were - without knowledge of MRI findings - assessed for nerve involvement with a simplified pain drawing and a structured physical examination. Agreement between findings was calculated as overall agreement, the p value for McNemar's exact test, specificity, sensitivity, and positive and negative predictive values. Results MRI-visible nerve involvement was significantly less common than, and showed weak agreement with, physical examination and pain drawing findings of nerve involvement in corresponding body segments. In spine segment L4-5, where most findings of nerve involvement were detected, the mean sensitivity of MRI-visible nerve involvement to a positive neurological test in the physical examination ranged from 16-37%. The mean specificity of MRI-visible nerve involvement in the same segment ranged from 61-77%. Positive and negative predictive values of MRI-visible nerve involvement in segment L4-5 ranged from 22-78% and 28-56% respectively. Conclusion In patients with long-standing nerve root symptoms referred for lumbar MRI, MRI-visible nerve involvement significantly underestimates the presence of nerve involvement detected by a physical examination and a pain drawing. A structured physical examination and a simplified pain drawing may reveal that many patients with "MRI-invisible" lumbar symptoms need treatment aimed at nerve involvement. Factors other than present MRI-visible nerve involvement may be responsible for findings of nerve involvement in the physical examination and the pain drawing. PMID:20831785

Radiosynthesis and in vivo evaluation of a series of substituted 11C-phenethylamines as 5-HT (2A) agonist PET tracers.

PubMed

Ettrup, Anders; Hansen, Martin; Santini, Martin A; Paine, James; Gillings, Nic; Palner, Mikael; Lehel, Szabolcs; Herth, Matthias M; Madsen, Jacob; Kristensen, Jesper; Begtrup, Mikael; Knudsen, Gitte M

2011-04-01

Positron emission tomography (PET) imaging of serotonin 2A (5-HT(2A)) receptors with agonist tracers holds promise for the selective labelling of 5-HT(2A) receptors in their high-affinity state. We have previously validated [(11)C]Cimbi-5 and found that it is a 5-HT(2A) receptor agonist PET tracer. In an attempt to further optimize the target-to-background binding ratio, we modified the chemical structure of the phenethylamine backbone and carbon-11 labelling site of [(11)C]Cimbi-5 in different ways. Here, we present the in vivo validation of nine novel 5-HT(2A) receptor agonist PET tracers in the pig brain. Each radiotracer was injected intravenously into anaesthetized Danish Landrace pigs, and the pigs were subsequently scanned for 90 min in a high-resolution research tomography scanner. To evaluate 5-HT(2A) receptor binding, cortical nondisplaceable binding potentials (BP(ND)) were calculated using the simplified reference tissue model with the cerebellum as a reference region. After intravenous injection, all compounds entered the brain and distributed preferentially into the cortical areas, in accordance with the known 5-HT(2A) receptor distribution. The largest target-to-background binding ratio was found for [(11)C]Cimbi-36 which also had a high brain uptake compared to its analogues. The cortical binding of [(11)C]Cimbi-36 was decreased by pretreatment with ketanserin, supporting 5-HT(2A) receptor selectivity in vivo. [(11)C]Cimbi-82 and [(11)C]Cimbi-21 showed lower cortical BP(ND), while [(11)C]Cimbi-27, [(11)C]Cimbi-29, [(11)C]Cimbi-31 and [(11)C]Cimbi-88 gave rise to cortical BP(ND) similar to that of [(11)C]Cimbi-5. [(11)C]Cimbi-36 is currently the most promising candidate for investigation of 5-HT(2A) receptor agonist binding in the living human brain with PET.

Acute effect of intravenously applied alcohol in the human striatal and extrastriatal D2 /D3 dopamine system.

PubMed

Pfeifer, Philippe; Tüscher, Oliver; Buchholz, Hans Georg; Gründer, Gerhard; Vernaleken, Ingo; Paulzen, Michael; Zimmermann, Ulrich S; Maus, Stephan; Lieb, Klaus; Eggermann, Thomas; Fehr, Christoph; Schreckenberger, Mathias

2017-09-01

Investigations on the acute effects of alcohol in the human mesolimbic dopamine D 2 /D 3 receptor system have yielded conflicting results. With respect to the effects of alcohol on extrastriatal D 2 /D 3 dopamine receptors no investigations have been reported yet. Therefore we applied PET imaging using the postsynaptic dopamine D 2 /D 3 receptor ligand [ 18 F]fallypride addressing the question, whether intravenously applied alcohol stimulates the extrastriatal and striatal dopamine system. We measured subjective effects of alcohol and made correlation analyses with the striatal and extrastriatal D 2 /D 3 binding potential. Twenty-four healthy male μ-opioid receptor (OPRM1)118G allele carriers underwent a standardized intravenous and placebo alcohol administration. The subjective effects of alcohol were measured with a visual analogue scale. For the evaluation of the dopamine response we calculated the binding potential (BP ND ) by using the simplified reference tissue model (SRTM). In addition, we calculated distribution volumes (target and reference regions) in 10 subjects for which metabolite corrected arterial samples were available. In the alcohol condition no significant dopamine response in terms of a reduction of BP ND was observed in striatal and extrastriatal brain regions. We found a positive correlation for 'liking' alcohol and the BP ND in extrastriatal brain regions (Inferior frontal cortex (IFC) (r = 0.533, p = 0.007), orbitofrontal cortex (OFC) (r = 0.416, p = 0.043) and prefrontal cortex (PFC) (r = 0.625, p = 0.001)). The acute alcohol effects on the D 2 /D 3 dopamine receptor binding potential of the striatal and extrastriatal system in our experiment were insignificant. A positive correlation of the subjective effect of 'liking' alcohol with cortical D 2 /D 3 receptors may hint at an addiction relevant trait. © 2016 Society for the Study of Addiction.

Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

NASA Astrophysics Data System (ADS)

Pu, Fei; Yang, Bingye; Ke, Caihuan

2015-07-01

Accurate quantification of transcripts using quantitative real-time polymerase chain reaction (qPCR) depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 ( ACT-2), elongation factor 1 alpha ( EF-1α), elongation factor 1 beta ( EF-1β), glyceraldehyde-3-phosphate dehydrogenase ( GAPDH), ubiquitin ( UBQ), β-tubulin ( β-TUB), and 18S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene ( Gβ) across tissue types was also examined and normalized to the expression of each or both of UBQ and β-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further functional genomics studies in this economically valuable marine bivalve.

In silico selection of expression reference genes with demonstrated stability in barley among a diverse set of tissues and cultivars

USDA-ARS?s Scientific Manuscript database

Premise of the study: Reference genes are selected based on the assumption of temporal and spatial expression stability and on their widespread use in model species. They are often used in new target species without validation, presumed as stable. For barley, reference gene validation is lacking, bu...

Modeling ultrasonic transient scattering from biological tissues including their dispersive properties directly in the time domain.

PubMed

Norton, G V; Novarini, J C

2007-06-01

Ultrasonic imaging in medical applications involves propagation and scattering of acoustic waves within and by biological tissues that are intrinsically dispersive. Analytical approaches for modeling propagation and scattering in inhomogeneous media are difficult and often require extremely simplifying approximations in order to achieve a solution. To avoid such approximations, the direct numerical solution of the wave equation via the method of finite differences offers the most direct tool, which takes into account diffraction and refraction. It also allows for detailed modeling of the real anatomic structure and combination/layering of tissues. In all cases the correct inclusion of the dispersive properties of the tissues can make the difference in the interpretation of the results. However, the inclusion of dispersion directly in the time domain proved until recently to be an elusive problem. In order to model the transient signal a convolution operator that takes into account the dispersive characteristics of the medium is introduced to the linear wave equation. To test the ability of this operator to handle scattering from localized scatterers, in this work, two-dimensional numerical modeling of scattering from an infinite cylinder with physical properties associated with biological tissue is calculated. The numerical solutions are compared with the exact solution synthesized from the frequency domain for a variety of tissues having distinct dispersive properties. It is shown that in all cases, the use of the convolutional propagation operator leads to the correct solution for the scattered field.

A DTI-based model for TMS using the independent impedance method with frequency-dependent tissue parameters

NASA Astrophysics Data System (ADS)

De Geeter, N.; Crevecoeur, G.; Dupré, L.; Van Hecke, W.; Leemans, A.

2012-04-01

Accurate simulations on detailed realistic head models are necessary to gain a better understanding of the response to transcranial magnetic stimulation (TMS). Hitherto, head models with simplified geometries and constant isotropic material properties are often used, whereas some biological tissues have anisotropic characteristics which vary naturally with frequency. Moreover, most computational methods do not take the tissue permittivity into account. Therefore, we calculate the electromagnetic behaviour due to TMS in a head model with realistic geometry and where realistic dispersive anisotropic tissue properties are incorporated, based on T1-weighted and diffusion-weighted magnetic resonance images. This paper studies the impact of tissue anisotropy, permittivity and frequency dependence, using the anisotropic independent impedance method. The results show that anisotropy yields differences up to 32% and 19% of the maximum induced currents and electric field, respectively. Neglecting the permittivity values leads to a decrease of about 72% and 24% of the maximum currents and field, respectively. Implementing the dispersive effects of biological tissues results in a difference of 6% of the maximum currents. The cerebral voxels show limited sensitivity of the induced electric field to changes in conductivity and permittivity, whereas the field varies approximately linearly with frequency. These findings illustrate the importance of including each of the above parameters in the model and confirm the need for accuracy in the applied patient-specific method, which can be used in computer-assisted TMS.

Multiparametric monitoring of tissue vitality in clinical situations

NASA Astrophysics Data System (ADS)

Mayevsky, Avraham; Manor, Tamar; Meilin, Sigal; Razon, Nisim; Ouknine, George E.; Ornstein, Eugene

2001-05-01

The monitoring of various tissue's physiological and biochemical parameters is one of the tools used by the clinicians to improve diagnosis capacity. As of today, the very few devices developed for real time clinical monitoring of tissue vitality are based on a single parameter measurement. Tissue energy balance could be defined as the ratio between oxygen or energy supply and demand. In order to determine the vitality of the brain, for example, it is necessary to measure at least the following 3 parameters: Energy Demand--potassium ion homeostasis; Energy Supply-- cerebral blood flow; Energy Balance--mitochondrial NADH redox state. For other tissues one can measure various energy demand processes specific to the tested organ. We have developed a unique multiparametric monitoring system tested in various experimental and clinical applications. The multiprobe assembly (MPA) consists of a fiber optic probe for measurement of tissue blood flow and mitochondrial NADH redox state, ion selective electrodes (K+, Ca2+, H+), electrodes for electrical activities (ECoG or ECG and DC potential), temperature probe and for monitoring the brain - Intra Cranial Pressure probe (ICP). The computerized monitoring system was used in the neurological intensive care unit to monitor comatose patients for a period of 24-48 hours. Also, a simplified MPA was used in the neurosurgical operating room or during organ transplantation procedure. It was found that the MPA could be used in clinical situations and that the data collected has a significant diagnosis value for the medical team.

Predator-prey Encounter Rates in Turbulent Environments: Consequences of Inertia Effects and Finite Sizes

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

Pecseli, H. L.; Trulsen, J.

2009-10-08

Experimental as well as theoretical studies have demonstrated that turbulence can play an important role for the biosphere in marine environments, in particular also by affecting prey-predator encounter rates. Reference models for the encounter rates rely on simplifying assumptions of predators and prey being described as point particles moving passively with the local flow velocity. Based on simple arguments that can be tested experimentally we propose corrections for the standard expression for the encounter rates, where now finite sizes and Stokes drag effects are included.

Calculation of load distribution in stiffened cylindrical shells

NASA Technical Reports Server (NTRS)

Ebner, H; Koller, H

1938-01-01

Thin-walled shells with strong longitudinal and transverse stiffening (for example, stressed-skin fuselages and wings) may, under certain simplifying assumptions, be treated as static systems with finite redundancies. In this report the underlying basis for this method of treatment of the problem is presented and a computation procedure for stiffened cylindrical shells with curved sheet panels indicated. A detailed discussion of the force distribution due to applied concentrated forces is given, and the discussion illustrated by numerical examples which refer to an experimentally determined circular cylindrical shell.

Optimal flight trajectories in the presence of windshear, 1984-86

NASA Technical Reports Server (NTRS)

Miele, A.

1986-01-01

Optimal flight trajectories were determined in the presence of windshear and guidance schemes were developed for near optimum flight in a windshear. This is a wind characterized by sharp change in intensity and direction over a relatively small region of space. This problem is important in the takeoff and landing of both civilian airplanes and military airplanes and is key to aircraft saftey. The topics covered in reference to takeoff problems are: equations of motion, problem formulation, algorithms, optimal flight trajectories, advanced guidance schemes, simplified guidance schemes, and piloting strategies.

Experimental evaluation of a 600 lbf spacecraft rocket engine.

NASA Technical Reports Server (NTRS)

Hoehn, F. W.

1972-01-01

Experimental results are presented for a long-duration-capability (1000-sec), space-storable, bipropellant liquid rocket motor burning fluorine/hydrazine or FLOX/monomethylhydrazine. The interrelationship between injected mixture ratio and the per cent film cooling on vacuum specific impulse performance and chamber heat transfer is given. Experimental sea level measurements are used to predict space vacuum performance based upon simplified JANNAF reference procedures. Dynamic combustion stability is demonstrated over a wide range of operating conditions. Analytical results of char penetration, erosion, and ablative wall temperature distributions are presented for prototype chamber designs.

Translation invariant time-dependent massive gravity: Hamiltonian analysis

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

Mourad, Jihad; Steer, Danièle A.; Noui, Karim, E-mail: mourad@apc.univ-paris7.fr, E-mail: karim.noui@lmpt.univ-tours.fr, E-mail: steer@apc.univ-paris7.fr

2014-09-01

The canonical structure of the massive gravity in the first order moving frame formalism is studied. We work in the simplified context of translation invariant fields, with mass terms given by general non-derivative interactions, invariant under the diagonal Lorentz group, depending on the moving frame as well as a fixed reference frame. We prove that the only mass terms which give 5 propagating degrees of freedom are the dRGT mass terms, namely those which are linear in the lapse. We also complete the Hamiltonian analysis with the dynamical evolution of the system.

FE Modelling of the Fluid-Structure-Acoustic Interaction for the Vocal Folds Self-Oscillation

NASA Astrophysics Data System (ADS)

Švancara, Pavel; Horáček, J.; Hrůza, V.

The flow induced self-oscillation of the human vocal folds in interaction with acoustic processes in the simplified vocal tract model was explored by three-dimensional (3D) finite element (FE) model. Developed FE model includes vocal folds pretension before phonation, large deformations of the vocal fold tissue, vocal folds contact, fluid-structure interaction, morphing the fluid mesh according the vocal folds motion (Arbitrary Lagrangian-Eulerian approach), unsteady viscous compressible airflow described by the Navier-Stokes equations and airflow separation during the glottis closure. Iterative partitioned approach is used for modelling the fluid-structure interaction. Computed results prove that the developed model can be used for simulation of the vocal folds self-oscillation and resulting acoustic waves. The developed model enables to numerically simulate an influence of some pathological changes in the vocal fold tissue on the voice production.

Semiautomated Device for Batch Extraction of Metabolites from Tissue Samples

PubMed Central

2012-01-01

Metabolomics has become a mainstream analytical strategy for investigating metabolism. The quality of data derived from these studies is proportional to the consistency of the sample preparation. Although considerable research has been devoted to finding optimal extraction protocols, most of the established methods require extensive sample handling. Manual sample preparation can be highly effective in the hands of skilled technicians, but an automated tool for purifying metabolites from complex biological tissues would be of obvious utility to the field. Here, we introduce the semiautomated metabolite batch extraction device (SAMBED), a new tool designed to simplify metabolomics sample preparation. We discuss SAMBED’s design and show that SAMBED-based extractions are of comparable quality to extracts produced through traditional methods (13% mean coefficient of variation from SAMBED versus 16% from manual extractions). Moreover, we show that aqueous SAMBED-based methods can be completed in less than a quarter of the time required for manual extractions. PMID:22292466

Brachytherapy devices and methods employing americium-241

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

Gray, L. A.

1985-04-16

Sources and methods for radiation therapy, particularly brachytherapy, employing americium-241 (60 keV gamma emission and 433 year half-life) provide major advantages for radiotherapy, including simplified radiation protection, dose reduction to healthy tissue, increased dose to tumor, and improved dose distributions. A number of apparent drawbacks and unfavorable considerations including low gamma factor, high self-absorption, increased activity required and alpha-particle generation leading to helium gas pressure buildup and potential neutron contamination in the generated radiation are all effectively dealt with and overcome through recognition of subtle favorable factors unique to americium-241 among brachytherapy sources and through suitable constructional techniques. Due tomore » an additional amount of radiation, in the order of 50%, provided primarily to nearby regions as a result of Compton scatter in tissue and water, higher dose rates occur than would be predicted by conventional calculations.« less

Acoustic dipole radiation model for magnetoacoustic tomography with magnetic induction

NASA Astrophysics Data System (ADS)

Li, Yi-Ling; Ma, Qing-Yu; Zhang, Dong; Xia, Rong-Min

2011-08-01

An acoustic dipole radiation model for magnetoacoustic tomography with magnetic induction (MAT-MI) is proposed, based on the analyses of one-dimensional tissue vibration, three-dimensional acoustic dipole radiation and acoustic waveform detection with a planar piston transducer. The collected waveforms provide information about the conductivity boundaries in various vibration intensities and phases due to the acoustic dipole radiation pattern. Combined with the simplified back projection algorithm, the conductivity configuration of the measured layer in terms of shape and size can be reconstructed with obvious border stripes. The numerical simulation is performed for a two-layer cylindrical phantom model and it is also verified by the experimental results of MAT-MI for a tissue-like sample phantom. The proposed model suggests a potential application of conductivity differentiation and provides a universal basis for the further study of conductivity reconstruction for MAT-MI.

Preparation of 3D fibroin/chitosan blend porous scaffold for tissue engineering via a simplified method.

PubMed

Ruan, Yuhui; Lin, Hong; Yao, Jinrong; Chen, Zhengrong; Shao, Zhengzhong

2011-03-10

In this work, we developed a simple and flexible method to manufacture a 3D porous scaffold based on the blend of regenerated silk fibroin (RSF) and chitosan (CS). No crosslinker or other toxic reagents were used in this method. The pores of resulted 3D scaffolds were connected with each other, and their sizes could be easily controlled by the concentration of the mixed solution. Compared with pure RSF scaffolds, the water absorptivities of these RSF/CS blend scaffolds with significantly enhanced mechanical properties were greatly increased. The results of MTT and RT-PCR tests indicated that the chondrocytes grew very well in these blend RSF/CS porous scaffolds. This suggested that the RSF/CS blend scaffold prepared by this new method could be a promising candidate for applications in tissue engineering. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the effect of computed tomography resolution to distinguish between abdominal aortic aneurysm wall tissue and calcification: A proof of concept.

PubMed

Barrett, H E; Cunnane, E M; O Brien, J M; Moloney, M A; Kavanagh, E G; Walsh, M T

2017-10-01

The purpose of this study is to determine the optimal target CT spatial resolution for accurately imaging abdominal aortic aneurysm (AAA) wall characteristics, distinguishing between tissue and calcification components, for an accurate assessment of rupture risk. Ruptured and non-ruptured AAA-wall samples were acquired from eight patients undergoing open surgical aneurysm repair upon institutional review board approval and informed consent was obtained from all patients. Physical measurements of AAA-wall cross-section were made using scanning electron microscopy. Samples were scanned using high resolution micro-CT scanning. A resolution range of 15.5-155μm was used to quantify the influence of decreasing resolution on wall area measurements, in terms of tissue and calcification. A statistical comparison between the reference resolution (15.5μm) and multi-detector CT resolution (744μm) was also made. Electron microscopy examination of ruptured AAAs revealed extremely thin outer tissue structure <200μm in radial distribution which is supporting the aneurysm wall along with large areas of adjacent medial calcifications far greater in area than the tissue layer. The spatial resolution of 155μm is a significant predictor of the reference AAA-wall tissue and calcification area measurements (r=0.850; p<0.001; r=0.999; p<0.001 respectively). The tissue and calcification area at 155μm is correct within 8.8%±1.86 and 26.13%±9.40 respectively with sensitivity of 87.17% when compared to the reference. The inclusion of AAA-wall measurements, through the use of high resolution-CT will elucidate the variations in AAA-wall tissue and calcification distributions across the wall which may help to leverage an improved assessment of AAA rupture risk. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface Entrapment of Fibronectin on Electrospun PLGA Scaffolds for Periodontal Tissue Engineering

PubMed Central

Gritsch, Kerstin; Salles, Vincent; Attik, Ghania N.; Grosgogeat, Brigitte

2014-01-01

Abstract Nowadays, the challenge in the tissue engineering field consists in the development of biomaterials designed to regenerate ad integrum damaged tissues. Despite the current use of bioresorbable polyesters such as poly(l-lactide) (PLA), poly(d,l-lactide-co-glycolide) (PLGA), and poly-ɛ-caprolactone in soft tissue regeneration researches, their hydrophobic properties negatively influence the cell adhesion. Here, to overcome it, we have developed a fibronectin (FN)-functionalized electrospun PLGA scaffold for periodontal ligament regeneration. Functionalization of electrospun PLGA scaffolds was performed by alkaline hydrolysis (0.1 or 0.01 M NaOH). Then, hydrolyzed scaffolds were coated by simple deposition of an FN layer (10 μg/mL). FN coating was evidenced by X-ray photoelectron analysis. A decrease of contact angle and greater cell adhesion to hydrolyzed, FN-coated PLGA scaffolds were noticed. Suitable degradation behavior without pH variations was observed for all samples up to 28 days. All treated materials presented strong shrinkage, fiber orientation loss, and collapsed fibers. However, functionalization process using 0.01 M NaOH concentration resulted in unchanged scaffold porosity, preserved chemical composition, and similar mechanical properties compared with untreated scaffolds. The proposed simplified method to functionalize electrospun PLGA fibers is an efficient route to make polyester scaffolds more biocompatible and shows potential for tissue engineering. PMID:24940563

The use of total human bone marrow fraction in a direct three-dimensional expansion approach for bone tissue engineering applications: focus on angiogenesis and osteogenesis.

PubMed

Guerrero, Julien; Oliveira, Hugo; Catros, Sylvain; Siadous, Robin; Derkaoui, Sidi-Mohammed; Bareille, Reine; Letourneur, Didier; Amédée, Joëlle

2015-03-01

Current approaches in bone tissue engineering have shown limited success, mostly owing to insufficient vascularization of the construct. A common approach consists of co-culture of endothelial cells and osteoblastic cells. This strategy uses cells from different sources and differentiation states, thus increasing the complexity upstream of a clinical application. The source of reparative cells is paramount for the success of bone tissue engineering applications. In this context, stem cells obtained from human bone marrow hold much promise. Here, we analyzed the potential of human whole bone marrow cells directly expanded in a three-dimensional (3D) polymer matrix and focused on the further characterization of this heterogeneous population and on their ability to promote angiogenesis and osteogenesis, both in vitro and in vivo, in a subcutaneous model. Cellular aggregates were formed within 24 h and over the 12-day culture period expressed endothelial and bone-specific markers and a specific junctional protein. Ectopic implantation of the tissue-engineered constructs revealed osteoid tissue and vessel formation both at the periphery and within the implant. This work sheds light on the potential clinical use of human whole bone marrow for bone regeneration strategies, focusing on a simplified approach to develop a direct 3D culture without two-dimensional isolation or expansion.

Reference-free determination of tissue absorption coefficient by modulation transfer function characterization in spatial frequency domain.

PubMed

Chen, Weiting; Zhao, Huijuan; Li, Tongxin; Yan, Panpan; Zhao, Kuanxin; Qi, Caixia; Gao, Feng

2017-08-08

Spatial frequency domain (SFD) measurement allows rapid and non-contact wide-field imaging of the tissue optical properties, thus has become a potential tool for assessing physiological parameters and therapeutic responses during photodynamic therapy of skin diseases. The conventional SFD measurement requires a reference measurement within the same experimental scenario as that for a test one to calibrate mismatch between the real measurements and the model predictions. Due to the individual physical and geometrical differences among different tissues, organs and patients, an ideal reference measurement might be unavailable in clinical trials. To address this problem, we present a reference-free SFD determination of absorption coefficient that is based on the modulation transfer function (MTF) characterization. Instead of the absolute amplitude that is used in the conventional SFD approaches, we herein employ the MTF to characterize the propagation of the modulated lights in tissues. With such a dimensionless relative quantity, the measurements can be naturally corresponded to the model predictions without calibrating the illumination intensity. By constructing a three-dimensional database that portrays the MTF as a function of the optical properties (both the absorption coefficient μ a and the reduced scattering coefficient [Formula: see text]) and the spatial frequency, a look-up table approach or a least-square curve-fitting method is readily applied to recover the absorption coefficient from a single frequency or multiple frequencies, respectively. Simulation studies have verified the feasibility of the proposed reference-free method and evaluated its accuracy in the absorption recovery. Experimental validations have been performed on homogeneous tissue-mimicking phantoms with μ a ranging from 0.01 to 0.07 mm -1 and [Formula: see text] = 1.0 or 2.0 mm -1 . The results have shown maximum errors of 4.86 and 7% for [Formula: see text] = 1.0 mm -1 and [Formula: see text] = 2.0 mm -1 , respectively. We have also presented quantitative ex vivo imaging of human lung cancer in a subcutaneous xenograft mouse model for further validation, and observed high absorption contrast in the tumor region. The proposed method can be applied to the rapid and accurate determination of the absorption coefficient, and better yet, in a reference-free way. We believe this reference-free strategy will facilitate the clinical translation of the SFD measurement to achieve enhanced intraoperative hemodynamic monitoring and personalized treatment planning in photodynamic therapy.

Analysis of Mass Averaged Tissue Doses in CAM, CAF, MAX, and FAX

NASA Technical Reports Server (NTRS)

Slaba, Tony C.; Qualls, Garry D.; Clowdsley, Martha S.; Blattnig, Steve R.; Simonsen, Lisa C.; Walker, Steven A.; Singleterry, Robert C.

2009-01-01

To estimate astronaut health risk due to space radiation, one must have the ability to calculate exposure-related quantities averaged over specific organs and tissue types. In this study, we first examine the anatomical properties of the Computerized Anatomical Man (CAM), Computerized Anatomical Female (CAF), Male Adult voXel (MAX), and Female Adult voXel (FAX) models by comparing the masses of various tissues to the reference values specified by the International Commission on Radiological Protection (ICRP). Major discrepancies are found between the CAM and CAF tissue masses and the ICRP reference data for almost all of the tissues. We next examine the distribution of target points used with the deterministic transport code HZETRN to compute mass averaged exposure quantities. A numerical algorithm is used to generate multiple point distributions for many of the effective dose tissues identified in CAM, CAF, MAX, and FAX. It is concluded that the previously published CAM and CAF point distributions were under-sampled and that the set of point distributions presented here should be adequate for future studies involving CAM, CAF, MAX, or FAX. It is concluded that MAX and FAX are more accurate than CAM and CAF for space radiation analyses.

Analysis of a new phase and height algorithm in phase measurement profilometry

NASA Astrophysics Data System (ADS)

Bian, Xintian; Zuo, Fen; Cheng, Ju

2018-04-01

Traditional phase measurement profilometry adopts divergent illumination to obtain the height distribution of a measured object accurately. However, the mapping relation between reference plane coordinates and phase distribution must be calculated before measurement. Data are then stored in a computer in the form of a data sheet for standby applications. This study improved the distribution of projected fringes and deducted the phase-height mapping algorithm when the two pupils of the projection and imaging systems are of unequal heights and when the projection and imaging axes are on different planes. With the algorithm, calculating the mapping relation between reference plane coordinates and phase distribution prior to measurement is unnecessary. Thus, the measurement process is simplified, and the construction of an experimental system is made easy. Computer simulation and experimental results confirm the effectiveness of the method.

Construction of Reference Data for Tissue Characterization of Arterial Wall Based on Elasticity Images

NASA Astrophysics Data System (ADS)

Inagaki, Jun; Hasegawa, Hideyuki; Kanai, Hiroshi; Ichiki, Masataka; Tezuka, Fumiaki

2005-06-01

Previously, we developed the phased tracking method [H. Kanai et al.: IEEE Trans. Ultrason. Ferroelectr. Freq. Control 43 (1996) 791] for measuring the minute change in thickness during one heartbeat and the elasticity of the arterial wall. By comparing pathological images with elasticity images measured with ultrasound, elasticity distributions for respective tissues in the arterial wall were determined. We have already measured the elasticity distributions for lipids and fibrous tissues (mixtures of smooth-muscle and collagen fiber) [H. Kanai et al.: Circulation 107 (2003) 3018]. In this study, elasticity distributions were measured for blood clots and calcified tissues. We discuss whether these elasticity distributions, which were measuerd in vitro, can be used as reference data for classifying cross-sectional elasticity images measured in vivo into respective tissues. In addition to the measurement of elasticity distributions, correlations between collagen content and elasticity were investigated with respect to fibrous tissue to estimate the collagen and smooth-muscle content based on elasticity. Collagen and smooth-muscle content may be important factors in determining the stability of the fibrous cap of atherosclerotic plaque. Therefore, correlations between elasticity and elements of the tissue in the arterial wall may provide useful information for the noninvasive diagnosis of plaque vulnerability.

Reference tissue quantification of DCE-MRI data without a contrast agent calibration

NASA Astrophysics Data System (ADS)

Walker-Samuel, Simon; Leach, Martin O.; Collins, David J.

2007-02-01

The quantification of dynamic contrast-enhanced (DCE) MRI data conventionally requires a conversion from signal intensity to contrast agent concentration by measuring a change in the tissue longitudinal relaxation rate, R1. In this paper, it is shown that the use of a spoiled gradient-echo acquisition sequence (optimized so that signal intensity scales linearly with contrast agent concentration) in conjunction with a reference tissue-derived vascular input function (VIF), avoids the need for the conversion to Gd-DTPA concentration. This study evaluates how to optimize such sequences and which dynamic time-series parameters are most suitable for this type of analysis. It is shown that signal difference and relative enhancement provide useful alternatives when full contrast agent quantification cannot be achieved, but that pharmacokinetic parameters derived from both contain sources of error (such as those caused by differences between reference tissue and region of interest proton density and native T1 values). It is shown in a rectal cancer study that these sources of uncertainty are smaller when using signal difference, compared with relative enhancement (15 ± 4% compared with 33 ± 4%). Both of these uncertainties are of the order of those associated with the conversion to Gd-DTPA concentration, according to literature estimates.

Determination of perfluorinated alkyl acid concentrations in biological standard reference materials.

PubMed

Reiner, Jessica L; O'Connell, Steven G; Butt, Craig M; Mabury, Scott A; Small, Jeff M; De Silva, Amila O; Muir, Derek C G; Delinsky, Amy D; Strynar, Mark J; Lindstrom, Andrew B; Reagen, William K; Malinsky, Michelle; Schäfer, Sandra; Kwadijk, Christiaan J A F; Schantz, Michele M; Keller, Jennifer M

2012-11-01

Standard reference materials (SRMs) are homogeneous, well-characterized materials used to validate measurements and improve the quality of analytical data. The National Institute of Standards and Technology (NIST) has a wide range of SRMs that have mass fraction values assigned for legacy pollutants. These SRMs can also serve as test materials for method development, method validation, and measurement for contaminants of emerging concern. Because inter-laboratory comparison studies have revealed substantial variability of measurements of perfluoroalkyl acids (PFAAs), future analytical measurements will benefit from determination of consensus values for PFAAs in SRMs to provide a means to demonstrate method-specific performance. To that end, NIST, in collaboration with other groups, has been measuring concentrations of PFAAs in a variety of SRMs. Here we report levels of PFAAs and perfluorooctane sulfonamide (PFOSA) determined in four biological SRMs: fish tissue (SRM 1946 Lake Superior Fish Tissue, SRM 1947 Lake Michigan Fish Tissue), bovine liver (SRM 1577c), and mussel tissue (SRM 2974a). We also report concentrations for three in-house quality-control materials: beluga whale liver, pygmy sperm whale liver, and white-sided dolphin liver. Measurements in SRMs show an array of PFAAs, with perfluorooctane sulfonate (PFOS) being the most frequently detected. Reference and information values are reported for PFAAs measured in these biological SRMs.

Evaluation of normalized metal artifact reduction (NMAR) in kVCT using MVCT prior images for radiotherapy treatment planning.

PubMed

Paudel, M R; Mackenzie, M; Fallone, B G; Rathee, S

2013-08-01

To evaluate the metal artifacts in kilovoltage computed tomography (kVCT) images that are corrected using a normalized metal artifact reduction (NMAR) method with megavoltage CT (MVCT) prior images. Tissue characterization phantoms containing bilateral steel inserts are used in all experiments. Two MVCT images, one without any metal artifact corrections and the other corrected using a modified iterative maximum likelihood polychromatic algorithm for CT (IMPACT) are translated to pseudo-kVCT images. These are then used as prior images without tissue classification in an NMAR technique for correcting the experimental kVCT image. The IMPACT method in MVCT included an additional model for the pair∕triplet production process and the energy dependent response of the MVCT detectors. An experimental kVCT image, without the metal inserts and reconstructed using the filtered back projection (FBP) method, is artificially patched with the known steel inserts to get a reference image. The regular NMAR image containing the steel inserts that uses tissue classified kVCT prior and the NMAR images reconstructed using MVCT priors are compared with the reference image for metal artifact reduction. The Eclipse treatment planning system is used to calculate radiotherapy dose distributions on the corrected images and on the reference image using the Anisotropic Analytical Algorithm with 6 MV parallel opposed 5×10 cm2 fields passing through the bilateral steel inserts, and the results are compared. Gafchromic film is used to measure the actual dose delivered in a plane perpendicular to the beams at the isocenter. The streaking and shading in the NMAR image using tissue classifications are significantly reduced. However, the structures, including metal, are deformed. Some uniform regions appear to have eroded from one side. There is a large variation of attenuation values inside the metal inserts. Similar results are seen in commercially corrected image. Use of MVCT prior images without tissue classification in NMAR significantly reduces these problems. The radiation dose calculated on the reference image is close to the dose measured using the film. Compared to the reference image, the calculated dose difference in the conventional NMAR image, the corrected images using uncorrected MVCT image, and IMPACT corrected MVCT image as priors is ∼15.5%, ∼5%, and ∼2.7%, respectively, at the isocenter. The deformation and erosion of the structures present in regular NMAR corrected images can be largely reduced by using MVCT priors without tissue segmentation. The attenuation value of metal being incorrect, large dose differences relative to the true value can result when using the conventional NMAR image. This difference can be significantly reduced if MVCT images are used as priors. Reduced tissue deformation, better tissue visualization, and correct information about the electron density of the tissues and metals in the artifact corrected images could help delineate the structures better, as well as calculate radiation dose more correctly, thus enhancing the quality of the radiotherapy treatment planning.

Evaluation on penetration rate of cloud for incoming solar radiation using geostationary satellite data

NASA Astrophysics Data System (ADS)

Yeom, Jong-Min; Han, Kyung-Soo; Kim, Jae-Jin

2012-05-01

Solar surface insolation (SSI) represents how much solar radiance reaches the Earth's surface in a specified area and is an important parameter in various fields such as surface energy research, meteorology, and climate change. This study calculates insolation using Multi-functional Transport Satellite (MTSAT-1R) data with a simplified cloud factor over Northeast Asia. For SSI retrieval from the geostationary satellite data, the physical model of Kawamura is modified to improve insolation estimation by considering various atmospheric constituents, such as Rayleigh scattering, water vapor, ozone, aerosols, and clouds. For more accurate atmospheric parameterization, satellite-based atmospheric constituents are used instead of constant values when estimating insolation. Cloud effects are a key problem in insolation estimation because of their complicated optical characteristics and high temporal and spatial variation. The accuracy of insolation data from satellites depends on how well cloud attenuation as a function of geostationary channels and angle can be inferred. This study uses a simplified cloud factor that depends on the reflectance and solar zenith angle. Empirical criteria to select reference data for fitting to the ground station data are applied to suggest simplified cloud factor methods. Insolation estimated using the cloud factor is compared with results of the unmodified physical model and with observations by ground-based pyranometers located in the Korean peninsula. The modified model results show far better agreement with ground truth data compared to estimates using the conventional method under overcast conditions.

Analytic Guidance for the First Entry in a Skip Atmospheric Entry

NASA Technical Reports Server (NTRS)

Garcia-Llama, Eduardo

2007-01-01

This paper presents an analytic method to generate a reference drag trajectory for the first entry portion of a skip atmospheric entry. The drag reference, expressed as a polynomial function of the velocity, will meet the conditions necessary to fit the requirements of the complete entry phase. The generic method proposed to generate the drag reference profile is further simplified by thinking of the drag and the velocity as density and cumulative distribution functions respectively. With this notion it will be shown that the reference drag profile can be obtained by solving a linear algebraic system of equations. The resulting drag profile is flown using the feedback linearization method of differential geometric control as guidance law with the error dynamics of a second order homogeneous equation in the form of a damped oscillator. This approach was first proposed as a revisited version of the Space Shuttle Orbiter entry guidance. However, this paper will show that it can be used to fly the first entry in a skip entry trajectory. In doing so, the gains in the error dynamics will be changed at a certain point along the trajectory to improve the tracking performance.

Identification of Reference Genes for Normalizing Quantitative Real-Time PCR in Urechis unicinctus

NASA Astrophysics Data System (ADS)

Bai, Yajiao; Zhou, Di; Wei, Maokai; Xie, Yueyang; Gao, Beibei; Qin, Zhenkui; Zhang, Zhifeng

2018-06-01

The reverse transcription quantitative real-time PCR (RT-qPCR) has become one of the most important techniques of studying gene expression. A set of valid reference genes are essential for the accurate normalization of data. In this study, five candidate genes were analyzed with geNorm, NormFinder, BestKeeper and ΔCt methods to identify the genes stably expressed in echiuran Urechis unicinctus, an important commercial marine benthic worm, under abiotic (sulfide stress) and normal (adult tissues, embryos and larvae at different development stages) conditions. The comprehensive results indicated that the expression of TBP was the most stable at sulfide stress and in developmental process, while the expression of EF- 1- α was the most stable at sulfide stress and in various tissues. TBP and EF- 1- α were recommended as a suitable reference gene combination to accurately normalize the expression of target genes at sulfide stress; and EF- 1- α, TBP and TUB were considered as a potential reference gene combination for normalizing the expression of target genes in different tissues. No suitable gene combination was obtained among these five candidate genes for normalizing the expression of target genes for developmental process of U. unicinctus. Our results provided a valuable support for quantifying gene expression using RT-qPCR in U. unicinctus.

Mammalian monoamine-oxidizing enzymes, with special reference to benzylamine oxidase in human tissues.

PubMed

Lewinsohn, R

1984-01-01

A review is presented of the monoamine-oxidizing enzymes with special reference to the activity of benzylamine oxidase (BzAO) in human tissues. Methods of study of amine oxidases, properties (chiefly of BzAO) and some problems concerning substrate and inhibitor specificity and multiple forms of monoamine oxidase (MAO) are surveyed. The substrate specificity of human plasma BzAO is compared with that of amine-oxidizing enzymes in plasma or serum of other species. Correlations of plasma BzAO and platelet MAO activity with clinical findings are discussed. The distribution of amine oxidase activities in solid human tissues is reviewed, in particular BzAO in blood vessels and richly-vascularized tissues, as well as kinetic constants and altered patterns of activity of BzAO in human atherosclerosis. Activities of the amine oxidases in non-vascular smooth muscle, in cultured cells, and in various tissues related to human gestation, are discussed. The present knowledge of BzAO is discussed in terms of its possible clinical relevance to several human disease states, and the importance of the enzyme in the human body.

PET brain kinetics studies of 11C-ITMM and 11C-ITDM,radioprobes for metabotropic glutamate receptor type 1, in a nonhuman primate

PubMed Central

Yamasaki, Tomoteru; Maeda, Jun; Fujinaga, Masayuki; Nagai, Yuji; Hatori, Akiko; Yui, Joji; Xie, Lin; Nengaki, Nobuki; Zhang, Ming-Rong

2014-01-01

The metabotropic glutamate receptor type 1 (mGluR1) is a novel target protein for the development of new drugs against central nervous system disorders. Recently, we have developed 11C-labeled PET probes 11C-ITMM and 11C-ITDM, which demonstrate similar profiles, for imaging of mGluR1. In the present study, we compared 11C-ITMM and 11C-ITDM PET imaging and quantitative analysis in the monkey brain. Respective PET images showed similar distribution of uptake in the cerebellum, thalamus, and cingulate cortex. Slightly higher uptake was detected with 11C-ITDM than with 11C-ITMM. For the kinetic analysis using the two-tissue compartment model (2-TCM), the distribution volume (VT) in the cerebellum, an mGluR1-rich region in the brain, was 2.5 mL∙cm-3 for 11C-ITMM and 3.6 mL∙cm-3 for 11C-ITDM. By contrast, the VT in the pons, a region with negligible mGluR1 expression, was similarly low for both radiopharmaceuticals. Based on these results, we performed noninvasive PET quantitative analysis with general reference tissue models using the time-activity curve of the pons as a reference region. We confirmed the relationship and differences between the reference tissue models and 2-TCM using correlational scatter plots and Bland-Altman plots analyses. Although the scattergrams of both radiopharmaceuticals showed over- or underestimations of reference tissue model-based the binding potentials against 2-TCM, there were no significant differences between the two kinetic analysis models. In conclusion, we first demonstrated the potentials of 11C-ITMM and 11C-ITDM for noninvasive PET quantitative analysis using reference tissue models. In addition, our findings suggest that 11C-ITDM may be superior to 11C-ITMM as a PET probe for imaging of mGluR1, because regional VT values in PET with 11C-ITDM were higher than those of 11C-ITMM. Clinical studies of 11C-ITDM in humans will be necessary in the future. PMID:24795840

PET brain kinetics studies of (11)C-ITMM and (11)C-ITDM,radioprobes for metabotropic glutamate receptor type 1, in a nonhuman primate.

PubMed

Yamasaki, Tomoteru; Maeda, Jun; Fujinaga, Masayuki; Nagai, Yuji; Hatori, Akiko; Yui, Joji; Xie, Lin; Nengaki, Nobuki; Zhang, Ming-Rong

2014-01-01

The metabotropic glutamate receptor type 1 (mGluR1) is a novel target protein for the development of new drugs against central nervous system disorders. Recently, we have developed (11)C-labeled PET probes (11)C-ITMM and (11)C-ITDM, which demonstrate similar profiles, for imaging of mGluR1. In the present study, we compared (11)C-ITMM and (11)C-ITDM PET imaging and quantitative analysis in the monkey brain. Respective PET images showed similar distribution of uptake in the cerebellum, thalamus, and cingulate cortex. Slightly higher uptake was detected with (11)C-ITDM than with (11)C-ITMM. For the kinetic analysis using the two-tissue compartment model (2-TCM), the distribution volume (VT) in the cerebellum, an mGluR1-rich region in the brain, was 2.5 mL∙cm(-3) for (11)C-ITMM and 3.6 mL∙cm(-3) for (11)C-ITDM. By contrast, the VT in the pons, a region with negligible mGluR1 expression, was similarly low for both radiopharmaceuticals. Based on these results, we performed noninvasive PET quantitative analysis with general reference tissue models using the time-activity curve of the pons as a reference region. We confirmed the relationship and differences between the reference tissue models and 2-TCM using correlational scatter plots and Bland-Altman plots analyses. Although the scattergrams of both radiopharmaceuticals showed over- or underestimations of reference tissue model-based the binding potentials against 2-TCM, there were no significant differences between the two kinetic analysis models. In conclusion, we first demonstrated the potentials of (11)C-ITMM and (11)C-ITDM for noninvasive PET quantitative analysis using reference tissue models. In addition, our findings suggest that (11)C-ITDM may be superior to (11)C-ITMM as a PET probe for imaging of mGluR1, because regional VT values in PET with (11)C-ITDM were higher than those of (11)C-ITMM. Clinical studies of (11)C-ITDM in humans will be necessary in the future.

Widespread abnormality of the γ-aminobutyric acid-ergic system in Tourette syndrome

PubMed Central

Bagic, Anto; Simmons, Janine M.; Mari, Zoltan; Bonne, Omer; Xu, Ben; Kazuba, Diane; Herscovitch, Peter; Carson, Richard E.; Murphy, Dennis L.; Drevets, Wayne C.; Hallett, Mark

2012-01-01

Dysfunction of the γ-aminobutyric acid-ergic system in Tourette syndrome may conceivably underlie the symptoms of motor disinhibition presenting as tics and psychiatric manifestations, such as attention deficit hyperactivity disorder and obsessive–compulsive disorder. The purpose of this study was to identify a possible dysfunction of the γ-aminobutyric acid-ergic system in Tourette patients, especially involving the basal ganglia-thalamo-cortical circuits and the cerebellum. We studied 11 patients with Tourette syndrome and 11 healthy controls. Positron emission tomography procedure: after injection of 20 mCi of [11C]flumazenil, dynamic emission images of the brain were acquired. Structural magnetic resonance imaging scans were obtained to provide an anatomical framework for the positron emission tomography data analysis. Images of binding potential were created using the two-step version of the simplified reference tissue model. The binding potential images then were spatially normalized, smoothed and compared between groups using statistical parametric mapping. We found decreased binding of GABAA receptors in Tourette patients bilaterally in the ventral striatum, globus pallidus, thalamus, amygdala and right insula. In addition, the GABAA receptor binding was increased in the bilateral substantia nigra, left periaqueductal grey, right posterior cingulate cortex and bilateral cerebellum. These results are consistent with the longstanding hypothesis that circuits involving the basal ganglia and thalamus are disinhibited in Tourette syndrome patients. In addition, the abnormalities in GABAA receptor binding in the insula and cerebellum appear particularly noteworthy based upon recent evidence implicating these structures in the generation of tics. PMID:22577221

Investigation of injection dose and camera integration time on quantifying pharmacokinetics of a Cy5.5-GX1 probe with dynamic fluorescence imaging in vivo

NASA Astrophysics Data System (ADS)

Dai, Yunpeng; Chen, Xueli; Yin, Jipeng; Kang, Xiaoyu; Wang, Guodong; Zhang, Xianghan; Nie, Yongzhan; Wu, Kaichun; Liang, Jimin

2016-08-01

The aim of this article is to investigate the influence of a tracer injection dose (ID) and camera integration time (IT) on quantifying pharmacokinetics of Cy5.5-GX1 in gastric cancer BGC-823 cell xenografted mice. Based on three factors, including whether or not to inject free GX1, the ID of Cy5.5-GX1, and the camera IT, 32 mice were randomly divided into eight groups and received 60-min dynamic fluorescence imaging. Gurfinkel exponential model (GEXPM) and Lammertsma simplified reference tissue model (SRTM) combined with a singular value decomposition analysis were used to quantitatively analyze the acquired dynamic fluorescent images. The binding potential (Bp) and the sum of the pharmacokinetic rate constants (SKRC) of Cy5.5-GX1 were determined by the SRTM and EXPM, respectively. In the tumor region, the SKRC value exhibited an obvious trend with change in the tracer ID, but the Bp value was not sensitive to it. Both the Bp and SKRC values were independent of the camera IT. In addition, the ratio of the tumor-to-muscle region was correlated with the camera IT but was independent of the tracer ID. Dynamic fluorescence imaging in conjunction with a kinetic analysis may provide more quantitative information than static fluorescence imaging, especially for a priori information on the optimal ID of targeted probes for individual therapy.

A Nth-order linear algorithm for extracting diffuse correlation spectroscopy blood flow indices in heterogeneous tissues.

PubMed

Shang, Yu; Yu, Guoqiang

2014-09-29

Conventional semi-infinite analytical solutions of correlation diffusion equation may lead to errors when calculating blood flow index (BFI) from diffuse correlation spectroscopy (DCS) measurements in tissues with irregular geometries. Very recently, we created an algorithm integrating a N th-order linear model of autocorrelation function with the Monte Carlo simulation of photon migrations in homogenous tissues with arbitrary geometries for extraction of BFI (i.e., αD B ). The purpose of this study is to extend the capability of the N th-order linear algorithm for extracting BFI in heterogeneous tissues with arbitrary geometries. The previous linear algorithm was modified to extract BFIs in different types of tissues simultaneously through utilizing DCS data at multiple source-detector separations. We compared the proposed linear algorithm with the semi-infinite homogenous solution in a computer model of adult head with heterogeneous tissue layers of scalp, skull, cerebrospinal fluid, and brain. To test the capability of the linear algorithm for extracting relative changes of cerebral blood flow (rCBF) in deep brain, we assigned ten levels of αD B in the brain layer with a step decrement of 10% while maintaining αD B values constant in other layers. Simulation results demonstrate the accuracy (errors < 3%) of high-order ( N  ≥ 5) linear algorithm in extracting BFIs in different tissue layers and rCBF in deep brain. By contrast, the semi-infinite homogenous solution resulted in substantial errors in rCBF (34.5% ≤ errors ≤ 60.2%) and BFIs in different layers. The N th-order linear model simplifies data analysis, thus allowing for online data processing and displaying. Future study will test this linear algorithm in heterogeneous tissues with different levels of blood flow variations and noises.

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

PubMed

Legeai, Fabrice; Gimenez, Sylvie; Duvic, Bernard; Escoubas, Jean-Michel; Gosselin Grenet, Anne-Sophie; Blanc, Florence; Cousserans, François; Séninet, Imène; Bretaudeau, Anthony; Mutuel, Doriane; Girard, Pierre-Alain; Monsempes, Christelle; Magdelenat, Ghislaine; Hilliou, Frédérique; Feyereisen, René; Ogliastro, Mylène; Volkoff, Anne-Nathalie; Jacquin-Joly, Emmanuelle; d'Alençon, Emmanuelle; Nègre, Nicolas; Fournier, Philippe

2014-08-23

Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and grass. In addition, the Sf9 cell line, widely used in biochemistry for in vitro protein production, is derived from S. frugiperda tissues. Many research groups are using S. frugiperda as a model organism to investigate questions such as plant adaptation, pest behavior or resistance to pesticides. In this study, we constructed a reference transcriptome assembly (Sf_TR2012b) of RNA sequences obtained from more than 35 S. frugiperda developmental time-points and tissue samples. We assessed the quality of this reference transcriptome by annotating a ubiquitous gene family--ribosomal proteins--as well as gene families that have a more constrained spatio-temporal expression and are involved in development, immunity and olfaction. We also provide a time-course of expression that we used to characterize the transcriptional regulation of the gene families studied. We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome. While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts. That allowed us to explore the spatial and temporal expression of genes and to observe that some olfactory receptors are expressed in antennae and palps but also in other non related tissues such as fat bodies. Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

A Simplified, Low-Cost Method for Polarized Light Microscopy

PubMed Central

Maude, Richard J.; Buapetch, Wanchana; Silamut, Kamolrat

2009-01-01

Malaria pigment is an intracellular inclusion body that appears in blood and tissue specimens on microscopic examination and can help in establishing the diagnosis of malaria. In simple light microscopy, it can be difficult to discern from cellular background and artifacts. It has long been known that if polarized light microscopy is used, malaria pigment can be much easier to distinguish. However, this technique is rarely used because of the need for a relatively costly polarization microscope. We describe a simple and economical technique to convert any standard light microscope suitable for examination of malaria films into a polarization microscope. PMID:19861611

A Guideline to Family-Wide Comparative State-of-the-Art Quantitative RT-PCR Analysis Exemplified with a Brassicaceae Cross-Species Seed Germination Case Study[W][OA

PubMed Central

Graeber, Kai; Linkies, Ada; Wood, Andrew T.A.; Leubner-Metzger, Gerhard

2011-01-01

Comparative biology includes the comparison of transcriptome and quantitative real-time RT-PCR (qRT-PCR) data sets in a range of species to detect evolutionarily conserved and divergent processes. Transcript abundance analysis of target genes by qRT-PCR requires a highly accurate and robust workflow. This includes reference genes with high expression stability (i.e., low intersample transcript abundance variation) for correct target gene normalization. Cross-species qRT-PCR for proper comparative transcript quantification requires reference genes suitable for different species. We addressed this issue using tissue-specific transcriptome data sets of germinating Lepidium sativum seeds to identify new candidate reference genes. We investigated their expression stability in germinating seeds of L. sativum and Arabidopsis thaliana by qRT-PCR, combined with in silico analysis of Arabidopsis and Brassica napus microarray data sets. This revealed that reference gene expression stability is higher for a given developmental process between distinct species than for distinct developmental processes within a given single species. The identified superior cross-species reference genes may be used for family-wide comparative qRT-PCR analysis of Brassicaceae seed germination. Furthermore, using germinating seeds, we exemplify optimization of the qRT-PCR workflow for challenging tissues regarding RNA quality, transcript stability, and tissue abundance. Our work therefore can serve as a guideline for moving beyond Arabidopsis by establishing high-quality cross-species qRT-PCR. PMID:21666000

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.

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

PubMed

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

2014-04-01

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

Evaluation of DNA damage induced by gamma radiation in gill and muscle tissues of Cyprinus carpio and their relative sensitivity.

PubMed

M K, Praveen Kumar; Shyama, Soorambail K; D'Costa, Avelyno; Kadam, Samit B; Sonaye, Bhagatsingh Harisingh; Chaubey, Ramesh Chandra

2017-10-01

The effect of radiation on the aquatic environment is of major concern in recent years. Limited data is available on the genotoxicity of gamma radiation on different tissues of aquatic organisms. Hence, the present investigation was carried out to study the DNA damage induced by gamma radiation in the gill and muscle tissues and their relative sensitivity using the comet assay in the freshwater teleost fish, common carp (Cyprinus carpio). The comet assay was optimized and validated in common carp using cyclophosphamide (CP), a reference genotoxic agent. The fish were exposed (acute) to various doses of gamma radiation (2, 4, 6, 8 and 10Gy) and samplings (gill and muscle tissue) were done at regular intervals (24, 48 and 72h) to assess the DNA damage. A significant increase in DNA damage was observed as indicated by an increase in % tail DNA for all doses of gamma radiation in both tissues. We also observed a dose-related increase and a time-dependent decrease of DNA damage. In comparison, DNA damage showed different sensitivity among the tissues at different doses. This shows that a particular dose may have different effects on different tissues which could be due to physiological factors of the particular tissue. Our study also suggests that the gills and muscle of fish are sensitive and reliable tissues for evaluating the genotoxic effects of reference and environmental agents, using the comet assay. Copyright © 2017. Published by Elsevier Inc.

Immunomagnetic separation can enrich fixed solid tumors for epithelial cells.

PubMed

Yaremko, M L; Kelemen, P R; Kutza, C; Barker, D; Westbrook, C A

1996-01-01

Immunomagnetic separation is a highly specific technique for the enrichment or isolation of cells from a variety of fresh tissues and microorganisms or molecules from suspensions. Because new techniques for molecular analysis of solid tumors are now applicable to fixed tissue but sometimes require or benefit from enrichment for tumor cells, we tested the efficacy of immunomagnetic separation for enriching fixed solid tumors for malignant epithelial cells. We applied it to two different tumors and fixation methods to separate neoplastic from non-neoplastic cells in primary colorectal cancers and metastatic breast cancers, and were able to enrich to a high degree of purity. Immunomagnetic separation was effective in unembedded fixed tissue as well as fixed paraffin-embedded tissue. The magnetically separated cells were amenable to fluorescence in situ hybridization and polymerase chain reaction amplification of their DNA with minimal additional manipulation. The high degree of enrichment achieved before amplification contributed to interpretation of loss of heterozygosity in metastatic breast cancers, and simplified fluorescence in situ hybridization analysis because only neoplastic cells were hybridized and counted. Immunomagnetic separation is effective for the enrichment of fixed solid tumors, can be performed with widely available commercial antibodies, and requires little specialized instrumentation. It can contribute to interpretation of results in situations where enrichment by other methods is difficult or not possible.

Managing tissue bank access to the OR for tissue recovery.

PubMed

Trim, Robert S

2011-08-01

Hospitals often have tissue recovery service agreements with regional tissue banks to facilitate the donation process. The agreements that outline the tissue bank-hospital relationship frequently allow tissue bank personnel to perform tissue recovery procedures in the referring hospital's OR and may or may not specify any preparatory orientation or any written protocols for tissue bank staff members to follow. This creates the potential for unintentional breaches of protocol that can affect operation of equipment or result in contamination that may put surgical patients and staff members at risk. The OR manager is responsible for establishing appropriate orientation plans for tissue bank employees to ensure they understand and adhere to the hospital's protocols. Copyright © 2011 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Korean anatomical reference data for adults for use in radiological protection

NASA Astrophysics Data System (ADS)

Choi, Chansoo; Yeom, Yeon Soo; Nguyen, Thang Tat; Lee, Hanjin; Han, Haegin; Shin, Bangho; Zhang, Xujia; Kim, Chan Hyeong; Chung, Beom Sun

2018-01-01

For radiological protection from exposure to ionizing radiation, in which a population-averaged dose evaluation is used, establishing a system of reference anatomical and physiological data for a specific population of interest is important. Some studies were done in the past to establish Korean reference data; however, the data provided the mass values only for a limited number of organs/tissues. In addition, the standing height and total body mass are based on 20-year-old data. In the present study, a new set of Korean reference anatomical values was established for use in the radiological protection of Korean workers and members of the public. The established Korean reference data provide the masses of 58 organs/tissues, including those needed to calculate the effective dose, which were derived by collecting and analyzing various scientific reports in the literature and data. In addition, the data provide not only standing height and total body mass, but also 131 additional anthropometric parameters; these values were derived from the most recent Korean national survey project, 7 th Size Korea. The characteristics of the data were also compared with several other population data, including the Asian and the International Commission on Radiological Protection (ICRP) reference data.

Impact of the residential conservation service program on natural gas and electric utilities. Appendix B

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

Not Available

An assessment of the RCS program is provided from the perspective of eleven case study utilities. First, an introduction to the role and value of conservation in utility strategic planning is presented. The interplay of various utility system characteristics is shown to be the primary determinant of the value of conservation efforts from the utility's point of view. Simplified typologies of utilities are developed to aid in the identification of those combinations of the utility characteristics that will favor the adoption of the utility sponsored strategic conservation efforts. The integration of the RCS program with other utility conservation and loadmore » management programs is explored for the eleven case study utilities. Reference is made to the simplified typologies in order to show, through actual program experience, how the strategic position of the utility company affects its adoption of this federal program. Evaluative studies done by the eleven case study utilities of the RCS program are reviewed. Results are presented and the methodologies are critiqued. Conclusions regarding the RCS program from the utility perspective are presented.« less

Optimization of wearable microwave antenna with simplified electromagnetic model of the human body

NASA Astrophysics Data System (ADS)

Januszkiewicz, Łukasz; Barba, Paolo Di; Hausman, Sławomir

2017-12-01

In this paper the problem of optimization design of a microwave wearable antenna is investigated. Reference is made to a specific antenna design that is a wideband Vee antenna the geometry of which is characterized by 6 parameters. These parameters were automatically adjusted with an evolution strategy based algorithm EStra to obtain the impedance matching of the antenna located in the proximity of the human body. The antenna was designed to operate in the ISM (industrial, scientific, medical) band which covers the frequency range of 2.4 GHz up to 2.5 GHz. The optimization procedure used the finite-difference time-domain method based full-wave simulator with a simplified human body model. In the optimization procedure small movements of antenna towards or away of the human body that are likely to happen during real use were considered. The stability of the antenna parameters irrespective of the movements of the user's body is an important factor in wearable antenna design. The optimization procedure allowed obtaining good impedance matching for a given range of antenna distances with respect to the human body.

Erosion estimation of guide vane end clearance in hydraulic turbines with sediment water flow

NASA Astrophysics Data System (ADS)

Han, Wei; Kang, Jingbo; Wang, Jie; Peng, Guoyi; Li, Lianyuan; Su, Min

2018-04-01

The end surface of guide vane or head cover is one of the most serious parts of sediment erosion for high-head hydraulic turbines. In order to investigate the relationship between erosion depth of wall surface and the characteristic parameter of erosion, an estimative method including a simplified flow model and a modificatory erosion calculative function is proposed in this paper. The flow between the end surfaces of guide vane and head cover is simplified as a clearance flow around a circular cylinder with a backward facing step. Erosion characteristic parameter of csws3 is calculated with the mixture model for multiphase flow and the renormalization group (RNG) k-𝜀 turbulence model under the actual working conditions, based on which, erosion depths of guide vane and head cover end surfaces are estimated with a modification of erosion coefficient K. The estimation results agree well with the actual situation. It is shown that the estimative method is reasonable for erosion prediction of guide vane and can provide a significant reference to determine the optimal maintenance cycle for hydraulic turbine in the future.

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions

PubMed Central

Acharya, Kamal R.; Dhand, Navneet K.; Whittington, Richard J.; Plain, Karren M.

2017-01-01

Johne’s disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen’s kappa statistic) and no significant difference to the reference tests (McNemar’s Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption. PMID:29312970

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions.

PubMed

Acharya, Kamal R; Dhand, Navneet K; Whittington, Richard J; Plain, Karren M

2017-01-01

Johne's disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen's kappa statistic) and no significant difference to the reference tests (McNemar's Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption.

Selecting and validating reference genes for quantitative real-time PCR in Plutella xylostella (L.).

PubMed

You, Yanchun; Xie, Miao; Vasseur, Liette; You, Minsheng

2018-05-01

Gene expression analysis provides important clues regarding gene functions, and quantitative real-time PCR (qRT-PCR) is a widely used method in gene expression studies. Reference genes are essential for normalizing and accurately assessing gene expression. In the present study, 16 candidate reference genes (ACTB, CyPA, EF1-α, GAPDH, HSP90, NDPk, RPL13a, RPL18, RPL19, RPL32, RPL4, RPL8, RPS13, RPS4, α-TUB, and β-TUB) from Plutella xylostella were selected to evaluate gene expression stability across different experimental conditions using five statistical algorithms (geNorm, NormFinder, Delta Ct, BestKeeper, and RefFinder). The results suggest that different reference genes or combinations of reference genes are suitable for normalization in gene expression studies of P. xylostella according to the different developmental stages, strains, tissues, and insecticide treatments. Based on the given experimental sets, the most stable reference genes were RPS4 across different developmental stages, RPL8 across different strains and tissues, and EF1-α across different insecticide treatments. A comprehensive and systematic assessment of potential reference genes for gene expression normalization is essential for post-genomic functional research in P. xylostella, a notorious pest with worldwide distribution and a high capacity to adapt and develop resistance to insecticides.

Agreement between diagnoses reached by clinical examination and available reference standards: a prospective study of 216 patients with lumbopelvic pain

PubMed Central

Laslett, Mark; McDonald, Barry; Tropp, Hans; Aprill, Charles N; Öberg, Birgitta

2005-01-01

Background The tissue origin of low back pain (LBP) or referred lower extremity symptoms (LES) may be identified in about 70% of cases using advanced imaging, discography and facet or sacroiliac joint blocks. These techniques are invasive and availability varies. A clinical examination is non-invasive and widely available but its validity is questioned. Diagnostic studies usually examine single tests in relation to single reference standards, yet in clinical practice, clinicians use multiple tests and select from a range of possible diagnoses. There is a need for studies that evaluate the diagnostic performance of clinical diagnoses against available reference standards. Methods We compared blinded clinical diagnoses with diagnoses based on available reference standards for known causes of LBP or LES such as discography, facet, sacroiliac or hip joint blocks, epidurals injections, advanced imaging studies or any combination of these tests. A prospective, blinded validity design was employed. Physiotherapists examined consecutive patients with chronic lumbopelvic pain and/or referred LES scheduled to receive the reference standard examinations. When diagnoses were in complete agreement regardless of complexity, "exact" agreement was recorded. When the clinical diagnosis was included within the reference standard diagnoses, "clinical agreement" was recorded. The proportional chance criterion (PCC) statistic was used to estimate agreement on multiple diagnostic possibilities because it accounts for the prevalence of individual categories in the sample. The kappa statistic was used to estimate agreement on six pathoanatomic diagnoses. Results In a sample of chronic LBP patients (n = 216) with high levels of disability and distress, 67% received a patho-anatomic diagnosis based on available reference standards, and 10% had more than one tissue origin of pain identified. For 27 diagnostic categories and combinations, chance clinical agreement (PCC) was estimated at 13%. "Exact" agreement between clinical and reference standard diagnoses was 32% and "clinical agreement" 51%. For six pathoanatomic categories (disc, facet joint, sacroiliac joint, hip joint, nerve root and spinal stenosis), PCC was 33% with actual agreement 56%. There was no overlap of 95% confidence intervals on any comparison. Diagnostic agreement on the six most common patho-anatomic categories produced a kappa of 0.31. Conclusion Clinical diagnoses agree with reference standards diagnoses more often than chance. Using available reference standards, most patients can have a tissue source of pain identified. PMID:15943873

Methods And Systems For Using Reference Images In Acoustic Image Processing

DOEpatents

Moore, Thomas L.; Barter, Robert Henry

2005-01-04

A method and system of examining tissue are provided in which a field, including at least a portion of the tissue and one or more registration fiducials, is insonified. Scattered acoustic information, including both transmitted and reflected waves, is received from the field. A representation of the field, including both the tissue and the registration fiducials, is then derived from the received acoustic radiation.

An atlas of DNA methylation in diverse bovine tissues

USDA-ARS?s Scientific Manuscript database

We launched an effort to produce a reference cattle DNA methylation resource to improve animal production. We will employ experimental pipelines built around next generation sequencing technologies to map DNA methylation in cultured cells and primary tissues systems frequently involved in animal pro...

FT-IR imaging for quantitative determination of liver fat content in non-alcoholic fatty liver.

PubMed

Kochan, K; Maslak, E; Chlopicki, S; Baranska, M

2015-08-07

In this work we apply FT-IR imaging of large areas of liver tissue cross-section samples (∼5 cm × 5 cm) for quantitative assessment of steatosis in murine model of Non-Alcoholic Fatty Liver (NAFLD). We quantified the area of liver tissue occupied by lipid droplets (LDs) by FT-IR imaging and Oil Red O (ORO) staining for comparison. Two alternative FT-IR based approaches are presented. The first, straightforward method, was based on average spectra from tissues and provided values of the fat content by using a PLS regression model and the reference method. The second one – the chemometric-based method – enabled us to determine the values of the fat content, independently of the reference method by means of k-means cluster (KMC) analysis. In summary, FT-IR images of large size liver sections may prove to be useful for quantifying liver steatosis without the need of tissue staining.

Examining the effects of metal mining mixtures on fathead minnow (Pimephales promelas) using field-based multi-trophic artificial streams.

PubMed

Rozon-Ramilo, Lisa D; Dubé, Monique G; Rickwood, Carrie J; Niyogi, Som

2011-09-01

This study illustrates the use of a mesocosm approach for assessing the independent effects of three treated metal mine effluents (MME) discharging into a common receiving environment and regulated under the same regulation. A field-based, multi-trophic artificial stream study was conducted in August 2008 to assess the effects of three metal mining effluents on fathead minnow (Pimephales promelas) in a 21-day reproduction bioassay. The nature of the approach allowed for assessment of both dietary and waterborne exposure pathways. Elements (e.g. Se, Co, Cl, Cu, Fe) were analyzed in several media (water, sediments) and tissues (biofilm, Chironomus dilutus, female fathead minnow (FHM) body, ovary, liver, gills). Significant increases in metal and micronutrient concentrations were observed in the water and biofilm tissues in all MME treatments [20% surface water effluent (SWE), 30% mine water effluent (MWE), and 45% process water effluent (PWE)], compared to reference. However, copper was the only element to significantly increase in the sediments when exposed to PWE. Co and Ni increased significantly in C. dilutus tissues in SWE (1.4- and 1.5-fold, respectively), Cu and Se also increased in chironomid tissues in PWE (5.2- and 3.3-fold, respectively); however, no significant increases in metals or micronutrients occurred in chironomid tissues when exposed to MWE compared to reference. There were no significant increases in metal concentrations in female FHM tissues (body, liver, gonads, gills) in any of the treatments suggesting that metals were either not bioavailable, lost from the females via the eggs, or naturally regulated through homeostatic mechanisms. Cumulative number of eggs per female per day increased significantly (∼127%) after exposure to SWE and decreased significantly (∼33%) after exposure to PWE when compared to reference. Mean total number of days to hatch was reduced in PWE compared to reference. This study shows the importance of isolating treatment streams in cumulative discharge environments to assess aquatic effects due to the different nature of the effluents. Copyright © 2011 Elsevier Inc. All rights reserved.

Selection and validation of reference genes for quantitative gene expression analyses in various tissues and seeds at different developmental stages in Bixa orellana L.

PubMed

Moreira, Viviane S; Soares, Virgínia L F; Silva, Raner J S; Sousa, Aurizangela O; Otoni, Wagner C; Costa, Marcio G C

2018-05-01

Bixa orellana L., popularly known as annatto, produces several secondary metabolites of pharmaceutical and industrial interest, including bixin, whose molecular basis of biosynthesis remain to be determined. Gene expression analysis by quantitative real-time PCR (qPCR) is an important tool to advance such knowledge. However, correct interpretation of qPCR data requires the use of suitable reference genes in order to reduce experimental variations. In the present study, we have selected four different candidates for reference genes in B. orellana , coding for 40S ribosomal protein S9 (RPS9), histone H4 (H4), 60S ribosomal protein L38 (RPL38) and 18S ribosomal RNA (18SrRNA). Their expression stabilities in different tissues (e.g. flower buds, flowers, leaves and seeds at different developmental stages) were analyzed using five statistical tools (NormFinder, geNorm, BestKeeper, ΔCt method and RefFinder). The results indicated that RPL38 is the most stable gene in different tissues and stages of seed development and 18SrRNA is the most unstable among the analyzed genes. In order to validate the candidate reference genes, we have analyzed the relative expression of a target gene coding for carotenoid cleavage dioxygenase 1 (CCD1) using the stable RPL38 and the least stable gene, 18SrRNA , for normalization of the qPCR data. The results demonstrated significant differences in the interpretation of the CCD1 gene expression data, depending on the reference gene used, reinforcing the importance of the correct selection of reference genes for normalization.

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples.

PubMed

Pine, P S; Boedigheimer, M; Rosenzweig, B A; Turpaz, Y; He, Y D; Delenstarr, G; Ganter, B; Jarnagin, K; Jones, W D; Reid, L H; Thompson, K L

2008-11-01

Effective use of microarray technology in clinical and regulatory settings is contingent on the adoption of standard methods for assessing performance. The MicroArray Quality Control project evaluated the repeatability and comparability of microarray data on the major commercial platforms and laid the groundwork for the application of microarray technology to regulatory assessments. However, methods for assessing performance that are commonly applied to diagnostic assays used in laboratory medicine remain to be developed for microarray assays. A reference system for microarray performance evaluation and process improvement was developed that includes reference samples, metrics and reference datasets. The reference material is composed of two mixes of four different rat tissue RNAs that allow defined target ratios to be assayed using a set of tissue-selective analytes that are distributed along the dynamic range of measurement. The diagnostic accuracy of detected changes in expression ratios, measured as the area under the curve from receiver operating characteristic plots, provides a single commutable value for comparing assay specificity and sensitivity. The utility of this system for assessing overall performance was evaluated for relevant applications like multi-laboratory proficiency testing programs and single-laboratory process drift monitoring. The diagnostic accuracy of detection of a 1.5-fold change in signal level was found to be a sensitive metric for comparing overall performance. This test approaches the technical limit for reliable discrimination of differences between two samples using this technology. We describe a reference system that provides a mechanism for internal and external assessment of laboratory proficiency with microarray technology and is translatable to performance assessments on other whole-genome expression arrays used for basic and clinical research.

Validation of Non-Invasive Tracer Kinetic Analysis of 18F-Florbetaben PET Using a Dual Time-Window Acquisition Protocol.

PubMed

Bullich, Santiago; Barthel, Henryk; Koglin, Norman; Becker, Georg A; De Santi, Susan; Jovalekic, Aleksandar; Stephens, Andrew W; Sabri, Osama

2017-11-24

Accurate amyloid PET quantification is necessary for monitoring amyloid-beta accumulation and response to therapy. Currently, most of the studies are analyzed using the static standardized uptake value ratio (SUVR) approach because of its simplicity. However, this approach may be influenced by changes in cerebral blood flow (CBF) or radiotracer clearance. Full tracer kinetic models require arterial blood sampling and dynamic image acquisition. The objectives of this work were: (1) to validate a non-invasive kinetic modeling approach for 18 F-florbetaben PET using an acquisition protocol with the best compromise between quantification accuracy and simplicity and (2) to assess the impact of CBF changes and radiotracer clearance on SUVRs and non-invasive kinetic modeling data in 18 F-florbetaben PET. Methods: Data from twenty subjects (10 patients with probable Alzheimer's dementia/ 10 healthy volunteers) were used to compare the binding potential (BP ND ) obtained from the full kinetic analysis to the SUVR and to non-invasive tracer kinetic methods (simplified reference tissue model (SRTM), and multilinear reference tissue model 2 (MRTM2)). Different approaches using shortened or interrupted acquisitions were compared to the results of the full acquisition (0-140 min). Simulations were carried out to assess the effect of CBF and radiotracer clearance changes on SUVRs and non-invasive kinetic modeling outputs. Results: A 0-30 and 120-140 min dual time-window acquisition protocol using appropriate interpolation of the missing time points provided the best compromise between patient comfort and quantification accuracy. Excellent agreement was found between BP ND obtained using full and dual time-window (2TW) acquisition protocols (BP ND,2TW =0.01+ 1.00 BP ND,FULL , R2=0.97 (MRTM2); BP ND,2TW = 0.05+ 0.92·BP ND,FULL , R2=0.93 (SRTM)). Simulations showed a limited impact of CBF and radiotracer clearance changes on MRTM parameters and SUVRs. Conclusion: This study demonstrates accurate non-invasive kinetic modeling of 18 F-florbetaben PET data using a dual time-window acquisition protocol, thus providing a good compromise between quantification accuracy, scan duration and patient burden. The influence of CBF and radiotracer clearance changes on amyloid-beta load estimates was small. For most clinical research applications, the SUVR approach is appropriate. However, for longitudinal studies in which a maximum quantification accuracy is desired, this non-invasive dual time-window acquisition protocol and kinetic analysis is recommended. Copyright © 2017 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Patterns of age related changes for phosphodiesterase type-10A in comparison with dopamine D2/3 receptors and sub-cortical volumes in the human basal ganglia: A PET study with 18F-MNI-659 and 11C-raclopride with correction for partial volume effect.

PubMed

Fazio, Patrik; Schain, Martin; Mrzljak, Ladislav; Amini, Nahid; Nag, Sangram; Al-Tawil, Nabil; Fitzer-Attas, Cheryl J; Bronzova, Juliana; Landwehrmeyer, Bernhard; Sampaio, Cristina; Halldin, Christer; Varrone, Andrea

2017-05-15

Phosphodiesterase 10A enzyme (PDE10A) is an important striatal target that has been shown to be affected in patients with neurodegenerative disorders, particularly Huntington´s disease (HD). PDE10A is expressed on striatal neurones in basal ganglia where other known molecular targets are enriched such as dopamine D 2/3 receptors (D 2/3 R). The aim of this study was to examine the availability of PDE10A enzyme in relation with age and gender and to compare those changes with those related to D 2/3 R and volumes in different regions of the basal ganglia. As a secondary objective we examined the relative distribution of D 2/3 R and PDE10A enzyme in the striatum and globus pallidus. Forty control subjects (20F/20M; age: 44±11y, age range 27-69) from an ongoing positron emission tomography (PET) study in HD gene expansion carriers were included. Subjects were examined with PET using the high-resolution research tomograph (HRRT) and with 3T magnetic resonance imaging (MRI). The PDE10A radioligand 18 F-MNI-659 and D 2/3 R radioligand 11 C-raclopride were used. The outcome measure was the binding potential (BP ND ) estimated with the two-tissue compartment model ( 18 F-MNI-659) and the simplified reference tissue model ( 11 C-raclopride) using the cerebellum as reference region. The PET data were corrected for partial volume effects. In the striatum, PDE10A availability showed a significant age-related decline that was larger compared to the age-related decline of D 2/3 R availability and to the age-related decline of volumes measured with MRI. In the globus pallidus, a less pronounced decline of PDE10A availability was observed, whereas D 2/3 R availability and volumes seemed to be rather stable with aging. The distribution of the PDE10A enzyme was different from the distribution of D 2/3 R, with higher availability in the globus pallidus. These results indicate that aging is associated with a considerable physiological reduction of the availability of PDE10A enzyme in the striatum. Moreover as result of the analysis, in the striatum for both the molecular targets, we observed a gender effect with higher BP ND the female group. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

PubMed Central

Salem, Mohamed; Paneru, Bam; Al-Tobasei, Rafet; Abdouni, Fatima; Thorgaard, Gary H.; Rexroad, Caird E.; Yao, Jianbo

2015-01-01

Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of ~1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000–32,000 genes (35–71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome. PMID:25793877

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.

[Role of chronic inflammation in adipose tissue in the pathophysiology of obesity].

PubMed

Suganami, Takayoshi; Ogawa, Yoshihiro

2013-02-01

Obesity may be viewed as a chronic low-grade inflammatory disease as well as a metabolic disease. Evidence has accumulated suggesting that chronic inflammation in adipose tissue leads to dramatic changes in number and cell type of stromal cells during the course of obesity, which is referred to as"adipose tissue remodeling". Among stromal cells, macrophages in obese adipose tissue are considered to be crucial for adipose tissue inflammation, which results in dysregulated adipocytokine production and ectopic fat accumulation. Understanding the molecular mechanism underlying adipose tissue inflammation would contribute to the identification of novel therapeutic strategies to prevent or treat obesity-induced metabolic derangements.

TH-CD-202-05: DECT Based Tissue Segmentation as Input to Monte Carlo Simulations for Proton Treatment Verification Using PET Imaging

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

Berndt, B; Wuerl, M; Dedes, G

Purpose: To improve agreement of predicted and measured positron emitter yields in patients, after proton irradiation for PET-based treatment verification, using a novel dual energy CT (DECT) tissue segmentation approach, overcoming known deficiencies from single energy CT (SECT). Methods: DECT head scans of 5 trauma patients were segmented and compared to existing decomposition methods with a first focus on the brain. For validation purposes, three brain equivalent solutions [water, white matter (WM) and grey matter (GM) – equivalent with respect to their reference carbon and oxygen contents and CT numbers at 90kVp and 150kVp] were prepared from water, ethanol, sucrosemore » and salt. The activities of all brain solutions, measured during a PET scan after uniform proton irradiation, were compared to Monte Carlo simulations. Simulation inputs were various solution compositions obtained from different segmentation approaches from DECT, SECT scans, and known reference composition. Virtual GM solution salt concentration corrections were applied based on DECT measurements of solutions with varying salt concentration. Results: The novel tissue segmentation showed qualitative improvements in %C for patient brain scans (ground truth unavailable). The activity simulations based on reference solution compositions agree with the measurement within 3–5% (4–8Bq/ml). These reference simulations showed an absolute activity difference between WM (20%C) and GM (10%C) to H2O (0%C) of 43 Bq/ml and 22 Bq/ml, respectively. Activity differences between reference simulations and segmented ones varied from −6 to 1 Bq/ml for DECT and −79 to 8 Bq/ml for SECT. Conclusion: Compared to the conventionally used SECT segmentation, the DECT based segmentation indicates a qualitative and quantitative improvement. In controlled solutions, a MC input based on DECT segmentation leads to better agreement with the reference. Future work will address the anticipated improvement of quantification accuracy in patients, comparing different tissue decomposition methods with an MR brain segmentation. Acknowledgement: DFG-MAP and HIT-Heidelberg Deutsche Forschungsgemeinschaft (MAP); Bundesministerium fur Bildung und Forschung (01IB13001)« less

Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Helicoverpa armigera (Lepidoptera: Noctuidae).

PubMed

Zhang, Songdou; An, Shiheng; Li, Zhen; Wu, Fengming; Yang, Qingpo; Liu, Yichen; Cao, Jinjun; Zhang, Huaijiang; Zhang, Qingwen; Liu, Xiaoxia

2015-01-25

Recent studies have focused on determining functional genes and microRNAs in the pest Helicoverpa armigera (Lepidoptera: Noctuidae). Most of these studies used quantitative real-time PCR (qRT-PCR). Suitable reference genes are necessary to normalize gene expression data of qRT-PCR. However, a comprehensive study on the reference genes in H. armigera remains lacking. Twelve candidate reference genes of H. armigera were selected and evaluated for their expression stability under different biotic and abiotic conditions. The comprehensive stability ranking of candidate reference genes was recommended by RefFinder and the optimal number of reference genes was calculated by geNorm. Two target genes, thioredoxin (TRX) and Cu/Zn superoxide dismutase (SOD), were used to validate the selection of reference genes. Results showed that the most suitable candidate combinations of reference genes were as follows: 28S and RPS15 for developmental stages; RPS15 and RPL13 for larvae tissues; EF and RPL27 for adult tissues; GAPDH, RPL27, and β-TUB for nuclear polyhedrosis virus infection; RPS15 and RPL32 for insecticide treatment; RPS15 and RPL27 for temperature treatment; and RPL32, RPS15, and RPL27 for all samples. This study not only establishes an accurate method for normalizing qRT-PCR data in H. armigera but also serve as a reference for further study on gene transcription in H. armigera and other insects. Copyright © 2014 Elsevier B.V. All rights reserved.

An alternative to fully coupled reactive transport simulations for long-term prediction of chemical reactions in complex geological systems

NASA Astrophysics Data System (ADS)

De Lucia, Marco; Kempka, Thomas; Kühn, Michael

2014-05-01

Fully-coupled reactive transport simulations involving multiphase hydrodynamics and chemical reactions in heterogeneous settings are extremely challenging from a computational point of view. This often leads to oversimplification of the investigated system: coarse spatial discretization, to keep the number of elements in the order of few thousands; simplified chemistry, disregarding many potentially important reactions. A novel approach for coupling non-reactive hydrodynamic simulations with the outcome of single batch geochemical simulations was therefore introduced to assess the potential long-term mineral trapping at the Ketzin pilot site for underground CO2 storage in Germany [1],[2]. The advantage of the coupling is the ability to use multi-million grid non-reactive hydrodynamics simulations on one side and few batch 0D geochemical simulations on the other, so that the complexity of both systems does not need to be reduced. This contribution shows the approach which was taken to validate this simplified coupling scheme. The procedure involved batch simulations of the reference geochemical model, then performing both non-reactive and fully coupled 1D and 3D reactive transport simulations and finally applying the simplified coupling scheme based on the non-reactive and geochemical batch model. The TOUGHREACT/ECO2N [3] simulator was adopted for the validation. The degree of refinement of the spatial grid and the complexity and velocity of the mineral reactions, along with a cut-off value for the minimum concentration of dissolved CO2 allowed to originate precipitates in the simplified approach were found out to be the governing parameters for the convergence of the two schemes. Systematic discrepancies between the approaches are not reducible, simply because there is no feedback between chemistry and hydrodynamics, and can reach 20 % - 30 % in unfavourable cases. However, even such discrepancy is completely acceptable, in our opinion, given the amount of uncertainty underlying the geochemical models. References [1] Klein, E., De Lucia, M., Kempka, T. Kühn, M. 2013. Evaluation of longterm mineral trapping at the Ketzin pilot site for CO2 storage: an integrative approach using geochemical modelling and reservoir simulation. International Journal of Greenhouse Gas Control 19: 720-730, doi:10.1016/j.ijggc.2013.05.014 [2] Kempka, T., Klein, E., De Lucia, M., Tillner, E. Kühn, M. 2013. Assessment of Long-term CO2 Trapping Mechanisms at the Ketzin Pilot Site (Germany) by Coupled Numerical Modelling. Energy Procedia 37: 5419-5426, doi:10.1016/j.egypro.2013.06.460 [3] Xu, T., Spycher, N., Sonnenthal, E., Zhang, G., Zheng, L., Pruess, K. 2010. TOUGHREACT Version 2.0: A simulator for subsurface reactive transport under non-isothermal multiphase flow conditions, Computers & Geosciences 37(6), doi:10.1016/j.cageo.2010.10.007

FDG-PET reproducibility in tumor-bearing mice: comparing a traditional SUV approach with a tumor-to-brain tissue ratio approach.

PubMed

Busk, Morten; Munk, Ole L; Jakobsen, Steen; Frøkiær, Jørgen; Overgaard, Jens; Horsman, Michael R

2017-05-01

Current [F-18]-fluorodeoxyglucose positron emission tomography (FDG-PET) procedures in tumor-bearing mice typically includes fasting, anesthesia, and standardized uptake value (SUV)-based quantification. Such procedures may be inappropriate for prolonged multiscan experiments. We hypothesize that normalization of tumor FDG retention relative to a suitable reference tissue may improve accuracy as this method may be less susceptible to uncontrollable day-to-day changes in blood glucose levels, physical activity, or unnoticed imperfect tail vein injections. Fed non-anesthetized tumor-bearing mice were administered FDG intravenously (i.v.) or intraperitoneally (i.p.) and PET scanned on consecutive days using a Mediso nanoScan PET/magnetic resonance imaging (MRI). Reproducibility of various PET-deduced measures of tumor FDG retention, including normalization to FDG signal in reference organs and a conventional SUV approach, was evaluated. Day-to-day variability in i.v. injected mice was lower when tumor FDG retention was normalized to brain signal (T/B), compared to normalization to other tissues or when using SUV-based normalization. Assessment of tissue radioactivity in dissected tissues confirmed the validity of PET-derived T/B ratios. Mean T/B and SUV values were similar in i.v. and i.p. administered animals, but SUV normalization was more robust in the i.p. group than in the i.v. group. Multimodality scanners allow tissue delineation and normalization of tumor FDG uptake relative to reference tissues. Normalization to brain, but not liver or kidney, improved scan reproducibility considerably and was superior to traditional SUV quantification in i.v. tracer-injected animals. Day-to-day variability in SUV's was lower in i.p. than in i.v. injected animals, and i.p. injections may therefore be a valuable alternative in prolonged rodent studies, where repeated vein injections are undesirable.

A novel technique for reference point generation to aid in intraoral scan alignment.

PubMed

Renne, Walter G; Evans, Zachary P; Mennito, Anthony; Ludlow, Mark

2017-11-12

When using a completely digital workflow on larger prosthetic cases it is often difficult to communicate to the laboratory or chairside Computer Aided Design and Computer Aided Manufacturing system the provisional prosthetic information. The problem arises when common hard tissue data points are limited or non-existent such as in complete arch cases in which the 3D model of the complete arch provisional restorations must be aligned perfectly with the 3D model of the complete arch preparations. In these instances, soft tissue is not enough to ensure an accurate automatic or manual alignment due to a lack of well-defined reference points. A new technique is proposed for the proper digital alignment of the 3D virtual model of the provisional prosthetic to the 3D virtual model of the prepared teeth in cases where common and coincident hard tissue data points are limited. Clinical considerations: A technique is described in which fiducial composite resin dots are temporarily placed on the intraoral keratinized tissue in strategic locations prior to final impressions. These fiducial dots provide coincident and clear 3D data points that when scanned into a digital impression allow superimposition of the 3D models. Composite resin dots on keratinized tissue were successful at allowing accurate merging of provisional restoration and post-preparation 3D models for the purpose of using the provisional restorations as a guide for final CLINICAL SIGNIFICANCE: Composite resin dots placed temporarily on attached tissue were successful at allowing accurate merging of the provisional restoration 3D models to the preparation 3D models for the purposes of using the provisional restorations as a guide for final restoration design and manufacturing. In this case, they allowed precise superimposition of the 3D models made in the absence of any other hard tissue reference points, resulting in the fabrication of ideal final restorations. © 2017 Wiley Periodicals, Inc.

Evaluation of architectural and histopathological biomarkers in the intestine of brown trout (Salmo trutta Linnaeus, 1758) challenged with environmental pollution.

PubMed

Barišić, Josip; Filipović Marijić, Vlatka; Mijošek, Tatjana; Čož-Rakovac, Rozelindra; Dragun, Zrinka; Krasnići, Nesrete; Ivanković, Dušica; Kružlicová, Dáša; Erk, Marijana

2018-06-14

In the present study novel histopathological approach, using fish intestine as a sensitive bioindicator organ of pollution impact in the freshwater ecosystem, was proposed. Histopathological alterations were compared between native brown trout (Salmo trutta Linnaeus, 1758) from the reference (Krka River spring) and pollution impacted location (influence of technological/municipal wastewaters and agricultural runoff near the Town of Knin) of the karst Krka River in Croatia. In brown trout from both locations, severe parasitic infestation with acanthocephalan species Dentitruncus trutae was found, enabling evaluation of acanthocephalan infestation histopathology, which indicated parasite tissue reaction in a form of inflammatory, necrotic and hyperplastic response that extended throughout lamina epithelialis mucosae, lamina propria, and lamina muscularis mucosae. New semi-quantitative histological approach was proposed in order to foresee alterations classified in three reaction patterns: control tissue appearance, moderate (progressive) tissue impairment and severe (regressive and inflammatory) tissue damage. The most frequent progressive alteration was hyperplasia of epithelium on the reference site, whereas the most frequent regressive alterations were atrophy and necrosis seen on the polluted site. Furthermore, histopathological approach was combined with micromorphological and macromorphological assessment as an additional indicator of pollution impact. Among 15 observed intestinal measures, two biomarkers of intestinal tissue damage were indicated as significant, height of supranuclear space (hSN) and number of mucous cells over 100 μm fold distance of intestinal mucosa (nM), which measures were significantly lower in fish from polluted area compared to the reference site. Obtained results indicated that combined histological and morphological approach on fish intestinal tissue might be used as a valuable biological tool for assessing pollution impact on aquatic organisms. Therefore, semi quantitative scoring and multiparametric morphological assessment of intestinal tissue lesion magnitude should become a common approach to handle environmental pollution impact. Copyright © 2018 Elsevier B.V. All rights reserved.

FISH TISSUE QUALITY IN NEAR-COASTAL AREAS OF THE GULF OF MEXICO RECEIVING POINT SOURCE DISCHARGES

EPA Science Inventory

The objective of this study was to determine inorganic and organic contaminant concentrations in edible tissue of fish collected from eight coastal areas receiving wastewater discharges and from two reference locations. Trace metal residues were statistically similar regardless o...

The impact of anthropometric patient-phantom matching on organ dose: A hybrid phantom study for fluoroscopy guided interventions

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

Johnson, Perry B.; Geyer, Amy; Borrego, David

Purpose: To investigate the benefits and limitations of patient-phantom matching for determining organ dose during fluoroscopy guided interventions. Methods: In this study, 27 CT datasets representing patients of different sizes and genders were contoured and converted into patient-specific computational models. Each model was matched, based on height and weight, to computational phantoms selected from the UF hybrid patient-dependent series. In order to investigate the influence of phantom type on patient organ dose, Monte Carlo methods were used to simulate two cardiac projections (PA/left lateral) and two abdominal projections (RAO/LPO). Organ dose conversion coefficients were then calculated for each patient-specific andmore » patient-dependent phantom and also for a reference stylized and reference hybrid phantom. The coefficients were subsequently analyzed for any correlation between patient-specificity and the accuracy of the dose estimate. Accuracy was quantified by calculating an absolute percent difference using the patient-specific dose conversion coefficients as the reference. Results: Patient-phantom matching was shown most beneficial for estimating the dose to heavy patients. In these cases, the improvement over using a reference stylized phantom ranged from approximately 50% to 120% for abdominal projections and for a reference hybrid phantom from 20% to 60% for all projections. For lighter individuals, patient-phantom matching was clearly superior to using a reference stylized phantom, but not significantly better than using a reference hybrid phantom for certain fields and projections. Conclusions: The results indicate two sources of error when patients are matched with phantoms: Anatomical error, which is inherent due to differences in organ size and location, and error attributed to differences in the total soft tissue attenuation. For small patients, differences in soft tissue attenuation are minimal and are exceeded by inherent anatomical differences. For large patients, difference in soft tissue attenuation can be large. In these cases, patient-phantom matching proves most effective as differences in soft tissue attenuation are mitigated. With increasing obesity rates, overweight patients will continue to make up a growing fraction of all patients undergoing medical imaging. Thus, having phantoms that better represent this population represents a considerable improvement over previous methods. In response to this study, additional phantoms representing heavier weight percentiles will be added to the UFHADM and UFHADF patient-dependent series.« less

Biomimetic Hybrid Feedback Feedforward Neural-Network Learning Control.

PubMed

Pan, Yongping; Yu, Haoyong

2017-06-01

This brief presents a biomimetic hybrid feedback feedforward neural-network learning control (NNLC) strategy inspired by the human motor learning control mechanism for a class of uncertain nonlinear systems. The control structure includes a proportional-derivative controller acting as a feedback servo machine and a radial-basis-function (RBF) NN acting as a feedforward predictive machine. Under the sufficient constraints on control parameters, the closed-loop system achieves semiglobal practical exponential stability, such that an accurate NN approximation is guaranteed in a local region along recurrent reference trajectories. Compared with the existing NNLC methods, the novelties of the proposed method include: 1) the implementation of an adaptive NN control to guarantee plant states being recurrent is not needed, since recurrent reference signals rather than plant states are utilized as NN inputs, which greatly simplifies the analysis and synthesis of the NNLC and 2) the domain of NN approximation can be determined a priori by the given reference signals, which leads to an easy construction of the RBF-NNs. Simulation results have verified the effectiveness of this approach.

Relative Photometry of HAT-P-1b Occultations

NASA Astrophysics Data System (ADS)

Béky, Bence; Holman, Matthew J.; Gilliland, Ronald L.; Bakos, Gáspár Á.; Winn, Joshua N.; Noyes, Robert W.; Sasselov, Dimitar D.

2013-06-01

We present Hubble Space Telescope (HST) Space Telescope Imaging Spectrograph observations of two occultations of the transiting exoplanet HAT-P-1b. By measuring the planet to star flux ratio near opposition, we constrain the geometric albedo of the planet, which is strongly linked to its atmospheric temperature gradient. An advantage of HAT-P-1 as a target is its binary companion ADS 16402 A, which provides an excellent photometric reference, simplifying the usual steps in removing instrumental artifacts from HST time-series photometry. We find that without this reference star, we would need to detrend the lightcurve with the time of the exposures as well as the first three powers of HST orbital phase, and this would introduce a strong bias in the results for the albedo. However, with this reference star, we only need to detrend the data with the time of the exposures to achieve the same per-point scatter, therefore we can avoid most of the bias associated with detrending. Our final result is a 2σ upper limit of 0.64 for the geometric albedo of HAT-P-1b between 577 and 947 nm.

Frequency-domain optical tomographic image reconstruction algorithm with the simplified spherical harmonics (SP3) light propagation model.

PubMed

Kim, Hyun Keol; Montejo, Ludguier D; Jia, Jingfei; Hielscher, Andreas H

2017-06-01

We introduce here the finite volume formulation of the frequency-domain simplified spherical harmonics model with n -th order absorption coefficients (FD-SP N ) that approximates the frequency-domain equation of radiative transfer (FD-ERT). We then present the FD-SP N based reconstruction algorithm that recovers absorption and scattering coefficients in biological tissue. The FD-SP N model with 3 rd order absorption coefficient (i.e., FD-SP 3 ) is used as a forward model to solve the inverse problem. The FD-SP 3 is discretized with a node-centered finite volume scheme and solved with a restarted generalized minimum residual (GMRES) algorithm. The absorption and scattering coefficients are retrieved using a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm. Finally, the forward and inverse algorithms are evaluated using numerical phantoms with optical properties and size that mimic small-volume tissue such as finger joints and small animals. The forward results show that the FD-SP 3 model approximates the FD-ERT (S 12 ) solution within relatively high accuracy; the average error in the phase (<3.7%) and the amplitude (<7.1%) of the partial current at the boundary are reported. From the inverse results we find that the absorption and scattering coefficient maps are more accurately reconstructed with the SP 3 model than those with the SP 1 model. Therefore, this work shows that the FD-SP 3 is an efficient model for optical tomographic imaging of small-volume media with non-diffuse properties both in terms of computational time and accuracy as it requires significantly lower CPU time than the FD-ERT (S 12 ) and also it is more accurate than the FD-SP 1 .

Simplified production and concentration of HIV-1-based lentiviral vectors using HYPERFlask vessels and anion exchange membrane chromatography

PubMed Central

Kutner, Robert H; Puthli, Sharon; Marino, Michael P; Reiser, Jakob

2009-01-01

Background During the past twelve years, lentiviral (LV) vectors have emerged as valuable tools for transgene delivery because of their ability to transduce nondividing cells and their capacity to sustain long-term transgene expression in target cells in vitro and in vivo. However, despite significant progress, the production and concentration of high-titer, high-quality LV vector stocks is still cumbersome and costly. Methods Here we present a simplified protocol for LV vector production on a laboratory scale using HYPERFlask vessels. HYPERFlask vessels are high-yield, high-performance flasks that utilize a multilayered gas permeable growth surface for efficient gas exchange, allowing convenient production of high-titer LV vectors. For subsequent concentration of LV vector stocks produced in this way, we describe a facile protocol involving Mustang Q anion exchange membrane chromatography. Results Our results show that unconcentrated LV vector stocks with titers in excess of 108 transduction units (TU) per ml were obtained using HYPERFlasks and that these titers were higher than those produced in parallel using regular 150-cm2 tissue culture dishes. We also show that up to 500 ml of an unconcentrated LV vector stock prepared using a HYPERFlask vessel could be concentrated using a single Mustang Q Acrodisc with a membrane volume of 0.18 ml. Up to 5.3 × 1010 TU were recovered from a single HYPERFlask vessel. Conclusion The protocol described here is easy to implement and should facilitate high-titer LV vector production for preclinical studies in animal models without the need for multiple tissue culture dishes and ultracentrifugation-based concentration protocols. PMID:19220915

Lq -Lp optimization for multigrid fluorescence tomography of small animals using simplified spherical harmonics

NASA Astrophysics Data System (ADS)

Edjlali, Ehsan; Bérubé-Lauzière, Yves

2018-01-01

We present the first Lq -Lp optimization scheme for fluorescence tomographic imaging. This is then applied to small animal imaging. Fluorescence tomography is an ill-posed, and in full generality, a nonlinear problem that seeks to image the 3D concentration distribution of a fluorescent agent inside a biological tissue. Standard candidates for regularization to deal with the ill-posedness of the image reconstruction problem include L1 and L2 regularization. In this work, a general Lq -Lp regularization framework (Lq discrepancy function - Lp regularization term) is introduced for fluorescence tomographic imaging. A method to calculate the gradient for this general framework is developed which allows evaluating the performance of different cost functions/regularization schemes in solving the fluorescence tomographic problem. The simplified spherical harmonics approximation is used to accurately model light propagation inside the tissue. Furthermore, a multigrid mesh is utilized to decrease the dimension of the inverse problem and reduce the computational cost of the solution. The inverse problem is solved iteratively using an lm-BFGS quasi-Newton optimization method. The simulations are performed under different scenarios of noisy measurements. These are carried out on the Digimouse numerical mouse model with the kidney being the target organ. The evaluation of the reconstructed images is performed both qualitatively and quantitatively using several metrics including QR, RMSE, CNR, and TVE under rigorous conditions. The best reconstruction results under different scenarios are obtained with an L1.5 -L1 scheme with premature termination of the optimization process. This is in contrast to approaches commonly found in the literature relying on L2 -L2 schemes.

Periodic Extraction of Interstitial Fluid from the Site of Subcutaneous Insulin Infusion for the Measurement of Glucose: A Novel Single-Port Technique for the Treatment of Type 1 Diabetes Patients

PubMed Central

Lindpointner, Stefan; Korsatko, Stefan; Tutkur, Dina; Bodenlenz, Manfred; Pieber, Thomas R.

2013-01-01

Abstract Background Treatment of type 1 diabetes patients could be simplified if the site of subcutaneous insulin infusion could also be used for the measurement of glucose. This study aimed to assess the agreement between blood glucose concentrations and glucose levels in the interstitial fluid (ISF) that is extracted from the insulin infusion site during periodic short-term interruptions of continuous subcutaneous insulin infusion (CSII). Subjects and Methods A perforated cannula (24 gauge) was inserted into subcutaneous adipose tissue of C-peptide-negative type 1 diabetes subjects (n=13) and used alternately to infuse rapid-acting insulin (100 U/mL) and to extract ISF glucose during a fasting period and after ingestion of a standard oral glucose load (75 g). Results Although periodically interrupted for extracting glucose (every hour for approximately 10 min), insulin infusion with the cannula was adequate to achieve euglycemia during fasting and to restore euglycemia after glucose ingestion. Furthermore, the ISF-derived estimates of plasma glucose levels agreed well with plasma glucose concentrations. Correlation coefficient and median absolute relative difference values were found to be 0.95 and 8.0%, respectively. Error grid analysis showed 99.0% of all ISF glucose values within clinically acceptable Zones A and B (83.5% Zone A, 15.5% Zone B). Conclusions Results show that ISF glucose concentrations measured at the insulin infusion site during periodic short-term interruptions of CSII closely reflect blood glucose levels, thus suggesting that glucose monitoring and insulin delivery may be performed alternately at the same tissue site. A single-port device of this type could be used to simplify and improve glucose management in diabetes. PMID:23126579

Quantitative analysis of in vivo mucosal bacterial biofilms.

PubMed

Singhal, Deepti; Boase, Sam; Field, John; Jardeleza, Camille; Foreman, Andrew; Wormald, Peter-John

2012-01-01

Quantitative assays of mucosal biofilms on ex vivo samples are challenging using the currently applied specialized microscopic techniques to identify them. The COMSTAT2 computer program has been applied to in vitro biofilm models for quantifying biofilm structures seen on confocal scanning laser microscopy (CSLM). The aim of this study was to quantify Staphylococcus aureus (S. aureus) biofilms seen via CSLM on ex situ samples of sinonasal mucosa, using the COMSTAT2 program. S. aureus biofilms were grown in frontal sinuses of 4 merino sheep as per a previously standardized sheep sinusitis model for biofilms. Two sinonasal mucosal samples, 10 mm × 10 mm in size, from each of the 2 sinuses of the 4 sheep were analyzed for biofilm presence with Baclight stain and CSLM. Two random image stacks of mucosa with S. aureus biofilm were recorded from each sample, and analyzed using COMSTAT2 software that translates image stacks into a simplified 3-dimensional matrix of biofilm mass by eliminating surrounding host tissue. Three independent observers analyzed images using COMSTAT2 and 3 repeated rounds of analyses were done to calculate biofilm biomass. The COMSTAT2 application uses an observer-dependent threshold setting to translate CSLM biofilm images into a simplified 3-dimensional output for quantitative analysis. Intraclass correlation coefficient (ICC) between thresholds set by the 3 observers for each image stacks was 0.59 (p = 0.0003). Threshold values set at different points of time by a single observer also showed significant correlation as seen by ICC of 0.80 (p < 0.001). COMSTAT2 can be applied to quantify and study the complex 3-dimensional biofilm structures that are recorded via CSLM on mucosal tissue like the sinonasal mucosa. Copyright © 2011 American Rhinologic Society-American Academy of Otolaryngic Allergy, LLC.

Combined Recirculatory-compartmental Population Pharmacokinetic Modeling of Arterial and Venous Plasma S(+) and R(-) Ketamine Concentrations.

PubMed

Henthorn, Thomas K; Avram, Michael J; Dahan, Albert; Gustafsson, Lars L; Persson, Jan; Krejcie, Tom C; Olofsen, Erik

2018-05-16

The pharmacokinetics of infused drugs have been modeled without regard for recirculatory or mixing kinetics. We used a unique ketamine dataset with simultaneous arterial and venous blood sampling, during and after separate S(+) and R(-) ketamine infusions, to develop a simplified recirculatory model of arterial and venous plasma drug concentrations. S(+) or R(-) ketamine was infused over 30 min on two occasions to 10 healthy male volunteers. Frequent, simultaneous arterial and forearm venous blood samples were obtained for up to 11 h. A multicompartmental pharmacokinetic model with front-end arterial mixing and venous blood components was developed using nonlinear mixed effects analyses. A three-compartment base pharmacokinetic model with additional arterial mixing and arm venous compartments and with shared S(+)/R(-) distribution kinetics proved superior to standard compartmental modeling approaches. Total pharmacokinetic flow was estimated to be 7.59 ± 0.36 l/min (mean ± standard error of the estimate), and S(+) and R(-) elimination clearances were 1.23 ± 0.04 and 1.06 ± 0.03 l/min, respectively. The arm-tissue link rate constant was 0.18 ± 0.01 min and the fraction of arm blood flow estimated to exchange with arm tissue was 0.04 ± 0.01. Arterial drug concentrations measured during drug infusion have two kinetically distinct components: partially or lung-mixed drug and fully mixed-recirculated drug. Front-end kinetics suggest the partially mixed concentration is proportional to the ratio of infusion rate and total pharmacokinetic flow. This simplified modeling approach could lead to more generalizable models for target-controlled infusions and improved methods for analyzing pharmacokinetic-pharmacodynamic data.

Plasma vs heart tissue concentration in humans - literature data analysis of drugs distribution.

PubMed

Tylutki, Zofia; Polak, Sebastian

2015-03-12

Little is known about the uptake of drugs into the human heart, although it is of great importance nowadays, when science desires to predict tissue level behavior rather than to measure it. Although the drug concentration in cardiac tissue seems a better predictor for physiological and electrophysiological changes than its level in plasma, knowledge of this value is very limited. Tissue to plasma partition coefficients (Kp) come to rescue since they characterize the distribution of a drug among tissues as being one of the input parameters in physiologically based pharmacokinetic (PBPK) models. The article reviews cardiac surgery and forensic medical studies to provide a reference for drug concentrations in human cardiac tissue. Firstly, the focus is on whether a drug penetrates into heart tissue at a therapeutic level; the provided values refer to antibiotics, antifungals and anticancer drugs. Drugs that directly affect cardiomyocyte electrophysiology are another group of interest. Measured levels of amiodarone, digoxin, perhexiline and verapamil in different sites in human cardiac tissue where the compounds might meet ion channels, gives an insight into how these more lipophilic drugs penetrate the heart. Much data are derived from postmortem studies and they provide insight to the cardiac distribution of more than 200 drugs. The analysis depicts potential problems in defining the active concentration location, what may indirectly suggest multiple mechanisms involved in the drug distribution within the heart. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Revisiting the Logan plot to account for non-negligible blood volume in brain tissue.

PubMed

Schain, Martin; Fazio, Patrik; Mrzljak, Ladislav; Amini, Nahid; Al-Tawil, Nabil; Fitzer-Attas, Cheryl; Bronzova, Juliana; Landwehrmeyer, Bernhard; Sampaio, Christina; Halldin, Christer; Varrone, Andrea

2017-08-18

Reference tissue-based quantification of brain PET data does not typically include correction for signal originating from blood vessels, which is known to result in biased outcome measures. The bias extent depends on the amount of radioactivity in the blood vessels. In this study, we seek to revisit the well-established Logan plot and derive alternative formulations that provide estimation of distribution volume ratios (DVRs) that are corrected for the signal originating from the vasculature. New expressions for the Logan plot based on arterial input function and reference tissue were derived, which included explicit terms for whole blood radioactivity. The new methods were evaluated using PET data acquired using [ 11 C]raclopride and [ 18 F]MNI-659. The two-tissue compartment model (2TCM), with which signal originating from blood can be explicitly modeled, was used as a gold standard. DVR values obtained for [ 11 C]raclopride using the either blood-based or reference tissue-based Logan plot were systematically underestimated compared to 2TCM, and for [ 18 F]MNI-659, a proportionality bias was observed, i.e., the bias varied across regions. The biases disappeared when optimal blood-signal correction was used for respective tracer, although for the case of [ 18 F]MNI-659 a small but systematic overestimation of DVR was still observed. The new method appears to remove the bias introduced due to absence of correction for blood volume in regular graphical analysis and can be considered in clinical studies. Further studies are however required to derive a generic mapping between plasma and whole-blood radioactivity levels.

Moon-based visibility analysis for the observation of “The Belt and Road”

NASA Astrophysics Data System (ADS)

REN, Yuanzhen; GUO, Huadong; LIU, Guang; YE, Hanlin; DING, Yixing; RUAN, Zhixing; LV, Mingyang

2016-11-01

Aiming at promoting the economic prosperity and regional economic cooperation, the “Silk Road Economic Belt” and the “21st Century Maritime Silk Road” (hereinafter referred to as the Belt and Road) was raised. To get a better understanding of “the Belt and Road” whole region, considering the large-scale characteristic, the Moon platform is a good choice. In this paper, the ephemeris is taken as data source and the positions and attitudes of Sun, Earth and Moon are obtained based on the reference systems transformation. Then we construct a simplified observation model and calculate the spatial and angular visibility of the Moon platform for “the Belt and Road” region. It turns out that Moon-based observation of this region shows a good performance of spatial visibility and variable angular visibility, indicating the Moon being a new potential platform for large-scale Earth observation.

Efficient chemoenzymatic dynamic kinetic resolution of 1-heteroaryl ethanols.

PubMed

Vallin, Karl S A; Wensbo Posaric, David; Hamersak, Zdenko; Svensson, Mats A; Minidis, Alexander B E

2009-12-18

The scope and limitation of the combined ruthenium-lipase induced dynamic kinetic resolution (DKR) through O-acetylation of racemic heteroaromatic secondary alcohols, i.e., 1-heteroaryl substituted ethanols, was investigated. After initial screening of reaction conditions, Candida antarctica lipase B (Novozyme 435, N435) together with 4-chloro-phenylacetate as acetyl-donor for kinetic resolution (KR), in conjunction with the ruthenium-based Shvo catalyst for substrate racemization in toluene at 80 degrees C, enabled DKR with high yields and stereoselectivity of various 1-heteroaryl ethanols, such as oxadiazoles, isoxazoles, 1H-pyrazole, or 1H-imidazole. In addition, DFT calculations based on a simplified catalyst complex model for the catalytic (de)hydrogenation step are in agreement with the previously reported outer sphere mechanism. These results support the further understanding of the mechanistic aspects behind the difference in reactivity of 1-heteroaryl substituted ethanols in comparison to reference substrates, as often referred to in the literature.

A new approach of active compliance control via fuzzy logic control for multifingered robot hand

NASA Astrophysics Data System (ADS)

Jamil, M. F. A.; Jalani, J.; Ahmad, A.

2016-07-01

Safety is a vital issue in Human-Robot Interaction (HRI). In order to guarantee safety in HRI, a model reference impedance control can be a very useful approach introducing a compliant control. In particular, this paper establishes a fuzzy logic compliance control (i.e. active compliance control) to reduce impact and forces during physical interaction between humans/objects and robots. Exploiting a virtual mass-spring-damper system allows us to determine a desired compliant level by understanding the behavior of the model reference impedance control. The performance of fuzzy logic compliant control is tested in simulation for a robotic hand known as the RED Hand. The results show that the fuzzy logic is a feasible control approach, particularly to control position and to provide compliant control. In addition, the fuzzy logic control allows us to simplify the controller design process (i.e. avoid complex computation) when dealing with nonlinearities and uncertainties.

Shack-Hartmann reflective micro profilometer

NASA Astrophysics Data System (ADS)

Gong, Hai; Soloviev, Oleg; Verhaegen, Michel; Vdovin, Gleb

2018-01-01

We present a quantitative phase imaging microscope based on a Shack-Hartmann sensor, that directly reconstructs the optical path difference (OPD) in reflective mode. Comparing with the holographic or interferometric methods, the SH technique needs no reference beam in the setup, which simplifies the system. With a preregistered reference, the OPD image can be reconstructed from a single shot. Also, the method has a rather relaxed requirement on the illumination coherence, thus a cheap light source such as a LED is feasible in the setup. In our previous research, we have successfully verified that a conventional transmissive microscope can be transformed into an optical path difference microscope by using a Shack-Hartmann wavefront sensor under incoherent illumination. The key condition is that the numerical aperture of illumination should be smaller than the numerical aperture of imaging lens. This approach is also applicable to characterization of reflective and slightly scattering surfaces.

Medical applications of model-based dynamic thermography

NASA Astrophysics Data System (ADS)

Nowakowski, Antoni; Kaczmarek, Mariusz; Ruminski, Jacek; Hryciuk, Marcin; Renkielska, Alicja; Grudzinski, Jacek; Siebert, Janusz; Jagielak, Dariusz; Rogowski, Jan; Roszak, Krzysztof; Stojek, Wojciech

2001-03-01

The proposal to use active thermography in medical diagnostics is promising in some applications concerning investigation of directly accessible parts of the human body. The combination of dynamic thermograms with thermal models of investigated structures gives attractive possibility to make internal structure reconstruction basing on different thermal properties of biological tissues. Measurements of temperature distribution synchronized with external light excitation allow registration of dynamic changes of local temperature dependent on heat exchange conditions. Preliminary results of active thermography applications in medicine are discussed. For skin and under- skin tissues an equivalent thermal model may be determined. For the assumed model its effective parameters may be reconstructed basing on the results of transient thermal processes. For known thermal diffusivity and conductivity of specific tissues the local thickness of a two or three layer structure may be calculated. Results of some medical cases as well as reference data of in vivo study on animals are presented. The method was also applied to evaluate the state of the human heart during the open chest cardio-surgical interventions. Reference studies of evoked heart infarct in pigs are referred, too. We see the proposed new in medical applications technique as a promising diagnostic tool. It is a fully non-invasive, clean, handy, fast and affordable method giving not only qualitative view of investigated surfaces but also an objective quantitative measurement result, accurate enough for many applications including fast screening of affected tissues.

Accuracy of magnetic resonance based susceptibility measurements

NASA Astrophysics Data System (ADS)

Erdevig, Hannah E.; Russek, Stephen E.; Carnicka, Slavka; Stupic, Karl F.; Keenan, Kathryn E.

2017-05-01

Magnetic Resonance Imaging (MRI) is increasingly used to map the magnetic susceptibility of tissue to identify cerebral microbleeds associated with traumatic brain injury and pathological iron deposits associated with neurodegenerative diseases such as Parkinson's and Alzheimer's disease. Accurate measurements of susceptibility are important for determining oxygen and iron content in blood vessels and brain tissue for use in noninvasive clinical diagnosis and treatment assessments. Induced magnetic fields with amplitude on the order of 100 nT, can be detected using MRI phase images. The induced field distributions can then be inverted to obtain quantitative susceptibility maps. The focus of this research was to determine the accuracy of MRI-based susceptibility measurements using simple phantom geometries and to compare the susceptibility measurements with magnetometry measurements where SI-traceable standards are available. The susceptibilities of paramagnetic salt solutions in cylindrical containers were measured as a function of orientation relative to the static MRI field. The observed induced fields as a function of orientation of the cylinder were in good agreement with simple models. The MRI susceptibility measurements were compared with SQUID magnetometry using NIST-traceable standards. MRI can accurately measure relative magnetic susceptibilities while SQUID magnetometry measures absolute magnetic susceptibility. Given the accuracy of moment measurements of tissue mimicking samples, and the need to look at small differences in tissue properties, the use of existing NIST standard reference materials to calibrate MRI reference structures is problematic and better reference materials are required.

Evaluation of a Post-Processing Approach for Multiscale Analysis of Biphasic Mechanics of Chondrocytes

PubMed Central

Sibole, Scott C.; Maas, Steve; Halloran, Jason P.; Weiss, Jeffrey A.; Erdemir, Ahmet

2014-01-01

Understanding the mechanical behavior of chondrocytes as a result of cartilage tissue mechanics has significant implications for both evaluation of mechanobiological function and to elaborate on damage mechanisms. A common procedure for prediction of chondrocyte mechanics (and of cell mechanics in general) relies on a computational post-processing approach where tissue level deformations drive cell level models. Potential loss of information in this numerical coupling approach may cause erroneous cellular scale results, particularly during multiphysics analysis of cartilage. The goal of this study was to evaluate the capacity of 1st and 2nd order data passing to predict chondrocyte mechanics by analyzing cartilage deformations obtained for varying complexity of loading scenarios. A tissue scale model with a sub-region incorporating representation of chondron size and distribution served as control. The postprocessing approach first required solution of a homogeneous tissue level model, results of which were used to drive a separate cell level model (same characteristics as the subregion of control model). The 1st data passing appeared to be adequate for simplified loading of the cartilage and for a subset of cell deformation metrics, e.g., change in aspect ratio. The 2nd order data passing scheme was more accurate, particularly when asymmetric permeability of the tissue boundaries were considered. Yet, the method exhibited limitations for predictions of instantaneous metrics related to the fluid phase, e.g., mass exchange rate. Nonetheless, employing higher-order data exchange schemes may be necessary to understand the biphasic mechanics of cells under lifelike tissue loading states for the whole time history of the simulation. PMID:23809004

Selection and evaluation of novel reference genes for quantitative reverse transcription PCR (qRT-PCR) based on genome and transcriptome data in Brassica napus L.

PubMed

Yang, Hongli; Liu, Jing; Huang, Shunmou; Guo, Tingting; Deng, Linbin; Hua, Wei

2014-03-15

Selection of reference genes in Brassica napus, a tetraploid (4×) species, is a very difficult task without information on genome and transcriptome. By now, only several traditional reference genes which show significant expression differentiation under different conditions are used in B. napus. In the present study, based on genome and transcriptome data of the rapeseed Zhongshuang-11 cultivar, 14 candidate reference genes were screened for investigation in different tissues, cultivars, and treated conditions of B. napus. These genes were as follows: ELF5, ENTH, F-BOX7, F-BOX2, FYPP1, GDI1, GYF, MCP2d, OTP80, PPR, SPOC, Unknown1, Unknown2 and UBA. Among them, excluding GYF and FYPP1, another 12 genes, were identified to perform better than traditional reference genes ACTIN7 and GAPDH. To further validate the accuracy of the newly developed reference genes in normalization, expression levels of BnCAT1 (B. napus catalase 1) in different rapeseed tissues and seedlings under stress conditions were normalized by the three most stable reference genes PPR, GDI1, and ENTH and little difference existed in normalization results. To the best of our knowledge, this is the first time B. napus reference genes have been provided with the help of complete genome and transcriptome information. The new reference genes provided in this study are more accurate than previously reported reference genes in quantifying expression levels of B. napus genes. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Evaluation of normalized metal artifact reduction (NMAR) in kVCT using MVCT prior images for radiotherapy treatment planning

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

Paudel, M. R.; Mackenzie, M.; Rathee, S.

2013-08-15

Purpose: To evaluate the metal artifacts in kilovoltage computed tomography (kVCT) images that are corrected using a normalized metal artifact reduction (NMAR) method with megavoltage CT (MVCT) prior images.Methods: Tissue characterization phantoms containing bilateral steel inserts are used in all experiments. Two MVCT images, one without any metal artifact corrections and the other corrected using a modified iterative maximum likelihood polychromatic algorithm for CT (IMPACT) are translated to pseudo-kVCT images. These are then used as prior images without tissue classification in an NMAR technique for correcting the experimental kVCT image. The IMPACT method in MVCT included an additional model formore » the pair/triplet production process and the energy dependent response of the MVCT detectors. An experimental kVCT image, without the metal inserts and reconstructed using the filtered back projection (FBP) method, is artificially patched with the known steel inserts to get a reference image. The regular NMAR image containing the steel inserts that uses tissue classified kVCT prior and the NMAR images reconstructed using MVCT priors are compared with the reference image for metal artifact reduction. The Eclipse treatment planning system is used to calculate radiotherapy dose distributions on the corrected images and on the reference image using the Anisotropic Analytical Algorithm with 6 MV parallel opposed 5 × 10 cm{sup 2} fields passing through the bilateral steel inserts, and the results are compared. Gafchromic film is used to measure the actual dose delivered in a plane perpendicular to the beams at the isocenter.Results: The streaking and shading in the NMAR image using tissue classifications are significantly reduced. However, the structures, including metal, are deformed. Some uniform regions appear to have eroded from one side. There is a large variation of attenuation values inside the metal inserts. Similar results are seen in commercially corrected image. Use of MVCT prior images without tissue classification in NMAR significantly reduces these problems. The radiation dose calculated on the reference image is close to the dose measured using the film. Compared to the reference image, the calculated dose difference in the conventional NMAR image, the corrected images using uncorrected MVCT image, and IMPACT corrected MVCT image as priors is ∼15.5%, ∼5%, and ∼2.7%, respectively, at the isocenter.Conclusions: The deformation and erosion of the structures present in regular NMAR corrected images can be largely reduced by using MVCT priors without tissue segmentation. The attenuation value of metal being incorrect, large dose differences relative to the true value can result when using the conventional NMAR image. This difference can be significantly reduced if MVCT images are used as priors. Reduced tissue deformation, better tissue visualization, and correct information about the electron density of the tissues and metals in the artifact corrected images could help delineate the structures better, as well as calculate radiation dose more correctly, thus enhancing the quality of the radiotherapy treatment planning.« less

Improved method for quantifying the avicide 3-chloro-p-toluidine hydrochloride in bird tissues using a deuterated surrogate/GC/MS method.

PubMed

Stahl, Randal S; Custer, Thomas W; Pochop, Patricia A; Johnston, John J

2002-02-13

A method using a deuterated surrogate of the avicide 3-chloro-p-toluidine hydrochloride (CPTH) was developed to quantify the CPTH residues in the gastrointestinal (GI) tract and breast muscle tissues in birds collected in CPTH-baited sunflower and rice fields. This method increased the range of a previous surrogate/gas chromatography/mass spectroscopy method from 0-2 to 0-20 microg/g in tissue samples and greatly simplified the extraction procedure. The modified method also sought to increase recoveries over a range of matrix effects introduced by analyzing tissues from birds collected in the field, where the GI tract contents would be affected by varying diet. The new method was used to determine the CPTH concentration in GI tract samples fortified with CPTH-treated rice bait to simulate the consumption of varying amounts of treated bait by two nontargeted bird species, pigeon (Columbia livia) and house sparrow (Passer domesticus). The new method was then used to examine the CPTH concentrations in the gizzard contents of the targeted bird species, red-winged black bird (Agelaius phoeniceus) and brown-headed cowbird (Molothrus ater), that were collected after feeding at a treated bait site. The method proved sufficiently sensitive to quantify CPTH in the breast muscle tissues and the gizzard contents of red-winged blackbirds and brown-headed cowbirds during an operational baiting program. The levels of CPTH determined for these birds in both tissue samples were determined to be highly correlated. The appearance of CPTH in the breast muscle tissue immediately after feeding was not anticipated. The potential secondary hazard posed by the targeted birds to potential scavengers and predators was also evaluated.

Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques.

PubMed

Barry, Christopher; Schmitz, Matthew T; Propson, Nicholas E; Hou, Zhonggang; Zhang, Jue; Nguyen, Bao K; Bolin, Jennifer M; Jiang, Peng; McIntosh, Brian E; Probasco, Mitchell D; Swanson, Scott; Stewart, Ron; Thomson, James A; Schwartz, Michael P; Murphy, William L

2017-11-01

The aim of the present study was to test sample reproducibility for model neural tissues formed on synthetic hydrogels. Human embryonic stem (ES) cell-derived precursor cells were cultured on synthetic poly(ethylene glycol) (PEG) hydrogels to promote differentiation and self-organization into model neural tissue constructs. Neural progenitor, vascular, and microglial precursor cells were combined on PEG hydrogels to mimic developmental timing, which produced multicomponent neural constructs with 3D neuronal and glial organization, organized vascular networks, and microglia with ramified morphologies. Spearman's rank correlation analysis of global gene expression profiles and a comparison of coefficient of variation for expressed genes demonstrated that replicate neural constructs were highly uniform to at least day 21 for samples from independent experiments. We also demonstrate that model neural tissues formed on PEG hydrogels using a simplified neural differentiation protocol correlated more strongly to in vivo brain development than samples cultured on tissue culture polystyrene surfaces alone. These results provide a proof-of-concept demonstration that 3D cellular models that mimic aspects of human brain development can be produced from human pluripotent stem cells with high sample uniformity between experiments by using standard culture techniques, cryopreserved cell stocks, and a synthetic extracellular matrix. Impact statement Pluripotent stem (PS) cells have been characterized by an inherent ability to self-organize into 3D "organoids" resembling stomach, intestine, liver, kidney, and brain tissues, offering a potentially powerful tool for modeling human development and disease. However, organoid formation must be quantitatively reproducible for applications such as drug and toxicity screening. Here, we report a strategy to produce uniform neural tissue constructs with reproducible global gene expression profiles for replicate samples from multiple experiments.

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

Shang, Yu; Yu, Guoqiang, E-mail: guoqiang.yu@uky.edu

Conventional semi-infinite analytical solutions of correlation diffusion equation may lead to errors when calculating blood flow index (BFI) from diffuse correlation spectroscopy (DCS) measurements in tissues with irregular geometries. Very recently, we created an algorithm integrating a Nth-order linear model of autocorrelation function with the Monte Carlo simulation of photon migrations in homogenous tissues with arbitrary geometries for extraction of BFI (i.e., αD{sub B}). The purpose of this study is to extend the capability of the Nth-order linear algorithm for extracting BFI in heterogeneous tissues with arbitrary geometries. The previous linear algorithm was modified to extract BFIs in different typesmore » of tissues simultaneously through utilizing DCS data at multiple source-detector separations. We compared the proposed linear algorithm with the semi-infinite homogenous solution in a computer model of adult head with heterogeneous tissue layers of scalp, skull, cerebrospinal fluid, and brain. To test the capability of the linear algorithm for extracting relative changes of cerebral blood flow (rCBF) in deep brain, we assigned ten levels of αD{sub B} in the brain layer with a step decrement of 10% while maintaining αD{sub B} values constant in other layers. Simulation results demonstrate the accuracy (errors < 3%) of high-order (N ≥ 5) linear algorithm in extracting BFIs in different tissue layers and rCBF in deep brain. By contrast, the semi-infinite homogenous solution resulted in substantial errors in rCBF (34.5% ≤ errors ≤ 60.2%) and BFIs in different layers. The Nth-order linear model simplifies data analysis, thus allowing for online data processing and displaying. Future study will test this linear algorithm in heterogeneous tissues with different levels of blood flow variations and noises.« less

Improved method for quantifying the avicide 3-chloro-p-toluidine hydrochloride in bird tissues using a deuterated surrogate/GC/MS method

USGS Publications Warehouse

Stahl, R.S.; Custer, T.W.; Pochop, P.A.; Johnston, J.J.

2002-01-01

A method using a deuterated surrogate of the avicide 3-chloro-p-toluidine hydrochloride (CPTH) was developed to quantify the CPTH residues in the gastrointestinal (Gl) tract and breast muscle tissues in birds collected in CPTH-baited sunflower and rice fields. This method increased the range of a previous surrogate/gas chromatography/mass spectroscopy method from 0-2 to 0-20mug/g in tissue samples and greatly simplified the extraction procedure. The modified method also sought to increase recoveries over a range of matrix effects introduced by analyzing tissues from birds collected in the field, where the GI tract contents would be affected by varying diet. The new method was used to determine the CPTH concentration In GI tract samples fortified with CPTH-treated rice bait to simulate the consumption of varying amounts of treated bait by two nontargeted bird species, pigeon (Columbia livia) and house sparrow (Passer domesticus). The new method was then used to examine the CPTH concentrations in the gizzard contents of the targeted bird species, red-winged black bird (Agelaius phoeniceus) and brown-headed cowbird (Molothrus ater) that were collected after feeding at a treated bait site. The method proved sufficiently sensitive to quantify CPTH in the breast muscle tissues and the gizzard contents of red-winged blackbirds and brown-headed cowbirds during an operational baiting program. The levels of CPTH determined for these birds in both tissue samples were determined to be highly correlated. The appearance of CPTH in the breast muscle tissue immediately after feeding was not anticipated. The potential secondary hazard posed by the targeted birds to potential scavengers and predators was also evaluated.

Identification and validation of quantitative real-time reverse transcription PCR reference genes for gene expression analysis in teak (Tectona grandis L.f.)

PubMed Central

2014-01-01

Background Teak (Tectona grandis L.f.) is currently the preferred choice of the timber trade for fabrication of woody products due to its extraordinary qualities and is widely grown around the world. Gene expression studies are essential to explore wood formation of vascular plants, and quantitative real-time reverse transcription PCR (qRT-PCR) is a sensitive technique employed for quantifying gene expression levels. One or more appropriate reference genes are crucial to accurately compare mRNA transcripts through different tissues/organs and experimental conditions. Despite being the focus of some genetic studies, a lack of molecular information has hindered genetic exploration of teak. To date, qRT-PCR reference genes have not been identified and validated for teak. Results Identification and cloning of nine commonly used qRT-PCR reference genes from teak, including ribosomal protein 60s (rp60s), clathrin adaptor complexes medium subunit family (Cac), actin (Act), histone 3 (His3), sand family (Sand), β-Tubulin (Β-Tub), ubiquitin (Ubq), elongation factor 1-α (Ef-1α), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Expression profiles of these genes were evaluated by qRT-PCR in six tissue and organ samples (leaf, flower, seedling, root, stem and branch secondary xylem) of teak. Appropriate gene cloning and sequencing, primer specificity and amplification efficiency was verified for each gene. Their stability as reference genes was validated by NormFinder, BestKeeper, geNorm and Delta Ct programs. Results obtained from all programs showed that TgUbq and TgEf-1α are the most stable genes to use as qRT-PCR reference genes and TgAct is the most unstable gene in teak. The relative expression of the teak cinnamyl alcohol dehydrogenase (TgCAD) gene in lignified tissues at different ages was assessed by qRT-PCR, using TgUbq and TgEf-1α as internal controls. These analyses exposed a consistent expression pattern with both reference genes. Conclusion This study proposes a first broad collection of teak tissue and organ mRNA expression data for nine selected candidate qRT-PCR reference genes. NormFinder, Bestkeeper, geNorm and Delta Ct analyses suggested that TgUbq and TgEf-1α have the highest expression stability and provided similar results when evaluating TgCAD gene expression, while the commonly used Act should be avoided. PMID:25048176

Tissue-specific selection of stable reference genes for real-time PCR normalization in an obese rat model.

PubMed

Cabiati, Manuela; Raucci, Serena; Caselli, Chiara; Guzzardi, Maria Angela; D'Amico, Andrea; Prescimone, Tommaso; Giannessi, Daniela; Del Ry, Silvia

2012-06-01

Obesity is a complex pathology with interacting and confounding causes due to the environment, hormonal signaling patterns, and genetic predisposition. At present, the Zucker rat is an eligible genetic model for research on obesity and metabolic syndrome, allowing scrutiny of gene expression profiles. Real-time PCR is the benchmark method for measuring mRNA expressions, but the accuracy and reproducibility of its data greatly depend on appropriate normalization strategies. In the Zucker rat model, no specific reference genes have been identified in myocardium, kidney, and lung, the main organs involved in this syndrome. The aim of this study was to select among ten candidates (Actb, Gapdh, Polr2a, Ywhag, Rpl13a, Sdha, Ppia, Tbp, Hprt1 and Tfrc) a set of reference genes that can be used for the normalization of mRNA expression data obtained by real-time PCR in obese and lean Zucker rats both at fasting and during acute hyperglycemia. The most stable genes in the heart were Sdha, Tbp, and Hprt1; in kidney, Tbp, Actb, and Gapdh were chosen, while Actb, Ywhag, and Sdha were selected as the most stably expressed set for pulmonary tissue. The normalization strategy was used to analyze mRNA expression of tumor necrosis factor α, the main inflammatory mediator in obesity, whose variations were more significant when normalized with the appropriately selected reference genes. The findings obtained in this study underline the importance of having three stably expressed reference gene sets for use in the cardiac, renal, and pulmonary tissues of an experimental model of obese and hyperglycemic Zucker rats.

Prototyping Faithful Execution in a Java virtual machine.

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

Tarman, Thomas David; Campbell, Philip LaRoche; Pierson, Lyndon George

2003-09-01

This report presents the implementation of a stateless scheme for Faithful Execution, the design for which is presented in a companion report, ''Principles of Faithful Execution in the Implementation of Trusted Objects'' (SAND 2003-2328). We added a simple cryptographic capability to an already simplified class loader and its associated Java Virtual Machine (JVM) to provide a byte-level implementation of Faithful Execution. The extended class loader and JVM we refer to collectively as the Sandia Faithfully Executing Java architecture (or JavaFE for short). This prototype is intended to enable exploration of more sophisticated techniques which we intend to implement in hardware.

A Quick Reference on Chloride.

PubMed

Bohn, Andrea A; de Morais, Helio Autran

2017-03-01

Chloride is an essential element, playing important roles in digestion, muscular activity, regulation of body fluids, and acid-base balance. As the most abundant anion in extracellular fluid, chloride plays a major role in maintaining electroneutrality. Chloride is intrinsically linked to sodium in maintaining osmolality and fluid balance and has an inverse relationship with bicarbonate in maintaining acid-base balance. It is likely because of these close ties that chloride does not get the individual attention it deserves; we can use these facts to simplify and interpret changes in serum chloride concentrations. Copyright © 2016 Elsevier Inc. All rights reserved.

Guidebook for analysis of tether applications

NASA Technical Reports Server (NTRS)

Carroll, J. A.

1985-01-01

This guidebook is intended as a tool to facilitate initial analyses of proposed tether applications in space. The guiding philosophy is that a brief analysis of all the common problem areas is far more useful than a detailed study in any one area. Such analyses can minimize the waste of resources on elegant but fatally flawed concepts, and can identify the areas where more effort is needed on concepts which do survive the initial analyses. The simplified formulas, approximations, and analytical tools included should be used only for preliminary analyses. For detailed analyses, the references with each topic and in the bibliography may be useful.

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

PubMed Central

Massa, Alicia N.; Childs, Kevin L.; Lin, Haining; Bryan, Glenn J.; Giuliano, Giovanni; Buell, C. Robin

2011-01-01

Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family. PMID:22046362

[Systemic lupus erythematosus and pregnancy].

PubMed

Basheva, S; Nikolov, A; Stoilov, R; Stoilov, N

2012-01-01

Connective-tissue disorders, also referred to as collagen-vascular disorders, are characterized by autoantibody-mediated connective-tissue abnormalities. These are also called immune-complex diseases because many involve deposition of immune complexes in specific organ or tissue sites. Some of these disorders are characterized by sterile inflammation, especially of the skin, joints, blood vessels, and kidneys, and are referred to as rheumatic diseases. For inexplicable reasons, many rheumatic diseases primarily affect women. Another major category of connective-tissue diseases includes inherited disorders of bone, skin, cartilage, blood vessels. Examples include Marfan syndrome, osteogenesis imperfecta, and Ehlers-Danlos syndrome. Lupus erythematosus (LE) is the main and most important disease in the group of systemic connective tissue diseases. It is heterogeneous, multiple organs autoimmune inflammatory disease with complex pathogenesis, which is the result of interaction between the susceptible genes and environmental factors that lead to abnormal immune response. In this review will consider: its incidence, pathogenesis, clinical forms and clinical features and diagnosis set based on generally accepted clinical criteria developed by the American College of Rheumatology (ACR), the course of pregnancy in patients suffering from LE, the most common complications of LE during pregnancy and antiphospholipid syndrome as part of LE.

New vibro-acoustic paradigms in biological tissues with application to diagnosis of pulmonary disorders

NASA Astrophysics Data System (ADS)

Zhang, Xiangling

The fundamental objective of the present study is to improve our understanding of audible sound propagation in the pulmonary system and torso. A related applied objective is to assess the feasibility of using audible acoustics for diagnosis of specific pulmonary conditions, such as pneumothorax (PTX). To accomplish these objectives, this study includes theoretical, computational and experimental developments aimed at: (1) better identifying the mechanical dynamic properties of soft biological tissues found in the torso region, (2) investigating the mechanisms of sound attenuation that occur when a PTX is present using greatly simplified theoretical and computational models, and (3) exploring the feasibility and utility of more comprehensive and precise computational finite element models of audible sound propagation in the pulmonary system and torso that would aid in related diagnostic developments. Mechanical material properties of soft biological tissue are studied for the low audible frequency range. The sensitivity to shear viscoelastic material constants of theoretical solutions for radiation impedance and surface wave motion are compared. Theoretical solutions are also compared to experimental measurements and numerical results from finite element analysis. It is found that, while prior theoretical solutions for radiation impedance are accurate, use of such measurements to estimate shear viscoelastic constants is not as precise as the use of surface wave measurements. The feasibility of using audible sound for diagnosis of pneumothorax is studied. Simplified one- and two-dimensional theoretical and numerical models of sound transmission through the pulmonary system and chest region to the chest wall surface are developed to more clearly understand the mechanism of energy loss when a pneumothorax is present, relative to a baseline case. A canine study on which these models are based predicts significant decreases in acoustic transmission strength when a pneumothorax is presented, in qualitative agreement with experimental measurements in dogs. Finally, the feasibility of building three-dimensional computational models is studied based on CT images of human subject or combination of the Horsfield airway model with geometry of other parts approximate from medical illustration. Preliminary results from these models show the same trend of acoustic energy loss when a PTX is present.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

NASA Astrophysics Data System (ADS)

Comi, Troy J.; Neumann, Elizabeth K.; Do, Thanh D.; Sweedler, Jonathan V.

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. [Figure not available: see fulltext.

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling.

PubMed

Comi, Troy J; Neumann, Elizabeth K; Do, Thanh D; Sweedler, Jonathan V

2017-09-01

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. Graphical Abstract ᅟ.

Effect of reference conditions on flow rate, modifier fraction and retention in supercritical fluid chromatography.

PubMed

De Pauw, Ruben; Shoykhet Choikhet, Konstantin; Desmet, Gert; Broeckhoven, Ken

2016-08-12

When using compressible mobile phases such as fluidic CO2, the density, the volumetric flow rates and volumetric fractions are pressure dependent. The pressure and temperature definition of these volumetric parameters (referred to as the reference conditions) may alter between systems, manufacturers and operating conditions. A supercritical fluid chromatography system was modified to operate in two modes with different definition of the eluent delivery parameters, referred to as fixed and variable mode. For the variable mode, the volumetric parameters are defined with reference to the pump operating pressure and actual pump head temperature. These conditions may vary when, e.g. changing the column length, permeability, flow rate, etc. and are thus variable reference conditions. For the fixed mode, the reference conditions were set at 150bar and 30°C, resulting in a mass flow rate and mass fraction of modifier definition which is independent of the operation conditions. For the variable mode, the mass flow rate of carbon dioxide increases with system pump operating pressure, decreasing the fraction of modifier. Comparing the void times and retention factor shows that the deviation between the two modes is almost independent of modifier percentage, but depends on the operating pressure. Recalculating the set volumetric fraction of modifier to the mass fraction results in the same retention behaviour for both modes. This shows that retention in SFC can be best modelled using the mass fraction of modifier. The fixed mode also simplifies method scaling as it only requires matching average column pressure. Copyright © 2016 Elsevier B.V. All rights reserved.

Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis in Isatis indigotica Fort.

PubMed Central

Li, Tao; Wang, Jing; Lu, Miao; Zhang, Tianyi; Qu, Xinyun; Wang, Zhezhi

2017-01-01

Due to its sensitivity and specificity, real-time quantitative PCR (qRT-PCR) is a popular technique for investigating gene expression levels in plants. Based on the Minimum Information for Publication of Real-Time Quantitative PCR Experiments (MIQE) guidelines, it is necessary to select and validate putative appropriate reference genes for qRT-PCR normalization. In the current study, three algorithms, geNorm, NormFinder, and BestKeeper, were applied to assess the expression stability of 10 candidate reference genes across five different tissues and three different abiotic stresses in Isatis indigotica Fort. Additionally, the IiYUC6 gene associated with IAA biosynthesis was applied to validate the candidate reference genes. The analysis results of the geNorm, NormFinder, and BestKeeper algorithms indicated certain differences for the different sample sets and different experiment conditions. Considering all of the algorithms, PP2A-4 and TUB4 were recommended as the most stable reference genes for total and different tissue samples, respectively. Moreover, RPL15 and PP2A-4 were considered to be the most suitable reference genes for abiotic stress treatments. The obtained experimental results might contribute to improved accuracy and credibility for the expression levels of target genes by qRT-PCR normalization in I. indigotica. PMID:28702046

A simplified fracture network model for studying the efficiency of a single well semi open loop heat exchanger in fractured crystalline rock

NASA Astrophysics Data System (ADS)

de La Bernardie, Jérôme; de Dreuzy, Jean-Raynald; Bour, Olivier; Thierion, Charlotte; Ausseur, Jean-Yves; Lesuer, Hervé; Le Borgne, Tanguy

2016-04-01

Geothermal energy is a renewable energy source particularly attractive due to associated low greenhouse gas emission rates. Crystalline rocks are in general considered of poor interest for geothermal applications at shallow depths (< 100m), because of the low permeability of the medium. In some cases, fractures may enhance permeability, but thermal energy storage at these shallow depths is still remaining very challenging because of the complexity of fractured media. The purpose of this study is to test the possibility of efficient thermal energy storage in shallow fractured rocks with a single well semi open loop heat exchanger (standing column well). For doing so, a simplified numerical model of fractured media is considered with few fractures. Here we present the different steps for building the model and for achieving the sensitivity analysis. First, an analytical and dimensional study on the equations has been achieved to highlight the main parameters that control the optimization of the system. In a second step, multiphysics software COMSOL was used to achieve numerical simulations in a very simplified model of fractured media. The objective was to test the efficiency of such a system to store and recover thermal energy depending on i) the few parameters controlling fracture network geometry (size and number of fractures) and ii) the frequency of cycles used to store and recover thermal energy. The results have then been compared to reference shallow geothermal systems already set up for porous media. Through this study, relationships between structure, heat exchanges and storage may be highlighted.

Realistic Vascular Replicator for TAVR Procedures.

PubMed

Rotman, Oren M; Kovarovic, Brandon; Sadasivan, Chander; Gruberg, Luis; Lieber, Baruch B; Bluestein, Danny

2018-04-13

Transcatheter aortic valve replacement (TAVR) is an over-the-wire procedure for treatment of severe aortic stenosis (AS). TAVR valves are conventionally tested using simplified left heart simulators (LHS). While those provide baseline performance reliably, their aortic root geometries are far from the anatomical in situ configuration, often overestimating the valves' performance. We report on a novel benchtop patient-specific arterial replicator designed for testing TAVR and training interventional cardiologists in the procedure. The Replicator is an accurate model of the human upper body vasculature for training physicians in percutaneous interventions. It comprises of fully-automated Windkessel mechanism to recreate physiological flow conditions. Calcified aortic valve models were fabricated and incorporated into the Replicator, then tested for performing TAVR procedure by an experienced cardiologist using the Inovare valve. EOA, pressures, and angiograms were monitored pre- and post-TAVR. A St. Jude mechanical valve was tested as a reference that is less affected by the AS anatomy. Results in the Replicator of both valves were compared to the performance in a commercial ISO-compliant LHS. The AS anatomy in the Replicator resulted in a significant decrease of the TAVR valve performance relative to the simplified LHS, with EOA and transvalvular pressures comparable to clinical data. Minor change was seen in the mechanical valve performance. The Replicator showed to be an effective platform for TAVR testing. Unlike a simplified geometric anatomy LHS, it conservatively provides clinically-relevant outcomes and complement it. The Replicator can be most valuable for testing new valves under challenging patient anatomies, physicians training, and procedural planning.

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean.

PubMed

Gao, Mengmeng; Liu, Yaping; Ma, Xiao; Shuai, Qin; Gai, Junyi; Li, Yan

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China. To identify the suitable reference genes for normalizing the expression levels of target genes by qRT-PCR in soybean response to Al, Cd and heat stresses, we studied the expression stability of ten commonly used housekeeping genes in soybean roots and leaves under these three abiotic stresses, using five approaches, BestKeeper, Delta Ct, geNorm, NormFinder and RefFinder. We found TUA4 is the most stable reference gene in soybean root tips under Al stress. Under Cd stress, Fbox and UKN2 are the most stable reference genes in roots and leaves, respectively, while 60S is the most suitable reference gene when analyzing both roots and leaves together. For heat stress, TUA4 and UKN2 are the most stable housekeeping genes in roots and leaves, respectively, and UKN2 is the best reference gene for analysis of roots and leaves together. To validate the reference genes, we quantified the relative expression levels of six target genes that were involved in soybean response to Al, Cd or heat stresses, respectively. The expression patterns of these target genes differed between using the most and least stable reference genes, suggesting the selection of a suitable reference gene is critical for gene expression studies.

A simplified strategy for studying the etiology of viral diseases: Apple stem grooving virus as a case study.

PubMed

Dhir, Sunny; Walia, Yashika; Zaidi, A A; Hallan, Vipin

2015-03-01

A simple method to amplify infective, complete genomes of single stranded RNA viruses by long distance PCR (LD PCR) from woody plant tissues is described in detail. The present protocol eliminates partial purification of viral particles and the amplification is achieved in three steps: (i) easy preparation of template RNA by incorporating a pre processing step before loading onto the column (ii) reverse transcription by AMV or Superscript reverse transcriptase and (iii) amplification of cDNA by LD PCR using LA or Protoscript Taq DNA polymerase. Incorporation of a preprocessing step helped to isolate consistent quality RNA from recalcitrant woody tissues such as apple, which was critical for efficient amplification of the complete genomes of Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV). Complete genome of ASGV was cloned under T7 RNA polymerase promoter and was confirmed to be infectious through transcript inoculation producing symptoms similar to the wild type virus. This is the first report for the largest RNA virus genome amplified by PCR from total nucleic acid extracts of woody plant tissues. Copyright © 2014 Elsevier B.V. All rights reserved.

[Maintainance of a research tissue bank. (Infra)structural and quality aspects].

PubMed

Schmitt, S; Kynast, K; Schirmacher, P; Herpel, E

2015-11-01

The availability of high quality human tissue samples and access to associated histopathological and clinical data are essential for biomedical research. Therefore, it is necessary to establish quality assured tissue biobanks that provide high quality tissue samples for research purposes. This entails quality concerns referring not only to the biomaterial specimen itself but encompassing all procedures related to biobanking, including the implementation of structural components, e.g. ethical and legal guidelines, quality management documentation as well as data and project management and information technology (IT) administration. Moreover, an integral aspect of tissue biobanks is the quality assured evaluation of every tissue specimen that is stored in a tissue biobank and used for projects to guarantee high quality assured biomaterial.

Evaluation of new antibiotic cocktails against contaminating bacteria found in allograft tissues.

PubMed

Serafini, Agnese; Riello, Erika; Trojan, Diletta; Cogliati, Elisa; Palù, Giorgio; Manganelli, Riccardo; Paolin, Adolfo

2016-12-01

Contamination of retrieved tissues is a major problem for allograft safety. Consequently, tissue banks have implemented decontamination protocols to eliminate microorganisms from tissues. Despite the widespread adoption of these protocols, few comprehensive studies validating such methods have been published. In this manuscript we compare the bactericidal activity of different antibiotic cocktails at different temperatures against a panel of bacterial species frequently isolated in allograft tissues collected at the Treviso Tissue Bank Foundation, a reference organization of the Veneto Region in Italy that was instituted to select, recover, process, store and distribute human tissues. We were able to identify at least two different formulations capable of killing most of the bacteria during prolonged incubation at 4 °C.

9 CFR 101.6 - Cell cultures.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Cell cultures. 101.6 Section 101.6..., SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS DEFINITIONS § 101.6 Cell cultures. When used in conjunction with or in reference to cell cultures, which may be referred to as tissue cultures...

9 CFR 101.6 - Cell cultures.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Cell cultures. 101.6 Section 101.6..., SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS DEFINITIONS § 101.6 Cell cultures. When used in conjunction with or in reference to cell cultures, which may be referred to as tissue cultures...

9 CFR 101.6 - Cell cultures.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Cell cultures. 101.6 Section 101.6..., SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS DEFINITIONS § 101.6 Cell cultures. When used in conjunction with or in reference to cell cultures, which may be referred to as tissue cultures...

9 CFR 101.6 - Cell cultures.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Cell cultures. 101.6 Section 101.6..., SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS DEFINITIONS § 101.6 Cell cultures. When used in conjunction with or in reference to cell cultures, which may be referred to as tissue cultures...

9 CFR 101.6 - Cell cultures.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Cell cultures. 101.6 Section 101.6..., SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS DEFINITIONS § 101.6 Cell cultures. When used in conjunction with or in reference to cell cultures, which may be referred to as tissue cultures...

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples

PubMed Central

2010-01-01

Background Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Results Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. Conclusions We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system. PMID:20492695

Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples.

PubMed

Mehta, Rohini; Birerdinc, Aybike; Hossain, Noreen; Afendy, Arian; Chandhoke, Vikas; Younossi, Zobair; Baranova, Ancha

2010-05-21

Given the epidemic proportions of obesity worldwide and the concurrent prevalence of metabolic syndrome, there is an urgent need for better understanding the underlying mechanisms of metabolic syndrome, in particular, the gene expression differences which may participate in obesity, insulin resistance and the associated series of chronic liver conditions. Real-time PCR (qRT-PCR) is the standard method for studying changes in relative gene expression in different tissues and experimental conditions. However, variations in amount of starting material, enzymatic efficiency and presence of inhibitors can lead to quantification errors. Hence the need for accurate data normalization is vital. Among several known strategies for data normalization, the use of reference genes as an internal control is the most common approach. Recent studies have shown that both obesity and presence of insulin resistance influence an expression of commonly used reference genes in omental fat. In this study we validated candidate reference genes suitable for qRT-PCR profiling experiments using visceral adipose samples from obese and lean individuals. Cross-validation of expression stability of eight selected reference genes using three popular algorithms, GeNorm, NormFinder and BestKeeper found ACTB and RPII as most stable reference genes. We recommend ACTB and RPII as stable reference genes most suitable for gene expression studies of human visceral adipose tissue. The use of these genes as a reference pair may further enhance the robustness of qRT-PCR in this model system.

Evaluation of Reference Genes for Quantitative Real-Time PCR in Songbirds

PubMed Central

Zinzow-Kramer, Wendy M.; Horton, Brent M.; Maney, Donna L.

2014-01-01

Quantitative real-time PCR (qPCR) is becoming a popular tool for the quantification of gene expression in the brain and endocrine tissues of songbirds. Accurate analysis of qPCR data relies on the selection of appropriate reference genes for normalization, yet few papers on songbirds contain evidence of reference gene validation. Here, we evaluated the expression of ten potential reference genes (18S, ACTB, GAPDH, HMBS, HPRT, PPIA, RPL4, RPL32, TFRC, and UBC) in brain, pituitary, ovary, and testis in two species of songbird: zebra finch and white-throated sparrow. We used two algorithms, geNorm and NormFinder, to assess the stability of these reference genes in our samples. We found that the suitability of some of the most popular reference genes for target gene normalization in mammals, such as 18S, depended highly on tissue type. Thus, they are not the best choices for brain and gonad in these songbirds. In contrast, we identified alternative genes, such as HPRT, RPL4 and PPIA, that were highly stable in brain, pituitary, and gonad in these species. Our results suggest that the validation of reference genes in mammals does not necessarily extrapolate to other taxonomic groups. For researchers wishing to identify and evaluate suitable reference genes for qPCR songbirds, our results should serve as a starting point and should help increase the power and utility of songbird models in behavioral neuroendocrinology. PMID:24780145

Assessment of the Risks from Imbedded Fragments of Depleted Uranium

DTIC Science & Technology

1993-03-01

for chronic kidney toxicity; the impact of fibrotic encapsulation , if it occurs; and the chemical form of the imbedded fragment. The potential for...Effects of Depleted Uranium Imbedded in Tissue Reference: Brigadier General Ronald R. Blanck (SGPS-PSP) letter of 26 February 1992 In response to your...the muscle and fatty tissue will probably occur and will occur in all other tissue types that elicit similar cellular responses to foreign bodies. It

Rice proteome analysis: a step toward functional analysis of the rice genome.

PubMed

Komatsu, Setsuko; Tanaka, Naoki

2005-03-01

The technique of proteome analysis using 2-DE has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this review, we describe construction of the rice proteome database, the cataloging of rice proteins, and the functional characterization of some of the proteins identified. Initially, proteins extracted from various tissues and organelles were separated by 2-DE and an image analyzer was used to construct a display or reference map of the proteins. The rice proteome database currently contains 23 reference maps based on 2-DE of proteins from different rice tissues and subcellular compartments. These reference maps comprise 13 129 rice proteins, and the amino acid sequences of 5092 of these proteins are entered in the database. Major proteins involved in growth or stress responses have been identified by using a proteomics approach and some of these proteins have unique functions. Furthermore, initial work has also begun on analyzing the phosphoproteome and protein-protein interactions in rice. The information obtained from the rice proteome database will aid in the molecular cloning of rice genes and in predicting the function of unknown proteins.