Computational design and engineering of polymeric orthodontic aligners.

PubMed

Barone, S; Paoli, A; Razionale, A V; Savignano, R

2016-10-05

Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner's effectiveness. Copyright © 2016 John Wiley & Sons, Ltd.

Anatomical parameterization for volumetric meshing of the liver

NASA Astrophysics Data System (ADS)

Vera, Sergio; González Ballester, Miguel A.; Gil, Debora

2014-03-01

A coordinate system describing the interior of organs is a powerful tool for a systematic localization of injured tissue. If the same coordinate values are assigned to specific anatomical landmarks, the coordinate system allows integration of data across different medical image modalities. Harmonic mappings have been used to produce parametric coordinate systems over the surface of anatomical shapes, given their flexibility to set values at specific locations through boundary conditions. However, most of the existing implementations in medical imaging restrict to either anatomical surfaces, or the depth coordinate with boundary conditions is given at sites of limited geometric diversity. In this paper we present a method for anatomical volumetric parameterization that extends current harmonic parameterizations to the interior anatomy using information provided by the volume medial surface. We have applied the methodology to define a common reference system for the liver shape and functional anatomy. This reference system sets a solid base for creating anatomical models of the patient's liver, and allows comparing livers from several patients in a common framework of reference.

[Age- and sex-specific reference intervals for 10 health examination items: mega-data from a Japanese Health Service Association].

PubMed

Suka, Machi; Yoshida, Katsumi; Kawai, Tadashi; Aoki, Yoshikazu; Yamane, Noriyuki; Yamauchi, Kuniaki

2005-07-01

To determine age- and sex-specific reference intervals for 10 health examination items in Japanese adults. Health examination data were accumulated from 24 different prefectural health service associations affiliated with the Japan Association of Health Service. Those who were non-smokers, drank less than 7 days/week, and had a body mass index of 18.5-24.9kg/m2 were sampled as a reference population (n = 737,538; 224,947 men and 512,591 women). After classified by age and sex, reference intervals for 10 health examination items (systolic blood pressure, diastolic blood pressure, total cholesterol, triglyceride, glucose, uric acid, AST, ALT, gamma-GT, and hemoglobin) were estimated using the parametric and nonparametric methods. In every item except for hemoglobin, men had higher reference intervals than women. Systolic blood pressure, total cholesterol, and glucose showed an upward trend in values with increasing age. Hemoglobin showed a downward trend in values with increasing age. Triglyceride, ALT, and gamma-GT reached a peak in middle age. Overall, parametric estimates showed narrower reference intervals than non-parametric estimates. Reference intervals vary with age and sex. Age- and sex-specific reference intervals may contribute to better assessment of health examination data.

Parametric mapping of [18F]fluoromisonidazole positron emission tomography using basis functions.

PubMed

Hong, Young T; Beech, John S; Smith, Rob; Baron, Jean-Claude; Fryer, Tim D

2011-02-01

In this study, we show a basis function method (BAFPIC) for voxelwise calculation of kinetic parameters (K(1), k(2), k(3), K(i)) and blood volume using an irreversible two-tissue compartment model. BAFPIC was applied to rat ischaemic stroke micro-positron emission tomography data acquired with the hypoxia tracer [(18)F]fluoromisonidazole because irreversible two-tissue compartmental modelling provided good fits to data from both hypoxic and normoxic tissues. Simulated data show that BAFPIC produces kinetic parameters with significantly lower variability and bias than nonlinear least squares (NLLS) modelling in hypoxic tissue. The advantage of BAFPIC over NLLS is less pronounced in normoxic tissue. K(i) determined from BAFPIC has lower variability than that from the Patlak-Gjedde graphical analysis (PGA) by up to 40% and lower bias, except for normoxic tissue at mid-high noise levels. Consistent with the simulation results, BAFPIC parametric maps of real data suffer less noise-induced variability than do NLLS and PGA. Delineation of hypoxia on BAFPIC k(3) maps is aided by low variability in normoxic tissue, which matches that in K(i) maps. BAFPIC produces K(i) values that correlate well with those from PGA (r(2)=0.93 to 0.97; slope 0.99 to 1.05, absolute intercept <0.00002 mL/g per min). BAFPIC is a computationally efficient method of determining parametric maps with low bias and variance.

Nakagami-m parametric imaging for characterization of thermal coagulation and cavitation erosion induced by HIFU.

PubMed

Han, Meng; Wang, Na; Guo, Shifang; Chang, Nan; Lu, Shukuan; Wan, Mingxi

2018-07-01

Nowadays, both thermal and mechanical ablation techniques of HIFU associated with cavitation have been developed for noninvasive treatment. A specific challenge for the successful clinical implementation of HIFU is to achieve real-time imaging for the evaluation and determination of therapy outcomes such as necrosis or homogenization. Ultrasound Nakagami-m parametric imaging highlights the degrading shadowing effects of bubbles and can be used for tissue characterization. The aim of this study is to investigate the performance of Nakagami-m parametric imaging for evaluating and differentiating thermal coagulation and cavitation erosion induced by HIFU. Lesions were induced in basic bovine serum albumin (BSA) phantoms and ex vivo porcine livers using a 1.6 MHz single-element transducer. Thermal and mechanical lesions induced by two types of HIFU sequences respectively were evaluated using Nakagami-m parametric imaging and ultrasound B-mode imaging. The lesion sizes estimated using Nakagami-m parametric imaging technique were all closer to the actual sizes than those of B-mode imaging. The p-value obtained from the t-test between the mean m values of thermal coagulation and cavitation erosion was smaller than 0.05, demonstrating that the m values of thermal lesions were significantly different from that of mechanical lesions, which was confirmed by ex vivo experiments and histologic examination showed that different changes result from HIFU exposure, one of tissue dehydration resulting from the thermal effect, and the other of tissue homogenate resulting from mechanical effect. This study demonstrated that Nakagami-m parametric imaging is a potential real-time imaging technique for evaluating and differentiating thermal coagulation and cavitation erosion. Copyright © 2018 Elsevier B.V. All rights reserved.

Parametric imaging using subharmonic signals from ultrasound contrast agents in patients with breast lesions.

PubMed

Eisenbrey, John R; Dave, Jaydev K; Merton, Daniel A; Palazzo, Juan P; Hall, Anne L; Forsberg, Flemming

2011-01-01

Parametric maps showing perfusion of contrast media can be useful tools for characterizing lesions in breast tissue. In this study we show the feasibility of parametric subharmonic imaging (SHI), which allows imaging of a vascular marker (the ultrasound contrast agent) while providing near complete tissue suppression. Digital SHI clips of 16 breast lesions from 14 women were acquired. Patients were scanned using a modified LOGIQ 9 scanner (GE Healthcare, Waukesha, WI) transmitting/receiving at 4.4/2.2 MHz. Using motion-compensated cumulative maximum intensity (CMI) sequences, parametric maps were generated for each lesion showing the time to peak (TTP), estimated perfusion (EP), and area under the time-intensity curve (AUC). Findings were grouped and compared according to biopsy results as benign lesions (n = 12, including 5 fibroadenomas and 3 cysts) and carcinomas (n = 4). For each lesion CMI, TTP, EP, and AUC parametric images were generated. No significant variations were detected with CMI (P = .80), TTP (P = .35), or AUC (P = .65). A statistically significant variation was detected for the average pixel EP (P = .002). Especially, differences were seen between carcinoma and benign lesions (mean ± SD, 0.10 ± 0.03 versus 0.05 ± 0.02 intensity units [IU]/s; P = .0014) and between carcinoma and fibroadenoma (0.10 ± 0.03 versus 0.04 ± 0.01 IU/s; P = .0044), whereas differences between carcinomas and cysts were found to be nonsignificant. In conclusion, a parametric imaging method for characterization of breast lesions using the high contrast to tissue signal provided by SHI has been developed. While the preliminary sample size was limited, results show potential for breast lesion characterization based on perfusion flow parameters.

Parametric approaches to micro-scale characterization of tissue volumes in vivo and ex vivo: Imaging microvasculature, attenuation, birefringence, and stiffness (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sampson, David D.; Chin, Lixin; Gong, Peijun; Wijesinghe, Philip; Es'haghian, Shaghayegh; Allen, Wesley M.; Klyen, Blake R.; Kirk, Rodney W.; Kennedy, Brendan F.; McLaughlin, Robert A.

2016-03-01

INVITED TALK Advances in imaging tissue microstructure in living subjects, or in freshly excised tissue with minimum preparation and processing, are important for future diagnosis and surgical guidance in the clinical setting, particularly for application to cancer. Whilst microscopy methods continue to advance on the cellular scale and medical imaging is well established on the scale of the whole tumor or organ, it is attractive to consider imaging the tumor environment on the micro-scale, between that of cells and whole tissues. Such a scenario is ideally suited to optical coherence tomography (OCT), with the twin attractions of requiring little or no tissue preparation, and in vivo capability. OCT's intrinsic scattering contrast reveals many morphological features of tumors, but is frequently ineffective in revealing other important aspects, such as microvasculature, or in reliably distinguishing tumor from uninvolved stroma. To address these shortcomings, we are developing several advances on the basic OCT approach. We are exploring speckle fluctuations to image tissue microvasculature and we have been developing several parametric approaches to tissue micro-scale characterization. Our approaches extract, from a three-dimensional OCT data set, a two-dimensional image of an optical parameter, such as attenuation or birefringence, or a mechanical parameter, such as stiffness, that aids in characterizing the tissue. This latter method, termed optical coherence elastography, parallels developments in ultrasound and magnetic resonance imaging. Parametric imaging of birefringence and of stiffness both show promise in addressing the important issue of differentiating cancer from uninvolved stroma in breast tissue.

The Absolute Stability Analysis in Fuzzy Control Systems with Parametric Uncertainties and Reference Inputs

NASA Astrophysics Data System (ADS)

Wu, Bing-Fei; Ma, Li-Shan; Perng, Jau-Woei

This study analyzes the absolute stability in P and PD type fuzzy logic control systems with both certain and uncertain linear plants. Stability analysis includes the reference input, actuator gain and interval plant parameters. For certain linear plants, the stability (i.e. the stable equilibriums of error) in P and PD types is analyzed with the Popov or linearization methods under various reference inputs and actuator gains. The steady state errors of fuzzy control systems are also addressed in the parameter plane. The parametric robust Popov criterion for parametric absolute stability based on Lur'e systems is also applied to the stability analysis of P type fuzzy control systems with uncertain plants. The PD type fuzzy logic controller in our approach is a single-input fuzzy logic controller and is transformed into the P type for analysis. In our work, the absolute stability analysis of fuzzy control systems is given with respect to a non-zero reference input and an uncertain linear plant with the parametric robust Popov criterion unlike previous works. Moreover, a fuzzy current controlled RC circuit is designed with PSPICE models. Both numerical and PSPICE simulations are provided to verify the analytical results. Furthermore, the oscillation mechanism in fuzzy control systems is specified with various equilibrium points of view in the simulation example. Finally, the comparisons are also given to show the effectiveness of the analysis method.

A non-invasive diffuse reflectance calibration-free method for absolute determination of exogenous biochemicals concentration in biological tissues

NASA Astrophysics Data System (ADS)

Lappa, Alexander V.; Kulikovskiy, Artem N.; Busarov, Oleg G.

2014-03-01

The paper presents a new method for distant non-destructive determination of concentration of light absorbing admixtures in turbid media. In particular, it is intended for non-invasive in vivo control of accumulation in patient tissues of various biochemicals introduced to the patients for chemotherapy, photodynamic therapy or diagnostics. It is require that the admixture absorption spectrum should have a clearly marked peak in the wavelength region where the pure medium one varies regularly. Fluorescence of admixtures is not required. The method uses the local diffuse reflectance spectroscopy with optical fiber probe including one emitting and two reading There are several features in the method: the value to be determined is absolute concentration of admixtures; the method needs no calibration measurements on phantoms; it needs no reference measurements on sample with zero admixture concentration; it uses a two parametric kinetic light propagation model and original algorithms to resolve direct and inverse tasks of radiation transport theory. Experimental testing passed with tissue equivalent phantoms and different admixtures, including a chlorine photosensitizer, showed accuracy under 10% in all cases.

A multicenter nationwide reference intervals study for common biochemical analytes in Turkey using Abbott analyzers.

PubMed

Ozarda, Yesim; Ichihara, Kiyoshi; Aslan, Diler; Aybek, Hulya; Ari, Zeki; Taneli, Fatma; Coker, Canan; Akan, Pinar; Sisman, Ali Riza; Bahceci, Onur; Sezgin, Nurzen; Demir, Meltem; Yucel, Gultekin; Akbas, Halide; Ozdem, Sebahat; Polat, Gurbuz; Erbagci, Ayse Binnur; Orkmez, Mustafa; Mete, Nuriye; Evliyaoglu, Osman; Kiyici, Aysel; Vatansev, Husamettin; Ozturk, Bahadir; Yucel, Dogan; Kayaalp, Damla; Dogan, Kubra; Pinar, Asli; Gurbilek, Mehmet; Cetinkaya, Cigdem Damla; Akin, Okhan; Serdar, Muhittin; Kurt, Ismail; Erdinc, Selda; Kadicesme, Ozgur; Ilhan, Necip; Atali, Dilek Sadak; Bakan, Ebubekir; Polat, Harun; Noyan, Tevfik; Can, Murat; Bedir, Abdulkerim; Okuyucu, Ali; Deger, Orhan; Agac, Suret; Ademoglu, Evin; Kaya, Ayşem; Nogay, Turkan; Eren, Nezaket; Dirican, Melahat; Tuncer, GulOzlem; Aykus, Mehmet; Gunes, Yeliz; Ozmen, Sevda Unalli; Kawano, Reo; Tezcan, Sehavet; Demirpence, Ozlem; Degirmen, Elif

2014-12-01

A nationwide multicenter study was organized to establish reference intervals (RIs) in the Turkish population for 25 commonly tested biochemical analytes and to explore sources of variation in reference values, including regionality. Blood samples were collected nationwide in 28 laboratories from the seven regions (≥400 samples/region, 3066 in all). The sera were collectively analyzed in Uludag University in Bursa using Abbott reagents and analyzer. Reference materials were used for standardization of test results. After secondary exclusion using the latent abnormal values exclusion method, RIs were derived by a parametric method employing the modified Box-Cox formula and compared with the RIs by the non-parametric method. Three-level nested ANOVA was used to evaluate variations among sexes, ages and regions. Associations between test results and age, body mass index (BMI) and region were determined by multiple regression analysis (MRA). By ANOVA, differences of reference values among seven regions were significant in none of the 25 analytes. Significant sex-related and age-related differences were observed for 10 and seven analytes, respectively. MRA revealed BMI-related changes in results for uric acid, glucose, triglycerides, high-density lipoprotein (HDL)-cholesterol, alanine aminotransferase, and γ-glutamyltransferase. Their RIs were thus derived by applying stricter criteria excluding individuals with BMI >28 kg/m2. Ranges of RIs by non-parametric method were wider than those by parametric method especially for those analytes affected by BMI. With the lack of regional differences and the well-standardized status of test results, the RIs derived from this nationwide study can be used for the entire Turkish population.

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

PubMed Central

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

2014-01-01

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

Establishment of reference intervals of clinical chemistry analytes for the adult population in Saudi Arabia: a study conducted as a part of the IFCC global study on reference values.

PubMed

Borai, Anwar; Ichihara, Kiyoshi; Al Masaud, Abdulaziz; Tamimi, Waleed; Bahijri, Suhad; Armbuster, David; Bawazeer, Ali; Nawajha, Mustafa; Otaibi, Nawaf; Khalil, Haitham; Kawano, Reo; Kaddam, Ibrahim; Abdelaal, Mohamed

2016-05-01

This study is a part of the IFCC-global study to derive reference intervals (RIs) for 28 chemistry analytes in Saudis. Healthy individuals (n=826) aged ≥18 years were recruited using the global study protocol. All specimens were measured using an Architect analyzer. RIs were derived by both parametric and non-parametric methods for comparative purpose. The need for secondary exclusion of reference values based on latent abnormal values exclusion (LAVE) method was examined. The magnitude of variation attributable to gender, ages and regions was calculated by the standard deviation ratio (SDR). Sources of variations: age, BMI, physical exercise and smoking levels were investigated by using the multiple regression analysis. SDRs for gender, age and regional differences were significant for 14, 8 and 2 analytes, respectively. BMI-related changes in test results were noted conspicuously for CRP. For some metabolic related parameters the ranges of RIs by non-parametric method were wider than by the parametric method and RIs derived using the LAVE method were significantly different than those without it. RIs were derived with and without gender partition (BMI, drugs and supplements were considered). RIs applicable to Saudis were established for the majority of chemistry analytes, whereas gender, regional and age RI partitioning was required for some analytes. The elevated upper limits of metabolic analytes reflects the existence of high prevalence of metabolic syndrome in Saudi population.

MRI-guided attenuation correction in whole-body PET/MR: assessment of the effect of bone attenuation.

PubMed

Akbarzadeh, A; Ay, M R; Ahmadian, A; Alam, N Riahi; Zaidi, H

2013-02-01

Hybrid PET/MRI presents many advantages in comparison with its counterpart PET/CT in terms of improved soft-tissue contrast, decrease in radiation exposure, and truly simultaneous and multi-parametric imaging capabilities. However, the lack of well-established methodology for MR-based attenuation correction is hampering further development and wider acceptance of this technology. We assess the impact of ignoring bone attenuation and using different tissue classes for generation of the attenuation map on the accuracy of attenuation correction of PET data. This work was performed using simulation studies based on the XCAT phantom and clinical input data. For the latter, PET and CT images of patients were used as input for the analytic simulation model using realistic activity distributions where CT-based attenuation correction was utilized as reference for comparison. For both phantom and clinical studies, the reference attenuation map was classified into various numbers of tissue classes to produce three (air, soft tissue and lung), four (air, lungs, soft tissue and cortical bones) and five (air, lungs, soft tissue, cortical bones and spongeous bones) class attenuation maps. The phantom studies demonstrated that ignoring bone increases the relative error by up to 6.8% in the body and up to 31.0% for bony regions. Likewise, the simulated clinical studies showed that the mean relative error reached 15% for lesions located in the body and 30.7% for lesions located in bones, when neglecting bones. These results demonstrate an underestimation of about 30% of tracer uptake when neglecting bone, which in turn imposes substantial loss of quantitative accuracy for PET images produced by hybrid PET/MRI systems. Considering bones in the attenuation map will considerably improve the accuracy of MR-guided attenuation correction in hybrid PET/MR to enable quantitative PET imaging on hybrid PET/MR technologies.

Optimised analytical models of the dielectric properties of biological tissue.

PubMed

Salahuddin, Saqib; Porter, Emily; Krewer, Finn; O' Halloran, Martin

2017-05-01

The interaction of electromagnetic fields with the human body is quantified by the dielectric properties of biological tissues. These properties are incorporated into complex numerical simulations using parametric models such as Debye and Cole-Cole, for the computational investigation of electromagnetic wave propagation within the body. These parameters can be acquired through a variety of optimisation algorithms to achieve an accurate fit to measured data sets. A number of different optimisation techniques have been proposed, but these are often limited by the requirement for initial value estimations or by the large overall error (often up to several percentage points). In this work, a novel two-stage genetic algorithm proposed by the authors is applied to optimise the multi-pole Debye parameters for 54 types of human tissues. The performance of the two-stage genetic algorithm has been examined through a comparison with five other existing algorithms. The experimental results demonstrate that the two-stage genetic algorithm produces an accurate fit to a range of experimental data and efficiently out-performs all other optimisation algorithms under consideration. Accurate values of the three-pole Debye models for 54 types of human tissues, over 500 MHz to 20 GHz, are also presented for reference. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

An Optical Parametric Amplifier for Profiling Gases of Atmospheric Interest

NASA Technical Reports Server (NTRS)

Heaps, William (Technical Monitor); Burris, John; Richter, Dale

2004-01-01

This paper describes the development of a lidar transmitter using an optical parametric amplifier. It is designed for profiling gases of atmospheric interest at high spatial and temporal precision in the near-IR. Discussions on desirable characteristics for such a transmitter with specific reference to the case of CO, are made.

A stereotaxic, population-averaged T1w ovine brain atlas including cerebral morphology and tissue volumes

PubMed Central

Nitzsche, Björn; Frey, Stephen; Collins, Louis D.; Seeger, Johannes; Lobsien, Donald; Dreyer, Antje; Kirsten, Holger; Stoffel, Michael H.; Fonov, Vladimir S.; Boltze, Johannes

2015-01-01

Standard stereotaxic reference systems play a key role in human brain studies. Stereotaxic coordinate systems have also been developed for experimental animals including non-human primates, dogs, and rodents. However, they are lacking for other species being relevant in experimental neuroscience including sheep. Here, we present a spatial, unbiased ovine brain template with tissue probability maps (TPM) that offer a detailed stereotaxic reference frame for anatomical features and localization of brain areas, thereby enabling inter-individual and cross-study comparability. Three-dimensional data sets from healthy adult Merino sheep (Ovis orientalis aries, 12 ewes and 26 neutered rams) were acquired on a 1.5 T Philips MRI using a T1w sequence. Data were averaged by linear and non-linear registration algorithms. Moreover, animals were subjected to detailed brain volume analysis including examinations with respect to body weight (BW), age, and sex. The created T1w brain template provides an appropriate population-averaged ovine brain anatomy in a spatial standard coordinate system. Additionally, TPM for gray (GM) and white (WM) matter as well as cerebrospinal fluid (CSF) classification enabled automatic prior-based tissue segmentation using statistical parametric mapping (SPM). Overall, a positive correlation of GM volume and BW explained about 15% of the variance of GM while a positive correlation between WM and age was found. Absolute tissue volume differences were not detected, indeed ewes showed significantly more GM per bodyweight as compared to neutered rams. The created framework including spatial brain template and TPM represent a useful tool for unbiased automatic image preprocessing and morphological characterization in sheep. Therefore, the reported results may serve as a starting point for further experimental and/or translational research aiming at in vivo analysis in this species. PMID:26089780

Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping

PubMed Central

Yarnykh, Vasily L.

2015-01-01

Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097

Accuracy and variability of tumor burden measurement on multi-parametric MRI

NASA Astrophysics Data System (ADS)

Salarian, Mehrnoush; Gibson, Eli; Shahedi, Maysam; Gaed, Mena; Gómez, José A.; Moussa, Madeleine; Romagnoli, Cesare; Cool, Derek W.; Bastian-Jordan, Matthew; Chin, Joseph L.; Pautler, Stephen; Bauman, Glenn S.; Ward, Aaron D.

2014-03-01

Measurement of prostate tumour volume can inform prognosis and treatment selection, including an assessment of the suitability and feasibility of focal therapy, which can potentially spare patients the deleterious side effects of radical treatment. Prostate biopsy is the clinical standard for diagnosis but provides limited information regarding tumour volume due to sparse tissue sampling. A non-invasive means for accurate determination of tumour burden could be of clinical value and an important step toward reduction of overtreatment. Multi-parametric magnetic resonance imaging (MPMRI) is showing promise for prostate cancer diagnosis. However, the accuracy and inter-observer variability of prostate tumour volume estimation based on separate expert contouring of T2-weighted (T2W), dynamic contrastenhanced (DCE), and diffusion-weighted (DW) MRI sequences acquired using an endorectal coil at 3T is currently unknown. We investigated this question using a histologic reference standard based on a highly accurate MPMRIhistology image registration and a smooth interpolation of planimetric tumour measurements on histology. Our results showed that prostate tumour volumes estimated based on MPMRI consistently overestimated histological reference tumour volumes. The variability of tumour volume estimates across the different pulse sequences exceeded interobserver variability within any sequence. Tumour volume estimates on DCE MRI provided the lowest inter-observer variability and the highest correlation with histology tumour volumes, whereas the apparent diffusion coefficient (ADC) maps provided the lowest volume estimation error. If validated on a larger data set, the observed correlations could support the development of automated prostate tumour volume segmentation algorithms as well as correction schemes for tumour burden estimation on MPMRI.

Automated unsupervised multi-parametric classification of adipose tissue depots in skeletal muscle

PubMed Central

Valentinitsch, Alexander; Karampinos, Dimitrios C.; Alizai, Hamza; Subburaj, Karupppasamy; Kumar, Deepak; Link, Thomas M.; Majumdar, Sharmila

2012-01-01

Purpose To introduce and validate an automated unsupervised multi-parametric method for segmentation of the subcutaneous fat and muscle regions in order to determine subcutaneous adipose tissue (SAT) and intermuscular adipose tissue (IMAT) areas based on data from a quantitative chemical shift-based water-fat separation approach. Materials and Methods Unsupervised standard k-means clustering was employed to define sets of similar features (k = 2) within the whole multi-modal image after the water-fat separation. The automated image processing chain was composed of three primary stages including tissue, muscle and bone region segmentation. The algorithm was applied on calf and thigh datasets to compute SAT and IMAT areas and was compared to a manual segmentation. Results The IMAT area using the automatic segmentation had excellent agreement with the IMAT area using the manual segmentation for all the cases in the thigh (R2: 0.96) and for cases with up to moderate IMAT area in the calf (R2: 0.92). The group with the highest grade of muscle fat infiltration in the calf had the highest error in the inner SAT contour calculation. Conclusion The proposed multi-parametric segmentation approach combined with quantitative water-fat imaging provides an accurate and reliable method for an automated calculation of the SAT and IMAT areas reducing considerably the total post-processing time. PMID:23097409

Linear time-dependent reference intervals where there is measurement error in the time variable-a parametric approach.

PubMed

Gillard, Jonathan

2015-12-01

This article re-examines parametric methods for the calculation of time specific reference intervals where there is measurement error present in the time covariate. Previous published work has commonly been based on the standard ordinary least squares approach, weighted where appropriate. In fact, this is an incorrect method when there are measurement errors present, and in this article, we show that the use of this approach may, in certain cases, lead to referral patterns that may vary with different values of the covariate. Thus, it would not be the case that all patients are treated equally; some subjects would be more likely to be referred than others, hence violating the principle of equal treatment required by the International Federation for Clinical Chemistry. We show, by using measurement error models, that reference intervals are produced that satisfy the requirement for equal treatment for all subjects. © The Author(s) 2011.

Tremor Detection Using Parametric and Non-Parametric Spectral Estimation Methods: A Comparison with Clinical Assessment

PubMed Central

Martinez Manzanera, Octavio; Elting, Jan Willem; van der Hoeven, Johannes H.; Maurits, Natasha M.

2016-01-01

In the clinic, tremor is diagnosed during a time-limited process in which patients are observed and the characteristics of tremor are visually assessed. For some tremor disorders, a more detailed analysis of these characteristics is needed. Accelerometry and electromyography can be used to obtain a better insight into tremor. Typically, routine clinical assessment of accelerometry and electromyography data involves visual inspection by clinicians and occasionally computational analysis to obtain objective characteristics of tremor. However, for some tremor disorders these characteristics may be different during daily activity. This variability in presentation between the clinic and daily life makes a differential diagnosis more difficult. A long-term recording of tremor by accelerometry and/or electromyography in the home environment could help to give a better insight into the tremor disorder. However, an evaluation of such recordings using routine clinical standards would take too much time. We evaluated a range of techniques that automatically detect tremor segments in accelerometer data, as accelerometer data is more easily obtained in the home environment than electromyography data. Time can be saved if clinicians only have to evaluate the tremor characteristics of segments that have been automatically detected in longer daily activity recordings. We tested four non-parametric methods and five parametric methods on clinical accelerometer data from 14 patients with different tremor disorders. The consensus between two clinicians regarding the presence or absence of tremor on 3943 segments of accelerometer data was employed as reference. The nine methods were tested against this reference to identify their optimal parameters. Non-parametric methods generally performed better than parametric methods on our dataset when optimal parameters were used. However, one parametric method, employing the high frequency content of the tremor bandwidth under consideration (High Freq) performed similarly to non-parametric methods, but had the highest recall values, suggesting that this method could be employed for automatic tremor detection. PMID:27258018

Characterization of the Embryogenic Tissue of the Norway Spruce Including a Transition Layer between the Tissue and the Culture Medium by Magnetic Resonance Imaging

NASA Astrophysics Data System (ADS)

Kořínek, R.; Mikulka, J.; Hřib, J.; Hudec, J.; Havel, L.; Bartušek, K.

2017-02-01

The paper describes the visualization of the cells (ESEs) and mucilage (ECMSN) in an embryogenic tissue via magnetic resonance imaging (MRI) relaxometry measurement combined with the subsequent multi-parametric segmentation. The computed relaxometry maps T1 and T2 show a thin layer (transition layer) between the culture medium and the embryogenic tissue. The ESEs, mucilage, and transition layer differ in their relaxation times T1 and T2; thus, these times can be used to characterize the individual parts within the embryogenic tissue. The observed mean values of the relaxation times T1 and T2 of the ESEs, mucilage, and transition layer are as follows: 1469 ± 324 and 53 ± 10 ms, 1784 ± 124 and 74 ± 8 ms, 929 ± 164 and 32 ± 4.7 ms, respectively. The multi-parametric segmentation exploiting the T1 and T2 relaxation times as a classifier shows the distribution of the ESEs and mucilage within the embryogenic tissue. The discussed T1 and T2 indicators can be utilized to characterize both the growth-related changes in an embryogenic tissue and the effect of biotic/abiotic stresses, thus potentially becoming a distinctive indicator of the state of any examined embryogenic tissue.

PARAMETRIC AND NON PARAMETRIC (MARS: MULTIVARIATE ADDITIVE REGRESSION SPLINES) LOGISTIC REGRESSIONS FOR PREDICTION OF A DICHOTOMOUS RESPONSE VARIABLE WITH AN EXAMPLE FOR PRESENCE/ABSENCE OF AMPHIBIANS

EPA Science Inventory

The purpose of this report is to provide a reference manual that could be used by investigators for making informed use of logistic regression using two methods (standard logistic regression and MARS). The details for analyses of relationships between a dependent binary response ...

Direct Bio-printing with Heterogeneous Topology Design.

PubMed

Ahsan, Amm Nazmul; Xie, Ruinan; Khoda, Bashir

2017-01-01

Bio-additive manufacturing is a promising tool to fabricate porous scaffold structures for expediting the tissue regeneration processes. Unlike the most traditional bulk material objects, the microstructures of tissue and organs are mostly highly anisotropic, heterogeneous, and porous in nature. However, modelling the internal heterogeneity of tissues/organs structures in the traditional CAD environment is difficult and oftentimes inaccurate. Besides, the de facto STL conversion of bio-models introduces loss of information and piles up more errors in each subsequent step (build orientation, slicing, tool-path planning) of the bio-printing process plan. We are proposing a topology based scaffold design methodology to accurately represent the heterogeneous internal architecture of tissues/organs. An image analysis technique is used that digitizes the topology information contained in medical images of tissues/organs. A weighted topology reconstruction algorithm is implemented to represent the heterogeneity with parametric functions. The parametric functions are then used to map the spatial material distribution. The generated information is directly transferred to the 3D bio-printer and heterogeneous porous tissue scaffold structure is manufactured without STL file. The proposed methodology is implemented to verify the effectiveness of the approach and the designed example structure is bio-fabricated with a deposition based bio-additive manufacturing system.

Parametric Method Performance for Dynamic 3'-Deoxy-3'-18F-Fluorothymidine PET/CT in Epidermal Growth Factor Receptor-Mutated Non-Small Cell Lung Carcinoma Patients Before and During Therapy.

PubMed

Kramer, Gerbrand Maria; Frings, Virginie; Heijtel, Dennis; Smit, E F; Hoekstra, Otto S; Boellaard, Ronald

2017-06-01

The objective of this study was to validate several parametric methods for quantification of 3'-deoxy-3'- 18 F-fluorothymidine ( 18 F-FLT) PET in advanced-stage non-small cell lung carcinoma (NSCLC) patients with an activating epidermal growth factor receptor mutation who were treated with gefitinib or erlotinib. Furthermore, we evaluated the impact of noise on accuracy and precision of the parametric analyses of dynamic 18 F-FLT PET/CT to assess the robustness of these methods. Methods : Ten NSCLC patients underwent dynamic 18 F-FLT PET/CT at baseline and 7 and 28 d after the start of treatment. Parametric images were generated using plasma input Logan graphic analysis and 2 basis functions-based methods: a 2-tissue-compartment basis function model (BFM) and spectral analysis (SA). Whole-tumor-averaged parametric pharmacokinetic parameters were compared with those obtained by nonlinear regression of the tumor time-activity curve using a reversible 2-tissue-compartment model with blood volume fraction. In addition, 2 statistically equivalent datasets were generated by countwise splitting the original list-mode data, each containing 50% of the total counts. Both new datasets were reconstructed, and parametric pharmacokinetic parameters were compared between the 2 replicates and the original data. Results: After the settings of each parametric method were optimized, distribution volumes (V T ) obtained with Logan graphic analysis, BFM, and SA all correlated well with those derived using nonlinear regression at baseline and during therapy ( R 2 ≥ 0.94; intraclass correlation coefficient > 0.97). SA-based V T images were most robust to increased noise on a voxel-level (repeatability coefficient, 16% vs. >26%). Yet BFM generated the most accurate K 1 values ( R 2 = 0.94; intraclass correlation coefficient, 0.96). Parametric K 1 data showed a larger variability in general; however, no differences were found in robustness between methods (repeatability coefficient, 80%-84%). Conclusion: Both BFM and SA can generate quantitatively accurate parametric 18 F-FLT V T images in NSCLC patients before and during therapy. SA was more robust to noise, yet BFM provided more accurate parametric K 1 data. We therefore recommend BFM as the preferred parametric method for analysis of dynamic 18 F-FLT PET/CT studies; however, SA can also be used. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Parametric Architecture in the Urban Space

NASA Astrophysics Data System (ADS)

Januszkiewicz, Krystyna; Kowalski, Karol G.

2017-10-01

The paper deals with the parametric architecture which is trying to introduce a new spatial language in the context for urban tissue that correspond to the artistic consciousness and the attitude of information and digital technologies era. The first part of the paper defines the main features of parametric architecture (such as: folding, continuity and curvilinearity) which are are characteristic of the new style of named the “parametricism”. This architecture is a strong emphasis on geometry, materiality, feasibility and sustainability, what emerges is an explicit agenda promoting material ornamentation, spatial spectacle and formal theatricality. The second part presents result of case study, especially parametric public use buildings, within the tissue of city. The analyzed objects are: The Sage Gateshead (1998-2004) in Gateshead, Kunsthaus in Graz (2000-2003), the Weltstadthaus (2003-2005) in Cologne, The Golden Terraces in Warsaw (2000-2007), the Metropol Parasol in Seville (2005-2011) the King Cross Station (2005-2012) in London, the headquarters of the Pathé Foundation (2006-2014) in Paris. Each of the enumerated examples shows a diverse approach to designing in the urban space, which reflect the age of digital technologies and the information society. In conclusion emphasizes, that new concept of the spatialization of architecture is the equivalent of the democratization of the political system, the liberalization of the economy, among other examples.

A non-parametric peak calling algorithm for DamID-Seq.

PubMed

Li, Renhua; Hempel, Leonie U; Jiang, Tingbo

2015-01-01

Protein-DNA interactions play a significant role in gene regulation and expression. In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription factor in sex determination, we applied the DNA adenine methylation identification (DamID) technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq). One feature of DamID-Seq data is that induced adenine methylation signals are not assured to be symmetrically distributed at TFBS, which renders the existing peak calling algorithms for ChIP-Seq, including SPP and MACS, inappropriate for DamID-Seq data. This challenged us to develop a new algorithm for peak calling. A challenge in peaking calling based on sequence data is estimating the averaged behavior of background signals. We applied a bootstrap resampling method to short sequence reads in the control (Dam only). After data quality check and mapping reads to a reference genome, the peaking calling procedure compromises the following steps: 1) reads resampling; 2) reads scaling (normalization) and computing signal-to-noise fold changes; 3) filtering; 4) Calling peaks based on a statistically significant threshold. This is a non-parametric method for peak calling (NPPC). We also used irreproducible discovery rate (IDR) analysis, as well as ChIP-Seq data to compare the peaks called by the NPPC. We identified approximately 6,000 peaks for DSX, which point to 1,225 genes related to the fat body tissue difference between female and male Drosophila. Statistical evidence from IDR analysis indicated that these peaks are reproducible across biological replicates. In addition, these peaks are comparable to those identified by use of ChIP-Seq on S2 cells, in terms of peak number, location, and peaks width.

Refining patterns of joint hypermobility, habitus, and orthopedic traits in joint hypermobility syndrome and Ehlers-Danlos syndrome, hypermobility type.

PubMed

Morlino, Silvia; Dordoni, Chiara; Sperduti, Isabella; Venturini, Marina; Celletti, Claudia; Camerota, Filippo; Colombi, Marina; Castori, Marco

2017-04-01

Joint hypermobility syndrome (JHS) and Ehlers-Danlos syndrome, hypermobility type (EDS-HT) are two overlapping heritable disorders (JHS/EDS-HT) recognized by separated sets of diagnostic criteria and still lack a confirmatory test. This descriptive research was aimed at better characterizing the clinical phenotype of JHS/EDS-HT with focus on available diagnostic criteria, and in order to propose novel features and assessment strategies. One hundred and eighty-nine (163 females, 26 males; age: 2-73 years) patients from two Italian reference centers were investigated for Beighton score, range of motion in 21 additional joints, rate and sites of dislocations and sprains, recurrent soft-tissue injuries, tendon and muscle ruptures, body mass index, arm span/height ratio, wrist and thumb signs, and 12 additional orthopedic features. Rough rates were compared by age, sex, and handedness with a series of parametric and non-parametric tools. Multiple correspondence analysis was carried out for possible co-segregations of features. Beighton score and hypermobility at other joints were influenced by age at diagnosis. Rate and sites of joint instability complications did not vary according to age at diagnosis except for soft-tissue injuries. No major difference was registered by sex and dominant versus non-dominant body side. At multiple correspondence analysis, selected features tend to co-segregate in a dichotomous distribution. Dolichostenomelia and arachnodactyly segregated independently. This study pointed out a more protean musculoskeletal phenotype than previously considered according to available diagnostic criteria for JHS/EDS-HT. Our findings corroborated the need for a re-thinking of JHS/EDS-HT on clinical grounds in order to find better therapeutic and research strategies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Kinetic modeling of PET-FDG in the brain without blood sampling.

PubMed

Bentourkia, M'hamed

2006-12-01

The aim in this work is to report a new method to calculate parametric images from a single scan acquisition with positron emission tomography (PET) and fluorodeoxyglucose (FDG) in the human brain without blood sampling. It is usually practical for research or clinical purposes to inject the patient in an isolated room and to start the PET acquisition only for some 10-20 min, about 30 min after FDG injection. In order to calculate the cerebral metabolic rates for glucose (CMRG), usually several blood samples are required. The proposed method considers the relation between the uptake of the tracer in the cerebellum as a reference tissue and the population based input curve. Similar results were obtained for CMRG values with the present method in comparison to the usual autoradiographic and the non-linear least squares fitting of regions of interest.

Usefulness of myocardial parametric imaging to evaluate myocardial viability in experimental and in clinical studies.

PubMed

Korosoglou, G; Hansen, A; Bekeredjian, R; Filusch, A; Hardt, S; Wolf, D; Schellberg, D; Katus, H A; Kuecherer, H

2006-03-01

To evaluate whether myocardial parametric imaging (MPI) is superior to visual assessment for the evaluation of myocardial viability. Myocardial contrast echocardiography (MCE) was assessed in 11 pigs before, during, and after left anterior descending coronary artery occlusion and in 32 patients with ischaemic heart disease by using intravenous SonoVue administration. In experimental studies perfusion defect area assessment by MPI was compared with visually guided perfusion defect planimetry. Histological assessment of necrotic tissue was the standard reference. In clinical studies viability was assessed on a segmental level by (1) visual analysis of myocardial opacification; (2) quantitative estimation of myocardial blood flow in regions of interest; and (3) MPI. Functional recovery between three and six months after revascularisation was the standard reference. In experimental studies, compared with visually guided perfusion defect planimetry, planimetric assessment of infarct size by MPI correlated more significantly with histology (r2 = 0.92 versus r2 = 0.56) and had a lower intraobserver variability (4% v 15%, p < 0.05). In clinical studies, MPI had higher specificity (66% v 43%, p < 0.05) than visual MCE and good accuracy (81%) for viability detection. It was less time consuming (3.4 (1.6) v 9.2 (2.4) minutes per image, p < 0.05) than quantitative blood flow estimation by regions of interest and increased the agreement between observers interpreting myocardial perfusion (kappa = 0.87 v kappa = 0.75, p < 0.05). MPI is useful for the evaluation of myocardial viability both in animals and in patients. It is less time consuming than quantification analysis by regions of interest and less observer dependent than visual analysis. Thus, strategies incorporating this technique may be valuable for the evaluation of myocardial viability in clinical routine.

Direct adaptive robust tracking control for 6 DOF industrial robot with enhanced accuracy.

PubMed

Yin, Xiuxing; Pan, Li

2018-01-01

A direct adaptive robust tracking control is proposed for trajectory tracking of 6 DOF industrial robot in the presence of parametric uncertainties, external disturbances and uncertain nonlinearities. The controller is designed based on the dynamic characteristics in the working space of the end-effector of the 6 DOF robot. The controller includes robust control term and model compensation term that is developed directly based on the input reference or desired motion trajectory. A projection-type parametric adaptation law is also designed to compensate for parametric estimation errors for the adaptive robust control. The feasibility and effectiveness of the proposed direct adaptive robust control law and the associated projection-type parametric adaptation law have been comparatively evaluated based on two 6 DOF industrial robots. The test results demonstrate that the proposed control can be employed to better maintain the desired trajectory tracking even in the presence of large parametric uncertainties and external disturbances as compared with PD controller and nonlinear controller. The parametric estimates also eventually converge to the real values along with the convergence of tracking errors, which further validate the effectiveness of the proposed parametric adaption law. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Age-dependent biochemical quantities: an approach for calculating reference intervals.

PubMed

Bjerner, J

2007-01-01

A parametric method is often preferred when calculating reference intervals for biochemical quantities, as non-parametric methods are less efficient and require more observations/study subjects. Parametric methods are complicated, however, because of three commonly encountered features. First, biochemical quantities seldom display a Gaussian distribution, and there must either be a transformation procedure to obtain such a distribution or a more complex distribution has to be used. Second, biochemical quantities are often dependent on a continuous covariate, exemplified by rising serum concentrations of MUC1 (episialin, CA15.3) with increasing age. Third, outliers often exert substantial influence on parametric estimations and therefore need to be excluded before calculations are made. The International Federation of Clinical Chemistry (IFCC) currently recommends that confidence intervals be calculated for the reference centiles obtained. However, common statistical packages allowing for the adjustment of a continuous covariate do not make this calculation. In the method described in the current study, Tukey's fence is used to eliminate outliers and two-stage transformations (modulus-exponential-normal) in order to render Gaussian distributions. Fractional polynomials are employed to model functions for mean and standard deviations dependent on a covariate, and the model is selected by maximum likelihood. Confidence intervals are calculated for the fitted centiles by combining parameter estimation and sampling uncertainties. Finally, the elimination of outliers was made dependent on covariates by reiteration. Though a good knowledge of statistical theory is needed when performing the analysis, the current method is rewarding because the results are of practical use in patient care.

Determination of in vivo mechanical properties of long bones from their impedance response curves

NASA Technical Reports Server (NTRS)

Borders, S. G.

1981-01-01

A mathematical model consisting of a uniform, linear, visco-elastic, Euler-Bernoulli beam to represent the ulna or tibia of the vibrating forearm or leg system is developed. The skin and tissue compressed between the probe and bone is represented by a spring in series with the beam. The remaining skin and tissue surrounding the bone is represented by a visco-elastic foundation with mass. An extensive parametric study is carried out to determine the effect of each parameter of the mathematical model on its impedance response. A system identification algorithm is developed and programmed on a digital computer to determine the parametric values of the model which best simulate the data obtained from an impedance test.

Parametric study of potential early commercial MHD power plants

NASA Technical Reports Server (NTRS)

Hals, F. A.

1979-01-01

Three different reference power plant configurations were considered with parametric variations of the various design parameters for each plant. Two of the reference plant designs were based on the use of high temperature regenerative air preheaters separately fired by a low Btu gas produced from a coal gasifier which was integrated with the power plant. The third reference plant design was based on the use of oxygen enriched combustion air preheated to a more moderate temperature in a tubular type metallic recuperative heat exchanger which is part of the bottoming plant heat recovery system. Comparative information was developed on plant performance and economics. The highest net plant efficiency of about 45 percent was attained by the reference plant design with the use of a high temperature air preheater separately fired with the advanced entrained bed gasifier. The use of oxygen enrichment of the combustion air yielded the lowest cost of generating electricity at a slightly lower plant efficiency. Both of these two reference plant designs are identified as potentially attractive for early MHD power plant applications.

Strategies for the generation of parametric images of [11C]PIB with plasma input functions considering discriminations and reproducibility.

PubMed

Edison, Paul; Brooks, David J; Turkheimer, Federico E; Archer, Hilary A; Hinz, Rainer

2009-11-01

Pittsburgh compound B or [11C]PIB is an amyloid imaging agent which shows a clear differentiation between subjects with Alzheimer's disease (AD) and controls. However the observed signal difference in other forms of dementia such as dementia with Lewy bodies (DLB) is smaller, and mild cognitively impaired (MCI) subjects and some healthy elderly normals may show intermediate levels of [11C]PIB binding. The cerebellum, a commonly used reference region for non-specific tracer uptake in [11C]PIB studies in AD may not be valid in Prion disorders or monogenic forms of AD. The aim of this work was to: 1-compare methods for generating parametric maps of [11C]PIB retention in tissue using a plasma input function in respect of their ability to discriminate between AD subjects and controls and 2-estimate the test-retest reproducibility in AD subjects. 12 AD subjects (5 of which underwent a repeat scan within 6 weeks) and 10 control subjects had 90 minute [11C]PIB dynamic PET scans, and arterial plasma input functions were measured. Parametric maps were generated with graphical analysis of reversible binding (Logan plot), irreversible binding (Patlak plot), and spectral analysis. Between group differentiation was calculated using Student's t-test and comparisons between different methods were made using p values. Reproducibility was assessed by intraclass correlation coefficients (ICC). We found that the 75 min value of the impulse response function showed the best group differentiation and had a higher ICC than volume of distribution maps generated from Logan and spectral analysis. Patlak analysis of [11C]PIB binding was the least reproducible.

Prospective multi-centre Voxel Based Morphometry study employing scanner specific segmentations: Procedure development using CaliBrain structural MRI data

PubMed Central

2009-01-01

Background Structural Magnetic Resonance Imaging (sMRI) of the brain is employed in the assessment of a wide range of neuropsychiatric disorders. In order to improve statistical power in such studies it is desirable to pool scanning resources from multiple centres. The CaliBrain project was designed to provide for an assessment of scanner differences at three centres in Scotland, and to assess the practicality of pooling scans from multiple-centres. Methods We scanned healthy subjects twice on each of the 3 scanners in the CaliBrain project with T1-weighted sequences. The tissue classifier supplied within the Statistical Parametric Mapping (SPM5) application was used to map the grey and white tissue for each scan. We were thus able to assess within scanner variability and between scanner differences. We have sought to correct for between scanner differences by adjusting the probability mappings of tissue occupancy (tissue priors) used in SPM5 for tissue classification. The adjustment procedure resulted in separate sets of tissue priors being developed for each scanner and we refer to these as scanner specific priors. Results Voxel Based Morphometry (VBM) analyses and metric tests indicated that the use of scanner specific priors reduced tissue classification differences between scanners. However, the metric results also demonstrated that the between scanner differences were not reduced to the level of within scanner variability, the ideal for scanner harmonisation. Conclusion Our results indicate the development of scanner specific priors for SPM can assist in pooling of scan resources from different research centres. This can facilitate improvements in the statistical power of quantitative brain imaging studies. PMID:19445668

Assessing noninferiority in a three-arm trial using the Bayesian approach.

PubMed

Ghosh, Pulak; Nathoo, Farouk; Gönen, Mithat; Tiwari, Ram C

2011-07-10

Non-inferiority trials, which aim to demonstrate that a test product is not worse than a competitor by more than a pre-specified small amount, are of great importance to the pharmaceutical community. As a result, methodology for designing and analyzing such trials is required, and developing new methods for such analysis is an important area of statistical research. The three-arm trial consists of a placebo, a reference and an experimental treatment, and simultaneously tests the superiority of the reference over the placebo along with comparing this reference to an experimental treatment. In this paper, we consider the analysis of non-inferiority trials using Bayesian methods which incorporate both parametric as well as semi-parametric models. The resulting testing approach is both flexible and robust. The benefit of the proposed Bayesian methods is assessed via simulation, based on a study examining home-based blood pressure interventions. Copyright © 2011 John Wiley & Sons, Ltd.

Future space transportation systems analysis study. Phase 1 extension: Transportation systems reference data, volume 2

NASA Technical Reports Server (NTRS)

1975-01-01

Transportation mass requirements are developed for various mission and transportation modes based on vehicle systems sized to fit the exact needs of each mission. The parametric data used to derive the mass requirements for each mission and transportation mode are presented to enable accommodation of possible changes in mode options or payload definitions. The vehicle sizing and functional requirements used to derive the parametric data are described.

Cardiac-gated parametric images from 82 Rb PET from dynamic frames and direct 4D reconstruction.

PubMed

Germino, Mary; Carson, Richard E

2018-02-01

Cardiac perfusion PET data can be reconstructed as a dynamic sequence and kinetic modeling performed to quantify myocardial blood flow, or reconstructed as static gated images to quantify function. Parametric images from dynamic PET are conventionally not gated, to allow use of all events with lower noise. An alternative method for dynamic PET is to incorporate the kinetic model into the reconstruction algorithm itself, bypassing the generation of a time series of emission images and directly producing parametric images. So-called "direct reconstruction" can produce parametric images with lower noise than the conventional method because the noise distribution is more easily modeled in projection space than in image space. In this work, we develop direct reconstruction of cardiac-gated parametric images for 82 Rb PET with an extension of the Parametric Motion compensation OSEM List mode Algorithm for Resolution-recovery reconstruction for the one tissue model (PMOLAR-1T). PMOLAR-1T was extended to accommodate model terms to account for spillover from the left and right ventricles into the myocardium. The algorithm was evaluated on a 4D simulated 82 Rb dataset, including a perfusion defect, as well as a human 82 Rb list mode acquisition. The simulated list mode was subsampled into replicates, each with counts comparable to one gate of a gated acquisition. Parametric images were produced by the indirect (separate reconstructions and modeling) and direct methods for each of eight low-count and eight normal-count replicates of the simulated data, and each of eight cardiac gates for the human data. For the direct method, two initialization schemes were tested: uniform initialization, and initialization with the filtered iteration 1 result of the indirect method. For the human dataset, event-by-event respiratory motion compensation was included. The indirect and direct methods were compared for the simulated dataset in terms of bias and coefficient of variation as a function of iteration. Convergence of direct reconstruction was slow with uniform initialization; lower bias was achieved in fewer iterations by initializing with the filtered indirect iteration 1 images. For most parameters and regions evaluated, the direct method achieved the same or lower absolute bias at matched iteration as the indirect method, with 23%-65% lower noise. Additionally, the direct method gave better contrast between the perfusion defect and surrounding normal tissue than the indirect method. Gated parametric images from the human dataset had comparable relative performance of indirect and direct, in terms of mean parameter values per iteration. Changes in myocardial wall thickness and blood pool size across gates were readily visible in the gated parametric images, with higher contrast between myocardium and left ventricle blood pool in parametric images than gated SUV images. Direct reconstruction can produce parametric images with less noise than the indirect method, opening the potential utility of gated parametric imaging for perfusion PET. © 2017 American Association of Physicists in Medicine.

Design and Parametric Study of the Magnetic Sensor for Position Detection in Linear Motor Based on Nonlinear Parametric Model Order Reduction

PubMed Central

Paul, Sarbajit; Chang, Junghwan

2017-01-01

This paper presents a design approach for a magnetic sensor module to detect mover position using the proper orthogonal decomposition-dynamic mode decomposition (POD-DMD)-based nonlinear parametric model order reduction (PMOR). The parameterization of the sensor module is achieved by using the multipolar moment matching method. Several geometric variables of the sensor module are considered while developing the parametric study. The operation of the sensor module is based on the principle of the airgap flux density distribution detection by the Hall Effect IC. Therefore, the design objective is to achieve a peak flux density (PFD) greater than 0.1 T and total harmonic distortion (THD) less than 3%. To fulfill the constraint conditions, the specifications for the sensor module is achieved by using POD-DMD based reduced model. The POD-DMD based reduced model provides a platform to analyze the high number of design models very fast, with less computational burden. Finally, with the final specifications, the experimental prototype is designed and tested. Two different modes, 90° and 120° modes respectively are used to obtain the position information of the linear motor mover. The position information thus obtained are compared with that of the linear scale data, used as a reference signal. The position information obtained using the 120° mode has a standard deviation of 0.10 mm from the reference linear scale signal, whereas the 90° mode position signal shows a deviation of 0.23 mm from the reference. The deviation in the output arises due to the mechanical tolerances introduced into the specification during the manufacturing process. This provides a scope for coupling the reliability based design optimization in the design process as a future extension. PMID:28671580

Design and Parametric Study of the Magnetic Sensor for Position Detection in Linear Motor Based on Nonlinear Parametric model order reduction.

PubMed

Paul, Sarbajit; Chang, Junghwan

2017-07-01

This paper presents a design approach for a magnetic sensor module to detect mover position using the proper orthogonal decomposition-dynamic mode decomposition (POD-DMD)-based nonlinear parametric model order reduction (PMOR). The parameterization of the sensor module is achieved by using the multipolar moment matching method. Several geometric variables of the sensor module are considered while developing the parametric study. The operation of the sensor module is based on the principle of the airgap flux density distribution detection by the Hall Effect IC. Therefore, the design objective is to achieve a peak flux density (PFD) greater than 0.1 T and total harmonic distortion (THD) less than 3%. To fulfill the constraint conditions, the specifications for the sensor module is achieved by using POD-DMD based reduced model. The POD-DMD based reduced model provides a platform to analyze the high number of design models very fast, with less computational burden. Finally, with the final specifications, the experimental prototype is designed and tested. Two different modes, 90° and 120° modes respectively are used to obtain the position information of the linear motor mover. The position information thus obtained are compared with that of the linear scale data, used as a reference signal. The position information obtained using the 120° mode has a standard deviation of 0.10 mm from the reference linear scale signal, whereas the 90° mode position signal shows a deviation of 0.23 mm from the reference. The deviation in the output arises due to the mechanical tolerances introduced into the specification during the manufacturing process. This provides a scope for coupling the reliability based design optimization in the design process as a future extension.

Direct Parametric Reconstruction With Joint Motion Estimation/Correction for Dynamic Brain PET Data.

PubMed

Jiao, Jieqing; Bousse, Alexandre; Thielemans, Kris; Burgos, Ninon; Weston, Philip S J; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Markiewicz, Pawel; Ourselin, Sebastien

2017-01-01

Direct reconstruction of parametric images from raw photon counts has been shown to improve the quantitative analysis of dynamic positron emission tomography (PET) data. However it suffers from subject motion which is inevitable during the typical acquisition time of 1-2 hours. In this work we propose a framework to jointly estimate subject head motion and reconstruct the motion-corrected parametric images directly from raw PET data, so that the effects of distorted tissue-to-voxel mapping due to subject motion can be reduced in reconstructing the parametric images with motion-compensated attenuation correction and spatially aligned temporal PET data. The proposed approach is formulated within the maximum likelihood framework, and efficient solutions are derived for estimating subject motion and kinetic parameters from raw PET photon count data. Results from evaluations on simulated [ 11 C]raclopride data using the Zubal brain phantom and real clinical [ 18 F]florbetapir data of a patient with Alzheimer's disease show that the proposed joint direct parametric reconstruction motion correction approach can improve the accuracy of quantifying dynamic PET data with large subject motion.

Multi-parametric monitoring of high intensity focused ultrasound (HIFU) treatment using harmonic motion imaging for focused ultrasound (HMIFU)

NASA Astrophysics Data System (ADS)

Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa

2012-11-01

Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and relative phase-shift during high energy HIFU where tissue boiling occurs. Forty three (n=18) thermal lesions were formed in ex vivo canine liver specimens. Two dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10-, 20-and 30-s HIFU durations at three different acoustic powers of 8, 10, and 11W. For the 10-, 20-, and 30-s treatment cases, a steady decrease in the displacement (-8.67±4.80, -14.44±7.77, 24.03±12.11μm), compressive strain -0.16±0.06, -0.71±0.30, -0.68±0.36 %, and phase shift +1.80±6.80, -15.80±9.44, -18.62±13.14 ° were obtained, respectively, indicating overall increase of relative stiffness and decrease of the viscosity-to-stiffness ratio during heating. After treatment, 2D HMI displacement images of the thermal lesions showed an increased lesion-to-background contrast of 1.34±0.19, 1.98±0.30, 2.26±0.80 and lesion size of 40.95±8.06, 47.6±4.87, and 52.23±2.19 mm2, respectively, which was validated again with pathology 25.17±6.99, 42.17±1.77, 47.17±3.10 mm2. Additionally, studies also investigated the performance of mutli-parametric monitoring under the influence of boiling and attenuation change due to tissue boiling, where discrepancies were found such as deteriorated displacement SNR and reversed lesion-to-background displacement contrast with indication on possible increase in attenuation and tissue gelatification or pulverization. Despite the challenge of the boiling mechanism, the relative phase shift served as consist biomechanical tissue response independent of changes in acoustic properties throughout the HIFU treatment. In addition, the 2D HMI displacement images were able to confirm and quantify the change in dimensions of the thermal lesion site. Therefore, the multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU treatment.

THz-wave parametric sources and imaging applications

NASA Astrophysics Data System (ADS)

Kawase, Kodo

2004-12-01

We have studied the generation of terahertz (THz) waves by optical parametric processes based on laser light scattering from the polariton mode of nonlinear crystals. Using parametric oscillation of MgO-doped LiNbO3 crystal pumped by a nano-second Q-switched Nd:YAG laser, we have realized a widely tunable coherent THz-wave sources with a simple configuration. We have also developed a novel basic technology for THz imaging, which allows detection and identification of chemicals by introducing the component spatial pattern analysis. The spatial distributions of the chemicals were obtained from terahertz multispectral trasillumination images, using absorption spectra previously measured with a widely tunable THz-wave parametric oscillator. Further we have applied this technique to the detection and identification of illicit drugs concealed in envelopes. The samples we used were methamphetamine and MDMA, two of the most widely consumed illegal drugs in Japan, and aspirin as a reference.

Josephson Parametric Reflection Amplifier with Integrated Directionality

NASA Astrophysics Data System (ADS)

Westig, M. P.; Klapwijk, T. M.

2018-06-01

A directional superconducting parametric amplifier in the GHz frequency range is designed and analyzed, suitable for low-power read-out of microwave kinetic inductance detectors employed in astrophysics and when combined with a nonreciprocal device at its input also for circuit quantum electrodynamics. It consists of a one-wavelength-long nondegenerate Josephson parametric reflection amplifier circuit. The device has two Josephson-junction oscillators, connected via a tailored impedance to an on-chip passive circuit which directs the in- to the output port. The amplifier provides a gain of 20 dB over a bandwidth of 220 MHz on the signal as well as on the idler portion of the amplified input and the total photon shot noise referred to the input corresponds to maximally approximately 1.3 photons per second per Hertz of bandwidth. We predict a factor of 4 increase in dynamic range compared to conventional Josephson parametric amplifiers.

Estimation of viscoelastic parameters in Prony series from shear wave propagation

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

Jung, Jae-Wook; Hong, Jung-Wuk, E-mail: j.hong@kaist.ac.kr, E-mail: jwhong@alum.mit.edu; Lee, Hyoung-Ki

2016-06-21

When acquiring accurate ultrasonic images, we must precisely estimate the mechanical properties of the soft tissue. This study investigates and estimates the viscoelastic properties of the tissue by analyzing shear waves generated through an acoustic radiation force. The shear waves are sourced from a localized pushing force acting for a certain duration, and the generated waves travel horizontally. The wave velocities depend on the mechanical properties of the tissue such as the shear modulus and viscoelastic properties; therefore, we can inversely calculate the properties of the tissue through parametric studies.

Building and using a statistical 3D motion atlas for analyzing myocardial contraction in MRI

NASA Astrophysics Data System (ADS)

Rougon, Nicolas F.; Petitjean, Caroline; Preteux, Francoise J.

2004-05-01

We address the issue of modeling and quantifying myocardial contraction from 4D MR sequences, and present an unsupervised approach for building and using a statistical 3D motion atlas for the normal heart. This approach relies on a state-of-the-art variational non rigid registration (NRR) technique using generalized information measures, which allows for robust intra-subject motion estimation and inter-subject anatomical alignment. The atlas is built from a collection of jointly acquired tagged and cine MR exams in short- and long-axis views. Subject-specific non parametric motion estimates are first obtained by incremental NRR of tagged images onto the end-diastolic (ED) frame. Individual motion data are then transformed into the coordinate system of a reference subject using subject-to-reference mappings derived by NRR of cine ED images. Finally, principal component analysis of aligned motion data is performed for each cardiac phase, yielding a mean model and a set of eigenfields encoding kinematic ariability. The latter define an organ-dedicated hierarchical motion basis which enables parametric motion measurement from arbitrary tagged MR exams. To this end, the atlas is transformed into subject coordinates by reference-to-subject NRR of ED cine frames. Atlas-based motion estimation is then achieved by parametric NRR of tagged images onto the ED frame, yielding a compact description of myocardial contraction during diastole.

Model for nucleon valence structure functions at all x, all p ⊥ and all Q 2 from the correspondence between QCD and DTU

NASA Astrophysics Data System (ADS)

Cohen-Tannoudji, G.; El Hassouni, A.; Mantrach, A.; Oudrhiri-Safiani, E. G.

1982-09-01

We propose a simple parametrization of the nucleon valence structure functions at all x, all p ⊥ and all Q 2. We use the DTU parton model to fix the parametrization at a reference point ( Q {0/2}=3 GeV2) and we mimic the QCD evolution by replacing the dimensioned parameters of the DTU parton model by functions depending on Q 2. Excellent agreement is obtained with existing data.

A Parametric Computational Analysis into Galvanic Coupling Intrabody Communication.

PubMed

Callejon, M Amparo; Del Campo, P; Reina-Tosina, Javier; Roa, Laura M

2017-08-02

Intrabody Communication (IBC) uses the human body tissues as transmission media for electrical signals to interconnect personal health devices in wireless body area networks. The main goal of this work is to conduct a computational analysis covering some bioelectric issues that still have not been fully explained, such as the modeling of the skin-electrode impedance, the differences associated to the use of constant voltage or current excitation modes, or the influence on attenuation of the subject's anthropometrical and bioelectric properties. With this aim, a computational finite element model has been developed, allowing the IBC channel attenuation as well as the electric field and current density through arm tissues to be computed as a function of these parameters. As a conclusion, this parametric analysis has in turn permitted us to disclose some knowledge about the causes and effects of the above-mentioned issues, thus explaining and complementing previous results reported in the literature.

Lung Motion Model Validation Experiments, Free-Breathing Tissue Densitometry, and Ventilation Mapping using Fast Helical CT Imaging

NASA Astrophysics Data System (ADS)

Dou, Hsiang-Tai

The uncertainties due to respiratory motion present significant challenges to accurate characterization of cancerous tissues both in terms of imaging and treatment. Currently available clinical lung imaging techniques are subject to inferior image quality and incorrect motion estimation, with consequences that can systematically impact the downstream treatment delivery and outcome. The main objective of this thesis is the development of the techniques of fast helical computed tomography (CT) imaging and deformable image registration for the radiotherapy applications in accurate breathing motion modeling, lung tissue density modeling and ventilation imaging. Fast helical CT scanning was performed on 64-slice CT scanner using the shortest available gantry rotation time and largest pitch value such that scanning of the thorax region amounts to just two seconds, which is less than typical breathing cycle in humans. The scanning was conducted under free breathing condition. Any portion of the lung anatomy undergoing such scanning protocol would be irradiated for only a quarter second, effectively removing any motion induced image artifacts. The resulting CT data were pristine volumetric images that record the lung tissue position and density in a fraction of the breathing cycle. Following our developed protocol, multiple fast helical CT scans were acquired to sample the tissue positions in different breathing states. To measure the tissue displacement, deformable image registration was performed that registers the non-reference images to the reference one. In modeling breathing motion, external breathing surrogate signal was recorded synchronously with the CT image slices. This allowed for the tissue-specific displacement to be modeled as parametrization of the recorded breathing signal using the 5D lung motion model. To assess the accuracy of the motion model in describing tissue position change, the model was used to simulate the original high-pitch helical CT scan geometries, employed as ground truth data. Image similarity between the simulated and ground truth scans was evaluated. The model validation experiments were conducted in a patient cohort of seventeen patients to assess the model robustness and inter-patient variation. The model error averaged over multiple tracked positions from several breathing cycles was found to be on the order of one millimeter. In modeling the density change under free breathing condition, the determinant of Jacobian matrix from the registration-derived deformation vector field yielded volume change information of the lung tissues. Correlation of the Jacobian values to the corresponding voxel Housfield units (HU) reveals that the density variation for the majority of lung tissues can be very well described by mass conservation relationship. Different tissue types were identified and separately modeled. Large trials of validation experiments were performed. The averaged deviation between the modeled and the reference lung density was 30 HU, which was estimated to be the background CT noise level. In characterizing the lung ventilation function, a novel method was developed to determine the extent of lung tissue volume change. Information on volume change was derived from the deformable image registration of the fast helical CT images in terms of Jacobian values with respect to a reference image. Assuming the multiple volume change measurements are independently and identically distributed, statistical formulation was derived to model ventilation distribution of each lung voxels and empirical minimum and maximum probability distribution of the Jacobian values was computed. Ventilation characteristic was evaluated as the difference of the expectation value from these extremal distributions. The resulting ventilation map was compared with an independently obtained ventilation image derived directly from the lung intensities and good correlation was found using statistical test. In addition, dynamic ventilation characterization was investigated by estimating the voxel-specific ventilation distribution. Ventilation maps were generated at different percentile levels using the tissue volume expansion metrics.

Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat

PubMed Central

Pérez-Rodríguez, Paulino; Gianola, Daniel; González-Camacho, Juan Manuel; Crossa, José; Manès, Yann; Dreisigacker, Susanne

2012-01-01

In genome-enabled prediction, parametric, semi-parametric, and non-parametric regression models have been used. This study assessed the predictive ability of linear and non-linear models using dense molecular markers. The linear models were linear on marker effects and included the Bayesian LASSO, Bayesian ridge regression, Bayes A, and Bayes B. The non-linear models (this refers to non-linearity on markers) were reproducing kernel Hilbert space (RKHS) regression, Bayesian regularized neural networks (BRNN), and radial basis function neural networks (RBFNN). These statistical models were compared using 306 elite wheat lines from CIMMYT genotyped with 1717 diversity array technology (DArT) markers and two traits, days to heading (DTH) and grain yield (GY), measured in each of 12 environments. It was found that the three non-linear models had better overall prediction accuracy than the linear regression specification. Results showed a consistent superiority of RKHS and RBFNN over the Bayesian LASSO, Bayesian ridge regression, Bayes A, and Bayes B models. PMID:23275882

Comparison between linear and non-parametric regression models for genome-enabled prediction in wheat.

PubMed

Pérez-Rodríguez, Paulino; Gianola, Daniel; González-Camacho, Juan Manuel; Crossa, José; Manès, Yann; Dreisigacker, Susanne

2012-12-01

In genome-enabled prediction, parametric, semi-parametric, and non-parametric regression models have been used. This study assessed the predictive ability of linear and non-linear models using dense molecular markers. The linear models were linear on marker effects and included the Bayesian LASSO, Bayesian ridge regression, Bayes A, and Bayes B. The non-linear models (this refers to non-linearity on markers) were reproducing kernel Hilbert space (RKHS) regression, Bayesian regularized neural networks (BRNN), and radial basis function neural networks (RBFNN). These statistical models were compared using 306 elite wheat lines from CIMMYT genotyped with 1717 diversity array technology (DArT) markers and two traits, days to heading (DTH) and grain yield (GY), measured in each of 12 environments. It was found that the three non-linear models had better overall prediction accuracy than the linear regression specification. Results showed a consistent superiority of RKHS and RBFNN over the Bayesian LASSO, Bayesian ridge regression, Bayes A, and Bayes B models.

Monte Carlo-based parametrization of the lateral dose spread for clinical treatment planning of scanned proton and carbon ion beams.

PubMed

Parodi, Katia; Mairani, Andrea; Sommerer, Florian

2013-07-01

Ion beam therapy using state-of-the-art pencil-beam scanning offers unprecedented tumour-dose conformality with superior sparing of healthy tissue and critical organs compared to conventional radiation modalities for external treatment of deep-seated tumours. For inverse plan optimization, the commonly employed analytical treatment-planning systems (TPSs) have to meet reasonable compromises in the accuracy of the pencil-beam modelling to ensure good performances in clinically tolerable execution times. In particular, the complex lateral spreading of ion beams in air and in the traversed tissue is typically approximated with ideal Gaussian-shaped distributions, enabling straightforward superimposition of several scattering contributions. This work presents the double Gaussian parametrization of scanned proton and carbon ion beams in water that has been introduced in an upgraded version of the worldwide first commercial ion TPS for clinical use at the Heidelberg Ion Beam Therapy Center (HIT). First, the Monte Carlo results obtained from a detailed implementation of the HIT beamline have been validated against available experimental data. Then, for generating the TPS lateral parametrization, radial beam broadening has been calculated in a water target placed at a representative position after scattering in the beamline elements and air for 20 initial beam energies for each ion species. The simulated profiles were finally fitted with an idealized double Gaussian distribution that did not perfectly describe the nature of the data, thus requiring a careful choice of the fitting conditions. The obtained parametrization is in clinical use not only at the HIT center, but also at the Centro Nazionale di Adroterapia Oncologica.

Monte Carlo-based parametrization of the lateral dose spread for clinical treatment planning of scanned proton and carbon ion beams

PubMed Central

Parodi, Katia; Mairani, Andrea; Sommerer, Florian

2013-01-01

Ion beam therapy using state-of-the-art pencil-beam scanning offers unprecedented tumour-dose conformality with superior sparing of healthy tissue and critical organs compared to conventional radiation modalities for external treatment of deep-seated tumours. For inverse plan optimization, the commonly employed analytical treatment-planning systems (TPSs) have to meet reasonable compromises in the accuracy of the pencil-beam modelling to ensure good performances in clinically tolerable execution times. In particular, the complex lateral spreading of ion beams in air and in the traversed tissue is typically approximated with ideal Gaussian-shaped distributions, enabling straightforward superimposition of several scattering contributions. This work presents the double Gaussian parametrization of scanned proton and carbon ion beams in water that has been introduced in an upgraded version of the worldwide first commercial ion TPS for clinical use at the Heidelberg Ion Beam Therapy Center (HIT). First, the Monte Carlo results obtained from a detailed implementation of the HIT beamline have been validated against available experimental data. Then, for generating the TPS lateral parametrization, radial beam broadening has been calculated in a water target placed at a representative position after scattering in the beamline elements and air for 20 initial beam energies for each ion species. The simulated profiles were finally fitted with an idealized double Gaussian distribution that did not perfectly describe the nature of the data, thus requiring a careful choice of the fitting conditions. The obtained parametrization is in clinical use not only at the HIT center, but also at the Centro Nazionale di Adroterapia Oncologica. PMID:23824133

Usefulness of myocardial parametric imaging to evaluate myocardial viability in experimental and in clinical studies

PubMed Central

Korosoglou, G; Hansen, A; Bekeredjian, R; Filusch, A; Hardt, S; Wolf, D; Schellberg, D; Katus, H A; Kuecherer, H

2006-01-01

Objective To evaluate whether myocardial parametric imaging (MPI) is superior to visual assessment for the evaluation of myocardial viability. Methods and results Myocardial contrast echocardiography (MCE) was assessed in 11 pigs before, during, and after left anterior descending coronary artery occlusion and in 32 patients with ischaemic heart disease by using intravenous SonoVue administration. In experimental studies perfusion defect area assessment by MPI was compared with visually guided perfusion defect planimetry. Histological assessment of necrotic tissue was the standard reference. In clinical studies viability was assessed on a segmental level by (1) visual analysis of myocardial opacification; (2) quantitative estimation of myocardial blood flow in regions of interest; and (3) MPI. Functional recovery between three and six months after revascularisation was the standard reference. In experimental studies, compared with visually guided perfusion defect planimetry, planimetric assessment of infarct size by MPI correlated more significantly with histology (r2  =  0.92 versus r2  =  0.56) and had a lower intraobserver variability (4% v 15%, p < 0.05). In clinical studies, MPI had higher specificity (66% v 43%, p < 0.05) than visual MCE and good accuracy (81%) for viability detection. It was less time consuming (3.4 (1.6) v 9.2 (2.4) minutes per image, p < 0.05) than quantitative blood flow estimation by regions of interest and increased the agreement between observers interpreting myocardial perfusion (κ  =  0.87 v κ  =  0.75, p < 0.05). Conclusion MPI is useful for the evaluation of myocardial viability both in animals and in patients. It is less time consuming than quantification analysis by regions of interest and less observer dependent than visual analysis. Thus, strategies incorporating this technique may be valuable for the evaluation of myocardial viability in clinical routine. PMID:15939722

DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

PubMed

Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

2013-09-10

A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

A generalized parametric response mapping method for analysis of multi-parametric imaging: A feasibility study with application to glioblastoma.

PubMed

Lausch, Anthony; Yeung, Timothy Pok-Chi; Chen, Jeff; Law, Elton; Wang, Yong; Urbini, Benedetta; Donelli, Filippo; Manco, Luigi; Fainardi, Enrico; Lee, Ting-Yim; Wong, Eugene

2017-11-01

Parametric response map (PRM) analysis of functional imaging has been shown to be an effective tool for early prediction of cancer treatment outcomes and may also be well-suited toward guiding personalized adaptive radiotherapy (RT) strategies such as sub-volume boosting. However, the PRM method was primarily designed for analysis of longitudinally acquired pairs of single-parameter image data. The purpose of this study was to demonstrate the feasibility of a generalized parametric response map analysis framework, which enables analysis of multi-parametric data while maintaining the key advantages of the original PRM method. MRI-derived apparent diffusion coefficient (ADC) and relative cerebral blood volume (rCBV) maps acquired at 1 and 3-months post-RT for 19 patients with high-grade glioma were used to demonstrate the algorithm. Images were first co-registered and then standardized using normal tissue image intensity values. Tumor voxels were then plotted in a four-dimensional Cartesian space with coordinate values equal to a voxel's image intensity in each of the image volumes and an origin defined as the multi-parametric mean of normal tissue image intensity values. Voxel positions were orthogonally projected onto a line defined by the origin and a pre-determined response vector. The voxels are subsequently classified as positive, negative or nil, according to whether projected positions along the response vector exceeded a threshold distance from the origin. The response vector was selected by identifying the direction in which the standard deviation of tumor image intensity values was maximally different between responding and non-responding patients within a training dataset. Voxel classifications were visualized via familiar three-class response maps and then the fraction of tumor voxels associated with each of the classes was investigated for predictive utility analogous to the original PRM method. Independent PRM and MPRM analyses of the contrast-enhancing lesion (CEL) and a 1 cm shell of surrounding peri-tumoral tissue were performed. Prediction using tumor volume metrics was also investigated. Leave-one-out cross validation (LOOCV) was used in combination with permutation testing to assess preliminary predictive efficacy and estimate statistically robust P-values. The predictive endpoint was overall survival (OS) greater than or equal to the median OS of 18.2 months. Single-parameter PRM and multi-parametric response maps (MPRMs) were generated for each patient and used to predict OS via the LOOCV. Tumor volume metrics (P ≥ 0.071 ± 0.01) and single-parameter PRM analyses (P ≥ 0.170 ± 0.01) were not found to be predictive of OS within this study. MPRM analysis of the peri-tumoral region but not the CEL was found to be predictive of OS with a classification sensitivity, specificity and accuracy of 80%, 100%, and 89%, respectively (P = 0.001 ± 0.01). The feasibility of a generalized MPRM analysis framework was demonstrated with improved prediction of overall survival compared to the original single-parameter method when applied to a glioblastoma dataset. The proposed algorithm takes the spatial heterogeneity in multi-parametric response into consideration and enables visualization. MPRM analysis of peri-tumoral regions was shown to have predictive potential supporting further investigation of a larger glioblastoma dataset. © 2017 American Association of Physicists in Medicine.

In-plane crashworthiness of bio-inspired hierarchical honeycombs

DOE PAGES

Yin, Hanfeng; Huang, Xiaofei; Scarpa, Fabrizio; ...

2018-03-13

Biological tissues like bone, wood, and sponge possess hierarchical cellular topologies, which are lightweight and feature an excellent energy absorption capability. Here we present a system of bio-inspired hierarchical honeycomb structures based on hexagonal, Kagome, and triangular tessellations. The hierarchical designs and a reference regular honeycomb configuration are subjected to simulated in-plane impact using the nonlinear finite element code LS-DYNA. The numerical simulation results show that the triangular hierarchical honeycomb provides the best performance compared to the other two hierarchical honeycombs, and features more than twice the energy absorbed by the regular honeycomb under similar loading conditions. We also proposemore » a parametric study correlating the microstructure parameters (hierarchical length ratio r and the number of sub cells N) to the energy absorption capacity of these hierarchical honeycombs. The triangular hierarchical honeycomb with N = 2 and r = 1/8 shows the highest energy absorption capacity among all the investigated cases, and this configuration could be employed as a benchmark for the design of future safety protective systems.« less

In-plane crashworthiness of bio-inspired hierarchical honeycombs

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

Yin, Hanfeng; Huang, Xiaofei; Scarpa, Fabrizio

Biological tissues like bone, wood, and sponge possess hierarchical cellular topologies, which are lightweight and feature an excellent energy absorption capability. Here we present a system of bio-inspired hierarchical honeycomb structures based on hexagonal, Kagome, and triangular tessellations. The hierarchical designs and a reference regular honeycomb configuration are subjected to simulated in-plane impact using the nonlinear finite element code LS-DYNA. The numerical simulation results show that the triangular hierarchical honeycomb provides the best performance compared to the other two hierarchical honeycombs, and features more than twice the energy absorbed by the regular honeycomb under similar loading conditions. We also proposemore » a parametric study correlating the microstructure parameters (hierarchical length ratio r and the number of sub cells N) to the energy absorption capacity of these hierarchical honeycombs. The triangular hierarchical honeycomb with N = 2 and r = 1/8 shows the highest energy absorption capacity among all the investigated cases, and this configuration could be employed as a benchmark for the design of future safety protective systems.« less

Spectral Clustering Predicts Tumor Tissue Heterogeneity Using Dynamic 18F-FDG PET: A Complement to the Standard Compartmental Modeling Approach.

PubMed

Katiyar, Prateek; Divine, Mathew R; Kohlhofer, Ursula; Quintanilla-Martinez, Leticia; Schölkopf, Bernhard; Pichler, Bernd J; Disselhorst, Jonathan A

2017-04-01

In this study, we described and validated an unsupervised segmentation algorithm for the assessment of tumor heterogeneity using dynamic 18 F-FDG PET. The aim of our study was to objectively evaluate the proposed method and make comparisons with compartmental modeling parametric maps and SUV segmentations using simulations of clinically relevant tumor tissue types. Methods: An irreversible 2-tissue-compartmental model was implemented to simulate clinical and preclinical 18 F-FDG PET time-activity curves using population-based arterial input functions (80 clinical and 12 preclinical) and the kinetic parameter values of 3 tumor tissue types. The simulated time-activity curves were corrupted with different levels of noise and used to calculate the tissue-type misclassification errors of spectral clustering (SC), parametric maps, and SUV segmentation. The utility of the inverse noise variance- and Laplacian score-derived frame weighting schemes before SC was also investigated. Finally, the SC scheme with the best results was tested on a dynamic 18 F-FDG measurement of a mouse bearing subcutaneous colon cancer and validated using histology. Results: In the preclinical setup, the inverse noise variance-weighted SC exhibited the lowest misclassification errors (8.09%-28.53%) at all noise levels in contrast to the Laplacian score-weighted SC (16.12%-31.23%), unweighted SC (25.73%-40.03%), parametric maps (28.02%-61.45%), and SUV (45.49%-45.63%) segmentation. The classification efficacy of both weighted SC schemes in the clinical case was comparable to the unweighted SC. When applied to the dynamic 18 F-FDG measurement of colon cancer, the proposed algorithm accurately identified densely vascularized regions from the rest of the tumor. In addition, the segmented regions and clusterwise average time-activity curves showed excellent correlation with the tumor histology. Conclusion: The promising results of SC mark its position as a robust tool for quantification of tumor heterogeneity using dynamic PET studies. Because SC tumor segmentation is based on the intrinsic structure of the underlying data, it can be easily applied to other cancer types as well. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

THz-wave parametric source and its imaging applications

NASA Astrophysics Data System (ADS)

Kawase, Kodo

2004-08-01

Widely tunable coherent terahertz (THz) wave generation has been demonstrated based on the parametric oscillation using MgO doped LiNbO3 crystal pumped by a Q-switched Nd:YAG laser. This method exhibits multiple advantages like wide tunability, coherency and compactness of its system. We have developed a novel basic technology for terahertz (THz) imaging, which allows detection and identification of chemicals by introducing the component spatial pattern analysis. The spatial distributions of the chemicals were obtained from terahertz multispectral transillumination images, using absorption spectra previously measured with a widely tunable THz-wave parametric oscillator. Further we have applied this technique to the detection and identification of illicit drugs concealed in envelopes. The samples we used were methamphetamine and MDMA, two of the most widely consumed illegal drugs in Japan, and aspirin as a reference.

Nonimaging optical illumination system

DOEpatents

Winston, R.; Ries, H.

1996-12-17

A nonimaging illumination optical device for producing a selected far field illuminance over an angular range. The optical device includes a light source, a light reflecting surface, and a family of light edge rays defined along a reference line with the reflecting surface defined in terms of the reference line as a parametric function R(t) where t is a scalar parameter position and R(t)=k(t)+Du(t) where k(t) is a parameterization of the reference line, and D is a distance from a point on the reference line to the reflection surface along the desired edge ray through the point. 35 figs.

Nonimaging optical illumination system

DOEpatents

Winston, R.; Ries, H.

1998-10-06

A nonimaging illumination optical device for producing a selected far field illuminance over an angular range. The optical device includes a light source a light reflecting surface, and a family of light edge rays defined along a reference line with the reflecting surface defined in terms of the reference lines a parametric function R(t) where t is a scalar parameter position and R(t)=k(t)+Du(t) where k(t) is a parameterization of the reference line, and D is a distance from a point on the reference line to the reflection surface along the desired edge ray through the point. 35 figs.

A first-in-man PET study of [18F]PSS232, a fluorinated ABP688 derivative for imaging metabotropic glutamate receptor subtype 5.

PubMed

Warnock, Geoffrey; Sommerauer, Michael; Mu, Linjing; Pla Gonzalez, Gloria; Geistlich, Susanne; Treyer, Valerie; Schibli, Roger; Buck, Alfred; Krämer, Stefanie D; Ametamey, Simon M

2018-06-01

Non-invasive imaging of metabotropic glutamate receptor 5 (mGlu 5 ) in the brain using PET is of interest in e.g., anxiety, depression, and Parkinson's disease. Widespread application of the most widely used mGlu 5 tracer, [ 11 C]ABP688, is limited by the short physical half-life of carbon-11. [ 18 F]PSS232 is a fluorinated analog with promising preclinical properties and high selectivity and specificity for mGlu 5 . In this first-in-man study, we evaluated the brain uptake pattern and kinetics of [ 18 F]PSS232 in healthy volunteers. [ 18 F]PSS232 PET was performed with ten healthy male volunteers aged 20-40 years. Seven of the subjects received a bolus injection and the remainder a bolus/infusion protocol. Cerebral blood flow was determined in seven subjects using [ 15 O]water PET. Arterial blood activity was measured using an online blood counter. Tracer kinetics were evaluated by compartment modeling and parametric maps were generated for both tracers. At 90 min post-injection, 59.2 ± 11.1% of total radioactivity in plasma corresponded to intact tracer. The regional first pass extraction fraction of [ 18 F]PSS232 ranged from 0.41 ± 0.06 to 0.55 ± 0.03 and brain distribution pattern matched that of [ 11 C]ABP688. Uptake kinetics followed a simple two-tissue compartment model. The volume of distribution of total tracer (V T , ml/cm 3 ) ranged from 1.18 ± 0.20 for white matter to 2.91 ± 0.51 for putamen. The respective mean distribution volume ratios (DVR) with cerebellum as the reference tissue were 0.88 ± 0.06 and 2.12 ± 0.10, respectively. The tissue/cerebellum ratios of a bolus/infusion protocol (30/70 dose ratio) were close to the DVR values. Brain uptake of [ 18 F]PSS232 matched the distribution of mGlu 5 and followed a two-tissue compartment model. The well-defined kinetics and the possibility to use reference tissue models, obviating the need for arterial blood sampling, make [ 18 F]PSS232 a promising fluorine-18 labeled radioligand for measuring mGlu 5 density in humans.

Diffusion tensor magnetic resonance imaging of the pancreas.

PubMed

Nissan, Noam; Golan, Talia; Furman-Haran, Edna; Apter, Sara; Inbar, Yael; Ariche, Arie; Bar-Zakay, Barak; Goldes, Yuri; Schvimer, Michael; Grobgeld, Dov; Degani, Hadassa

2014-01-01

To develop a diffusion-tensor-imaging (DTI) protocol that is sensitive to the complex diffusion and perfusion properties of the healthy and malignant pancreas tissues. Twenty-eight healthy volunteers and nine patients with pancreatic-ductal-adenocacinoma (PDAC), were scanned at 3T with T2-weighted and DTI sequences. Healthy volunteers were also scanned with multi-b diffusion-weighted-imaging (DWI), whereas a standard clinical protocol complemented the PDAC patients' scans. Image processing at pixel resolution yielded parametric maps of three directional diffusion coefficients λ1, λ2, λ3, apparent diffusion coefficient (ADC), and fractional anisotropy (FA), as well as a λ1-vector map, and a main diffusion-direction map. DTI measurements of healthy pancreatic tissue at b-values 0,500 s/mm² yielded: λ1 = (2.65±0.35)×10⁻³, λ2 = (1.87±0.22)×10⁻³, λ3 = (1.20±0.18)×10⁻³, ADC = (1.91±0.22)×10⁻³ (all in mm²/s units) and FA = 0.38±0.06. Using b-values of 100,500 s/mm² led to a significant reduction in λ1, λ2, λ3 and ADC (p<.0001) and a significant increase (p<0.0001) in FA. The reduction in the diffusion coefficients suggested a contribution of a fast intra-voxel-incoherent-motion (IVIM) component at b≤100 s/mm², which was confirmed by the multi-b DWI results. In PDACs, λ1, λ2, λ3 and ADC in both 0,500 s/mm² and 100,500 s/mm² b-values sets, as well as the reduction in these diffusion coefficients between the two sets, were significantly lower in comparison to the distal normal pancreatic tissue, suggesting higher cellularity and diminution of the fast-IVIM component in the cancer tissue. DTI using two reference b-values 0 and 100 s/mm² enabled characterization of the water diffusion and anisotropy of the healthy pancreas, taking into account a contribution of IVIM. The reduction in the diffusion coefficients of PDAC, as compared to normal pancreatic tissue, and the smaller change in these coefficients in PDAC when the reference b-value was modified from 0 to 100 s/mm², helped identifying the presence of malignancy.

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.

Molecular fingerprint-region spectroscopy from 5 to 12  μm using an orientation-patterned gallium phosphide optical parametric oscillator.

PubMed

Maidment, Luke; Schunemann, Peter G; Reid, Derryck T

2016-09-15

We report a femtosecond optical parametric oscillator (OPO) based on the new semiconductor gain material orientation-patterned gallium phosphide (OP-GaP), which enables the production of high-repetition-rate femtosecond pulses spanning 5-12 μm with average powers in the few to tens of milliwatts range. This is the first example of a broadband OPO operating across the molecular fingerprint region, and we demonstrate its potential by conducting broadband Fourier-transform spectroscopy using water vapor and a polystyrene reference standard.

Preclinical evaluation of parametric image reconstruction of [18F]FMISO PET: correlation with ex vivo immunohistochemistry

NASA Astrophysics Data System (ADS)

Cheng, Xiaoyin; Bayer, Christine; Maftei, Constantin-Alin; Astner, Sabrina T.; Vaupel, Peter; Ziegler, Sibylle I.; Shi, Kuangyu

2014-01-01

Compared to indirect methods, direct parametric image reconstruction (PIR) has the advantage of high quality and low statistical errors. However, it is not yet clear if this improvement in quality is beneficial for physiological quantification. This study aimed to evaluate direct PIR for the quantification of tumor hypoxia using the hypoxic fraction (HF) assessed from immunohistological data as a physiological reference. Sixteen mice with xenografted human squamous cell carcinomas were scanned with dynamic [18F]FMISO PET. Afterward, tumors were sliced and stained with H&E and the hypoxia marker pimonidazole. The hypoxic signal was segmented using k-means clustering and HF was specified as the ratio of the hypoxic area over the viable tumor area. The parametric Patlak slope images were obtained by indirect voxel-wise modeling on reconstructed images using filtered back projection and ordered-subset expectation maximization (OSEM) and by direct PIR (e.g., parametric-OSEM, POSEM). The mean and maximum Patlak slopes of the tumor area were investigated and compared with HF. POSEM resulted in generally higher correlations between slope and HF among the investigated methods. A strategy for the delineation of the hypoxic tumor volume based on thresholding parametric images at half maximum of the slope is recommended based on the results of this study.

WE-D-BRF-05: Quantitative Dual-Energy CT Imaging for Proton Stopping Power Computation

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

Han, D; Williamson, J; Siebers, J

2014-06-15

Purpose: To extend the two-parameter separable basis-vector model (BVM) to estimation of proton stopping power from dual-energy CT (DECT) imaging. Methods: BVM assumes that the photon cross sections of any unknown material can be represented as a linear combination of the corresponding quantities for two bracketing basis materials. We show that both the electron density (ρe) and mean excitation energy (Iex) can be modeled by BVM, enabling stopping power to be estimated from the Bethe-Bloch equation. We have implemented an idealized post-processing dual energy imaging (pDECT) simulation consisting of monogenetic 45 keV and 80 keV scanning beams with polystyrene-water andmore » water-CaCl2 solution basis pairs for soft tissues and bony tissues, respectively. The coefficients of 24 standard ICRU tissue compositions were estimated by pDECT. The corresponding ρe, Iex, and stopping power tables were evaluated via BVM and compared to tabulated ICRU 44 reference values. Results: BVM-based pDECT was found to estimate ρe and Iex with average and maximum errors of 0.5% and 2%, respectively, for the 24 tissues. Proton stopping power values at 175 MeV, show average/maximum errors of 0.8%/1.4%. For adipose, muscle and bone, these errors result range prediction accuracies less than 1%. Conclusion: A new two-parameter separable DECT model (BVM) for estimating proton stopping power was developed. Compared to competing parametric fit DECT models, BVM has the comparable prediction accuracy without necessitating iterative solution of nonlinear equations or a sample-dependent empirical relationship between effective atomic number and Iex. Based on the proton BVM, an efficient iterative statistical DECT reconstruction model is under development.« less

Reference intervals for selected serum biochemistry analytes in cheetahs Acinonyx jubatus.

PubMed

Hudson-Lamb, Gavin C; Schoeman, Johan P; Hooijberg, Emma H; Heinrich, Sonja K; Tordiffe, Adrian S W

2016-02-26

Published haematologic and serum biochemistry reference intervals are very scarce for captive cheetahs and even more for free-ranging cheetahs. The current study was performed to establish reference intervals for selected serum biochemistry analytes in cheetahs. Baseline serum biochemistry analytes were analysed from 66 healthy Namibian cheetahs. Samples were collected from 30 captive cheetahs at the AfriCat Foundation and 36 free-ranging cheetahs from central Namibia. The effects of captivity-status, age, sex and haemolysis score on the tested serum analytes were investigated. The biochemistry analytes that were measured were sodium, potassium, magnesium, chloride, urea and creatinine. The 90% confidence interval of the reference limits was obtained using the non-parametric bootstrap method. Reference intervals were preferentially determined by the non-parametric method and were as follows: sodium (128 mmol/L - 166 mmol/L), potassium (3.9 mmol/L - 5.2 mmol/L), magnesium (0.8 mmol/L - 1.2 mmol/L), chloride (97 mmol/L - 130 mmol/L), urea (8.2 mmol/L - 25.1 mmol/L) and creatinine (88 µmol/L - 288 µmol/L). Reference intervals from the current study were compared with International Species Information System values for cheetahs and found to be narrower. Moreover, age, sex and haemolysis score had no significant effect on the serum analytes in this study. Separate reference intervals for captive and free-ranging cheetahs were also determined. Captive cheetahs had higher urea values, most likely due to dietary factors. This study is the first to establish reference intervals for serum biochemistry analytes in cheetahs according to international guidelines. These results can be used for future health and disease assessments in both captive and free-ranging cheetahs.

Sensitivity and specificity of normality tests and consequences on reference interval accuracy at small sample size: a computer-simulation study.

PubMed

Le Boedec, Kevin

2016-12-01

According to international guidelines, parametric methods must be chosen for RI construction when the sample size is small and the distribution is Gaussian. However, normality tests may not be accurate at small sample size. The purpose of the study was to evaluate normality test performance to properly identify samples extracted from a Gaussian population at small sample sizes, and assess the consequences on RI accuracy of applying parametric methods to samples that falsely identified the parent population as Gaussian. Samples of n = 60 and n = 30 values were randomly selected 100 times from simulated Gaussian, lognormal, and asymmetric populations of 10,000 values. The sensitivity and specificity of 4 normality tests were compared. Reference intervals were calculated using 6 different statistical methods from samples that falsely identified the parent population as Gaussian, and their accuracy was compared. Shapiro-Wilk and D'Agostino-Pearson tests were the best performing normality tests. However, their specificity was poor at sample size n = 30 (specificity for P < .05: .51 and .50, respectively). The best significance levels identified when n = 30 were 0.19 for Shapiro-Wilk test and 0.18 for D'Agostino-Pearson test. Using parametric methods on samples extracted from a lognormal population but falsely identified as Gaussian led to clinically relevant inaccuracies. At small sample size, normality tests may lead to erroneous use of parametric methods to build RI. Using nonparametric methods (or alternatively Box-Cox transformation) on all samples regardless of their distribution or adjusting, the significance level of normality tests depending on sample size would limit the risk of constructing inaccurate RI. © 2016 American Society for Veterinary Clinical Pathology.

Macrophages Under Low Oxygen Culture Conditions Respond to Ion Parametric Resonance Magnetic Fields

EPA Science Inventory

Macrophages, when entering inflamed tissue, encounter low oxygen tension due to the impairment of blood supply and/or the massive infiltration of cells that consume oxygen. Previously, we showed that such macrophages release more bacteriotoxic hydrogen peroxide (H202) when expose...

Macrophages Under Low Oxygen Culture ConditionsRespond to Ion Parametric Resonance Magnetic Fields

EPA Science Inventory

Macrophages, when entering inflamed tissue, encounter low oxygen tension due to the impairment of blood supply and/or the massive infiltration of cells that consume oxygen. Previously, we showed that such macrophages release more bacteriotoxic hydrogen peroxide (H202) when expose...

A physiology-based parametric imaging method for FDG-PET data

NASA Astrophysics Data System (ADS)

Scussolini, Mara; Garbarino, Sara; Sambuceti, Gianmario; Caviglia, Giacomo; Piana, Michele

2017-12-01

Parametric imaging is a compartmental approach that processes nuclear imaging data to estimate the spatial distribution of the kinetic parameters governing tracer flow. The present paper proposes a novel and efficient computational method for parametric imaging which is potentially applicable to several compartmental models of diverse complexity and which is effective in the determination of the parametric maps of all kinetic coefficients. We consider applications to [18 F]-fluorodeoxyglucose positron emission tomography (FDG-PET) data and analyze the two-compartment catenary model describing the standard FDG metabolization by an homogeneous tissue and the three-compartment non-catenary model representing the renal physiology. We show uniqueness theorems for both models. The proposed imaging method starts from the reconstructed FDG-PET images of tracer concentration and preliminarily applies image processing algorithms for noise reduction and image segmentation. The optimization procedure solves pixel-wise the non-linear inverse problem of determining the kinetic parameters from dynamic concentration data through a regularized Gauss-Newton iterative algorithm. The reliability of the method is validated against synthetic data, for the two-compartment system, and experimental real data of murine models, for the renal three-compartment system.

Nonimaging optical illumination system

DOEpatents

Winston, Roland; Ries, Harald

2000-01-01

A nonimaging illumination optical device for producing a selected far field illuminance over an angular range. The optical device includes a light source 102, a light reflecting surface 108, and a family of light edge rays defined along a reference line 104 with the reflecting surface 108 defined in terms of the reference line 104 as a parametric function R(t) where t is a scalar parameter position and R(t)=k(t)+Du(t) where k(t) is a parameterization of the reference line 104, and D is a distance from a point on the reference line 104 to the reflection surface 108 along the desired edge ray through the point.

Nonimaging optical illumination system

DOEpatents

Winston, Roland; Ries, Harald

1998-01-01

A nonimaging illumination optical device for producing a selected far field illuminance over an angular range. The optical device includes a light source 102, a light reflecting surface 108, and a family of light edge rays defined along a reference line 104 with the reflecting surface 108 defined in terms of the reference line 104 as a parametric function R(t) where t is a scalar parameter position and R(t)=k(t)+Du(t) where k(t) is a parameterization of the reference line 104, and D is a distance from a point on the reference line 104 to the reflection surface 108 along the desired edge ray through the point.

Nonimaging optical illumination system

DOEpatents

Winston, Roland; Ries, Harald

1996-01-01

A nonimaging illumination optical device for producing a selected far field illuminance over an angular range. The optical device includes a light source 102, a light reflecting surface 108, and a family of light edge rays defined along a reference line 104 with the reflecting surface 108 defined in terms of the reference line 104 as a parametric function R(t) where t is a scalar parameter position and R(t)=k(t)+Du(t) where k(t) is a parameterization of the reference line 104, and D is a distance from a point on the reference line 104 to the reflection surface 108 along the desired edge ray through the point.

Effect of Logarithmic and Linear Frequency Scales on Parametric Modelling of Tissue Dielectric Data.

PubMed

Salahuddin, Saqib; Porter, Emily; Meaney, Paul M; O'Halloran, Martin

2017-02-01

The dielectric properties of biological tissues have been studied widely over the past half-century. These properties are used in a vast array of applications, from determining the safety of wireless telecommunication devices to the design and optimisation of medical devices. The frequency-dependent dielectric properties are represented in closed-form parametric models, such as the Cole-Cole model, for use in numerical simulations which examine the interaction of electromagnetic (EM) fields with the human body. In general, the accuracy of EM simulations depends upon the accuracy of the tissue dielectric models. Typically, dielectric properties are measured using a linear frequency scale; however, use of the logarithmic scale has been suggested historically to be more biologically descriptive. Thus, the aim of this paper is to quantitatively compare the Cole-Cole fitting of broadband tissue dielectric measurements collected with both linear and logarithmic frequency scales. In this way, we can determine if appropriate choice of scale can minimise the fit error and thus reduce the overall error in simulations. Using a well-established fundamental statistical framework, the results of the fitting for both scales are quantified. It is found that commonly used performance metrics, such as the average fractional error, are unable to examine the effect of frequency scale on the fitting results due to the averaging effect that obscures large localised errors. This work demonstrates that the broadband fit for these tissues is quantitatively improved when the given data is measured with a logarithmic frequency scale rather than a linear scale, underscoring the importance of frequency scale selection in accurate wideband dielectric modelling of human tissues.

Effect of Logarithmic and Linear Frequency Scales on Parametric Modelling of Tissue Dielectric Data

PubMed Central

Salahuddin, Saqib; Porter, Emily; Meaney, Paul M.; O’Halloran, Martin

2016-01-01

The dielectric properties of biological tissues have been studied widely over the past half-century. These properties are used in a vast array of applications, from determining the safety of wireless telecommunication devices to the design and optimisation of medical devices. The frequency-dependent dielectric properties are represented in closed-form parametric models, such as the Cole-Cole model, for use in numerical simulations which examine the interaction of electromagnetic (EM) fields with the human body. In general, the accuracy of EM simulations depends upon the accuracy of the tissue dielectric models. Typically, dielectric properties are measured using a linear frequency scale; however, use of the logarithmic scale has been suggested historically to be more biologically descriptive. Thus, the aim of this paper is to quantitatively compare the Cole-Cole fitting of broadband tissue dielectric measurements collected with both linear and logarithmic frequency scales. In this way, we can determine if appropriate choice of scale can minimise the fit error and thus reduce the overall error in simulations. Using a well-established fundamental statistical framework, the results of the fitting for both scales are quantified. It is found that commonly used performance metrics, such as the average fractional error, are unable to examine the effect of frequency scale on the fitting results due to the averaging effect that obscures large localised errors. This work demonstrates that the broadband fit for these tissues is quantitatively improved when the given data is measured with a logarithmic frequency scale rather than a linear scale, underscoring the importance of frequency scale selection in accurate wideband dielectric modelling of human tissues. PMID:28191324

TU-H-CAMPUS-IeP3-04: Evaluation of Changes in Quantitative Ultrasound Parameters During Prostate Radiotherapy

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

Najafi, M; El Kaffas, A; Han, B

Purpose: Clarity Autoscan ultrasound monitoring system allows acquisition of raw radiofrequency (RF) ultrasound data prior and during radiotherapy. This enables the computation of 3D Quantitative Ultrasound (QUS) tissue parametric maps from. We aim to evaluate whether QUS parameters undergo changes with radiotherapy and thus potentially be used as early predictors and/or markers of treatment response in prostate cancer patients. Methods: In-vivo evaluation was performed under IRB protocol to allow data collection in prostate patients treated with VMAT whereby prostate was imaged through the acoustic window of the perineum. QUS spectroscopy analysis was carried out by computing a tissue power spectrummore » normalized to the power spectrum obtained from a quartz to remove system transfer function effects. A ROI was selected within the 3D image volume of the prostate. Because longitudinal registration was optimal, the same features could be used to select ROIs at roughly the same location in images acquired on different days. Parametric maps were generated within the rectangular ROIs with window sizes that were approximately 8 times the wavelength of the ultrasound. The mid-band fit (MBF), spectral slope (SS) and spectral intercept (SI) QUS parameters were computed for each window within the ROI and displayed as parametric maps. Quantitative parameters were obtained by averaging each of the spectral parameters over the whole ROI. Results: Data was acquired for over 21 treatment fractions. Preliminary results show changes in the parametric maps. MBF values decreased from −33.9 dB to −38.7 dB from pre-treatment to the last day of treatment. The spectral slope increased from −1.1 a.u. to −0.5 a.u., and spectral intercept decreased from −28.2 dB to −36.3 dB over the 21 treatment regimen. Conclusion: QUS parametric maps change over the course of treatment which warrants further investigation in their potential use for treatment planning and predicting treatment outcomes. Research was supported by Elekta.« less

Brain tissues volume measurements from 2D MRI using parametric approach

NASA Astrophysics Data System (ADS)

L'vov, A. A.; Toropova, O. A.; Litovka, Yu. V.

2018-04-01

The purpose of the paper is to propose a fully automated method of volume assessment of structures within human brain. Our statistical approach uses maximum interdependency principle for decision making process of measurements consistency and unequal observations. Detecting outliers performed using maximum normalized residual test. We propose a statistical model which utilizes knowledge of tissues distribution in human brain and applies partial data restoration for precision improvement. The approach proposes completed computationally efficient and independent from segmentation algorithm used in the application.

In vivo multiphoton microscopy beyond 1 mm in the brain

NASA Astrophysics Data System (ADS)

Miller, David R.; Medina, Flor A.; Hassan, Ahmed; Perillo, Evan P.; Hagan, Kristen; Kazmi, S. M. Shams; Zemelman, Boris V.; Dunn, Andrew K.

2017-02-01

We perform high-resolution, non-invasive, in vivo deep-tissue imaging of the mouse neocortex using multiphoton microscopy with a high repetition rate optical parametric amplifier laser source tunable between λ=1,100 and 1,400 nm. We demonstrate an imaging depth of 1,200 μm in vasculature and 1,160 μm in neurons. We also demonstrate deep-tissue imaging using Indocyanine Green (ICG), which is FDA approved and a promising route to translate multiphoton microscopy to human applications.

Design Automation Using Script Languages. High-Level CAD Templates in Non-Parametric Programs

NASA Astrophysics Data System (ADS)

Moreno, R.; Bazán, A. M.

2017-10-01

The main purpose of this work is to study the advantages offered by the application of traditional techniques of technical drawing in processes for automation of the design, with non-parametric CAD programs, provided with scripting languages. Given that an example drawing can be solved with traditional step-by-step detailed procedures, is possible to do the same with CAD applications and to generalize it later, incorporating references. In today’s modern CAD applications, there are striking absences of solutions for building engineering: oblique projections (military and cavalier), 3D modelling of complex stairs, roofs, furniture, and so on. The use of geometric references (using variables in script languages) and their incorporation into high-level CAD templates allows the automation of processes. Instead of repeatedly creating similar designs or modifying their data, users should be able to use these templates to generate future variations of the same design. This paper presents the automation process of several complex drawing examples based on CAD script files aided with parametric geometry calculation tools. The proposed method allows us to solve complex geometry designs not currently incorporated in the current CAD applications and to subsequently create other new derivatives without user intervention. Automation in the generation of complex designs not only saves time but also increases the quality of the presentations and reduces the possibility of human errors.

Risk indicators related to peri-implant disease: an observational retrospective cohort study

PubMed Central

2016-01-01

Purpose The aim of the present study was to retrospectively investigate the influence of potential risk indicators on the development of peri-implant disease. Methods Overall, 103 patients referred for implant treatment from 2000 to 2012 were randomly enrolled. The study sample consisted of 421 conventional-length (>6 mm) non-turned titanium implants that were evaluated clinically and radiographically according to pre-established clinical and patient-related parameters by a single investigator. A non-parametric Mann-Whitney U test or Kruskal-Wallis rank test and a logistic regression model were used for the statistical analysis of the recorded data at the implant level. Results The diagnosis of peri-implant mucositis and peri-implantitis was made for 173 (41.1%) and 19 (4.5%) implants, respectively. Age (≥65 years), patient adherence (professional hygiene recalls <2/year) and the presence of plaque were associated with higher peri-implant probing-depth values and bleeding-on-probing scores. The logistic regression analysis indicated that age (P=0.001), patient adherence (P=0.03), the absence of keratinized tissue (P=0.03), implants placed in pristine bone (P=0.04), and the presence of peri-implant soft-tissue recession (P=0.000) were strongly associated with the event of peri-implantitis. Conclusions Within the limitations of this study, patients aged ≥65 years and non-adherent subjects were more prone to develop peri-implant disease. Therefore, early diagnosis and a systematic maintenance-care program are essential for maintaining peri-implant tissue health, especially in older patients. PMID:27588216

Creating a Strong Foundation with Engineering Design Graphics.

ERIC Educational Resources Information Center

Newcomer, Jeffrey L.; McKell, Eric K.; Raudebaugh, Robert A.; Kelley, David S.

2001-01-01

Describes the two-course engineering design graphics sequence on introductory design and graphics topics. The first course focuses on conceptual design and the development of visualization and sketching skills while the second one concentrates on detail design and parametric modeling. (Contains 28 references.) (Author/ASK)

Parametric Criticality Safety Calculations for Arrays of TRU Waste Containers

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

Gough, Sean T.

The Nuclear Criticality Safety Division (NCSD) has performed criticality safety calculations for finite and infinite arrays of transuranic (TRU) waste containers. The results of these analyses may be applied in any technical area onsite (e.g., TA-54, TA-55, etc.), as long as the assumptions herein are met. These calculations are designed to update the existing reference calculations for waste arrays documented in Reference 1, in order to meet current guidance on calculational methodology.

DFTB Parameters for the Periodic Table, Part 2: Energies and Energy Gradients from Hydrogen to Calcium.

PubMed

Oliveira, Augusto F; Philipsen, Pier; Heine, Thomas

2015-11-10

In the first part of this series, we presented a parametrization strategy to obtain high-quality electronic band structures on the basis of density-functional-based tight-binding (DFTB) calculations and published a parameter set called QUASINANO2013.1. Here, we extend our parametrization effort to include the remaining terms that are needed to compute the total energy and its gradient, commonly referred to as repulsive potential. Instead of parametrizing these terms as a two-body potential, we calculate them explicitly from the DFTB analogues of the Kohn-Sham total energy expression. This strategy requires only two further numerical parameters per element. Thus, the atomic configuration and four real numbers per element are sufficient to define the DFTB model at this level of parametrization. The QUASINANO2015 parameter set allows the calculation of energy, structure, and electronic structure of all systems composed of elements ranging from H to Ca. Extensive benchmarks show that the overall accuracy of QUASINANO2015 is comparable to that of well-established methods, including PM7 and hand-tuned DFTB parameter sets, while coverage of a much larger range of chemical systems is available.

A parametric model order reduction technique for poroelastic finite element models.

PubMed

Lappano, Ettore; Polanz, Markus; Desmet, Wim; Mundo, Domenico

2017-10-01

This research presents a parametric model order reduction approach for vibro-acoustic problems in the frequency domain of systems containing poroelastic materials (PEM). The method is applied to the Finite Element (FE) discretization of the weak u-p integral formulation based on the Biot-Allard theory and makes use of reduced basis (RB) methods typically employed for parametric problems. The parametric reduction is obtained rewriting the Biot-Allard FE equations for poroelastic materials using an affine representation of the frequency (therefore allowing for RB methods) and projecting the frequency-dependent PEM system on a global reduced order basis generated with the proper orthogonal decomposition instead of standard modal approaches. This has proven to be better suited to describe the nonlinear frequency dependence and the strong coupling introduced by damping. The methodology presented is tested on two three-dimensional systems: in the first experiment, the surface impedance of a PEM layer sample is calculated and compared with results of the literature; in the second, the reduced order model of a multilayer system coupled to an air cavity is assessed and the results are compared to those of the reference FE model.

MR PROSTATE SEGMENTATION VIA DISTRIBUTED DISCRIMINATIVE DICTIONARY (DDD) LEARNING.

PubMed

Guo, Yanrong; Zhan, Yiqiang; Gao, Yaozong; Jiang, Jianguo; Shen, Dinggang

2013-01-01

Segmenting prostate from MR images is important yet challenging. Due to non-Gaussian distribution of prostate appearances in MR images, the popular active appearance model (AAM) has its limited performance. Although the newly developed sparse dictionary learning method[1, 2] can model the image appearance in a non-parametric fashion, the learned dictionaries still lack the discriminative power between prostate and non-prostate tissues, which is critical for accurate prostate segmentation. In this paper, we propose to integrate deformable model with a novel learning scheme, namely the Distributed Discriminative Dictionary ( DDD ) learning, which can capture image appearance in a non-parametric and discriminative fashion. In particular, three strategies are designed to boost the tissue discriminative power of DDD. First , minimum Redundancy Maximum Relevance (mRMR) feature selection is performed to constrain the dictionary learning in a discriminative feature space. Second , linear discriminant analysis (LDA) is employed to assemble residuals from different dictionaries for optimal separation between prostate and non-prostate tissues. Third , instead of learning the global dictionaries, we learn a set of local dictionaries for the local regions (each with small appearance variations) along prostate boundary, thus achieving better tissue differentiation locally. In the application stage, DDDs will provide the appearance cues to robustly drive the deformable model onto the prostate boundary. Experiments on 50 MR prostate images show that our method can yield a Dice Ratio of 88% compared to the manual segmentations, and have 7% improvement over the conventional AAM.

Dorsomedial SCN neuronal subpopulations subserve different functions in human dementia.

PubMed

Harper, David G; Stopa, Edward G; Kuo-Leblanc, Victoria; McKee, Ann C; Asayama, Kentaro; Volicer, Ladislav; Kowall, Neil; Satlin, Andrew

2008-06-01

The suprachiasmatic nuclei (SCN) are necessary and sufficient for the maintenance of circadian rhythms in primate and other mammalian species. The human dorsomedial SCN contains populations of non-species-specific vasopressin and species-specific neurotensin neurons. We made time-series recordings of core body temperature and locomotor activity in 19 elderly, male, end-stage dementia patients and 8 normal elderly controls. Following the death of the dementia patients, neuropathological diagnostic information and tissue samples from the hypothalamus were obtained. Hypothalamic tissue was also obtained from eight normal control cases that had not had activity or core temperature recordings previously. Core temperature was analysed for parametric, circadian features, and activity was analysed for non-parametric and parametric circadian features. These indices were then correlated with the degree of degeneration seen in the SCN (glia/neuron ratio) and neuronal counts from the dorsomedial SCN (vasopressin, neurotensin). Specific loss of SCN neurotensin neurons was associated with loss of activity and temperature amplitude without increase in activity fragmentation. Loss of SCN vasopressin neurons was associated with increased activity fragmentation but not loss of amplitude. Evidence for a circadian rhythm of vasopressinergic activity was seen in the dementia cases but no evidence was seen for a circadian rhythm in neurotensinergic activity. These results provide evidence that the SCN is necessary for the maintenance of the circadian rhythm in humans, information on the role of neuronal subpopulations in subserving this function and the utility of dementia in elaborating brain-behaviour relationships in the human.

Teledetection passive et processus decisionnel a reference spatiale: Application a l'aquaculture en milieu marin

NASA Astrophysics Data System (ADS)

Habbane, Mohamed

L'objectif de cette etude est d'elaborer un processus decisionnel a reference spatiale (PDRS) pour la mariculture. Le PDRS est applique aux eaux cotieres de la baie des Chaleurs, dans le golfe du Saint-Laurent (Canada). Une carte preliminaire regionale d'indices du potentiel maricole, d'une limite de resolution spatiale de 1 kmsp2, est produite avec des parametres du niveau 1. Ces parametres englobent la temperature de l'eau de surface, extraite des images AVHRR, la salinite, les courants ainsi que les pigments chlorophylliens, quantifies a l'aide de mesures in situ. Les images AVHRR, prises en 1994, ont ete utiliees comme reference primaire pour selectionner des aires pouvant supporter une activite maricole sur la cote nord de la baie des Chaleurs. La temperature de surface extraite de ces images permet une analyse mesoechelle a la fois qualitative et quantitative des processus cotiers observes pendant la periode d'acquisition des donnees. Les autres donnees, soit la salinite, les courants et les concentrations en pigments chlorophylliens, sont analysees de facon a identifier la variabilite spatio-temporelle des caracteristiques des eaux de surface. L'ensemble des informations permet de produire une carte preliminaire regionale d'indices du potentiel maricole de la partie centrale de la baie des Chaleurs. Selon cet indice (defini entre 0 et 1), le secteur de potentiel aquicole de 0,5 a 0,75 s'etend sur une superficie d'environ 300 kmsp2. La localisation de cette aire potentielle est en accord avec les fortes concentrations en pigments chlrophylliens, presentant des conditions environnementales ideales a une haute productivite biologique. Par la suite la carte preliminaire est modifiee en tenant compte des parametres du niveau 2. Ces parametres sont la geomorphologie littorale, la bathymetrie, les sediments en suspension, les vents, les vagues, le debit d'eau douce, la glace marine, le carbone organique dissous, les aires de peche et les sources de pollution. Ces parametres sont compares deux a deux par rapport a la carte preliminaire regionale d'indices du potentiel maricole pour determiner leur poids relatif. La carte finale produite avec ces parametres du niveau 2 presente un secteur ou les indices du potentiel maricole sont de 0,5 a 0,75. Ce secteur longe la cote et epouse les isobathes de 10 a 30 m de profondeur. L'effet de la profondeur d'eau semble avoir jouer un role important. Le secteur de potentiel maricole de 0,25 a 0,5 est toujours present et couvre une superficie d'environ 426 kmsp2. L'etude necessitera toujours un suivi des conditions environnementales prevalant dans la region. Ce suivi peut etre effectue a l'aide d'un outil de vision aerospatiale (capteurs de teledetection) et d'analyse spatio-temporelle (SIG-PDRS). (Abstract shortened by UMI.)

Multi-parametric monitoring and assessment of high-intensity focused ultrasound (HIFU) boiling by harmonic motion imaging for focused ultrasound (HMIFU): an ex vivo feasibility study

NASA Astrophysics Data System (ADS)

Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa E.

2014-03-01

Harmonic motion imaging for focused ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and change in relative phase shift during high energy HIFU treatment with tissue boiling. Forty three (n = 43) thermal lesions were formed in ex vivo canine liver specimens (n = 28). Two-dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10 s, 20 s and 30 s HIFU durations at three different acoustic powers of 8, 10, and 11 W, which were selected and verified as treatment parameters capable of inducing boiling using both thermocouple and passive cavitation detection (PCD) measurements. Although a steady decrease in the displacement, compressive strain, and relative change in the focal phase shift (Δϕ) were obtained in numerous cases, indicating an overall increase in relative stiffness, the study outcomes also showed that during boiling, a reverse lesion-to-background displacement contrast was detected, indicating potential change in tissue absorption, geometrical change and/or, mechanical gelatification or pulverization. Following treatment, corresponding 2D HMI displacement images of the thermal lesions also mapped consistent discrepancy in the lesion-to-background displacement contrast. Despite the expectedly chaotic changes in acoustic properties with boiling, the relative change in phase shift showed a consistent decrease, indicating its robustness to monitor biomechanical properties independent of the acoustic property changes throughout the HIFU treatment. In addition, the 2D HMI displacement images confirmed and indicated the increase in the thermal lesion size with treatment duration, which was validated against pathology. In conclusion, multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU boiling, some of which were independent of the acoustic parameter changes.

Multi-parametric monitoring and assessment of High Intensity Focused Ultrasound (HIFU) boiling by Harmonic Motion Imaging for Focused Ultrasound (HMIFU): An ex vivo feasibility study

PubMed Central

Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa E.

2014-01-01

Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and change in relative phase-shift during high energy HIFU treatment with tissue boiling. Forty three (n=43) thermal lesions were formed in ex vivo canine liver specimens (n=28). Two dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10-s, 20-s and 30-s HIFU durations at three different acoustic powers of 8, 10, and 11W, which were selected and verified as treatment parameters capable of inducing boiling using both thermocouple and Passive Cavitation Detection (PCD) measurements. Although a steady decrease in the displacement, compressive strain, and relative change in the focal phase shift (Δφ) were obtained in numerous cases, indicating an overall increase in relative stiffness, the study outcomes also showed that during boiling, a reverse lesion-to-background displacement contrast was detected, indicating potential change in tissue absorption, geometrical change and/or, mechanical gelatification or pulverization. Following treatment, corresponding 2D HMI displacement images of the thermal lesions also mapped consistent discrepancy in the lesion-to-background displacement contrast. Despite unpredictable changes in acoustic properties with boiling, the relative change in phase shift showed a consistent decrease, indicating its robustness to monitor biomechanical properties independent of the acoustic property change throughout the HIFU treatment. In addition, the 2D HMI displacement images confirmed and indicated the increase in the thermal lesion size with treatment duration, which was validated against pathology. In conclusion, multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU boiling, some of which were independent of the acoustic parameter changes. PMID:24556974

Multi-parametric monitoring and assessment of high-intensity focused ultrasound (HIFU) boiling by harmonic motion imaging for focused ultrasound (HMIFU): an ex vivo feasibility study.

PubMed

Hou, Gary Y; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa E

2014-03-07

Harmonic motion imaging for focused ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and change in relative phase shift during high energy HIFU treatment with tissue boiling. Forty three (n = 43) thermal lesions were formed in ex vivo canine liver specimens (n = 28). Two-dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10 s, 20 s and 30 s HIFU durations at three different acoustic powers of 8, 10, and 11 W, which were selected and verified as treatment parameters capable of inducing boiling using both thermocouple and passive cavitation detection (PCD) measurements. Although a steady decrease in the displacement, compressive strain, and relative change in the focal phase shift (Δϕ) were obtained in numerous cases, indicating an overall increase in relative stiffness, the study outcomes also showed that during boiling, a reverse lesion-to-background displacement contrast was detected, indicating potential change in tissue absorption, geometrical change and/or, mechanical gelatification or pulverization. Following treatment, corresponding 2D HMI displacement images of the thermal lesions also mapped consistent discrepancy in the lesion-to-background displacement contrast. Despite the expectedly chaotic changes in acoustic properties with boiling, the relative change in phase shift showed a consistent decrease, indicating its robustness to monitor biomechanical properties independent of the acoustic property changes throughout the HIFU treatment. In addition, the 2D HMI displacement images confirmed and indicated the increase in the thermal lesion size with treatment duration, which was validated against pathology. In conclusion, multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU boiling, some of which were independent of the acoustic parameter changes.

Design for disassembly and sustainability assessment to support aircraft end-of-life treatment

NASA Astrophysics Data System (ADS)

Savaria, Christian

Gas turbine engine design is a multidisciplinary and iterative process. Many design iterations are necessary to address the challenges among the disciplines. In the creation of a new engine architecture, the design time is crucial in capturing new business opportunities. At the detail design phase, it was proven very difficult to correct an unsatisfactory design. To overcome this difficulty, the concept of Multi-Disciplinary Optimization (MDO) at the preliminary design phase (Preliminary MDO or PMDO) is used allowing more freedom to perform changes in the design. PMDO also reduces the design time at the preliminary design phase. The concept of PMDO was used was used to create parametric models, and new correlations for high pressure gas turbine housing and shroud segments towards a new design process. First, dedicated parametric models were created because of their reusability and versatility. Their ease of use compared to non-parameterized models allows more design iterations thus reduces set up and design time. Second, geometry correlations were created to minimize the number of parameters used in turbine housing and shroud segment design. Since the turbine housing and the shroud segment geometries are required in tip clearance analyses, care was taken as to not oversimplify the parametric formulation. In addition, a user interface was developed to interact with the parametric models and improve the design time. Third, the cooling flow predictions require many engine parameters (i.e. geometric and performance parameters and air properties) and a reference shroud segments. A second correlation study was conducted to minimize the number of engine parameters required in the cooling flow predictions and to facilitate the selection of a reference shroud segment. Finally, the parametric models, the geometry correlations, and the user interface resulted in a time saving of 50% and an increase in accuracy of 56% in the new design system compared to the existing design system. Also, regarding the cooling flow correlations, the number of engine parameters was reduced by a factor of 6 to create a simplified prediction model and hence a faster shroud segment selection process. None

18F-FLT uptake kinetics in head and neck squamous cell carcinoma: a PET imaging study.

PubMed

Liu, Dan; Chalkidou, Anastasia; Landau, David B; Marsden, Paul K; Fenwick, John D

2014-04-01

To analyze the kinetics of 3(')-deoxy-3(')-[F-18]-fluorothymidine (18F-FLT) uptake by head and neck squamous cell carcinomas and involved nodes imaged using positron emission tomography (PET). Two- and three-tissue compartment models were fitted to 12 tumor time-activity-curves (TACs) obtained for 6 structures (tumors or involved nodes) imaged in ten dynamic PET studies of 1 h duration, carried out for five patients. The ability of the models to describe the data was assessed using a runs test, the Akaike information criterion (AIC) and leave-one-out cross-validation. To generate parametric maps the models were also fitted to TACs of individual voxels. Correlations between maps of different parameters were characterized using Pearson'sr coefficient; in particular the phosphorylation rate-constants k3-2tiss and k5 of the two- and three-tissue models were studied alongside the flux parameters KFLT- 2tiss and KFLT of these models, and standardized uptake values (SUV). A methodology based on expectation-maximization clustering and the Bayesian information criterion ("EM-BIC clustering") was used to distil the information from noisy parametric images. Fits of two-tissue models 2C3K and 2C4K and three-tissue models 3C5K and 3C6K comprising three, four, five, and six rate-constants, respectively, pass the runs test for 4, 8, 10, and 11 of 12 tumor TACs. The three-tissue models have lower AIC and cross-validation scores for nine of the 12 tumors. Overall the 3C6K model has the lowest AIC and cross-validation scores and its fitted parameter values are of the same orders of magnitude as literature estimates. Maps of KFLT and KFLT- 2tiss are strongly correlated (r = 0.85) and also correlate closely with SUV maps (r = 0.72 for KFLT- 2tiss, 0.64 for KFLT). Phosphorylation rate-constant maps are moderately correlated with flux maps (r = 0.48 for k3-2tiss vs KFLT- 2tiss and r = 0.68 for k5 vs KFLT); however, neither phosphorylation rate-constant correlates significantly with SUV. EM-BIC clustering reduces the parametric maps to a small number of levels--on average 5.8, 3.5, 3.4, and 1.4 for KFLT- 2tiss, KFLT, k3-2tiss, and k5. This large simplification is potentially useful for radiotherapy dose-painting, but demonstrates the high noise in some maps. Statistical simulations show that voxel level noise degrades TACs generated from the 3C6K model sufficiently that the average AIC score, parameter bias, and total uncertainty of 2C4K model fits are similar to those of 3C6K fits, whereas at the whole tumor level the scores are lower for 3C6K fits. For the patients studied here, whole tumor FLT uptake time-courses are represented better overall by a three-tissue than by a two-tissue model. EM-BIC clustering simplifies noisy parametric maps, providing the best description of the underlying information they contain and is potentially useful for radiotherapy dose-painting. However, the clustering highlights the large degree of noise present in maps of the phosphorylation rate-constantsk5 and k3-2tiss, which are conceptually tightly linked to cellular proliferation. Methods must be found to make these maps more robust-either by constraining other model parameters or modifying dynamic imaging protocols. © 2014 American Association of Physicists in Medicine.

Characterization of Vertical Impact Device Acceleration Pulses Using Parametric Assessment: Phase I

DTIC Science & Technology

2015-04-01

vehicle seating systems. Previous research on the VID (Knox, T., Pellettiere, J., Perry, C., Plaga , J., Bonfeld, J., 2008; Veridian Contract Report...BIBLIOGRAPHY/REFERENCES Knox, T., Pellettiere, J., Perry, C., Plaga , J., Bonfeld, J. (2008). New Sensors to Track Head Acceleration During Possible

Noninvasive bi-graphical analysis for the quantification of slowly reversible radioligand binding

NASA Astrophysics Data System (ADS)

Seo, Seongho; Kim, Su Jin; Yoo, Hye Bin; Lee, Jee-Young; Kyeong Kim, Yu; Lee, Dong Soo; Zhou, Yun; Lee, Jae Sung

2016-09-01

In this paper, we presented a novel reference-region-based (noninvasive) bi-graphical analysis for the quantification of a reversible radiotracer binding that may be too slow to reach relative equilibrium (RE) state during positron emission tomography (PET) scans. The proposed method indirectly implements the noninvasive Logan plot, through arithmetic combination of the parameters of two other noninvasive methods and the apparent tissue-to-plasma efflux rate constant for the reference region (k2\\prime ). We investigated its validity and statistical properties, by performing a simulation study with various noise levels and k2\\prime values, and also evaluated its feasibility for [18F]FP-CIT PET in human brain. The results revealed that the proposed approach provides distribution volume ratio estimation comparable to the Logan plot at low noise levels while improving underestimation caused by non-RE state differently depending on k2\\prime . Furthermore, the proposed method was able to avoid noise-induced bias of the Logan plot, and the variability of its results was less dependent on k2\\prime than the Logan plot. Therefore, this approach, without issues related to arterial blood sampling given a pre-estimate of k2\\prime (e.g. population-based), could be useful in parametric image generation for slow kinetic tracers staying in a non-RE state within a PET scan.

[Technical background of data collection for parametric observation of total mesorectal excision (TME) in rectal cancer].

PubMed

Bláha, M; Hoch, J; Ferko, A; Ryška, A; Hovorková, E

Improvement in any human activity is preconditioned by inspection of results and providing feedback used for modification of the processes applied. Comparison of experts experience in the given field is another indispensable part leading to optimisation and improvement of processes, and optimally to implementation of standards. For the purpose of objective comparison and assessment of the processes, it is always necessary to describe the processes in a parametric way, to obtain representative data, to assess the achieved results, and to provide unquestionable and data-driven feedback based on such analysis. This may lead to a consensus on the definition of standards in the given area of health care. Total mesorectal excision (TME) is a standard procedure of rectal cancer (C20) surgical treatment. However, the quality of performed procedures varies in different health care facilities, which is given, among others, by internal processes and surgeons experience. Assessment of surgical treatment results is therefore of key importance. A pathologist who assesses the resected tissue can provide valuable feedback in this respect. An information system for the parametric assessment of TME performance is described in our article, including technical background in the form of a multicentre clinical registry and the structure of observed parameters. We consider the proposed system of TME parametric assessment as significant for improvement of TME performance, aimed at reducing local recurrences and at improving the overall prognosis of patients. rectal cancer total mesorectal excision parametric data clinical registries TME registry.

Parametric mapping using spectral analysis for 11C-PBR28 PET reveals neuroinflammation in mild cognitive impairment subjects.

PubMed

Fan, Zhen; Dani, Melanie; Femminella, Grazia D; Wood, Melanie; Calsolaro, Valeria; Veronese, Mattia; Turkheimer, Federico; Gentleman, Steve; Brooks, David J; Hinz, Rainer; Edison, Paul

2018-07-01

Neuroinflammation and microglial activation play an important role in amnestic mild cognitive impairment (MCI) and Alzheimer's disease. In this study, we investigated the spatial distribution of neuroinflammation in MCI subjects, using spectral analysis (SA) to generate parametric maps and quantify 11 C-PBR28 PET, and compared these with compartmental and other kinetic models of quantification. Thirteen MCI and nine healthy controls were enrolled in this study. Subjects underwent 11 C-PBR28 PET scans with arterial cannulation. Spectral analysis with an arterial plasma input function was used to generate 11 C-PBR28 parametric maps. These maps were then compared with regional 11 C-PBR28 V T (volume of distribution) using a two-tissue compartment model and Logan graphic analysis. Amyloid load was also assessed with 18 F-Flutemetamol PET. With SA, three component peaks were identified in addition to blood volume. The 11 C-PBR28 impulse response function (IRF) at 90 min produced the lowest coefficient of variation. Single-subject analysis using this IRF demonstrated microglial activation in five out of seven amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake revealed a group-wise significant increase in neuroinflammation in amyloid-positive MCI subjects versus HC in multiple cortical association areas, and particularly in the temporal lobe. Interestingly, compartmental analysis detected group-wise increase in 11 C-PBR28 binding in the thalamus of amyloid-positive MCI subjects, while Logan parametric maps did not perform well. This study demonstrates for the first time that spectral analysis can be used to generate parametric maps of 11 C-PBR28 uptake, and is able to detect microglial activation in amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake allow voxel-wise single-subject analysis and could be used to evaluate microglial activation in individual subjects.

Nonlinearity Role in Long-Term Interaction of the Ocean Gravity Waves

DTIC Science & Technology

2012-09-30

3 4 =s We found that in the fetch-limited case the wind forcing index s is similar to the time domain situation, and the wind forcing is given by...of its evolution. Fig.5 gives a graphical summary of four reference cases of self-similar evolution of wind-driven waves. These cases are shown as...different R, tangents of one-parametric dependencies H~TR height-to-period in logarithmic axes. Reference cases of growing wind sea are shown as

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

PubMed

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

2014-09-18

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

Serum prolactin revisited: parametric reference intervals and cross platform evaluation of polyethylene glycol precipitation-based methods for discrimination between hyperprolactinemia and macroprolactinemia.

PubMed

Overgaard, Martin; Pedersen, Susanne Møller

2017-10-26

Hyperprolactinemia diagnosis and treatment is often compromised by the presence of biologically inactive and clinically irrelevant higher-molecular-weight complexes of prolactin, macroprolactin. The objective of this study was to evaluate the performance of two macroprolactin screening regimes across commonly used automated immunoassay platforms. Parametric total and monomeric gender-specific reference intervals were determined for six immunoassay methods using female (n=96) and male sera (n=127) from healthy donors. The reference intervals were validated using 27 hyperprolactinemic and macroprolactinemic sera, whose presence of monomeric and macroforms of prolactin were determined using gel filtration chromatography (GFC). Normative data for six prolactin assays included the range of values (2.5th-97.5th percentiles). Validation sera (hyperprolactinemic and macroprolactinemic; n=27) showed higher discordant classification [mean=2.8; 95% confidence interval (CI) 1.2-4.4] for the monomer reference interval method compared to the post-polyethylene glycol (PEG) recovery cutoff method (mean=1.8; 95% CI 0.8-2.8). The two monomer/macroprolactin discrimination methods did not differ significantly (p=0.089). Among macroprolactinemic sera evaluated by both discrimination methods, the Cobas and Architect/Kryptor prolactin assays showed the lowest and the highest number of misclassifications, respectively. Current automated immunoassays for prolactin testing require macroprolactin screening methods based on PEG precipitation in order to discriminate truly from falsely elevated serum prolactin. While the recovery cutoff and monomeric reference interval macroprolactin screening methods demonstrate similar discriminative ability, the latter method also provides the clinician with an easy interpretable monomeric prolactin concentration along with a monomeric reference interval.

A global multicenter study on reference values: 1. Assessment of methods for derivation and comparison of reference intervals.

PubMed

Ichihara, Kiyoshi; Ozarda, Yesim; Barth, Julian H; Klee, George; Qiu, Ling; Erasmus, Rajiv; Borai, Anwar; Evgina, Svetlana; Ashavaid, Tester; Khan, Dilshad; Schreier, Laura; Rolle, Reynan; Shimizu, Yoshihisa; Kimura, Shogo; Kawano, Reo; Armbruster, David; Mori, Kazuo; Yadav, Binod K

2017-04-01

The IFCC Committee on Reference Intervals and Decision Limits coordinated a global multicenter study on reference values (RVs) to explore rational and harmonizable procedures for derivation of reference intervals (RIs) and investigate the feasibility of sharing RIs through evaluation of sources of variation of RVs on a global scale. For the common protocol, rather lenient criteria for reference individuals were adopted to facilitate harmonized recruitment with planned use of the latent abnormal values exclusion (LAVE) method. As of July 2015, 12 countries had completed their study with total recruitment of 13,386 healthy adults. 25 analytes were measured chemically and 25 immunologically. A serum panel with assigned values was measured by all laboratories. RIs were derived by parametric and nonparametric methods. The effect of LAVE methods is prominent in analytes which reflect nutritional status, inflammation and muscular exertion, indicating that inappropriate results are frequent in any country. The validity of the parametric method was confirmed by the presence of analyte-specific distribution patterns and successful Gaussian transformation using the modified Box-Cox formula in all countries. After successful alignment of RVs based on the panel test results, nearly half the analytes showed variable degrees of between-country differences. This finding, however, requires confirmation after adjusting for BMI and other sources of variation. The results are reported in the second part of this paper. The collaborative study enabled us to evaluate rational methods for deriving RIs and comparing the RVs based on real-world datasets obtained in a harmonized manner. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Parametric Net Influx Rate Images of 68Ga-DOTATOC and 68Ga-DOTATATE: Quantitative Accuracy and Improved Image Contrast.

PubMed

Ilan, Ezgi; Sandström, Mattias; Velikyan, Irina; Sundin, Anders; Eriksson, Barbro; Lubberink, Mark

2017-05-01

68 Ga-DOTATOC and 68 Ga-DOTATATE are radiolabeled somatostatin analogs used for the diagnosis of somatostatin receptor-expressing neuroendocrine tumors (NETs), and SUV measurements are suggested for treatment monitoring. However, changes in net influx rate ( K i ) may better reflect treatment effects than those of the SUV, and accordingly there is a need to compute parametric images showing K i at the voxel level. The aim of this study was to evaluate parametric methods for computation of parametric K i images by comparison to volume of interest (VOI)-based methods and to assess image contrast in terms of tumor-to-liver ratio. Methods: Ten patients with metastatic NETs underwent a 45-min dynamic PET examination followed by whole-body PET/CT at 1 h after injection of 68 Ga-DOTATOC and 68 Ga-DOTATATE on consecutive days. Parametric K i images were computed using a basis function method (BFM) implementation of the 2-tissue-irreversible-compartment model and the Patlak method using a descending aorta image-derived input function, and mean tumor K i values were determined for 50% isocontour VOIs and compared with K i values based on nonlinear regression (NLR) of the whole-VOI time-activity curve. A subsample of healthy liver was delineated in the whole-body and K i images, and tumor-to-liver ratios were calculated to evaluate image contrast. Correlation ( R 2 ) and agreement between VOI-based and parametric K i values were assessed using regression and Bland-Altman analysis. Results: The R 2 between NLR-based and parametric image-based (BFM) tumor K i values was 0.98 (slope, 0.81) and 0.97 (slope, 0.88) for 68 Ga-DOTATOC and 68 Ga-DOTATATE, respectively. For Patlak analysis, the R 2 between NLR-based and parametric-based (Patlak) tumor K i was 0.95 (slope, 0.71) and 0.92 (slope, 0.74) for 68 Ga-DOTATOC and 68 Ga-DOTATATE, respectively. There was no bias between NLR and parametric-based K i values. Tumor-to-liver contrast was 1.6 and 2.0 times higher in the parametric BFM K i images and 2.3 and 3.0 times in the Patlak images than in the whole-body images for 68 Ga-DOTATOC and 68 Ga-DOTATATE, respectively. Conclusion: A high R 2 and agreement between NLR- and parametric-based K i values was found, showing that K i images are quantitatively accurate. In addition, tumor-to-liver contrast was superior in the parametric K i images compared with whole-body images for both 68 Ga-DOTATOC and 68 Ga DOTATATE. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Optimized statistical parametric mapping for partial-volume-corrected amyloid positron emission tomography in patients with Alzheimer's disease and Lewy body dementia

NASA Astrophysics Data System (ADS)

Oh, Jungsu S.; Kim, Jae Seung; Chae, Sun Young; Oh, Minyoung; Oh, Seung Jun; Cha, Seung Nam; Chang, Ho-Jong; Lee, Chong Sik; Lee, Jae Hong

2017-03-01

We present an optimized voxelwise statistical parametric mapping (SPM) of partial-volume (PV)-corrected positron emission tomography (PET) of 11C Pittsburgh Compound B (PiB), incorporating the anatomical precision of magnetic resonance image (MRI) and amyloid β (A β) burden-specificity of PiB PET. First, we applied region-based partial-volume correction (PVC), termed the geometric transfer matrix (GTM) method, to PiB PET, creating MRI-based lobar parcels filled with mean PiB uptakes. Then, we conducted a voxelwise PVC by multiplying the original PET by the ratio of a GTM-based PV-corrected PET to a 6-mm-smoothed PV-corrected PET. Finally, we conducted spatial normalizations of the PV-corrected PETs onto the study-specific template. As such, we increased the accuracy of the SPM normalization and the tissue specificity of SPM results. Moreover, lobar smoothing (instead of whole-brain smoothing) was applied to increase the signal-to-noise ratio in the image without degrading the tissue specificity. Thereby, we could optimize a voxelwise group comparison between subjects with high and normal A β burdens (from 10 patients with Alzheimer's disease, 30 patients with Lewy body dementia, and 9 normal controls). Our SPM framework outperformed than the conventional one in terms of the accuracy of the spatial normalization (85% of maximum likelihood tissue classification volume) and the tissue specificity (larger gray matter, and smaller cerebrospinal fluid volume fraction from the SPM results). Our SPM framework optimized the SPM of a PV-corrected A β PET in terms of anatomical precision, normalization accuracy, and tissue specificity, resulting in better detection and localization of A β burdens in patients with Alzheimer's disease and Lewy body dementia.

Noninvasive parametric blood flow imaging of head and neck tumours using [15O]H2O and PET/CT.

PubMed

Komar, Gaber; Oikonen, Vesa; Sipilä, Hannu; Seppänen, Marko; Minn, Heikki

2012-11-01

The aim of this study was to develop a simple noninvasive method for measuring blood flow using [15O]H2O PET/CT for the head and neck area applicable in daily clinical practice. Fifteen dynamic [15O]H2O PET emission scans with simultaneous online radioactivity measurements of radial arterial blood [Blood-input functions (IFs)] were performed. Two noninvasively obtained population-based input functions were calculated by averaging all Blood-IF curves corrected for patients' body mass and injected dose [standardized uptake value (SUV)-IF] and for body surface area (BSA-IF) and injected dose. Parametric perfusion images were calculated for each set of IFs using a linearized two-compartment model, and values for several tissues were compared using Blood-IF as the gold standard. On comparing all tissues, the correlation between blood flow obtained with the invasive Blood-IF and both SUV-IF and BSA-IF was significant (R2=0.785 with P<0.001 and R2=0.813 with P<0.001, respectively). In individual tissues, the performance of the two noninvasive methods was most reliable in resting muscle and slightly less reliable in tumour and cerebellar regions. In these two tissues, only BSA-IF showed a significant correlation with Blood-IF (R2=0.307 with P=0.032 in tumours and R2=0.398 with P<0.007 in the cerebellum). The BSA-based noninvasive method enables clinically relevant delineation between areas of low and high blood flow in tumours. The blood flow of low-perfusion tissues can be reliably quantified using either of the evaluated noninvasive methods.

Is there more valuable information in PWI datasets for a voxel-wise acute ischemic stroke tissue outcome prediction than what is represented by typical perfusion maps?

NASA Astrophysics Data System (ADS)

Forkert, Nils Daniel; Siemonsen, Susanne; Dalski, Michael; Verleger, Tobias; Kemmling, Andre; Fiehler, Jens

2014-03-01

The acute ischemic stroke is a leading cause for death and disability in the industry nations. In case of a present acute ischemic stroke, the prediction of the future tissue outcome is of high interest for the clinicians as it can be used to support therapy decision making. Within this context, it has already been shown that the voxel-wise multi-parametric tissue outcome prediction leads to more promising results compared to single channel perfusion map thresholding. Most previously published multi-parametric predictions employ information from perfusion maps derived from perfusion-weighted MRI together with other image sequences such as diffusion-weighted MRI. However, it remains unclear if the typically calculated perfusion maps used for this purpose really include all valuable information from the PWI dataset for an optimal tissue outcome prediction. To investigate this problem in more detail, two different methods to predict tissue outcome using a k-nearest-neighbor approach were developed in this work and evaluated based on 18 datasets of acute stroke patients with known tissue outcome. The first method integrates apparent diffusion coefficient and perfusion parameter (Tmax, MTT, CBV, CBF) information for the voxel-wise prediction, while the second method employs also apparent diffusion coefficient information but the complete perfusion information in terms of the voxel-wise residue functions instead of the perfusion parameter maps for the voxel-wise prediction. Overall, the comparison of the results of the two prediction methods for the 18 patients using a leave-one-out cross validation revealed no considerable differences. Quantitatively, the parameter-based prediction of tissue outcome led to a mean Dice coefficient of 0.474, while the prediction using the residue functions led to a mean Dice coefficient of 0.461. Thus, it may be concluded from the results of this study that the perfusion parameter maps typically derived from PWI datasets include all valuable perfusion information required for a voxel-based tissue outcome prediction, while the complete analysis of the residue functions does not add further benefits for the voxel-wise tissue outcome prediction and is also computationally more expensive.

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

PubMed

Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav

2013-10-28

We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

Separation and purification of enzymes by continuous pH-parametric pumping

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

Huang, S.Y.; Lin, C.K.; Juang, L.Y.

1985-10-01

Trypsin and chymotrypsin were separated from porcine pancreas extract by continuous pH-parametric pumping. CHOM (chicken ovomucoid) was convalently bound to laboratory-prepared crab chitin with glutaraldehyde to form an affinity adsorbent of trypsin. The pH levels of top and bottom feeds were 8.0 and 2.5, respectively. Similar inhibitor, DKOM (duck ovomucoid), and pH levels 8.0 and 2.0 for top and bottom feeds, respectively, were used for separation and purification of chymotrypsin. e-Amino caproyl-D-tryptophan methyl ester was coupled to chitosan to form an affinity adsorbent for stem bromelain. The pH levels were 8.7 and 3.0. Separation continued fairly well with high yield,more » e.g., 95% recovery of trypsin after continuous pumping of 10 cycles. Optimum operational conditions for concentration and purification of these enzymes were investigated. The results showed that the continuous pH-parametric pumping coupled with affinity chromatography is effective for concentration and purification of enzymes. 19 references.« less

Diffusion Tensor Magnetic Resonance Imaging of the Pancreas

PubMed Central

Nissan, Noam; Golan, Talia; Furman-Haran, Edna; Apter, Sara; Inbar, Yael; Ariche, Arie; Bar-Zakay, Barak; Goldes, Yuri; Schvimer, Michael; Grobgeld, Dov; Degani, Hadassa

2014-01-01

Purpose To develop a diffusion-tensor-imaging (DTI) protocol that is sensitive to the complex diffusion and perfusion properties of the healthy and malignant pancreas tissues. Materials and Methods Twenty-eight healthy volunteers and nine patients with pancreatic-ductal-adenocacinoma (PDAC), were scanned at 3T with T2-weighted and DTI sequences. Healthy volunteers were also scanned with multi-b diffusion-weighted-imaging (DWI), whereas a standard clinical protocol complemented the PDAC patients’ scans. Image processing at pixel resolution yielded parametric maps of three directional diffusion coefficients λ1, λ2, λ3, apparent diffusion coefficient (ADC), and fractional anisotropy (FA), as well as a λ1-vector map, and a main diffusion-direction map. Results DTI measurements of healthy pancreatic tissue at b-values 0,500 s/mm2yielded: λ1 = (2.65±0.35)×10−3, λ2 = (1.87±0.22)×10−3, λ3 = (1.20±0.18)×10−3, ADC = (1.91±0.22)×10−3 (all in mm2/s units) and FA = 0.38±0.06. Using b-values of 100,500 s/mm2 led to a significant reduction in λ1, λ2, λ3 and ADC (p<.0001) and a significant increase (p<0.0001) in FA. The reduction in the diffusion coefficients suggested a contribution of a fast intra-voxel-incoherent-motion (IVIM) component at b≤100 s/mm2, which was confirmed by the multi-b DWI results. In PDACs, λ1, λ2, λ3 and ADC in both 0,500 s/mm2 and 100,500 s/mm2 b-values sets, as well as the reduction in these diffusion coefficients between the two sets, were significantly lower in comparison to the distal normal pancreatic tissue, suggesting higher cellularity and diminution of the fast-IVIM component in the cancer tissue. Conclusion DTI using two reference b-values 0 and 100 s/mm2 enabled characterization of the water diffusion and anisotropy of the healthy pancreas, taking into account a contribution of IVIM. The reduction in the diffusion coefficients of PDAC, as compared to normal pancreatic tissue, and the smaller change in these coefficients in PDAC when the reference b-value was modified from 0 to 100 s/mm2, helped identifying the presence of malignancy. PMID:25549366

Thermal therapy of pancreatic tumors using endoluminal ultrasound: parametric and patient-specific modeling

PubMed Central

Adams, Matthew S.; Scott, Serena J.; Salgaonkar, Vasant A.; Sommer, Graham; Diederich, Chris J.

2016-01-01

Purpose To investigate endoluminal ultrasound applicator configurations for volumetric thermal ablation and hyperthermia of pancreatic tumors using 3D acoustic and biothermal finite element models. Materials and Methods Parametric studies compared endoluminal heating performance for varying applicator transducer configurations (planar, curvilinear-focused, or radial-diverging), frequencies (1–5 MHz), and anatomical conditions. Patient-specific pancreatic head and body tumor models were used to evaluate feasibility of generating hyperthermia and thermal ablation using an applicator positioned in the duodenal or stomach lumen. Temperature and thermal dose were calculated to define ablation (>240 EM43°C) and moderate hyperthermia (40–45 °C) boundaries, and to assess sparing of sensitive tissues. Proportional-integral control was incorporated to regulate maximum temperature to 70–80 °C for ablation and 45 °C for hyperthermia in target regions. Results Parametric studies indicated that 1–3 MHz planar transducers are most suitable for volumetric ablation, producing 5–8 cm3 lesion volumes for a stationary 5 minute sonication. Curvilinear-focused geometries produce more localized ablation to 20–45 mm depth from the GI tract and enhance thermal sparing (Tmax<42 °C) of the luminal wall. Patient anatomy simulations show feasibility in ablating 60.1–92.9% of head/body tumor volumes (4.3–37.2 cm3) with dose <15 EM43°C in the luminal wall for 18–48 min treatment durations, using 1–3 applicator placements in GI lumen. For hyperthermia, planar and radial-diverging transducers could maintain up to 8 cm3 and 15 cm3 of tissue, respectively, between 40–45 °C for a single applicator placement. Conclusions Modeling studies indicate the feasibility of endoluminal ultrasound for volumetric thermal ablation or hyperthermia treatment of pancreatic tumor tissue. PMID:27097663

Assessing statistical differences between parameters estimates in Partial Least Squares path modeling.

PubMed

Rodríguez-Entrena, Macario; Schuberth, Florian; Gelhard, Carsten

2018-01-01

Structural equation modeling using partial least squares (PLS-SEM) has become a main-stream modeling approach in various disciplines. Nevertheless, prior literature still lacks a practical guidance on how to properly test for differences between parameter estimates. Whereas existing techniques such as parametric and non-parametric approaches in PLS multi-group analysis solely allow to assess differences between parameters that are estimated for different subpopulations, the study at hand introduces a technique that allows to also assess whether two parameter estimates that are derived from the same sample are statistically different. To illustrate this advancement to PLS-SEM, we particularly refer to a reduced version of the well-established technology acceptance model.

3-D Human body models in C.A.D. : Anthropometric Aspects

NASA Astrophysics Data System (ADS)

Renaud, C.; Steck, R.; Pineau, J. C.

1986-07-01

Modeling and simulation methods of man-machine systems are developed at the laboratory by interactive infography and C.A.D. technics. In order to better apprehend the morphological variability of populations we have enriched the 3-D model with a parametric function using classical anthropometric dimensions. We have selected reference, associate and complementary dimensions : lengths, breadths, circumferences and depths, which depend on operator's tasks and characteristics of workplaces. All anthropometric values come from the International Data Bank of Human Biometry of ERGODATA System. The utilization of the parametric function brings a quick and accurate description of morphology for theoretic subjects and can be used in C.A.D. analysis.

A linear, separable two-parameter model for dual energy CT imaging of proton stopping power computation

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

Han, Dong, E-mail: radon.han@gmail.com; Williamson, Jeffrey F.; Siebers, Jeffrey V.

2016-01-15

Purpose: To evaluate the accuracy and robustness of a simple, linear, separable, two-parameter model (basis vector model, BVM) in mapping proton stopping powers via dual energy computed tomography (DECT) imaging. Methods: The BVM assumes that photon cross sections (attenuation coefficients) of unknown materials are linear combinations of the corresponding radiological quantities of dissimilar basis substances (i.e., polystyrene, CaCl{sub 2} aqueous solution, and water). The authors have extended this approach to the estimation of electron density and mean excitation energy, which are required parameters for computing proton stopping powers via the Bethe–Bloch equation. The authors compared the stopping power estimation accuracymore » of the BVM with that of a nonlinear, nonseparable photon cross section Torikoshi parametric fit model (VCU tPFM) as implemented by the authors and by Yang et al. [“Theoretical variance analysis of single- and dual-energy computed tomography methods for calculating proton stopping power ratios of biological tissues,” Phys. Med. Biol. 55, 1343–1362 (2010)]. Using an idealized monoenergetic DECT imaging model, proton ranges estimated by the BVM, VCU tPFM, and Yang tPFM were compared to International Commission on Radiation Units and Measurements (ICRU) published reference values. The robustness of the stopping power prediction accuracy of tissue composition variations was assessed for both of the BVM and VCU tPFM. The sensitivity of accuracy to CT image uncertainty was also evaluated. Results: Based on the authors’ idealized, error-free DECT imaging model, the root-mean-square error of BVM proton stopping power estimation for 175 MeV protons relative to ICRU reference values for 34 ICRU standard tissues is 0.20%, compared to 0.23% and 0.68% for the Yang and VCU tPFM models, respectively. The range estimation errors were less than 1 mm for the BVM and Yang tPFM models, respectively. The BVM estimation accuracy is not dependent on tissue type and proton energy range. The BVM is slightly more vulnerable to CT image intensity uncertainties than the tPFM models. Both the BVM and tPFM prediction accuracies were robust to uncertainties of tissue composition and independent of the choice of reference values. This reported accuracy does not include the impacts of I-value uncertainties and imaging artifacts and may not be achievable on current clinical CT scanners. Conclusions: The proton stopping power estimation accuracy of the proposed linear, separable BVM model is comparable to or better than that of the nonseparable tPFM models proposed by other groups. In contrast to the tPFM, the BVM does not require an iterative solving for effective atomic number and electron density at every voxel; this improves the computational efficiency of DECT imaging when iterative, model-based image reconstruction algorithms are used to minimize noise and systematic imaging artifacts of CT images.« less

Bim and Gis: when Parametric Modeling Meets Geospatial Data

NASA Astrophysics Data System (ADS)

Barazzetti, L.; Banfi, F.

2017-12-01

Geospatial data have a crucial role in several projects related to infrastructures and land management. GIS software are able to perform advanced geospatial analyses, but they lack several instruments and tools for parametric modelling typically available in BIM. At the same time, BIM software designed for buildings have limited tools to handle geospatial data. As things stand at the moment, BIM and GIS could appear as complementary solutions, notwithstanding research work is currently under development to ensure a better level of interoperability, especially at the scale of the building. On the other hand, the transition from the local (building) scale to the infrastructure (where geospatial data cannot be neglected) has already demonstrated that parametric modelling integrated with geoinformation is a powerful tool to simplify and speed up some phases of the design workflow. This paper reviews such mixed approaches with both simulated and real examples, demonstrating that integration is already a reality at specific scales, which are not dominated by "pure" GIS or BIM. The paper will also demonstrate that some traditional operations carried out with GIS software are also available in parametric modelling software for BIM, such as transformation between reference systems, DEM generation, feature extraction, and geospatial queries. A real case study is illustrated and discussed to show the advantage of a combined use of both technologies. BIM and GIS integration can generate greater usage of geospatial data in the AECOO (Architecture, Engineering, Construction, Owner and Operator) industry, as well as new solutions for parametric modelling with additional geoinformation.

Dielectric properties of dog brain tissue measured in vitro across the 0.3-3 GHz band.

PubMed

Mohammed, Beadaa; Bialkowski, Konstanty; Abbosh, Amin; Mills, Paul C; Bradley, Andrew P

2016-09-22

Dielectric properties of dead Greyhound female dogs' brain tissues at different ages were measured at room temperature across the frequency range of 0.3-3 GHz. Measurements were made on excised tissues, in vitro in the laboratory, to carry out dielectric tests on sample tissues. Each dataset for a brain tissue was parametrized using the Cole-Cole expression, and the relevant Cole-Cole parameters for four tissue types are provided. A comparison was made with the database available in literature for other animals and human brain tissue. Results of two types of tissues (white matter and skull) showed systematic variation in dielectric properties as a function of animal age, whereas no significant change related to age was noticed for other tissues. Results provide critical information regarding dielectric properties of animal tissues for a realistic animal head model that can be used to verify the validity and reliability of a microwave head scanner for animals prior to testing on live animals. Bioelectromagnetics. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Generalized Beer-Lambert model for near-infrared light propagation in thick biological tissues

NASA Astrophysics Data System (ADS)

Bhatt, Manish; Ayyalasomayajula, Kalyan R.; Yalavarthy, Phaneendra K.

2016-07-01

The attenuation of near-infrared (NIR) light intensity as it propagates in a turbid medium like biological tissue is described by modified the Beer-Lambert law (MBLL). The MBLL is generally used to quantify the changes in tissue chromophore concentrations for NIR spectroscopic data analysis. Even though MBLL is effective in terms of providing qualitative comparison, it suffers from its applicability across tissue types and tissue dimensions. In this work, we introduce Lambert-W function-based modeling for light propagation in biological tissues, which is a generalized version of the Beer-Lambert model. The proposed modeling provides parametrization of tissue properties, which includes two attenuation coefficients μ0 and η. We validated our model against the Monte Carlo simulation, which is the gold standard for modeling NIR light propagation in biological tissue. We included numerous human and animal tissues to validate the proposed empirical model, including an inhomogeneous adult human head model. The proposed model, which has a closed form (analytical), is first of its kind in providing accurate modeling of NIR light propagation in biological tissues.

Detailing the relation between renal T2* and renal tissue pO2 using an integrated approach of parametric magnetic resonance imaging and invasive physiological measurements.

PubMed

Pohlmann, Andreas; Arakelyan, Karen; Hentschel, Jan; Cantow, Kathleen; Flemming, Bert; Ladwig, Mechthild; Waiczies, Sonia; Seeliger, Erdmann; Niendorf, Thoralf

2014-08-01

This study was designed to detail the relation between renal T2* and renal tissue pO2 using an integrated approach that combines parametric magnetic resonance imaging (MRI) and quantitative physiological measurements (MR-PHYSIOL). Experiments were performed in 21 male Wistar rats. In vivo modulation of renal hemodynamics and oxygenation was achieved by brief periods of aortic occlusion, hypoxia, and hyperoxia. Renal perfusion pressure (RPP), renal blood flow (RBF), local cortical and medullary tissue pO2, and blood flux were simultaneously recorded together with T2*, T2 mapping, and magnetic resonance-based kidney size measurements (MR-PHYSIOL). Magnetic resonance imaging was carried out on a 9.4-T small-animal magnetic resonance system. Relative changes in the invasive quantitative parameters were correlated with relative changes in the parameters derived from MRI using Spearman analysis and Pearson analysis. Changes in T2* qualitatively reflected tissue pO2 changes induced by the interventions. T2* versus pO2 Spearman rank correlations were significant for all interventions, yet quantitative translation of T2*/pO2 correlations obtained for one intervention to another intervention proved not appropriate. The closest T2*/pO2 correlation was found for hypoxia and recovery. The interlayer comparison revealed closest T2*/pO2 correlations for the outer medulla and showed that extrapolation of results obtained for one renal layer to other renal layers must be made with due caution. For T2* to RBF relation, significant Spearman correlations were deduced for all renal layers and for all interventions. T2*/RBF correlations for the cortex and outer medulla were even superior to those between T2* and tissue pO2. The closest T2*/RBF correlation occurred during hypoxia and recovery. Close correlations were observed between T2* and kidney size during hypoxia and recovery and for occlusion and recovery. In both cases, kidney size correlated well with renal vascular conductance, as did renal vascular conductance with T2*. Our findings indicate that changes in T2* qualitatively mirror changes in renal tissue pO2 but are also associated with confounding factors including vascular volume fraction and tubular volume fraction. Our results demonstrate that MR-PHYSIOL is instrumental to detail the link between renal tissue pO2 and T2* in vivo. Unravelling the link between regional renal T2* and tissue pO2, including the role of the T2* confounding parameters vascular and tubular volume fraction and oxy-hemoglobin dissociation curve, requires further research. These explorations are essential before the quantitative capabilities of parametric MRI can be translated from experimental research to improved clinical understanding of hemodynamics/oxygenation in kidney disorders.

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.

LoCoH: Non-parameteric kernel methods for constructing home ranges and utilization distributions

USGS Publications Warehouse

Getz, Wayne M.; Fortmann-Roe, Scott; Cross, Paul C.; Lyons, Andrew J.; Ryan, Sadie J.; Wilmers, Christopher C.

2007-01-01

Parametric kernel methods currently dominate the literature regarding the construction of animal home ranges (HRs) and utilization distributions (UDs). These methods frequently fail to capture the kinds of hard boundaries common to many natural systems. Recently a local convex hull (LoCoH) nonparametric kernel method, which generalizes the minimum convex polygon (MCP) method, was shown to be more appropriate than parametric kernel methods for constructing HRs and UDs, because of its ability to identify hard boundaries (e.g., rivers, cliff edges) and convergence to the true distribution as sample size increases. Here we extend the LoCoH in two ways: ‘‘fixed sphere-of-influence,’’ or r -LoCoH (kernels constructed from all points within a fixed radius r of each reference point), and an ‘‘adaptive sphere-of-influence,’’ or a -LoCoH (kernels constructed from all points within a radius a such that the distances of all points within the radius to the reference point sum to a value less than or equal to a ), and compare them to the original ‘‘fixed-number-of-points,’’ or k -LoCoH (all kernels constructed from k -1 nearest neighbors of root points). We also compare these nonparametric LoCoH to parametric kernel methods using manufactured data and data collected from GPS collars on African buffalo in the Kruger National Park, South Africa. Our results demonstrate that LoCoH methods are superior to parametric kernel methods in estimating areas used by animals, excluding unused areas (holes) and, generally, in constructing UDs and HRs arising from the movement of animals influenced by hard boundaries and irregular structures (e.g., rocky outcrops). We also demonstrate that a -LoCoH is generally superior to k - and r -LoCoH (with software for all three methods available at http://locoh.cnr.berkeley.edu).

An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

PubMed Central

Valdés-Hernández, Pedro Antonio; Sumiyoshi, Akira; Nonaka, Hiroi; Haga, Risa; Aubert-Vásquez, Eduardo; Ogawa, Takeshi; Iturria-Medina, Yasser; Riera, Jorge J.; Kawashima, Ryuta

2011-01-01

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies. PMID:22275894

Improved estimation of parametric images of cerebral glucose metabolic rate from dynamic FDG-PET using volume-wise principle component analysis

NASA Astrophysics Data System (ADS)

Dai, Xiaoqian; Tian, Jie; Chen, Zhe

2010-03-01

Parametric images can represent both spatial distribution and quantification of the biological and physiological parameters of tracer kinetics. The linear least square (LLS) method is a well-estimated linear regression method for generating parametric images by fitting compartment models with good computational efficiency. However, bias exists in LLS-based parameter estimates, owing to the noise present in tissue time activity curves (TTACs) that propagates as correlated error in the LLS linearized equations. To address this problem, a volume-wise principal component analysis (PCA) based method is proposed. In this method, firstly dynamic PET data are properly pre-transformed to standardize noise variance as PCA is a data driven technique and can not itself separate signals from noise. Secondly, the volume-wise PCA is applied on PET data. The signals can be mostly represented by the first few principle components (PC) and the noise is left in the subsequent PCs. Then the noise-reduced data are obtained using the first few PCs by applying 'inverse PCA'. It should also be transformed back according to the pre-transformation method used in the first step to maintain the scale of the original data set. Finally, the obtained new data set is used to generate parametric images using the linear least squares (LLS) estimation method. Compared with other noise-removal method, the proposed method can achieve high statistical reliability in the generated parametric images. The effectiveness of the method is demonstrated both with computer simulation and with clinical dynamic FDG PET study.

Parametric Effects of Word Frequency in Memory for Mixed Frequency Lists

ERIC Educational Resources Information Center

Lohnas, Lynn J.; Kahana, Michael J.

2013-01-01

The "word frequency paradox" refers to the finding that low frequency words are better recognized than high frequency words yet high frequency words are better recalled than low frequency words. Rather than comparing separate groups of low and high frequency words, we sought to quantify the functional relation between word frequency and…

Resampling methods in Microsoft Excel® for estimating reference intervals

PubMed Central

Theodorsson, Elvar

2015-01-01

Computer- intensive resampling/bootstrap methods are feasible when calculating reference intervals from non-Gaussian or small reference samples. Microsoft Excel® in version 2010 or later includes natural functions, which lend themselves well to this purpose including recommended interpolation procedures for estimating 2.5 and 97.5 percentiles.
The purpose of this paper is to introduce the reader to resampling estimation techniques in general and in using Microsoft Excel® 2010 for the purpose of estimating reference intervals in particular.
Parametric methods are preferable to resampling methods when the distributions of observations in the reference samples is Gaussian or can transformed to that distribution even when the number of reference samples is less than 120. Resampling methods are appropriate when the distribution of data from the reference samples is non-Gaussian and in case the number of reference individuals and corresponding samples are in the order of 40. At least 500-1000 random samples with replacement should be taken from the results of measurement of the reference samples. PMID:26527366

Resampling methods in Microsoft Excel® for estimating reference intervals.

PubMed

Theodorsson, Elvar

2015-01-01

Computer-intensive resampling/bootstrap methods are feasible when calculating reference intervals from non-Gaussian or small reference samples. Microsoft Excel® in version 2010 or later includes natural functions, which lend themselves well to this purpose including recommended interpolation procedures for estimating 2.5 and 97.5 percentiles. 
The purpose of this paper is to introduce the reader to resampling estimation techniques in general and in using Microsoft Excel® 2010 for the purpose of estimating reference intervals in particular.
 Parametric methods are preferable to resampling methods when the distributions of observations in the reference samples is Gaussian or can transformed to that distribution even when the number of reference samples is less than 120. Resampling methods are appropriate when the distribution of data from the reference samples is non-Gaussian and in case the number of reference individuals and corresponding samples are in the order of 40. At least 500-1000 random samples with replacement should be taken from the results of measurement of the reference samples.

Pixel-based parametric source depth map for Cerenkov luminescence imaging

NASA Astrophysics Data System (ADS)

Altabella, L.; Boschi, F.; Spinelli, A. E.

2016-01-01

Optical tomography represents a challenging problem in optical imaging because of the intrinsically ill-posed inverse problem due to photon diffusion. Cerenkov luminescence tomography (CLT) for optical photons produced in tissues by several radionuclides (i.e.: 32P, 18F, 90Y), has been investigated using both 3D multispectral approach and multiviews methods. Difficult in convergence of 3D algorithms can discourage to use this technique to have information of depth and intensity of source. For these reasons, we developed a faster 2D corrected approach based on multispectral acquisitions, to obtain source depth and its intensity using a pixel-based fitting of source intensity. Monte Carlo simulations and experimental data were used to develop and validate the method to obtain the parametric map of source depth. With this approach we obtain parametric source depth maps with a precision between 3% and 7% for MC simulation and 5-6% for experimental data. Using this method we are able to obtain reliable information about the source depth of Cerenkov luminescence with a simple and flexible procedure.

Reference Charts for Fetal Cerebellar Vermis Height: A Prospective Cross-Sectional Study of 10605 Fetuses

PubMed Central

Cignini, Pietro; Giorlandino, Maurizio; Brutti, Pierpaolo; Mangiafico, Lucia; Aloisi, Alessia; Giorlandino, Claudio

2016-01-01

Objective To establish reference charts for fetal cerebellar vermis height in an unselected population. Methods A prospective cross-sectional study between September 2009 and December 2014 was carried out at ALTAMEDICA Fetal–Maternal Medical Centre, Rome, Italy. Of 25203 fetal biometric measurements, 12167 (48%) measurements of the cerebellar vermis were available. After excluding 1562 (12.8%) measurements, a total of 10605 (87.2%) fetuses were considered and analyzed once only. Parametric and nonparametric quantile regression models were used for the statistical analysis. In order to evaluate the robustness of the proposed reference charts regarding various distributional assumptions on the ultrasound measurements at hand, we compared the gestational age-specific reference curves we produced through the statistical methods used. Normal mean height based on parametric and nonparametric methods were defined for each week of gestation and the regression equation expressing the height of the cerebellar vermis as a function of gestational age was calculated. Finally the correlation between dimension/gestation was measured. Results The mean height of the cerebellar vermis was 12.7mm (SD, 1.6mm; 95% confidence interval, 12.7–12.8mm). The regression equation expressing the height of the CV as a function of the gestational age was: height (mm) = -4.85+0.78 x gestational age. The correlation between dimension/gestation was expressed by the coefficient r = 0.87. Conclusion This is the first prospective cross-sectional study on fetal cerebellar vermis biometry with such a large sample size reported in literature. It is a detailed statistical survey and contains new centile-based reference charts for fetal height of cerebellar vermis measurements. PMID:26812238

Photon Entanglement Through Brain Tissue.

PubMed

Shi, Lingyan; Galvez, Enrique J; Alfano, Robert R

2016-12-20

Photon entanglement, the cornerstone of quantum correlations, provides a level of coherence that is not present in classical correlations. Harnessing it by study of its passage through organic matter may offer new possibilities for medical diagnosis technique. In this work, we study the preservation of photon entanglement in polarization, created by spontaneous parametric down-conversion, after one entangled photon propagates through multiphoton-scattering brain tissue slices with different thickness. The Tangle-Entropy (TS) plots show the strong preservation of entanglement of photons propagating in brain tissue. By spatially filtering the ballistic scattering of an entangled photon, we find that its polarization entanglement is preserved and non-locally correlated with its twin in the TS plots. The degree of entanglement correlates better with structure and water content than with sample thickness.

Photon Entanglement Through Brain Tissue

NASA Astrophysics Data System (ADS)

Shi, Lingyan; Galvez, Enrique J.; Alfano, Robert R.

2016-12-01

Photon entanglement, the cornerstone of quantum correlations, provides a level of coherence that is not present in classical correlations. Harnessing it by study of its passage through organic matter may offer new possibilities for medical diagnosis technique. In this work, we study the preservation of photon entanglement in polarization, created by spontaneous parametric down-conversion, after one entangled photon propagates through multiphoton-scattering brain tissue slices with different thickness. The Tangle-Entropy (TS) plots show the strong preservation of entanglement of photons propagating in brain tissue. By spatially filtering the ballistic scattering of an entangled photon, we find that its polarization entanglement is preserved and non-locally correlated with its twin in the TS plots. The degree of entanglement correlates better with structure and water content than with sample thickness.

A Frequency-Domain Multipath Parameter Estimation and Mitigation Method for BOC-Modulated GNSS Signals

PubMed Central

Sun, Chao; Feng, Wenquan; Du, Songlin

2018-01-01

As multipath is one of the dominating error sources for high accuracy Global Navigation Satellite System (GNSS) applications, multipath mitigation approaches are employed to minimize this hazardous error in receivers. Binary offset carrier modulation (BOC), as a modernized signal structure, is adopted to achieve significant enhancement. However, because of its multi-peak autocorrelation function, conventional multipath mitigation techniques for binary phase shift keying (BPSK) signal would not be optimal. Currently, non-parametric and parametric approaches have been studied specifically aiming at multipath mitigation for BOC signals. Non-parametric techniques, such as Code Correlation Reference Waveforms (CCRW), usually have good feasibility with simple structures, but suffer from low universal applicability for different BOC signals. Parametric approaches can thoroughly eliminate multipath error by estimating multipath parameters. The problems with this category are at the high computation complexity and vulnerability to the noise. To tackle the problem, we present a practical parametric multipath estimation method in the frequency domain for BOC signals. The received signal is transferred to the frequency domain to separate out the multipath channel transfer function for multipath parameter estimation. During this process, we take the operations of segmentation and averaging to reduce both noise effect and computational load. The performance of the proposed method is evaluated and compared with the previous work in three scenarios. Results indicate that the proposed averaging-Fast Fourier Transform (averaging-FFT) method achieves good robustness in severe multipath environments with lower computational load for both low-order and high-order BOC signals. PMID:29495589

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.

Comparison of unsupervised classification methods for brain tumor segmentation using multi-parametric MRI.

PubMed

Sauwen, N; Acou, M; Van Cauter, S; Sima, D M; Veraart, J; Maes, F; Himmelreich, U; Achten, E; Van Huffel, S

2016-01-01

Tumor segmentation is a particularly challenging task in high-grade gliomas (HGGs), as they are among the most heterogeneous tumors in oncology. An accurate delineation of the lesion and its main subcomponents contributes to optimal treatment planning, prognosis and follow-up. Conventional MRI (cMRI) is the imaging modality of choice for manual segmentation, and is also considered in the vast majority of automated segmentation studies. Advanced MRI modalities such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have already shown their added value in tumor tissue characterization, hence there have been recent suggestions of combining different MRI modalities into a multi-parametric MRI (MP-MRI) approach for brain tumor segmentation. In this paper, we compare the performance of several unsupervised classification methods for HGG segmentation based on MP-MRI data including cMRI, DWI, MRSI and PWI. Two independent MP-MRI datasets with a different acquisition protocol were available from different hospitals. We demonstrate that a hierarchical non-negative matrix factorization variant which was previously introduced for MP-MRI tumor segmentation gives the best performance in terms of mean Dice-scores for the pathologic tissue classes on both datasets.

Parametric Study of Wall Shear Stress in Idealized Avian Airways

NASA Astrophysics Data System (ADS)

Farnsworth, Michael S.; Riede, Tobias; Thomson, Scott L.

2017-11-01

Because wall shear stress (WSS) affects cell response, WSS patterns in avian respiratory airways may be related to the origin of the syrinx and corresponding voice-producing tissue structures (e.g., membranes or vocal folds) in birds. To explore possible linkages between WSS patterns and the locations of avian voice-producing structures, a computational model of flow through an idealized portion of the avian respiratory airway, including trachea and primary bronchi sections, has been developed. The flow is governed by the Navier-Stokes equations, with velocity boundary conditions derived from pressure-flow data in an adult zebra finch during quiet respiration. Geometric parameters such as tracheal/bronchial diameter and length, as well as bronchial branching angle, are parametrically varied based on data for different avian species. Simulation results predict elevated WSS in the vicinity of the tracheobronchial juncture, the location at which voice-producing tissues are found in avian species. In this presentation, the model will be described and spatial distributions of WSS during inspiration and expiration will be presented and compared for different geometric configurations and respiration rates and waveforms. Funding for this project from the Gordon and Betty Moore Foundation (Grant 4498) is gratefully acknowledged.

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.

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach

PubMed Central

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M.; El Fakhri, Georges

2013-01-01

Purpose: Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Methods: Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. Results: At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%–29% and 32%–70% for 50 × 106 and 10 × 106 detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40–50 iterations), while more than 500 iterations were needed for CG. Conclusions: The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method. PMID:24089922

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach.

PubMed

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M; El Fakhri, Georges

2013-10-01

Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%-29% and 32%-70% for 50 × 10(6) and 10 × 10(6) detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40-50 iterations), while more than 500 iterations were needed for CG. The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method.

Sci-Thur PM - Colourful Interactions: Highlights 04: A Fast Quantitative MRI Acquisition and Processing Pipeline for Radiation Treatment Planning and Simulation

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

Jutras, Jean-David

MRI-only Radiation Treatment Planning (RTP) is becoming increasingly popular because of a simplified work-flow, and less inconvenience to the patient who avoids multiple scans. The advantages of MRI-based RTP over traditional CT-based RTP lie in its superior soft-tissue contrast, and absence of ionizing radiation dose. The lack of electron-density information in MRI can be addressed by automatic tissue classification. To distinguish bone from air, which both appear dark in MRI, an ultra-short echo time (UTE) pulse sequence may be used. Quantitative MRI parametric maps can provide improved tissue segmentation/classification and better sensitivity in monitoring disease progression and treatment outcome thanmore » standard weighted images. Superior tumor contrast can be achieved on pure T{sub 1} images compared to conventional T{sub 1}-weighted images acquired in the same scan duration and voxel resolution. In this study, we have developed a robust and fast quantitative MRI acquisition and post-processing work-flow that integrates these latest advances into the MRI-based RTP of brain lesions. Using 3D multi-echo FLASH images at two different optimized flip angles (both acquired in under 9 min, and 1mm isotropic resolution), parametric maps of T{sub 1}, proton-density (M{sub 0}), and T{sub 2}{sup *} are obtained with high contrast-to-noise ratio, and negligible geometrical distortions, water-fat shifts and susceptibility effects. An additional 3D UTE MRI dataset is acquired (in under 4 min) and post-processed to classify tissues for dose simulation. The pipeline was tested on four healthy volunteers and a clinical trial on brain cancer patients is underway.« less

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

PubMed

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

2012-05-01

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

Acoustic radiation force impulse (ARFI) imaging: Characterizing the mechanical properties of tissues using their transient response to localized force

NASA Astrophysics Data System (ADS)

Nightingale, Kathryn R.; Palmeri, Mark L.; Congdon, Amy N.; Frinkely, Kristin D.; Trahey, Gregg E.

2004-05-01

Acoustic radiation force impulse (ARFI) imaging utilizes brief, high energy, focused acoustic pulses to generate radiation force in tissue, and conventional diagnostic ultrasound methods to detect the resulting tissue displacements in order to image the relative mechanical properties of tissue. The magnitude and spatial extent of the applied force is dependent upon the transmit beam parameters and the tissue attenuation. Forcing volumes are on the order of 5 mm3, pulse durations are less than 1 ms, and tissue displacements are typically several microns. Images of tissue displacement reflect local tissue stiffness, with softer tissues (e.g., fat) displacing farther than stiffer tissues (e.g., muscle). Parametric images of maximum displacement, time to peak displacement, and recovery time provide information about tissue material properties and structure. In both in vivo and ex vivo data, structures shown in matched B-mode images are in good agreement with those shown in ARFI images, with comparable resolution. Potential clinical applications under investigation include soft tissue lesion characterization, assessment of focal atherosclerosis, and imaging of thermal lesion formation during tissue ablation procedures. Results from ongoing studies will be presented. [Work supported by NIH Grant R01 EB002132-03, and the Whitaker Foundation. System support from Siemens Medical Solutions USA, Inc.

Non-transference of biological reference interval of TSH by electrochemiluminescence immunoassay: an Indian population perspective.

PubMed

Sarkar, Rajarshi

2013-08-23

Although TSH measurement by electrochemiluminescence immunoassay has become commonplace in India, significant discrepancy has been observed on interpretation of the test results when the manufacturer supplied biological reference interval (BRI) criteria were applied. This report determined whether the manufacturer's BRI (Roche Cobas) is transferable to the Indian population. Three hundred seventy-eight age- and sex-matched healthy subjects were selected from an urban Indian population. TSH reference measurements were acquired, and the reference data were statistically analysed. BRI of the Indian urban reference population was determined by non-parametric means. BRI was found to be 1.134 to 7.280μIU/ml. BRI thus calculated was found to be significantly different from that mentioned by the manufacturer (0.27 to 4.20μIU/ml), which, needless to mention, has profound clinical implications in this part of the globe. Copyright © 2013 Elsevier B.V. All rights reserved.

{sup 18}F-FLT uptake kinetics in head and neck squamous cell carcinoma: A PET imaging study

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

Liu, Dan, E-mail: dan.liu@oncology.ox.ac.uk; Fenwick, John D.; Chalkidou, Anastasia

2014-04-15

Purpose: To analyze the kinetics of 3{sup ′}-deoxy-3{sup ′}-[F-18]-fluorothymidine (18F-FLT) uptake by head and neck squamous cell carcinomas and involved nodes imaged using positron emission tomography (PET). Methods: Two- and three-tissue compartment models were fitted to 12 tumor time-activity-curves (TACs) obtained for 6 structures (tumors or involved nodes) imaged in ten dynamic PET studies of 1 h duration, carried out for five patients. The ability of the models to describe the data was assessed using a runs test, the Akaike information criterion (AIC) and leave-one-out cross-validation. To generate parametric maps the models were also fitted to TACs of individual voxels.more » Correlations between maps of different parameters were characterized using Pearson'sr coefficient; in particular the phosphorylation rate-constants k{sub 3-2tiss} and k{sub 5} of the two- and three-tissue models were studied alongside the flux parameters K{sub FLT-2tiss} and K{sub FLT} of these models, and standardized uptake values (SUV). A methodology based on expectation-maximization clustering and the Bayesian information criterion (“EM-BIC clustering”) was used to distil the information from noisy parametric images. Results: Fits of two-tissue models 2C3K and 2C4K and three-tissue models 3C5K and 3C6K comprising three, four, five, and six rate-constants, respectively, pass the runs test for 4, 8, 10, and 11 of 12 tumor TACs. The three-tissue models have lower AIC and cross-validation scores for nine of the 12 tumors. Overall the 3C6K model has the lowest AIC and cross-validation scores and its fitted parameter values are of the same orders of magnitude as literature estimates. Maps ofK{sub FLT} and K{sub FLT-2tiss} are strongly correlated (r = 0.85) and also correlate closely with SUV maps (r = 0.72 for K{sub FLT-2tiss}, 0.64 for K{sub FLT}). Phosphorylation rate-constant maps are moderately correlated with flux maps (r = 0.48 for k{sub 3-2tiss} vs K{sub FLT-2tiss} and r = 0.68 for k{sub 5} vs K{sub FLT}); however, neither phosphorylation rate-constant correlates significantly with SUV. EM-BIC clustering reduces the parametric maps to a small number of levels—on average 5.8, 3.5, 3.4, and 1.4 for K{sub FLT-2tiss}, K{sub FLT}, k{sub 3-2tiss}, and k{sub 5.} This large simplification is potentially useful for radiotherapy dose-painting, but demonstrates the high noise in some maps. Statistical simulations show that voxel level noise degrades TACs generated from the 3C6K model sufficiently that the average AIC score, parameter bias, and total uncertainty of 2C4K model fits are similar to those of 3C6K fits, whereas at the whole tumor level the scores are lower for 3C6K fits. Conclusions: For the patients studied here, whole tumor FLT uptake time-courses are represented better overall by a three-tissue than by a two-tissue model. EM-BIC clustering simplifies noisy parametric maps, providing the best description of the underlying information they contain and is potentially useful for radiotherapy dose-painting. However, the clustering highlights the large degree of noise present in maps of the phosphorylation rate-constantsk{sub 5} and k{sub 3-2tiss}, which are conceptually tightly linked to cellular proliferation. Methods must be found to make these maps more robust—either by constraining other model parameters or modifying dynamic imaging protocols.« less

High-intensity-focused-ultrasound (HIFU) induced homeostasis and tissue ablation

NASA Astrophysics Data System (ADS)

Chauhan, Sunita; Michel, M. S.; Alken, Peter; Kohrmann, K. U.; Haecker, Axel

2003-06-01

At high intensity levels, ultrasound energy focused into remote tissue targets in human body has shown to produce thermal necrosis in circumscribed regions with sub-millimeter accuracy. The non-invasive modality known as HIFU has enormous potential for thermal ablation of cancers/tumors of the human body without any adverse effects in the surrounding normal tissue. In this paper, empirical results for parametric assessment and interdependence of several exposure variables are presented for producing thermal necrosis as well as hemostasis. Multiple HIFU transducers in selective spatial configuration have been deployed using a suitably designed experiemntal harness, with and without motorized jig scanning. The pre-planning and on-line procedure for treatment and specified instrumentation is described. Custom designed 25mm aperture HIFU probes resonating at 2 MHz focused at 64 and 80 mm are used. Results have been obtained in ex-vivo animal tissue and in vitro biological phantoms for hemostasis.

Next-Generation Pathology.

PubMed

Caie, Peter D; Harrison, David J

2016-01-01

The field of pathology is rapidly transforming from a semiquantitative and empirical science toward a big data discipline. Large data sets from across multiple omics fields may now be extracted from a patient's tissue sample. Tissue is, however, complex, heterogeneous, and prone to artifact. A reductionist view of tissue and disease progression, which does not take this complexity into account, may lead to single biomarkers failing in clinical trials. The integration of standardized multi-omics big data and the retention of valuable information on spatial heterogeneity are imperative to model complex disease mechanisms. Mathematical modeling through systems pathology approaches is the ideal medium to distill the significant information from these large, multi-parametric, and hierarchical data sets. Systems pathology may also predict the dynamical response of disease progression or response to therapy regimens from a static tissue sample. Next-generation pathology will incorporate big data with systems medicine in order to personalize clinical practice for both prognostic and predictive patient care.

Simultaneous K-edge subtraction tomography for tracing strontium using parametric X-ray radiation

NASA Astrophysics Data System (ADS)

Hayakawa, Y.; Hayakawa, K.; Kaneda, T.; Nogami, K.; Sakae, T.; Sakai, T.; Sato, I.; Takahashi, Y.; Tanaka, T.

2017-07-01

The X-ray source based on parametric X-ray radiation (PXR) has been regularly providing a coherent X-ray beam for application studies at Nihon University. Recently, three dimensional (3D) computed tomography (CT) has become one of the most important applications of the PXR source. The methodology referred to as K-edge subtraction (KES) imaging is a particularly successful application utilizing the energy selectivity of PXR. In order to demonstrate the applicability of PXR-KES, a simultaneous KES experiment for a specimen containing strontium was performed using a PXR beam having an energy near the Sr K-edge of 16.1 keV. As a result, the 3D distribution of Sr was obtained by subtraction between the two simultaneously acquired tomographic images.

Radiofrequency Ablation, MR Thermometry, and High-Spatial-Resolution MR Parametric Imaging with a Single, Minimally Invasive Device.

PubMed

Ertürk, M Arcan; Sathyanarayana Hegde, Shashank; Bottomley, Paul A

2016-12-01

Purpose To develop and demonstrate in vitro and in vivo a single interventional magnetic resonance (MR)-active device that integrates the functions of precise identification of a tissue site with the delivery of radiofrequency (RF) energy for ablation, high-spatial-resolution thermal mapping to monitor thermal dose, and quantitative MR imaging relaxometry to document ablation-induced tissue changes for characterizing ablated tissue. Materials and Methods All animal studies were approved by the institutional animal care and use committee. A loopless MR imaging antenna composed of a tuned microcable either 0.8 or 2.2 mm in diameter with an extended central conductor was switched between a 3-T MR imaging unit and an RF power source to monitor and perform RF ablation in bovine muscle and human artery samples in vitro and in rabbits in vivo. High-spatial-resolution (250-300-μm) proton resonance frequency shift MR thermometry was interleaved with ablations. Quantitative spin-lattice (T1) and spin-spin (T2) relaxation time MR imaging mapping was performed before and after ablation. These maps were compared with findings from gross tissue examination of the region of ablated tissue after MR imaging. Results High-spatial-resolution MR imaging afforded temperature mapping in less than 8 seconds for monitoring ablation temperatures in excess of 85°C delivered by the same device. This produced irreversible thermal injury and necrosis. Quantitative MR imaging relaxation time maps demonstrated up to a twofold variation in mean regional T1 and T2 after ablation versus before ablation. Conclusion A simple, integrated, minimally invasive interventional probe that provides image-guided therapy delivery, thermal mapping of dose, and detection of ablation-associated MR imaging parametric changes was developed and demonstrated. With this single-device approach, coupling-related safety concerns associated with multiple conductor approaches were avoided. © RSNA, 2016 Online supplemental material is available for this article.

Photon Entanglement Through Brain Tissue

PubMed Central

Shi, Lingyan; Galvez, Enrique J.; Alfano, Robert R.

2016-01-01

Photon entanglement, the cornerstone of quantum correlations, provides a level of coherence that is not present in classical correlations. Harnessing it by study of its passage through organic matter may offer new possibilities for medical diagnosis technique. In this work, we study the preservation of photon entanglement in polarization, created by spontaneous parametric down-conversion, after one entangled photon propagates through multiphoton-scattering brain tissue slices with different thickness. The Tangle-Entropy (TS) plots show the strong preservation of entanglement of photons propagating in brain tissue. By spatially filtering the ballistic scattering of an entangled photon, we find that its polarization entanglement is preserved and non-locally correlated with its twin in the TS plots. The degree of entanglement correlates better with structure and water content than with sample thickness. PMID:27995952

Model reference tracking control of an aircraft: a robust adaptive approach

NASA Astrophysics Data System (ADS)

Tanyer, Ilker; Tatlicioglu, Enver; Zergeroglu, Erkan

2017-05-01

This work presents the design and the corresponding analysis of a nonlinear robust adaptive controller for model reference tracking of an aircraft that has parametric uncertainties in its system matrices and additive state- and/or time-dependent nonlinear disturbance-like terms in its dynamics. Specifically, robust integral of the sign of the error feedback term and an adaptive term is fused with a proportional integral controller. Lyapunov-based stability analysis techniques are utilised to prove global asymptotic convergence of the output tracking error. Extensive numerical simulations are presented to illustrate the performance of the proposed robust adaptive controller.

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.

Design of tissue engineering scaffolds based on hyperbolic surfaces: structural numerical evaluation.

PubMed

Almeida, Henrique A; Bártolo, Paulo J

2014-08-01

Tissue engineering represents a new field aiming at developing biological substitutes to restore, maintain, or improve tissue functions. In this approach, scaffolds provide a temporary mechanical and vascular support for tissue regeneration while tissue in-growth is being formed. These scaffolds must be biocompatible, biodegradable, with appropriate porosity, pore structure and distribution, and optimal vascularization with both surface and structural compatibility. The challenge is to establish a proper balance between porosity and mechanical performance of scaffolds. This work investigates the use of two different types of triple periodic minimal surfaces, Schwarz and Schoen, in order to design better biomimetic scaffolds with high surface-to-volume ratio, high porosity and good mechanical properties. The mechanical behaviour of these structures is assessed through the finite element method software Abaqus. The effect of two parametric parameters (thickness and surface radius) is also evaluated regarding its porosity and mechanical behaviour. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data.

PubMed

Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro

2007-05-01

Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent's non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent's method is not suitable for ROKU.

Biotrichotomy: The Neuroscientific and Neurobiological Systemology, Epistemology, and Methodology of the Tri-Squared Test and Tri-Center Analysis in Biostatistics

ERIC Educational Resources Information Center

Osler, James Edward

2015-01-01

This monograph provides a neuroscience-based systemological, epistemological, and methodological rational for the design of an advanced and novel parametric statistical analytics designed for the biological sciences referred to as "Biotrichotomy". The aim of this new arena of statistics is to provide dual metrics designed to analyze the…

Parametric Study of Diffusion-Enhancement Networks for Spatiotemporal Grouping in Real-Time Artificial Vision

DTIC Science & Technology

1991-06-04

1972). 2. M. Wertheimer. Experimentelle studien uber das sehen von bewegung. Z. fur Psych. 61, 161-265 (1912). Translated in part in Classics in...REFERENCES (Continued) 17. J.P.H. van Santen-and G. Sperling . "Elaborated Reichardt detectors." J. Opt. Soc. America A2, 300-321 (1985). 18. A.M. Waxman. J

A class of stochastic optimization problems with one quadratic & several linear objective functions and extended portfolio selection model

NASA Astrophysics Data System (ADS)

Xu, Jiuping; Li, Jun

2002-09-01

In this paper a class of stochastic multiple-objective programming problems with one quadratic, several linear objective functions and linear constraints has been introduced. The former model is transformed into a deterministic multiple-objective nonlinear programming model by means of the introduction of random variables' expectation. The reference direction approach is used to deal with linear objectives and results in a linear parametric optimization formula with a single linear objective function. This objective function is combined with the quadratic function using the weighted sums. The quadratic problem is transformed into a linear (parametric) complementary problem, the basic formula for the proposed approach. The sufficient and necessary conditions for (properly, weakly) efficient solutions and some construction characteristics of (weakly) efficient solution sets are obtained. An interactive algorithm is proposed based on reference direction and weighted sums. Varying the parameter vector on the right-hand side of the model, the DM can freely search the efficient frontier with the model. An extended portfolio selection model is formed when liquidity is considered as another objective to be optimized besides expectation and risk. The interactive approach is illustrated with a practical example.

Premix fuels study applicable to duct burner conditions for a variable cycle engine

NASA Technical Reports Server (NTRS)

Venkataramani, K. S.

1978-01-01

Emission levels and performance of a premixing Jet-A/air duct burner were measured at reference conditions representative of take-off and cruise for a variable cycle engine. In a parametric variation sequence of tests, data were obtained at inlet temperatures of 400, 500 and 600K at equivalence ratios varying from 0.9 to the lean stability limit. Ignition was achieved at all the reference conditions although the CO levels were very high. Significant nonuniformity across the combustor was observed for the emissions at the take-off condition. At a reference Mach number of 0.117 and an inlet temperature of 600K, corresponding to a simulated cruise condition, the NOx emission level was approximately 1 gm/kg-fuel.

[Clinical values of hemodynamics assessment by parametric color coding of digital subtraction angiography before and after endovascular therapy for critical limb ischaemia].

PubMed

Su, Haobo; Lou, Wensheng; Gu, Jianping

2015-10-06

To investigate the feasibility of parametric color coding of digital subtraction angiography (Syngo iFlow) for hemodynamics assessment in patients with critical limb ischemia in pre- and post-endovascular therapy. To explore the correlation between Syngo iFlow and the conventional techniques. from January 2013 to December 2014, Clinical data of 21 patients with TASC II type B and type C femoropopliteal arteriosclerotic occlusive disease who were treated by percutaneous transluminal angioplasty and/or primary stent implantation in Nanjing first hospital were analyzed retrospectively. Of these patients there were 10 males and 11 females with an average age of (72±6) years (range from 58-85 years). The treatment efficacy was assessed by the variation of a series of clinical symptoms indexes (such as pain score, cold sensation score and intermittent claudication score), ankle braehial index (ABI) and transcutaneous oxygen pressure (TcPO2). Angiography was performed with the same protocol before and after treatment and parametric color coding of digital subtraction angiography was created by Syngo iFlow software on a dedicated workstation. The time to peak (TTP) of artery and tissue perfusion selected at the same regions of foot and ankle were measured and analyzed to evaluate the improvement of microcirculation and hemodynamics of the ischemic limb. The correlations between Syngo iFlow and the traditional clinical evaluation methods were explored using the Spearman rank correlation test. All patients (21 limbs) underwent successful endovaseular therapy. The mean pain score, cold sensation score, intermittent claudication score, ABI and TcPO2 before treatment were (0.48±0.68), (2.71±0.72), (2.86±0.85), ABI (0.33±0.07), TcPO2 (26.83±3.41) mmHg. While 1 week after treatment all above indicators were (2.57±0.93), (0.33±0.48), (0.90±0.54), (0.69±0.11), TcPO2 (53.75±3.60) mmHg respectively. There were significant statistical differences between pre- and post-treatment (P<0.05). The pre- and post-operative TTP of artery and tissue perfusion were (14.07±1.77) vs (10.43±2.05) s, (18.75±2.72) vs (15.38±2.78) s. For assessment of hemodynamic changes during and after treatment, parametric color coding of digital subtraction angiography (Syngo iFlow) was assumed to show the limb blood flow and perfusion were improved and the differences were statistically significant. The Spearman rank correlation test showed the TTP of artery was positively correlated with ABI, TcPO2 (r=0.65, 0.73, P<0.05), the TTP of tissue perfusion was also positively correlated with ABI, TcPO2 (r=0.60, 0.60, P<0.05). Parametric color coding of digital subtraction angiography (Syngo iFlow) is a real-time, sensitive and quantitative tool that might provide additional support in the hemodynamics evaluation of endovascular treatment for patients with lower extremity peripheral arterial occlusion disease.

Method for Separation of Blood Vessels on the Three-Color Images of Biological Tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.

2017-07-01

A new technology was developed to improve the visibility of blood vessels on images of tissues of hollow human organs(the alimentary tract and respiratory system) based on the relation between the color components of the image, the scattering properties of the tissue, and its hemoglobin content. A statistical operator was presented to convert the three-color image of the tissue into a parametric map objectively characterizing the concentration of hemoglobin in the tissue regardless of the illumination and shooting conditions. An algorithm for obtaining conversion parameters for image systems with known spectral characteristics was presented. An image of a multilayer multiple-scattering medium modeling bronchial tissue was synthesized and was used to evaluate the efficiency of the proposed conversion system. It was shown that the conversion made it possible to increase the contrast of the blood vessels by almost two orders of magnitude, to significantly improve the clarity of the display of their borders, and to eliminate almost completely the influence of background and nonuniform illumination of the medium in comparison with the original image.

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.

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping.

PubMed

Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

2015-01-01

A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility.

Parametric system identification of resonant micro/nanosystems operating in a nonlinear response regime

NASA Astrophysics Data System (ADS)

Sabater, A. B.; Rhoads, J. F.

2017-02-01

The parametric system identification of macroscale resonators operating in a nonlinear response regime can be a challenging research problem, but at the micro- and nanoscales, experimental constraints add additional complexities. For example, due to the small and noisy signals micro/nanoresonators produce, a lock-in amplifier is commonly used to characterize the amplitude and phase responses of the systems. While the lock-in enables detection, it also prohibits the use of established time-domain, multi-harmonic, and frequency-domain methods, which rely upon time-domain measurements. As such, the only methods that can be used for parametric system identification are those based on fitting experimental data to an approximate solution, typically derived via perturbation methods and/or Galerkin methods, of a reduced-order model. Thus, one could view the parametric system identification of micro/nanosystems operating in a nonlinear response regime as the amalgamation of four coupled sub-problems: nonparametric system identification, or proper experimental design and data acquisition; the generation of physically consistent reduced-order models; the calculation of accurate approximate responses; and the application of nonlinear least-squares parameter estimation. This work is focused on the theoretical foundations that underpin each of these sub-problems, as the methods used to address one sub-problem can strongly influence the results of another. To provide context, an electromagnetically transduced microresonator is used as an example. This example provides a concrete reference for the presented findings and conclusions.

Robust non-parametric one-sample tests for the analysis of recurrent events.

PubMed

Rebora, Paola; Galimberti, Stefania; Valsecchi, Maria Grazia

2010-12-30

One-sample non-parametric tests are proposed here for inference on recurring events. The focus is on the marginal mean function of events and the basis for inference is the standardized distance between the observed and the expected number of events under a specified reference rate. Different weights are considered in order to account for various types of alternative hypotheses on the mean function of the recurrent events process. A robust version and a stratified version of the test are also proposed. The performance of these tests was investigated through simulation studies under various underlying event generation processes, such as homogeneous and nonhomogeneous Poisson processes, autoregressive and renewal processes, with and without frailty effects. The robust versions of the test have been shown to be suitable in a wide variety of event generating processes. The motivating context is a study on gene therapy in a very rare immunodeficiency in children, where a major end-point is the recurrence of severe infections. Robust non-parametric one-sample tests for recurrent events can be useful to assess efficacy and especially safety in non-randomized studies or in epidemiological studies for comparison with a standard population. Copyright © 2010 John Wiley & Sons, Ltd.

Non-intrusive reduced order modeling of nonlinear problems using neural networks

NASA Astrophysics Data System (ADS)

Hesthaven, J. S.; Ubbiali, S.

2018-06-01

We develop a non-intrusive reduced basis (RB) method for parametrized steady-state partial differential equations (PDEs). The method extracts a reduced basis from a collection of high-fidelity solutions via a proper orthogonal decomposition (POD) and employs artificial neural networks (ANNs), particularly multi-layer perceptrons (MLPs), to accurately approximate the coefficients of the reduced model. The search for the optimal number of neurons and the minimum amount of training samples to avoid overfitting is carried out in the offline phase through an automatic routine, relying upon a joint use of the Latin hypercube sampling (LHS) and the Levenberg-Marquardt (LM) training algorithm. This guarantees a complete offline-online decoupling, leading to an efficient RB method - referred to as POD-NN - suitable also for general nonlinear problems with a non-affine parametric dependence. Numerical studies are presented for the nonlinear Poisson equation and for driven cavity viscous flows, modeled through the steady incompressible Navier-Stokes equations. Both physical and geometrical parametrizations are considered. Several results confirm the accuracy of the POD-NN method and show the substantial speed-up enabled at the online stage as compared to a traditional RB strategy.

Out-of-Sample Extensions for Non-Parametric Kernel Methods.

PubMed

Pan, Binbin; Chen, Wen-Sheng; Chen, Bo; Xu, Chen; Lai, Jianhuang

2017-02-01

Choosing suitable kernels plays an important role in the performance of kernel methods. Recently, a number of studies were devoted to developing nonparametric kernels. Without assuming any parametric form of the target kernel, nonparametric kernel learning offers a flexible scheme to utilize the information of the data, which may potentially characterize the data similarity better. The kernel methods using nonparametric kernels are referred to as nonparametric kernel methods. However, many nonparametric kernel methods are restricted to transductive learning, where the prediction function is defined only over the data points given beforehand. They have no straightforward extension for the out-of-sample data points, and thus cannot be applied to inductive learning. In this paper, we show how to make the nonparametric kernel methods applicable to inductive learning. The key problem of out-of-sample extension is how to extend the nonparametric kernel matrix to the corresponding kernel function. A regression approach in the hyper reproducing kernel Hilbert space is proposed to solve this problem. Empirical results indicate that the out-of-sample performance is comparable to the in-sample performance in most cases. Experiments on face recognition demonstrate the superiority of our nonparametric kernel method over the state-of-the-art parametric kernel methods.

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

PubMed Central

2011-01-01

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with several previous glycosidic torsion parametrizations. PMID:21921995

Neurodynamics in the Sensorimotor Loop: Representing Behavior Relevant External Situations

PubMed Central

Pasemann, Frank

2017-01-01

In the context of the dynamical system approach to cognition and supposing that brains or brain-like systems controlling the behavior of autonomous systems are permanently driven by their sensor signals, the paper approaches the question of neurodynamics in the sensorimotor loop in a purely formal way. This is carefully done by addressing the problem in three steps, using the time-discrete dynamics of standard neural networks and a fiber space representation for better clearness. Furthermore, concepts like meta-transients, parametric stability and dynamical forms are introduced, where meta-transients describe the effect of realistic sensor inputs, parametric stability refers to a class of sensor inputs all generating the “same type” of dynamic behavior, and a dynamical form comprises the corresponding class of parametrized dynamical systems. It is argued that dynamical forms are the essential internal representatives of behavior relevant external situations. Consequently, it is suggested that dynamical forms are the basis for a memory of these situations. Finally, based on the observation that not all brain process have a direct effect on the motor activity, a natural splitting of neurodynamics into vertical (internal) and horizontal (effective) parts is introduced. PMID:28217092

The minimal number of parameters in triclinic crystal-field potentials

NASA Astrophysics Data System (ADS)

Mulak, J.

2003-09-01

The optimal parametrization schemes of the crystal-field (CF) potential in fitting procedures are those based on the smallest numbers of parameters. The surplus parametrizations usually lead to artificial and non-physical solutions. Therefore, the symmetry adapted reference systems are commonly used. Instead of them, however, the coordinate systems with the z-axis directed along the principal axes of the CF multipoles (2 k-poles) can be applied successfully, particularly for triclinic CF potentials. Due to the irreducibility of the D(k) representations such a choice can reduce the number of the k-order parameters by 2 k: from 2 k+1 (in the most general case) to only 1 (the axial one). Unfortunately, in general, the numbers of other order CF parameters stay then unrestricted. In this way, the number of parameters for the k-even triclinic CF potentials can be reduced by 4, 8 or 12, for k=2,4 or 6, respectively. Hence, the parametrization schemes based on maximum 14 parameters can be in use solely. For higher point symmetries this number is usually greater than that for the symmetry adapted systems. Nonetheless, many instructive correlations between the multipole contributions to the CF interaction are attainable in this way.

Measures of Situation Awareness: An Experimental Evaluation

DTIC Science & Technology

1991-10-01

occurrence from non- occurrence of the target event, referred to as sensitivity (Macmillan and Creelman , 1990). Because sensitivity declines if pilots are...Pollack and Norman, 1964; see also Craig, 1979; Macmillan and Creelman , 1990). Finally, avoidance failures were measured simply as the number of times...Wesley. Macmillan, N. A., & Creelman , C. D. (1990). Response bias: Characteristics of detection theory, threshold theory, and "non- parametric" indexes

Hypothesis Support Mechanism for Mid-Level Visual Pattern Recognition

NASA Technical Reports Server (NTRS)

Amador, Jose J (Inventor)

2007-01-01

A method of mid-level pattern recognition provides for a pose invariant Hough Transform by parametrizing pairs of points in a pattern with respect to at least two reference points, thereby providing a parameter table that is scale- or rotation-invariant. A corresponding inverse transform may be applied to test hypothesized matches in an image and a distance transform utilized to quantify the level of match.

Known-component 3D-2D registration for quality assurance of spine surgery pedicle screw placement

NASA Astrophysics Data System (ADS)

Uneri, A.; De Silva, T.; Stayman, J. W.; Kleinszig, G.; Vogt, S.; Khanna, A. J.; Gokaslan, Z. L.; Wolinsky, J.-P.; Siewerdsen, J. H.

2015-10-01

A 3D-2D image registration method is presented that exploits knowledge of interventional devices (e.g. K-wires or spine screws—referred to as ‘known components’) to extend the functionality of intraoperative radiography/fluoroscopy by providing quantitative measurement and quality assurance (QA) of the surgical product. The known-component registration (KC-Reg) algorithm uses robust 3D-2D registration combined with 3D component models of surgical devices known to be present in intraoperative 2D radiographs. Component models were investigated that vary in fidelity from simple parametric models (e.g. approximation of a screw as a simple cylinder, referred to as ‘parametrically-known’ component [pKC] registration) to precise models based on device-specific CAD drawings (referred to as ‘exactly-known’ component [eKC] registration). 3D-2D registration from three intraoperative radiographs was solved using the covariance matrix adaptation evolution strategy (CMA-ES) to maximize image-gradient similarity, relating device placement relative to 3D preoperative CT of the patient. Spine phantom and cadaver studies were conducted to evaluate registration accuracy and demonstrate QA of the surgical product by verification of the type of devices delivered and conformance within the ‘acceptance window’ of the spinal pedicle. Pedicle screws were successfully registered to radiographs acquired from a mobile C-arm, providing TRE 1-4 mm and  <5° using simple parametric (pKC) models, further improved to  <1 mm and  <1° using eKC registration. Using advanced pKC models, screws that did not match the device models specified in the surgical plan were detected with an accuracy of  >99%. Visualization of registered devices relative to surgical planning and the pedicle acceptance window provided potentially valuable QA of the surgical product and reliable detection of pedicle screw breach. 3D-2D registration combined with 3D models of known surgical devices offers a novel method for intraoperative QA. The method provides a near-real-time independent check against pedicle breach, facilitating revision within the same procedure if necessary and providing more rigorous verification of the surgical product.

Development of a computer aided diagnosis model for prostate cancer classification on multi-parametric MRI

NASA Astrophysics Data System (ADS)

Alfano, R.; Soetemans, D.; Bauman, G. S.; Gibson, E.; Gaed, M.; Moussa, M.; Gomez, J. A.; Chin, J. L.; Pautler, S.; Ward, A. D.

2018-02-01

Multi-parametric MRI (mp-MRI) is becoming a standard in contemporary prostate cancer screening and diagnosis, and has shown to aid physicians in cancer detection. It offers many advantages over traditional systematic biopsy, which has shown to have very high clinical false-negative rates of up to 23% at all stages of the disease. However beneficial, mp-MRI is relatively complex to interpret and suffers from inter-observer variability in lesion localization and grading. Computer-aided diagnosis (CAD) systems have been developed as a solution as they have the power to perform deterministic quantitative image analysis. We measured the accuracy of such a system validated using accurately co-registered whole-mount digitized histology. We trained a logistic linear classifier (LOGLC), support vector machine (SVC), k-nearest neighbour (KNN) and random forest classifier (RFC) in a four part ROI based experiment against: 1) cancer vs. non-cancer, 2) high-grade (Gleason score ≥4+3) vs. low-grade cancer (Gleason score <4+3), 3) high-grade vs. other tissue components and 4) high-grade vs. benign tissue by selecting the classifier with the highest AUC using 1-10 features from forward feature selection. The CAD model was able to classify malignant vs. benign tissue and detect high-grade cancer with high accuracy. Once fully validated, this work will form the basis for a tool that enhances the radiologist's ability to detect malignancies, potentially improving biopsy guidance, treatment selection, and focal therapy for prostate cancer patients, maximizing the potential for cure and increasing quality of life.

Direct reconstruction of parametric images for brain PET with event-by-event motion correction: evaluation in two tracers across count levels

NASA Astrophysics Data System (ADS)

Germino, Mary; Gallezot, Jean-Dominque; Yan, Jianhua; Carson, Richard E.

2017-07-01

Parametric images for dynamic positron emission tomography (PET) are typically generated by an indirect method, i.e. reconstructing a time series of emission images, then fitting a kinetic model to each voxel time activity curve. Alternatively, ‘direct reconstruction’, incorporates the kinetic model into the reconstruction algorithm itself, directly producing parametric images from projection data. Direct reconstruction has been shown to achieve parametric images with lower standard error than the indirect method. Here, we present direct reconstruction for brain PET using event-by-event motion correction of list-mode data, applied to two tracers. Event-by-event motion correction was implemented for direct reconstruction in the Parametric Motion-compensation OSEM List-mode Algorithm for Resolution-recovery reconstruction. The direct implementation was tested on simulated and human datasets with tracers [11C]AFM (serotonin transporter) and [11C]UCB-J (synaptic density), which follow the 1-tissue compartment model. Rigid head motion was tracked with the Vicra system. Parametric images of K 1 and distribution volume (V T  =  K 1/k 2) were compared to those generated by the indirect method by regional coefficient of variation (CoV). Performance across count levels was assessed using sub-sampled datasets. For simulated and real datasets at high counts, the two methods estimated K 1 and V T with comparable accuracy. At lower count levels, the direct method was substantially more robust to outliers than the indirect method. Compared to the indirect method, direct reconstruction reduced regional K 1 CoV by 35-48% (simulated dataset), 39-43% ([11C]AFM dataset) and 30-36% ([11C]UCB-J dataset) across count levels (averaged over regions at matched iteration); V T CoV was reduced by 51-58%, 54-60% and 30-46%, respectively. Motion correction played an important role in the dataset with larger motion: correction increased regional V T by 51% on average in the [11C]UCB-J dataset. Direct reconstruction of dynamic brain PET with event-by-event motion correction is achievable and dramatically more robust to noise in V T images than the indirect method.

Kinetics model for initiation and promotion for describing tumor prevalence from HZE radiation

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.

1994-01-01

A kinetics model for cellular repair and misrepair for multiple radiation-induced lesions (mutation-inactivation) is coupled to a two-mutation model of initiation and promotion in tissue to provide a parametric description of tumor prevalence in the Harderian gland in a mouse. Dose-response curves are described for gamma-rays and relativistic ions. The effects of nuclear fragmentation are also considered for high-energy proton and alpha particle exposures The model described provides a parametric description of age-dependent cancer induction for a wide range of radiation fields. We also consider the two hypotheses that radiation acts either solely as an initiator or as both initiator and promoter and make model calculations for fractionation exposures from gamma-rays and relativistic Fe ions. For fractionated Fe exposures, an inverse dose-rate effect is provided by a promotion hypothesis using a mutation rate for promotion typical of single-gene mutations.

Performance Guaranteed Inertia Emulation forDiesel-Wind System Feed Microgrid via ModelReference Control

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

Melin, Alexander M.; Zhang, Yichen; Djouadi, Seddik

In this paper, a model reference control based inertia emulation strategy is proposed. Desired inertia can be precisely emulated through this control strategy so that guaranteed performance is ensured. A typical frequency response model with parametrical inertia is set to be the reference model. A measurement at a specific location delivers the information of disturbance acting on the diesel-wind system to the referencemodel. The objective is for the speed of the diesel-wind system to track the reference model. Since active power variation is dominantly governed by mechanical dynamics and modes, only mechanical dynamics and states, i.e., a swing-engine-governor system plusmore » a reduced-order wind turbine generator, are involved in the feedback control design. The controller is implemented in a three-phase diesel-wind system feed microgrid. The results show exact synthetic inertia is emulated, leading to guaranteed performance and safety bounds.« less

Quantitative imaging of protein targets in the human brain with PET

NASA Astrophysics Data System (ADS)

Gunn, Roger N.; Slifstein, Mark; Searle, Graham E.; Price, Julie C.

2015-11-01

PET imaging of proteins in the human brain with high affinity radiolabelled molecules has a history stretching back over 30 years. During this period the portfolio of protein targets that can be imaged has increased significantly through successes in radioligand discovery and development. This portfolio now spans six major categories of proteins; G-protein coupled receptors, membrane transporters, ligand gated ion channels, enzymes, misfolded proteins and tryptophan-rich sensory proteins. In parallel to these achievements in radiochemical sciences there have also been significant advances in the quantitative analysis and interpretation of the imaging data including the development of methods for image registration, image segmentation, tracer compartmental modeling, reference tissue kinetic analysis and partial volume correction. In this review, we analyze the activity of the field around each of the protein targets in order to give a perspective on the historical focus and the possible future trajectory of the field. The important neurobiology and pharmacology is introduced for each of the six protein classes and we present established radioligands for each that have successfully transitioned to quantitative imaging in humans. We present a standard quantitative analysis workflow for these radioligands which takes the dynamic PET data, associated blood and anatomical MRI data as the inputs to a series of image processing and bio-mathematical modeling steps before outputting the outcome measure of interest on either a regional or parametric image basis. The quantitative outcome measures are then used in a range of different imaging studies including tracer discovery and development studies, cross sectional studies, classification studies, intervention studies and longitudinal studies. Finally we consider some of the confounds, challenges and subtleties that arise in practice when trying to quantify and interpret PET neuroimaging data including motion artifacts, partial volume effects, age effects, image registration and normalization, input functions and metabolites, parametric imaging, receptor internalization and genetic factors.

The moon illusion: II. A reference theory.

PubMed

Baird, J C

1982-09-01

The present theory provides explanations for the moon illusion and related issues involving size and distance perception in natural, outdoor settings. Although some assumptions of previous theories are rejected, other pivotal aspects are retained in this formulation. In particular, the present theory states that both the sky and ground are important referents in judging the spatial extent of the moon. Neither factor alone can account for all the available data, but quantitative models incorporating both factors do quite well when applied to the parametric findings of Holway and Boring, as well as to the results obtained by Kaufman and Rock. The reference theory and its associated class of specific models suggest new theoretical directions and experimental tests to narrow yet further the selection of appropriate explanations for one of visual perception's oldest unsolved puzzles.

Ultrasound Imaging of DNA-Damage Effects in Live Cultured Cells and in Brain Tissue.

PubMed

Tadayyon, Hadi; Gangeh, Mehrdad J; Vlad, Roxana; Kolios, Michael C; Czarnota, Gregory J

2017-01-01

High-frequency ultrasound (>20 MHz) spectroscopy can be used to detect noninvasively DNA damage in cell samples in vitro, and in live tissue both ex vivo and in vivo. This chapter focuses on the former two aspects. Experimental evidence suggests that morphological changes that occur in cells undergoing apoptosis result in changes in frequency-dependent ultrasound backscatter. With advances in research, ultrasound spectroscopy is advancing the boundaries of fast, label-free, noninvasive DNA damage detection technology with potential use in personalized medicine and early therapy response monitoring. Depending on the desired resolution, parametric ultrasound images can be computed and displayed within minutes to hours after ultrasound examination for cell death.

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.

Accurate determination of brain metabolite concentrations using ERETIC as external reference.

PubMed

Zoelch, Niklaus; Hock, Andreas; Heinzer-Schweizer, Susanne; Avdievitch, Nikolai; Henning, Anke

2017-08-01

Magnetic Resonance Spectroscopy (MRS) can provide in vivo metabolite concentrations in standard concentration units if a reliable reference signal is available. For 1 H MRS in the human brain, typically the signal from the tissue water is used as the (internal) reference signal. However, a concentration determination based on the tissue water signal most often requires a reliable estimate of the water concentration present in the investigated tissue. Especially in clinically interesting cases, this estimation might be difficult. To avoid assumptions about the water in the investigated tissue, the Electric REference To access In vivo Concentrations (ERETIC) method has been proposed. In this approach, the metabolite signal is compared with a reference signal acquired in a phantom and potential coil-loading differences are corrected using a synthetic reference signal. The aim of this study, conducted with a transceiver quadrature head coil, was to increase the accuracy of the ERETIC method by correcting the influence of spatial B 1 inhomogeneities and to simplify the quantification with ERETIC by incorporating an automatic phase correction for the ERETIC signal. Transmit field ( B1+) differences are minimized with a volume-selective power optimization, whereas reception sensitivity changes are corrected using contrast-minimized images of the brain and by adapting the voxel location in the phantom measurement closely to the position measured in vivo. By applying the proposed B 1 correction scheme, the mean metabolite concentrations determined with ERETIC in 21 healthy subjects at three different positions agree with concentrations derived with the tissue water signal as reference. In addition, brain water concentrations determined with ERETIC were in agreement with estimations derived using tissue segmentation and literature values for relative water densities. Based on the results, the ERETIC method presented here is a valid tool to derive in vivo metabolite concentration, with potential advantages compared with internal water referencing in diseased tissue. Copyright © 2017 John Wiley & Sons, Ltd.

Analyzing and Improving Image Quality in Reflective Ghost Imaging

DTIC Science & Technology

2011-02-01

photon quantum entanglement ," Phys. Rev. A 52, 3429 (1995). [2] A. Valencia, G. Scarcelli. M. D. Angelo, and Y. Shih. "Two- photon imaging with thermal...and reference fields, which were generated by spontaneous parametric downconversion (SPDC) and post- selection [1]. Because biphotons are entangled ...envelopes about center frequency we of linearly-polarized light fields normalized to have V/ photons /m 2s units as functions of their transverse

Large-Scale Urban Localisation with a Pushbroom LIDAR

DTIC Science & Technology

2012-10-01

the sole means of gen- erating full 6-DOF poses from a previously-surveyed workspace. In this approach, Normalised Information Distance is used as the...vehicle to have good knowledge of its position at system- initialization. We now turn to an overview of the use of point-based registration methods for...combination of reference vertices, and provides a convenient representation for the intersection test . Using this parametric representation, the coordinates

USSR Report, Engineering and Equipment.

DTIC Science & Technology

1987-02-18

VISNYK AKADEMIYI NAUK UKRAYINSKOYI RSR, No 6, Jun 86) 10 Local Energy Losses in a Piezoceramic Resonator Upon Electric Excitation (A.V. Mezheritskiy...MATEMATIKA I MEKHANIKA, No 2, Mar-Apr 86) 76 Simulation of Resonant Vibrations of Vibration Insulation System Under Effect of Low-Frequency Parametric...references 19: 17 Russian, 2 Western. 12172/13046 CSO: 1861/535 10 UDC 621.372.412/.414:537.228.1 LOCAL ENERGY LOSSES IN A PIEZOCERAMIC RESONATOR UPON

Applications of high average power nonlinear optics

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

Velsko, S.P.; Krupke, W.F.

1996-02-05

Nonlinear optical frequency convertors (harmonic generators and optical parametric oscillators are reviewed with an emphasis on high average power performance and limitations. NLO materials issues and NLO device designs are discussed in reference to several emerging scientific, military and industrial commercial applications requiring {approx} 100 watt average power level in the visible and infrared spectral regions. Research efforts required to enable practical {approx} 100 watt class NLO based laser systems are identified.

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Three-Dimensional Modeling of Aircraft High-Lift Components with Vehicle Sketch Pad

NASA Technical Reports Server (NTRS)

Olson, Erik D.

2016-01-01

Vehicle Sketch Pad (OpenVSP) is a parametric geometry modeler that has been used extensively for conceptual design studies of aircraft, including studies using higher-order analysis. OpenVSP can model flap and slat surfaces using simple shearing of the airfoil coordinates, which is an appropriate level of complexity for lower-order aerodynamic analysis methods. For three-dimensional analysis, however, there is not a built-in method for defining the high-lift components in OpenVSP in a realistic manner, or for controlling their complex motions in a parametric manner that is intuitive to the designer. This paper seeks instead to utilize OpenVSP's existing capabilities, and establish a set of best practices for modeling high-lift components at a level of complexity suitable for higher-order analysis methods. Techniques are described for modeling the flap and slat components as separate three-dimensional surfaces, and for controlling their motion using simple parameters defined in the local hinge-axis frame of reference. To demonstrate the methodology, an OpenVSP model for the Energy-Efficient Transport (EET) AR12 wind-tunnel model has been created, taking advantage of OpenVSP's Advanced Parameter Linking capability to translate the motions of the high-lift components from the hinge-axis coordinate system to a set of transformations in OpenVSP's frame of reference.

Evaluation of Two Outlier-Detection-Based Methods for Detecting Tissue-Selective Genes from Microarray Data

PubMed Central

Kadota, Koji; Konishi, Tomokazu; Shimizu, Kentaro

2007-01-01

Large-scale expression profiling using DNA microarrays enables identification of tissue-selective genes for which expression is considerably higher and/or lower in some tissues than in others. Among numerous possible methods, only two outlier-detection-based methods (an AIC-based method and Sprent’s non-parametric method) can treat equally various types of selective patterns, but they produce substantially different results. We investigated the performance of these two methods for different parameter settings and for a reduced number of samples. We focused on their ability to detect selective expression patterns robustly. We applied them to public microarray data collected from 36 normal human tissue samples and analyzed the effects of both changing the parameter settings and reducing the number of samples. The AIC-based method was more robust in both cases. The findings confirm that the use of the AIC-based method in the recently proposed ROKU method for detecting tissue-selective expression patterns is correct and that Sprent’s method is not suitable for ROKU. PMID:19936074

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.

Simulation-assisted design of microfluidic sample traps for optimal trapping and culture of non-adherent single cells, tissues, and spheroids.

PubMed

Rousset, Nassim; Monet, Frédéric; Gervais, Thomas

2017-03-21

This work focuses on modelling design and operation of "microfluidic sample traps" (MSTs). MSTs regroup a widely used class of microdevices that incorporate wells, recesses or chambers adjacent to a channel to individually trap, culture and/or release submicroliter 3D tissue samples ranging from simple cell aggregates and spheroids, to ex vivo tissue samples and other submillimetre-scale tissue models. Numerous MST designs employing various trapping mechanisms have been proposed in the literature, spurring the development of 3D tissue models for drug discovery and personalized medicine. Yet, there lacks a general framework to optimize trapping stability, trapping time, shear stress, and sample metabolism. Herein, the effects of hydrodynamics and diffusion-reaction on tissue viability and device operation are investigated using analytical and finite element methods with systematic parametric sweeps over independent design variables chosen to correspond to the four design degrees of freedom. Combining different results, we show that, for a spherical tissue of diameter d < 500 μm, the simplest, closest to optimal trap shape is a cube of dimensions w equal to twice the tissue diameter: w = 2d. Furthermore, to sustain tissues without perfusion, available medium volume per trap needs to be 100× the tissue volume to ensure optimal metabolism for at least 24 hours.

Efficient Verification of Holograms Using Mobile Augmented Reality.

PubMed

Hartl, Andreas Daniel; Arth, Clemens; Grubert, Jens; Schmalstieg, Dieter

2016-07-01

Paper documents such as passports, visas and banknotes are frequently checked by inspection of security elements. In particular, optically variable devices such as holograms are important, but difficult to inspect. Augmented Reality can provide all relevant information on standard mobile devices. However, hologram verification on mobiles still takes long and provides lower accuracy than inspection by human individuals using appropriate reference information. We aim to address these drawbacks by automatic matching combined with a special parametrization of an efficient goal-oriented user interface which supports constrained navigation. We first evaluate a series of similarity measures for matching hologram patches to provide a sound basis for automatic decisions. Then a re-parametrized user interface is proposed based on observations of typical user behavior during document capture. These measures help to reduce capture time to approximately 15 s with better decisions regarding the evaluated samples than what can be achieved by untrained users.

Fast, precise, and widely tunable frequency control of an optical parametric oscillator referenced to a frequency comb.

PubMed

Prehn, Alexander; Glöckner, Rosa; Rempe, Gerhard; Zeppenfeld, Martin

2017-03-01

Optical frequency combs (OFCs) provide a convenient reference for the frequency stabilization of continuous-wave lasers. We demonstrate a frequency control method relying on tracking over a wide range and stabilizing the beat note between the laser and the OFC. The approach combines fast frequency ramps on a millisecond timescale in the entire mode-hop free tuning range of the laser and precise stabilization to single frequencies. We apply it to a commercially available optical parametric oscillator (OPO) and demonstrate tuning over more than 60 GHz with a ramping speed up to 3 GHz/ms. Frequency ramps spanning 15 GHz are performed in less than 10 ms, with the OPO instantly relocked to the OFC after the ramp at any desired frequency. The developed control hardware and software are able to stabilize the OPO to sub-MHz precision and to perform sequences of fast frequency ramps automatically.

Conditional parametric models for storm sewer runoff

NASA Astrophysics Data System (ADS)

Jonsdottir, H.; Nielsen, H. Aa; Madsen, H.; Eliasson, J.; Palsson, O. P.; Nielsen, M. K.

2007-05-01

The method of conditional parametric modeling is introduced for flow prediction in a sewage system. It is a well-known fact that in hydrological modeling the response (runoff) to input (precipitation) varies depending on soil moisture and several other factors. Consequently, nonlinear input-output models are needed. The model formulation described in this paper is similar to the traditional linear models like final impulse response (FIR) and autoregressive exogenous (ARX) except that the parameters vary as a function of some external variables. The parameter variation is modeled by local lines, using kernels for local linear regression. As such, the method might be referred to as a nearest neighbor method. The results achieved in this study were compared to results from the conventional linear methods, FIR and ARX. The increase in the coefficient of determination is substantial. Furthermore, the new approach conserves the mass balance better. Hence this new approach looks promising for various hydrological models and analysis.

Structure of the alexithymic brain: A parametric coordinate-based meta-analysis.

PubMed

Xu, Pengfei; Opmeer, Esther M; van Tol, Marie-José; Goerlich, Katharina S; Aleman, André

2018-04-01

Alexithymia refers to deficiencies in identifying and expressing emotions. This might be related to changes in structural brain volumes, but its neuroanatomical basis remains uncertain as studies have shown heterogeneous findings. Therefore, we conducted a parametric coordinate-based meta-analysis. We identified seventeen structural neuroimaging studies (including a total of 2586 individuals with different levels of alexithymia) investigating the association between gray matter volume and alexithymia. Volumes of the left insula, left amygdala, orbital frontal cortex and striatum were consistently smaller in people with high levels of alexithymia. These areas are important for emotion perception and emotional experience. Smaller volumes in these areas might lead to deficiencies in appropriately identifying and expressing emotions. These findings provide the first quantitative integration of results pertaining to the structural neuroanatomical basis of alexithymia. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

CHRONOBIOLOGY OF HIGH BLOOD PRESSURE

PubMed Central

Cornélissen, G.; Halberg, F.; Bakken, E. E.; Wang, Z.; Tarquini, R.; Perfetto, F.; Laffi, G.; Maggioni, C.; Kumagai, Y.; Homolka, P.; Havelková, A.; Dušek, J.; Svačinová, H.; Siegelová, J.; Fišer, B.

2008-01-01

BIOCOS, the project aimed at studying BIOlogical systems in their COSmos, has obtained a great deal of expertise in the fields of blood pressure (BP) and heart rate (HR) monitoring and of marker rhythmometry for the purposes of screening, diagnosis, treatment, and prognosis. Prolonging the monitoring reduces the uncertainty in the estimation of circadian parameters; the current recommendation of BIOCOS requires monitoring for at least 7 days. The BIOCOS approach consists of a parametric and a non-parametric analysis of the data, in which the results from the individual subject are being compared with gender- and age-specified reference values in health. Chronobiological designs can offer important new information regarding the optimization of treatment by timing its administration as a function of circadian and other rhythms. New technological developments are needed to close the loop between the monitoring of blood pressure and the administration of antihypertensive drugs. PMID:19122770

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.

Broadband midinfrared frequency comb with tooth scanning

NASA Astrophysics Data System (ADS)

Lee, Kevin F.; Masłowski, P.; Mills, A.; Mohr, C.; Jiang, Jie; Schunemann, Peter G.; Fermann, M. E.

2015-03-01

Frequency combs are a massively parallel source of extremely accurate optical frequencies. Frequency combs generally operate at the visible or near-infrared wavelengths, but fundamental molecular vibrations occur at midinfrared wavelengths. We demonstrate an optically-referenced, broadband midinfrared frequency comb based on a doublyresonant optical parametric oscillator (OPO). By tuning the wavelength of the reference laser, the comb line frequencies are tuned as well. By scanning the reference wavelength, any frequency can be accessed, not just the frequencies of the base comb. Combined with our comb-resolving Fourier transform spectrometer, we can measure 200 wavenumber wide broadband absorption spectra with 200 kHz linewidth comb teeth. Our OPO is pumped by an amplified Tm fiber frequency comb, with phase-locked carrier envelope offset frequency, and repetition rate fixed by phase-locking a frequency comb line to a narrow linewidth diode laser at a telecom channel. The frequency comb is referenced to GPS by long-term stabilization of the repetition rate to a selected value using the temperature of the reference laser as the control. The resulting pump comb is about 3W of 100 fs pulses at 418 MHz repetition rate at 1950 nm. Part of the comb is used for supercontinuum generation for frequency stabilization, and the rest pumps an orientation-patterned gallium arsenide (OP-GaAs) crystal in a doubly-resonant optical parametric oscillator cavity, yielding collinear signal and idler beams from about 3 to 5.5 μm. We verify comb scanning by resolving the 200 MHz wide absorption lines of the entire fundamental CO vibrational manifold at 11 Torr pressure.

Mimicking biological stress-strain behaviour with synthetic elastomers

NASA Astrophysics Data System (ADS)

Vatankhah-Varnosfaderani, Mohammad; Daniel, William F. M.; Everhart, Matthew H.; Pandya, Ashish A.; Liang, Heyi; Matyjaszewski, Krzysztof; Dobrynin, Andrey V.; Sheiko, Sergei S.

2017-09-01

Despite the versatility of synthetic chemistry, certain combinations of mechanical softness, strength, and toughness can be difficult to achieve in a single material. These combinations are, however, commonplace in biological tissues, and are therefore needed for applications such as medical implants, tissue engineering, soft robotics, and wearable electronics. Present materials synthesis strategies are predominantly Edisonian, involving the empirical mixing of assorted monomers, crosslinking schemes, and occluded swelling agents, but this approach yields limited property control. Here we present a general strategy for mimicking the mechanical behaviour of biological materials by precisely encoding their stress-strain curves in solvent-free brush- and comb-like polymer networks (elastomers). The code consists of three independent architectural parameters—network strand length, side-chain length and grafting density. Using prototypical poly(dimethylsiloxane) elastomers, we illustrate how this parametric triplet enables the replication of the strain-stiffening characteristics of jellyfish, lung, and arterial tissues.

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

Parametric Interactions between Alfven waves in LaPD

NASA Astrophysics Data System (ADS)

Brugman, B.; Carter, T. A.; Cowley, S. C.; Pribyl, P.; Lybarger, W.

2004-11-01

The physics governing interactions between large amplitude Alfvén waves, which are relevant to plasmas in space as well as the laboratory, is at present not well understood. A major class of such interactions which are believed to occur in compressible plasmas is referred to as parametric decay. We will present the results of a series of experiments involving the interactions of large amplitude LHP Alfvén wave conducted on the Large Plasma Device (LaPD); where β ≪ 1, n ˜ 10^12 frac1cm^3 and B0 in (200,2500) G. These experiments show strong signs of one form of parametric decay, known as the Modulational Instability, which represents the interaction of two Alfvén waves and a low frequency density perturbation. This interaction is believed to occur in plasmas with β < 1 as well as β > 1, over a broad range of wavevector space, and for RHP as well as LHP Alfvén waves - distinguishing it from the Beat and Decay instabilities. Details of this interaction, in particular the structure of the incident waves as well as that of their byproducts, will be shown in physical as well as wavevector space. The generation of large amplitude waves using both an Alfvén wave MASER and high current loop antennas will also be illustrated. Lastly theoretical descriptions of parametric decay will be presented and compared to observations. Future work will also include comparisons of experimental results with applicable simulations, such as GS2. Work supported by DOE grant number DE-FG03-02ER54688

Interrelationships between fish tissue mercury concentrations and water quality for South Dakota natural lakes and impoundments

USGS Publications Warehouse

Chipps, Steven R.; Stetler, Larry; Stone, James J.; McCutcheon, Cindy M.

2011-01-01

The purpose of this study was to determine whether water quality parameters commonly associated with primary productivity may be used to predict the susceptibility of a specific water body to exceed proposed fish consumption advisory limitation of 0.3 mg kg−1. South Dakota currently has nine lakes and impoundments that exceed fish tissue mercury advisory limits of 1.0 mg kg−1 total mercury, far exceeding US Environmental Protection Agency and Food and Drug Administration 0.3 mg kg−1 consumption criteria. Previous studies suggest that increased aquatic productivity may mitigate the effects of biological production and subsequent uptake of methyl mercury through bio-dilution; however, it is uncertain whether these trends may exist within highly alkaline and highly productive aquatic conditions common to South Dakota lakes and impoundments. Water quality parameters and fish tissue mercury data for northern pike and walleye were collected and assessed using existing South Dakota Department of Environment and Natural Resources and Game Fish and Parks data. The data was initially screened using both parametric linear regression and non-parametric Mann–Whitney rank sum comparisons and further assessed using binary logistic regression and stepwise logistic regression methodology. Three separate phosphorus measurements (total, total dissolved, and Trophic State Index) and pH were determined to significantly correlate with increased mercury concentrations for the northern pike-in-impoundments model. However, phosphorus surprisingly was not a strong predictor for the remaining scenarios modeled. For the northern pike-in-natural lakes models, alkalinity was the most significant water quality parameter predicting increased mercury concentrations. Mercury concentrations for the walleye-in-natural lakes models were further influenced by pH and alkalinity. The water quality and fish tissue mercury interrelationships determined within this study suggest aquatic productivity, and consequential eutrophication processes appear to be reasonable indicators of fish tissue mercury susceptibility for aquatic conditions common to South Dakota and highlight the continuing need to minimize eutrophication through effective watershed management strategies.

Real-Time Assessment of Mechanical Tissue Trauma in Surgery.

PubMed

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

2017-10-01

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

Standards of ultrasound imaging of the adrenal glands

PubMed Central

Jakubowski, Wiesław S.; Dobruch-Sobczak, Katarzyna; Kasperlik-Załuska, Anna A.

2015-01-01

Adrenal glands are paired endocrine glands located over the upper renal poles. Adrenal pathologies have various clinical presentations. They can coexist with the hyperfunction of individual cortical zones or the medulla, insufficiency of the adrenal cortex or retained normal hormonal function. The most common adrenal masses are tumors incidentally detected in imaging examinations (ultrasound, tomography, magnetic resonance imaging), referred to as incidentalomas. They include a range of histopathological entities but cortical adenomas without hormonal hyperfunction are the most common. Each abdominal ultrasound scan of a child or adult should include the assessment of the suprarenal areas. If a previously non-reported, incidental solid focal lesion exceeding 1 cm (incidentaloma) is detected in the suprarenal area, computed tomography or magnetic resonance imaging should be conducted to confirm its presence and for differentiation and the tumor functional status should be determined. Ultrasound imaging is also used to monitor adrenal incidentaloma that is not eligible for a surgery. The paper presents recommendations concerning the performance and assessment of ultrasound examinations of the adrenal glands and their pathological lesions. The article includes new ultrasound techniques, such as tissue harmonic imaging, spatial compound imaging, three-dimensional ultrasound, elastography, contrast-enhanced ultrasound and parametric imaging. The guidelines presented above are consistent with the recommendations of the Polish Ultrasound Society. PMID:26807295

An open source multivariate framework for n-tissue segmentation with evaluation on public data.

PubMed

Avants, Brian B; Tustison, Nicholas J; Wu, Jue; Cook, Philip A; Gee, James C

2011-12-01

We introduce Atropos, an ITK-based multivariate n-class open source segmentation algorithm distributed with ANTs ( http://www.picsl.upenn.edu/ANTs). The Bayesian formulation of the segmentation problem is solved using the Expectation Maximization (EM) algorithm with the modeling of the class intensities based on either parametric or non-parametric finite mixtures. Atropos is capable of incorporating spatial prior probability maps (sparse), prior label maps and/or Markov Random Field (MRF) modeling. Atropos has also been efficiently implemented to handle large quantities of possible labelings (in the experimental section, we use up to 69 classes) with a minimal memory footprint. This work describes the technical and implementation aspects of Atropos and evaluates its performance on two different ground-truth datasets. First, we use the BrainWeb dataset from Montreal Neurological Institute to evaluate three-tissue segmentation performance via (1) K-means segmentation without use of template data; (2) MRF segmentation with initialization by prior probability maps derived from a group template; (3) Prior-based segmentation with use of spatial prior probability maps derived from a group template. We also evaluate Atropos performance by using spatial priors to drive a 69-class EM segmentation problem derived from the Hammers atlas from University College London. These evaluation studies, combined with illustrative examples that exercise Atropos options, demonstrate both performance and wide applicability of this new platform-independent open source segmentation tool.

An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data

PubMed Central

Tustison, Nicholas J.; Wu, Jue; Cook, Philip A.; Gee, James C.

2012-01-01

We introduce Atropos, an ITK-based multivariate n-class open source segmentation algorithm distributed with ANTs (http://www.picsl.upenn.edu/ANTs). The Bayesian formulation of the segmentation problem is solved using the Expectation Maximization (EM) algorithm with the modeling of the class intensities based on either parametric or non-parametric finite mixtures. Atropos is capable of incorporating spatial prior probability maps (sparse), prior label maps and/or Markov Random Field (MRF) modeling. Atropos has also been efficiently implemented to handle large quantities of possible labelings (in the experimental section, we use up to 69 classes) with a minimal memory footprint. This work describes the technical and implementation aspects of Atropos and evaluates its performance on two different ground-truth datasets. First, we use the BrainWeb dataset from Montreal Neurological Institute to evaluate three-tissue segmentation performance via (1) K-means segmentation without use of template data; (2) MRF segmentation with initialization by prior probability maps derived from a group template; (3) Prior-based segmentation with use of spatial prior probability maps derived from a group template. We also evaluate Atropos performance by using spatial priors to drive a 69-class EM segmentation problem derived from the Hammers atlas from University College London. These evaluation studies, combined with illustrative examples that exercise Atropos options, demonstrate both performance and wide applicability of this new platform-independent open source segmentation tool. PMID:21373993

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.

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.

Controllers for Battery Chargers and Battery Chargers Therefrom

NASA Technical Reports Server (NTRS)

Elmes, John (Inventor); Kersten, Rene (Inventor); Pepper, Michael (Inventor)

2014-01-01

A controller for a battery charger that includes a power converter has parametric sensors for providing a sensed Vin signal, a sensed Vout signal and a sensed Iout signal. A battery current regulator (BCR) is coupled to receive the sensed Iout signal and an Iout reference, and outputs a first duty cycle control signal. An input voltage regulator (IVR) receives the sensed Vin signal and a Vin reference. The IVR provides a second duty cycle control signal. A processor receives the sensed Iout signal and utilizes a Maximum Power Point Tracking (MPPT) algorithm, and provides the Vin reference to the IVR. A selection block forwards one of the first and second duty cycle control signals as a duty cycle control signal to the power converter. Dynamic switching between the first and second duty cycle control signals maximizes the power delivered to the battery.

Adjusting Expected Mortality Rates Using Information From a Control Population: An Example Using Socioeconomic Status.

PubMed

Bower, Hannah; Andersson, Therese M-L; Crowther, Michael J; Dickman, Paul W; Lambe, Mats; Lambert, Paul C

2018-04-01

Expected or reference mortality rates are commonly used in the calculation of measures such as relative survival in population-based cancer survival studies and standardized mortality ratios. These expected rates are usually presented according to age, sex, and calendar year. In certain situations, stratification of expected rates by other factors is required to avoid potential bias if interest lies in quantifying measures according to such factors as, for example, socioeconomic status. If data are not available on a population level, information from a control population could be used to adjust expected rates. We have presented two approaches for adjusting expected mortality rates using information from a control population: a Poisson generalized linear model and a flexible parametric survival model. We used a control group from BCBaSe-a register-based, matched breast cancer cohort in Sweden with diagnoses between 1992 and 2012-to illustrate the two methods using socioeconomic status as a risk factor of interest. Results showed that Poisson and flexible parametric survival approaches estimate similar adjusted mortality rates according to socioeconomic status. Additional uncertainty involved in the methods to estimate stratified, expected mortality rates described in this study can be accounted for using a parametric bootstrap, but this might make little difference if using a large control population.

Evaluation of model-based versus non-parametric monaural noise-reduction approaches for hearing aids.

PubMed

Harlander, Niklas; Rosenkranz, Tobias; Hohmann, Volker

2012-08-01

Single channel noise reduction has been well investigated and seems to have reached its limits in terms of speech intelligibility improvement, however, the quality of such schemes can still be advanced. This study tests to what extent novel model-based processing schemes might improve performance in particular for non-stationary noise conditions. Two prototype model-based algorithms, a speech-model-based, and a auditory-model-based algorithm were compared to a state-of-the-art non-parametric minimum statistics algorithm. A speech intelligibility test, preference rating, and listening effort scaling were performed. Additionally, three objective quality measures for the signal, background, and overall distortions were applied. For a better comparison of all algorithms, particular attention was given to the usage of the similar Wiener-based gain rule. The perceptual investigation was performed with fourteen hearing-impaired subjects. The results revealed that the non-parametric algorithm and the auditory model-based algorithm did not affect speech intelligibility, whereas the speech-model-based algorithm slightly decreased intelligibility. In terms of subjective quality, both model-based algorithms perform better than the unprocessed condition and the reference in particular for highly non-stationary noise environments. Data support the hypothesis that model-based algorithms are promising for improving performance in non-stationary noise conditions.

Toward uniform implementation of parametric map Digital Imaging and Communication in Medicine standard in multisite quantitative diffusion imaging studies.

PubMed

Malyarenko, Dariya; Fedorov, Andriy; Bell, Laura; Prah, Melissa; Hectors, Stefanie; Arlinghaus, Lori; Muzi, Mark; Solaiyappan, Meiyappan; Jacobs, Michael; Fung, Maggie; Shukla-Dave, Amita; McManus, Kevin; Boss, Michael; Taouli, Bachir; Yankeelov, Thomas E; Quarles, Christopher Chad; Schmainda, Kathleen; Chenevert, Thomas L; Newitt, David C

2018-01-01

This paper reports on results of a multisite collaborative project launched by the MRI subgroup of Quantitative Imaging Network to assess current capability and provide future guidelines for generating a standard parametric diffusion map Digital Imaging and Communication in Medicine (DICOM) in clinical trials that utilize quantitative diffusion-weighted imaging (DWI). Participating sites used a multivendor DWI DICOM dataset of a single phantom to generate parametric maps (PMs) of the apparent diffusion coefficient (ADC) based on two models. The results were evaluated for numerical consistency among models and true phantom ADC values, as well as for consistency of metadata with attributes required by the DICOM standards. This analysis identified missing metadata descriptive of the sources for detected numerical discrepancies among ADC models. Instead of the DICOM PM object, all sites stored ADC maps as DICOM MR objects, generally lacking designated attributes and coded terms for quantitative DWI modeling. Source-image reference, model parameters, ADC units and scale, deemed important for numerical consistency, were either missing or stored using nonstandard conventions. Guided by the identified limitations, the DICOM PM standard has been amended to include coded terms for the relevant diffusion models. Open-source software has been developed to support conversion of site-specific formats into the standard representation.

Brain tissue segmentation based on DTI data

PubMed Central

Liu, Tianming; Li, Hai; Wong, Kelvin; Tarokh, Ashley; Guo, Lei; Wong, Stephen T.C.

2008-01-01

We present a method for automated brain tissue segmentation based on the multi-channel fusion of diffusion tensor imaging (DTI) data. The method is motivated by the evidence that independent tissue segmentation based on DTI parametric images provides complementary information of tissue contrast to the tissue segmentation based on structural MRI data. This has important applications in defining accurate tissue maps when fusing structural data with diffusion data. In the absence of structural data, tissue segmentation based on DTI data provides an alternative means to obtain brain tissue segmentation. Our approach to the tissue segmentation based on DTI data is to classify the brain into two compartments by utilizing the tissue contrast existing in a single channel. Specifically, because the apparent diffusion coefficient (ADC) values in the cerebrospinal fluid (CSF) are more than twice that of gray matter (GM) and white matter (WM), we use ADC images to distinguish CSF and non-CSF tissues. Additionally, fractional anisotropy (FA) images are used to separate WM from non-WM tissues, as highly directional white matter structures have much larger fractional anisotropy values. Moreover, other channels to separate tissue are explored, such as eigenvalues of the tensor, relative anisotropy (RA), and volume ratio (VR). We developed an approach based on the Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm that combines these two-class maps to obtain a complete tissue segmentation map of CSF, GM, and WM. Evaluations are provided to demonstrate the performance of our approach. Experimental results of applying this approach to brain tissue segmentation and deformable registration of DTI data and spoiled gradient-echo (SPGR) data are also provided. PMID:17804258

A finite element model of remote palpation of breast lesions using radiation force: factors affecting tissue displacement.

PubMed

Nightingale, K R; Nightingale, R W; Palmeri, M L; Trahey, G E

2000-01-01

The early detection of breast cancer reduces patient mortality. The most common method of breast cancer detection is palpation. However, lesions that lie deep within the breast are difficult to palpate when they are small. Thus, a method of remote palpation, which may allow the detection of small lesions lying deep within the breast, is currently under investigation. In this method, acoustic radiation force is used to apply localized forces within tissue (to tissue volumes on the order of 2 mm3) and the resulting tissue displacements are mapped using ultrasonic correlation based methods. A volume of tissue that is stiffer than the surrounding medium (i.e., a lesion) distributes the force throughout the tissue beneath it, resulting in larger regions of displacement, and smaller maximum displacements. The resulting displacement maps may be used to image tissue stiffness. A finite-element-model (FEM) of acoustic remote palpation is presented in this paper. Using this model, a parametric analysis of the affect of varying tissue and acoustic beam characteristics on radiation force induced tissue displacements is performed. The results are used to evaluate the potential of acoustic remote palpation to provide useful diagnostic information in a clinical setting. The potential for using a single diagnostic transducer to both generate radiation force and track the resulting displacements is investigated.

Deformation and reperfusion damages and their accumulation in subcutaneous tissues during loading and unloading: a theoretical modeling of deep tissue injuries.

PubMed

Mak, Arthur F T; Yu, Yanyan; Kwan, Linda P C; Sun, Lei; Tam, Eric W C

2011-11-21

Deep tissue injuries (DTI) involve damages in the subcutaneous tissues under intact skin incurred by prolonged excessive epidermal loadings. This paper presents a new theoretical model for the development of DTI, broadly based on the experimental evidence in the literatures. The model covers the loading damages implicitly inclusive of both the direct mechanical and ischemic injuries, and the additional reperfusion damages and the competing healing processes during the unloading phase. Given the damage accumulated at the end of the loading period, the relative strength of the reperfusion and the healing capacity of the involved tissues system, the model provides a description of the subsequent damage evolution during unloading. The model is used to study parametrically the scenario when reperfusion damage dominates over healing upon unloading and the opposite scenario when the loading and subsequent reperfusion damages remain small relative to the healing capacity of the tissues system. The theoretical model provides an integrated understanding of how tissue damage may further build-up paradoxically even with unloading, how long it would take for the loading and reperfusion damages in the tissues to become fully recovered, and how such loading and reperfusion damages, if not given sufficient time for recovery, may accumulate over multiple loading and unloading cycles, leading to clinical deep tissues ulceration. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

Generating Three-Dimensional Surface Models of Solid Objects from Multiple Projections.

DTIC Science & Technology

1982-10-01

volume descriptions. The surface models are composed of curved, topologically rectangular, parametric patches. The data required to define these patches...geometry directly from image data .__ This method generates 3D surface descriptions of only those parts of the object that are illuminated by the pro- jected...objects. Generation of such models inherently requires the acquisition and analysis of 3D surface data . In this context, acquisition refers to the

Generalized Convexity and Concavity Properties of the Optimal Value Function in Parametric Nonlinear Programming.

DTIC Science & Technology

1983-04-11

existing ones. * -37- !I T-472 REFERENCES [1] Avriel, M., W. E. Diewert, S. Schaible and W. T. Ziemba (1981). Introduction to concave and generalized concave...functions. In Generalized Concavity in Optimization and Economics (S. Schaible and W. T. Ziemba , eds.), Academic Press, New York, pp. 21-50. (21 Bank...Optimality conditions involving generalized convex mappings. In Generalized Concavity in Optimization and Economics (S. Schaible and W. T. Ziemba

Compliant Robotic Structures. Part 2

DTIC Science & Technology

1986-07-01

Nonaxially Homogeneous Stresses and Strains 44 Parametric Studies 52 % References 65 III. LARGE DEFLECTIONS OF CONTINUOUS ELASTIC ’- STRUCTURES 66...APPENDIX C: Computer Program for the Element String 133 -° SUMMARY This is the second year report which is a part of a three- year study on compliant...ratios as high as 10/1 for laboratory-scale models and up to 3/1 for full-scale prototype arms. The first two years of this study have involved the

Sci—Fri PM: Topics — 06: The influence of regional dose sensitivity on salivary loss and recovery in the parotid gland

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

Clark, H; BC Cancer Agency, Surrey, B.C.; BC Cancer Agency, Vancouver, B.C.

Purpose: The Quantitative Analyses of Normal Tissue Effects in the Clinic (QUANTEC 2010) survey of radiation dose-volume effects on salivary gland function has called for improved understanding of intragland dose sensitivity and the effectiveness of partial sparing in salivary glands. Regional dose susceptibility of sagittally- and coronally-sub-segmented parotid gland has been studied. Specifically, we examine whether individual consideration of sub-segments leads to improved prediction of xerostomia compared with whole parotid mean dose. Methods: Data from 102 patients treated for head-and-neck cancers at the BC Cancer Agency were used in this study. Whole mouth stimulated saliva was collected before (baseline), threemore » months, and one year after cessation of radiotherapy. Organ volumes were contoured using treatment planning CT images and sub-segmented into regional portions. Both non-parametric (local regression) and parametric (mean dose exponential fitting) methods were employed. A bootstrap technique was used for reliability estimation and cross-comparison. Results: Salivary loss is described well using non-parametric and mean dose models. Parametric fits suggest a significant distinction in dose response between medial-lateral and anterior-posterior aspects of the parotid (p<0.01). Least-squares and least-median squares estimates differ significantly (p<0.00001), indicating fits may be skewed by noise or outliers. Salivary recovery exhibits a weakly arched dose response: the highest recovery is seen at intermediate doses. Conclusions: Salivary function loss is strongly dose dependent. In contrast no useful dose dependence was observed for function recovery. Regional dose dependence was observed, but may have resulted from a bias in dose distributions.« less

Development and Validation of a Statistical Shape Modeling-Based Finite Element Model of the Cervical Spine Under Low-Level Multiple Direction Loading Conditions

PubMed Central

Bredbenner, Todd L.; Eliason, Travis D.; Francis, W. Loren; McFarland, John M.; Merkle, Andrew C.; Nicolella, Daniel P.

2014-01-01

Cervical spinal injuries are a significant concern in all trauma injuries. Recent military conflicts have demonstrated the substantial risk of spinal injury for the modern warfighter. Finite element models used to investigate injury mechanisms often fail to examine the effects of variation in geometry or material properties on mechanical behavior. The goals of this study were to model geometric variation for a set of cervical spines, to extend this model to a parametric finite element model, and, as a first step, to validate the parametric model against experimental data for low-loading conditions. Individual finite element models were created using cervical spine (C3–T1) computed tomography data for five male cadavers. Statistical shape modeling (SSM) was used to generate a parametric finite element model incorporating variability of spine geometry, and soft-tissue material property variation was also included. The probabilistic loading response of the parametric model was determined under flexion-extension, axial rotation, and lateral bending and validated by comparison to experimental data. Based on qualitative and quantitative comparison of the experimental loading response and model simulations, we suggest that the model performs adequately under relatively low-level loading conditions in multiple loading directions. In conclusion, SSM methods coupled with finite element analyses within a probabilistic framework, along with the ability to statistically validate the overall model performance, provide innovative and important steps toward describing the differences in vertebral morphology, spinal curvature, and variation in material properties. We suggest that these methods, with additional investigation and validation under injurious loading conditions, will lead to understanding and mitigating the risks of injury in the spine and other musculoskeletal structures. PMID:25506051

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

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.

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.

SU-G-JeP2-02: A Unifying Multi-Atlas Approach to Electron Density Mapping Using Multi-Parametric MRI for Radiation Treatment Planning

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

Ren, S; Tianjin University, Tianjin; Hara, W

Purpose: MRI has a number of advantages over CT as a primary modality for radiation treatment planning (RTP). However, one key bottleneck problem still remains, which is the lack of electron density information in MRI. In the work, a reliable method to map electron density is developed by leveraging the differential contrast of multi-parametric MRI. Methods: We propose a probabilistic Bayesian approach for electron density mapping based on T1 and T2-weighted MRI, using multiple patients as atlases. For each voxel, we compute two conditional probabilities: (1) electron density given its image intensity on T1 and T2-weighted MR images, and (2)more » electron density given its geometric location in a reference anatomy. The two sources of information (image intensity and spatial location) are combined into a unifying posterior probability density function using the Bayesian formalism. The mean value of the posterior probability density function provides the estimated electron density. Results: We evaluated the method on 10 head and neck patients and performed leave-one-out cross validation (9 patients as atlases and remaining 1 as test). The proposed method significantly reduced the errors in electron density estimation, with a mean absolute HU error of 138, compared with 193 for the T1-weighted intensity approach and 261 without density correction. For bone detection (HU>200), the proposed method had an accuracy of 84% and a sensitivity of 73% at specificity of 90% (AUC = 87%). In comparison, the AUC for bone detection is 73% and 50% using the intensity approach and without density correction, respectively. Conclusion: The proposed unifying method provides accurate electron density estimation and bone detection based on multi-parametric MRI of the head with highly heterogeneous anatomy. This could allow for accurate dose calculation and reference image generation for patient setup in MRI-based radiation treatment planning.« less

Dynamic whole body PET parametric imaging: II. Task-oriented statistical estimation

PubMed Central

Karakatsanis, Nicolas A.; Lodge, Martin A.; Zhou, Y.; Wahl, Richard L.; Rahmim, Arman

2013-01-01

In the context of oncology, dynamic PET imaging coupled with standard graphical linear analysis has been previously employed to enable quantitative estimation of tracer kinetic parameters of physiological interest at the voxel level, thus, enabling quantitative PET parametric imaging. However, dynamic PET acquisition protocols have been confined to the limited axial field-of-view (~15–20cm) of a single bed position and have not been translated to the whole-body clinical imaging domain. On the contrary, standardized uptake value (SUV) PET imaging, considered as the routine approach in clinical oncology, commonly involves multi-bed acquisitions, but is performed statically, thus not allowing for dynamic tracking of the tracer distribution. Here, we pursue a transition to dynamic whole body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. In a companion study, we presented a novel clinically feasible dynamic (4D) multi-bed PET acquisition protocol as well as the concept of whole body PET parametric imaging employing Patlak ordinary least squares (OLS) regression to estimate the quantitative parameters of tracer uptake rate Ki and total blood distribution volume V. In the present study, we propose an advanced hybrid linear regression framework, driven by Patlak kinetic voxel correlations, to achieve superior trade-off between contrast-to-noise ratio (CNR) and mean squared error (MSE) than provided by OLS for the final Ki parametric images, enabling task-based performance optimization. Overall, whether the observer's task is to detect a tumor or quantitatively assess treatment response, the proposed statistical estimation framework can be adapted to satisfy the specific task performance criteria, by adjusting the Patlak correlation-coefficient (WR) reference value. The multi-bed dynamic acquisition protocol, as optimized in the preceding companion study, was employed along with extensive Monte Carlo simulations and an initial clinical FDG patient dataset to validate and demonstrate the potential of the proposed statistical estimation methods. Both simulated and clinical results suggest that hybrid regression in the context of whole-body Patlak Ki imaging considerably reduces MSE without compromising high CNR. Alternatively, for a given CNR, hybrid regression enables larger reductions than OLS in the number of dynamic frames per bed, allowing for even shorter acquisitions of ~30min, thus further contributing to the clinical adoption of the proposed framework. Compared to the SUV approach, whole body parametric imaging can provide better tumor quantification, and can act as a complement to SUV, for the task of tumor detection. PMID:24080994

Dynamic whole-body PET parametric imaging: II. Task-oriented statistical estimation.

PubMed

Karakatsanis, Nicolas A; Lodge, Martin A; Zhou, Y; Wahl, Richard L; Rahmim, Arman

2013-10-21

In the context of oncology, dynamic PET imaging coupled with standard graphical linear analysis has been previously employed to enable quantitative estimation of tracer kinetic parameters of physiological interest at the voxel level, thus, enabling quantitative PET parametric imaging. However, dynamic PET acquisition protocols have been confined to the limited axial field-of-view (~15-20 cm) of a single-bed position and have not been translated to the whole-body clinical imaging domain. On the contrary, standardized uptake value (SUV) PET imaging, considered as the routine approach in clinical oncology, commonly involves multi-bed acquisitions, but is performed statically, thus not allowing for dynamic tracking of the tracer distribution. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. In a companion study, we presented a novel clinically feasible dynamic (4D) multi-bed PET acquisition protocol as well as the concept of whole-body PET parametric imaging employing Patlak ordinary least squares (OLS) regression to estimate the quantitative parameters of tracer uptake rate Ki and total blood distribution volume V. In the present study, we propose an advanced hybrid linear regression framework, driven by Patlak kinetic voxel correlations, to achieve superior trade-off between contrast-to-noise ratio (CNR) and mean squared error (MSE) than provided by OLS for the final Ki parametric images, enabling task-based performance optimization. Overall, whether the observer's task is to detect a tumor or quantitatively assess treatment response, the proposed statistical estimation framework can be adapted to satisfy the specific task performance criteria, by adjusting the Patlak correlation-coefficient (WR) reference value. The multi-bed dynamic acquisition protocol, as optimized in the preceding companion study, was employed along with extensive Monte Carlo simulations and an initial clinical (18)F-deoxyglucose patient dataset to validate and demonstrate the potential of the proposed statistical estimation methods. Both simulated and clinical results suggest that hybrid regression in the context of whole-body Patlak Ki imaging considerably reduces MSE without compromising high CNR. Alternatively, for a given CNR, hybrid regression enables larger reductions than OLS in the number of dynamic frames per bed, allowing for even shorter acquisitions of ~30 min, thus further contributing to the clinical adoption of the proposed framework. Compared to the SUV approach, whole-body parametric imaging can provide better tumor quantification, and can act as a complement to SUV, for the task of tumor detection.

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.

Automated processing for proton spectroscopic imaging using water reference deconvolution.

PubMed

Maudsley, A A; Wu, Z; Meyerhoff, D J; Weiner, M W

1994-06-01

Automated formation of MR spectroscopic images (MRSI) is necessary before routine application of these methods is possible for in vivo studies; however, this task is complicated by the presence of spatially dependent instrumental distortions and the complex nature of the MR spectrum. A data processing method is presented for completely automated formation of in vivo proton spectroscopic images, and applied for analysis of human brain metabolites. This procedure uses the water reference deconvolution method (G. A. Morris, J. Magn. Reson. 80, 547(1988)) to correct for line shape distortions caused by instrumental and sample characteristics, followed by parametric spectral analysis. Results for automated image formation were found to compare favorably with operator dependent spectral integration methods. While the water reference deconvolution processing was found to provide good correction of spatially dependent resonance frequency shifts, it was found to be susceptible to errors for correction of line shape distortions. These occur due to differences between the water reference and the metabolite distributions.

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

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.

Multiparametric, Longitudinal Optical Coherence Tomography Imaging Reveals Acute Injury and Chronic Recovery in Experimental Ischemic Stroke

PubMed Central

Srinivasan, Vivek J.; Mandeville, Emiri T.; Can, Anil; Blasi, Francesco; Climov, Mihail; Daneshmand, Ali; Lee, Jeong Hyun; Yu, Esther; Radhakrishnan, Harsha; Lo, Eng H.; Sakadžić, Sava; Eikermann-Haerter, Katharina; Ayata, Cenk

2013-01-01

Progress in experimental stroke and translational medicine could be accelerated by high-resolution in vivo imaging of disease progression in the mouse cortex. Here, we introduce optical microscopic methods that monitor brain injury progression using intrinsic optical scattering properties of cortical tissue. A multi-parametric Optical Coherence Tomography (OCT) platform for longitudinal imaging of ischemic stroke in mice, through thinned-skull, reinforced cranial window surgical preparations, is described. In the acute stages, the spatiotemporal interplay between hemodynamics and cell viability, a key determinant of pathogenesis, was imaged. In acute stroke, microscopic biomarkers for eventual infarction, including capillary non-perfusion, cerebral blood flow deficiency, altered cellular scattering, and impaired autoregulation of cerebral blood flow, were quantified and correlated with histology. Additionally, longitudinal microscopy revealed remodeling and flow recovery after one week of chronic stroke. Intrinsic scattering properties serve as reporters of acute cellular and vascular injury and recovery in experimental stroke. Multi-parametric OCT represents a robust in vivo imaging platform to comprehensively investigate these properties. PMID:23940761

Accuracy and the Effect of Possible Subject-Based Confounders of Magnitude-Based MRI for Estimating Hepatic Proton Density Fat Fraction in Adults, Using MR Spectroscopy as Reference

PubMed Central

Heba, Elhamy R.; Desai, Ajinkya; Zand, Kevin A.; Hamilton, Gavin; Wolfson, Tanya; Schlein, Alexandra N.; Gamst, Anthony; Loomba, Rohit; Sirlin, Claude B.; Middleton, Michael S.

2016-01-01

Purpose To determine the accuracy and the effect of possible subject-based confounders of magnitude-based magnetic resonance imaging (MRI) for estimating hepatic proton density fat fraction (PDFF) for different numbers of echoes in adults with known or suspected nonalcoholic fatty liver disease, using MR spectroscopy (MRS) as a reference. Materials and Methods In this retrospective analysis of 506 adults, hepatic PDFF was estimated by unenhanced 3.0T MRI, using right-lobe MRS as reference. Regions of interest placed on source images and on six-echo parametric PDFF maps were colocalized to MRS voxel location. Accuracy using different numbers of echoes was assessed by regression and Bland–Altman analysis; slope, intercept, average bias, and R2 were calculated. The effect of age, sex, and body mass index (BMI) on hepatic PDFF accuracy was investigated using multivariate linear regression analyses. Results MRI closely agreed with MRS for all tested methods. For three- to six-echo methods, slope, regression intercept, average bias, and R2 were 1.01–0.99, 0.11–0.62%, 0.24–0.56%, and 0.981–0.982, respectively. Slope was closest to unity for the five-echo method. The two-echo method was least accurate, underestimating PDFF by an average of 2.93%, compared to an average of 0.23–0.69% for the other methods. Statistically significant but clinically nonmeaningful effects on PDFF error were found for subject BMI (P range: 0.0016 to 0.0783), male sex (P range: 0.015 to 0.037), and no statistically significant effect was found for subject age (P range: 0.18–0.24). Conclusion Hepatic magnitude-based MRI PDFF estimates using three, four, five, and six echoes, and six-echo parametric maps are accurate compared to reference MRS values, and that accuracy is not meaningfully confounded by age, sex, or BMI. PMID:26201284

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.

The influence of intraocular pressure and air jet pressure on corneal contactless tonometry tests.

PubMed

Simonini, Irene; Pandolfi, Anna

2016-05-01

The air puff is a dynamic contactless tonometer test used in ophthalmology clinical practice to assess the biomechanical properties of the human cornea and the intraocular pressure due to the filling fluids of the eye. The test is controversial, since the dynamic response of the cornea is governed by the interaction of several factors which cannot be discerned within a single measurement. In this study we describe a numerical model of the air puff tests, and perform a parametric analysis on the major action parameters (jet pressure and intraocular pressure) to assess their relevance on the mechanical response of a patient-specific cornea. The particular cornea considered here has been treated with laser reprofiling to correct myopia, and the parametric study has been conducted on both the preoperative and postoperative geometries. The material properties of the cornea have been obtained by means of an identification procedure that compares the static biomechanical response of preoperative and postoperative corneas under the physiological IOP. The parametric study on the intraocular pressure suggests that the displacement of the cornea׳s apex can be a reliable indicator for tonometry, and the one on the air jet pressure predicts the outcomes of two or more distinct measurements on the same cornea, which can be used in inverse procedures to estimate the material properties of the tissue. Copyright © 2015 Elsevier Ltd. All rights reserved.

USSR and Eastern Europe Scientific Abstracts, Engineering and Equipment, Number 31

DTIC Science & Technology

1977-04-18

average coefficient of air absorption is computed by the method of approximate replacement of the real spectrum by the graduated one. The entire range...end of transition area with an accuracy of 15%. Figures 5; References 7. USSR UDC 541.24:532.5 PARAMETRIC METHOD OF CALCULATION OF THERMODYNAMIC...12, 1976 Abstract No 12B723 by V. A. Polyanskiy] GLEBOV, G. A., and KOSHKIN, V. K. [Text] A method is presented for calculation of thermodynamic

Nonlinear Scaling Laws for Parametric Receiving Arrays. Part II. Numerical Analysis

DTIC Science & Technology

1976-06-30

SECTION 3U SUBROUTINE WRITE -UP» JPL» MAY 1969. 2, F. T, KROGH» »ON TESTING A SUBROUTINE FOR THE NUMERICAL INTEGRATION OF ORDINARY DIFFERENTIAL...WHICH IS ENTIRELY DOUBLE PRECISION. SEE THEIR WRITE -UPS FOR MINOR DIFFERENCES IN USAGE. 12.1.1.5. REMARKS THE ORDINARY DIFFERENTIAL EQUATIONS MAY BE...OF THE DEPENDENT VARIABLES» OR VALUES OF AUXILIARY FUNCTIONS. ONLY THE FIRST TWO OF THESE FEATURES ARE DESCRIBED IN THIS WRITE -UP. SEE REFERENCE 1

Power System Overview for the Small RPS Centaur Flyby and the Mars Polar Hard Lander NASA COMPASS Studies

NASA Technical Reports Server (NTRS)

Cataldo, Robert L.

2014-01-01

The NASA Glenn Research Center (GRC) Radioisotope Power System Program Office (RPSPO) sponsored two studies lead by their mission analysis team. The studies were performed by NASA GRCs Collaborative Modeling for Parametric Assessment of Space Systems (COMPASS) team. Typically a complete toplevel design reference mission (DRM) is performed assessing conceptual spacecraft design, launch mass, trajectory, science strategy and sub-system design such as, power, propulsion, structure and thermal.

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.

On the sensitivity of teleseismic full-waveform inversion to earth parametrization, initial model and acquisition design

NASA Astrophysics Data System (ADS)

Beller, S.; Monteiller, V.; Combe, L.; Operto, S.; Nolet, G.

2018-02-01

Full-waveform inversion (FWI) is not yet a mature imaging technology for lithospheric imaging from teleseismic data. Therefore, its promise and pitfalls need to be assessed more accurately according to the specifications of teleseismic experiments. Three important issues are related to (1) the choice of the lithospheric parametrization for optimization and visualization, (2) the initial model and (3) the acquisition design, in particular in terms of receiver spread and sampling. These three issues are investigated with a realistic synthetic example inspired by the CIFALPS experiment in the Western Alps. Isotropic elastic FWI is implemented with an adjoint-state formalism and aims to update three parameter classes by minimization of a classical least-squares difference-based misfit function. Three different subsurface parametrizations, combining density (ρ) with P and S wave speeds (Vp and Vs) , P and S impedances (Ip and Is), or elastic moduli (λ and μ) are first discussed based on their radiation patterns before their assessment by FWI. We conclude that the (ρ, λ, μ) parametrization provides the FWI models that best correlate with the true ones after recombining a posteriori the (ρ, λ, μ) optimization parameters into Ip and Is. Owing to the low frequency content of teleseismic data, 1-D reference global models as PREM provide sufficiently accurate initial models for FWI after smoothing that is necessary to remove the imprint of the layering. Two kinds of station deployments are assessed: coarse areal geometry versus dense linear one. We unambiguously conclude that a coarse areal geometry should be favoured as it dramatically increases the penetration in depth of the imaging as well as the horizontal resolution. This results because the areal geometry significantly increases local wavenumber coverage, through a broader sampling of the scattering and dip angles, compared to a linear deployment.

Development of a new mini-invasive tumour hyperthermia probe using high-temperature water vapour.

PubMed

Yu, Tian-Hua; Zhou, Yi-Xin; Liu, Jing

2004-01-01

A new mini-invasive hyperthermia probe using high-temperature water vapour for deep regional tumour treatment was developed in this paper. The vacuum insulation mechanism was incorporated into the probe to avoid heating damage to the normal tissues around the edge of the insertion path. To better understand the heat transfer behaviour in living tissues due to operation of the probe, theoretical models based on the Pennes' equation were established and two closed form analytical solutions under constant flux or temperature heating at the tip of probe were obtained. Parametric studies were performed to investigate the influence of various parameters on the temperature response of tissues heated by the probe. Further, several simulating experiments on the actual heating performance of the probe fabricated in this paper were conducted on the in vitro biological materials (fresh pork) and phantom gel. It was demonstrated that the probe can cause a high enough temperature over the treatment area to thermally destroy the tumour tissue in due time, while the temperature over the surrounding healthy tissues can be kept below a safe threshold value. This mini-invasive heating probe may have significant applications in future clinical tumour hyperthermia.

Subcutaneous Connective Tissue Reaction to a New Nano Zinc-Oxide Eugenol Sealer in Rat Model

PubMed Central

Omidi, Salma; Javidi, Maryam; Zarei, Mina; Mushakhian, Siavash; Jafarian, Amirhossein

2017-01-01

Introduction: The aim of this animal study was to evaluate the histological response of the new nano zinc-oxide eugenol (NZOE) sealer in comparison with Pulp Canal Sealer (ZOE based) and AH-26 (epoxy resin sealer). Methods and Materials: A total of 27 Wistar rats were used. Four polyethylene tubes were implanted in the back of each rat (three tubes containing the test materials and an empty tube as a control). Then, 9 animals were sacrificed at each interval of 15, 30 and 60 days, and the implants were removed with the surrounding tissues.Samples were evaluated for the presence of inflammatory cell (mononuclear cell), vascular changes, fibrous tissue formation and present of giant cell. Comparisons between groups and time-periods were performed using the Kruskal-Wallis and Mann-Whitney U non-parametric tests. The level of significance was set at 0.05. Results: No significant difference was observed in tissue reactions and biocompatibility pattern of three sealers during 3 experimental periods (P<0.05). In all groups the tissue behavior showed tendency to decrease the irritation effect over time. Conclusion: The new nano zinc-oxide eugenol sealer has histocompatibility properties comparable to conventional commercial sealers. PMID:28179927

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.

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.

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks.

PubMed

Jambusaria, Ankit; Klomp, Jeff; Hong, Zhigang; Rafii, Shahin; Dai, Yang; Malik, Asrar B; Rehman, Jalees

2018-06-07

The heterogeneity of cells across tissue types represents a major challenge for studying biological mechanisms as well as for therapeutic targeting of distinct tissues. Computational prediction of tissue-specific gene regulatory networks may provide important insights into the mechanisms underlying the cellular heterogeneity of cells in distinct organs and tissues. Using three pathway analysis techniques, gene set enrichment analysis (GSEA), parametric analysis of gene set enrichment (PGSEA), alongside our novel model (HeteroPath), which assesses heterogeneously upregulated and downregulated genes within the context of pathways, we generated distinct tissue-specific gene regulatory networks. We analyzed gene expression data derived from freshly isolated heart, brain, and lung endothelial cells and populations of neurons in the hippocampus, cingulate cortex, and amygdala. In both datasets, we found that HeteroPath segregated the distinct cellular populations by identifying regulatory pathways that were not identified by GSEA or PGSEA. Using simulated datasets, HeteroPath demonstrated robustness that was comparable to what was seen using existing gene set enrichment methods. Furthermore, we generated tissue-specific gene regulatory networks involved in vascular heterogeneity and neuronal heterogeneity by performing motif enrichment of the heterogeneous genes identified by HeteroPath and linking the enriched motifs to regulatory transcription factors in the ENCODE database. HeteroPath assesses contextual bidirectional gene expression within pathways and thus allows for transcriptomic assessment of cellular heterogeneity. Unraveling tissue-specific heterogeneity of gene expression can lead to a better understanding of the molecular underpinnings of tissue-specific phenotypes.

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.

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

PubMed

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

2018-05-10

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

Noninvasive Quantitative Imaging of Collagen Microstructure in Three-Dimensional Hydrogels Using High-Frequency Ultrasound

PubMed Central

Mercado, Karla P.; Helguera, María; Hocking, Denise C.

2015-01-01

Collagen I is widely used as a natural component of biomaterials for both tissue engineering and regenerative medicine applications. The physical and biological properties of fibrillar collagens are strongly tied to variations in collagen fiber microstructure. The goal of this study was to develop the use of high-frequency quantitative ultrasound to assess collagen microstructure within three-dimensional (3D) hydrogels noninvasively and nondestructively. The integrated backscatter coefficient (IBC) was employed as a quantitative ultrasound parameter to detect, image, and quantify spatial variations in collagen fiber density and diameter. Collagen fiber microstructure was varied by fabricating hydrogels with different collagen concentrations or polymerization temperatures. IBC values were computed from measurements of the backscattered radio-frequency ultrasound signals collected using a single-element transducer (38-MHz center frequency, 13–47 MHz bandwidth). The IBC increased linearly with increasing collagen concentration and decreasing polymerization temperature. Parametric 3D images of the IBC were generated to visualize and quantify regional variations in collagen microstructure throughout the volume of hydrogels fabricated in standard tissue culture plates. IBC parametric images of corresponding cell-embedded collagen gels showed cell accumulation within regions having elevated collagen IBC values. The capability of this ultrasound technique to noninvasively detect and quantify spatial differences in collagen microstructure offers a valuable tool to monitor the structural properties of collagen scaffolds during fabrication, to detect functional differences in collagen microstructure, and to guide fundamental research on the interactions of cells and collagen matrices. PMID:25517512

Noninvasive Quantitative Imaging of Collagen Microstructure in Three-Dimensional Hydrogels Using High-Frequency Ultrasound.

PubMed

Mercado, Karla P; Helguera, María; Hocking, Denise C; Dalecki, Diane

2015-07-01

Collagen I is widely used as a natural component of biomaterials for both tissue engineering and regenerative medicine applications. The physical and biological properties of fibrillar collagens are strongly tied to variations in collagen fiber microstructure. The goal of this study was to develop the use of high-frequency quantitative ultrasound to assess collagen microstructure within three-dimensional (3D) hydrogels noninvasively and nondestructively. The integrated backscatter coefficient (IBC) was employed as a quantitative ultrasound parameter to detect, image, and quantify spatial variations in collagen fiber density and diameter. Collagen fiber microstructure was varied by fabricating hydrogels with different collagen concentrations or polymerization temperatures. IBC values were computed from measurements of the backscattered radio-frequency ultrasound signals collected using a single-element transducer (38-MHz center frequency, 13-47 MHz bandwidth). The IBC increased linearly with increasing collagen concentration and decreasing polymerization temperature. Parametric 3D images of the IBC were generated to visualize and quantify regional variations in collagen microstructure throughout the volume of hydrogels fabricated in standard tissue culture plates. IBC parametric images of corresponding cell-embedded collagen gels showed cell accumulation within regions having elevated collagen IBC values. The capability of this ultrasound technique to noninvasively detect and quantify spatial differences in collagen microstructure offers a valuable tool to monitor the structural properties of collagen scaffolds during fabrication, to detect functional differences in collagen microstructure, and to guide fundamental research on the interactions of cells and collagen matrices.

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

Method of development of the program of forming of parametrical drawings of details in the AutoCAD software product

NASA Astrophysics Data System (ADS)

Alshakova, E. L.

2017-01-01

The program in the AutoLISP language allows automatically to form parametrical drawings during the work in the AutoCAD software product. Students study development of programs on AutoLISP language with the use of the methodical complex containing methodical instructions in which real examples of creation of images and drawings are realized. Methodical instructions contain reference information necessary for the performance of the offered tasks. The method of step-by-step development of the program is the basis for training in programming on AutoLISP language: the program draws elements of the drawing of a detail by means of definitely created function which values of arguments register in that sequence in which AutoCAD gives out inquiries when performing the corresponding command in the editor. The process of the program design is reduced to the process of step-by-step formation of functions and sequence of their calls. The author considers the development of the AutoLISP program for the creation of parametrical drawings of details, the defined design, the user enters the dimensions of elements of details. These programs generate variants of tasks of the graphic works performed in educational process of "Engineering graphics", "Engineering and computer graphics" disciplines. Individual tasks allow to develop at students skills of independent work in reading and creation of drawings, as well as 3D modeling.

Signature of charge migration in modulations of double ionization

NASA Astrophysics Data System (ADS)

Mauger, François; Abanador, Paul M.; Bruner, Adam; Sissay, Adonay; Gaarde, Mette B.; Lopata, Kenneth; Schafer, Kenneth J.

2018-04-01

We present a theoretical investigation of charge migration following strong-field ionization in a multielectron system. We study a model homonuclear molecule with two electrons, each restricted to one dimension (1 +1 D ), interacting with a strong, static electric field. We show that in this system charge migration results from the interplay between multiple ionization channels that overlap in space, creating a coherent electron-hole wave packet in the cation. We also find that, in our case, charge migration following the first ionization manifests as a modulation of the subsequent double-ionization signal. We derive a parametrized semiclassical model from the full multielectron system and we discuss the importance of the choice of cation electronic-structure basis for the efficacy of the semiclassical representation. We use the ab initio solution of the full 1 +1 D system as a reference for the qualitative and quantitative results of the parametrized semiclassical model. We discuss the extension of our model to long-wavelength time-dependent fields with full-dimension, many-electron targets.

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.

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.

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

PubMed

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

2016-01-01

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

Dynamical prediction of flu seasonality driven by ambient temperature: influenza vs. common cold

NASA Astrophysics Data System (ADS)

Postnikov, Eugene B.

2016-01-01

This work presents a comparative analysis of Influenzanet data for influenza itself and common cold in the Netherlands during the last 5 years, from the point of view of modelling by linearised SIRS equations parametrically driven by the ambient temperature. It is argued that this approach allows for the forecast of common cold, but not of influenza in a strict sense. The difference in their kinetic models is discussed with reference to the clinical background.

Widely-Tunable Parametric Short-Wave Infrared Transmitter for CO2 Trace Detection (POSTPRINT)

DTIC Science & Technology

2013-01-01

F. Amzajerdian, J. Yu, R. E. Davis, S. Ismail, S. Vay, M. J. Kavaya, and U. N. Singh, “ Coherent differential absorption lidar measurements of CO2... Doppler lidar system for wind sensing,” Appl. Opt. 46(11), 1953–1962 (2007). 1. Introduction Over the short-wave infrared (SWIR) spectrum, which is...fiber. References and links 1. M. Ebrahim-Zadeh, and I. T. Sorokina, eds., Mid-Infrared Coherent Sources and Applications (Springer, 2007). 2. C

Next Generation Data Collection System for Mobile Detection and Discrimination of Unexploded Ordnance

DTIC Science & Technology

2008-09-10

parametric form in which the i−th principal polarization is given by Li(t) = kit −βie− t γi ( Pasion and Oldenburg, 2001). The model parameters m contain the lo...66 September 2008 6 REFERENCES Billings, S. D., Pasion , L. R., Beran, L., Oldenburg, D., Sinex, D., Song, L., Lhomme, N., 2007, ESTCP MM-0504...Office. Billings, S. D., Pasion , L. R., Beran, L., Oldenburg, D., Sinex, D., Song, L., Lhomme, N., 2008, ESTCP MM-0504, Practical Discrimination

Urban Modelling with Typological Approach. Case Study: Merida, Yucatan, Mexico

NASA Astrophysics Data System (ADS)

Rodriguez, A.

2017-08-01

In three-dimensional models of urban historical reconstruction, missed contextual architecture faces difficulties because it does not have much written references in contrast to the most important monuments. This is the case of Merida, Yucatan, Mexico during the Colonial Era (1542-1810), which has lost much of its heritage. An alternative to offer a hypothetical view of these elements is a typological - parametric definition that allows a 3D modeling approach to the most common features of this heritage evidence.

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.

Optimal temperature control of tissue embedded with gold nanoparticles for enhanced thermal therapy based on two-energy equation model.

PubMed

Wang, Shen-Ling; Qi, Hong; Ren, Ya-Tao; Chen, Qin; Ruan, Li-Ming

2018-05-01

Thermal therapy is a very promising method for cancer treatment, which can be combined with chemotherapy, radiotherapy and other programs for enhanced cancer treatment. In order to get a better effect of thermal therapy in clinical applications, optimal internal temperature distribution of the tissue embedded with gold nanoparticles (GNPs) for enhanced thermal therapy was investigated in present research. The Monte Carlo method was applied to calculate the heat generation of the tissue embedded with GNPs irradiated by continuous laser. To have a better insight into the physical problem of heat transfer in tissues, the two-energy equation was employed to calculate the temperature distribution of the tissue in the process of GNPs enhanced therapy. The Arrhenius equation was applied to evaluate the degree of permanent thermal damage. A parametric study was performed to investigate the influence factors on the tissue internal temperature distribution, such as incident light intensity, the GNPs volume fraction, the periodic heating and cooling time, and the incident light position. It was found that period heating and cooling strategy can effectively avoid overheating of skin surface and heat damage of healthy tissue. Lower GNPs volume fraction will be better for the heat source distribution. Furthermore, the ring heating strategy is superior to the central heating strategy in the treatment effect. All the analysis provides theoretical guidance for optimal temperature control of tissue embedded with GNP for enhanced thermal therapy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Parametric study of irreversible electroporation with different needle electrodes: electrical and thermal analysis.

PubMed

Nickfarjam, Abolfazl; Firoozabadi, S Mohammad P

2014-08-01

Irreversible electroporation (IRE) is a new tumour ablation method used in cancer treatment procedures. In a successful IRE treatment it is crucial to impose minimum thermal damage to the tumour and its surrounding healthy tissue, while subjecting the entire tumour to a strong electric field. Here we present a 3D model of a subcutaneous tumour in a four-layer skin using a geometry-based finite element approach. Four common needle electrode configurations were studied in this paper. The study evaluated six essential factors which are important in the electrical and thermal distributions in tumour and normal tissue. The results revealed that a hexagonal 3 × 3 geometry provides the maximum electrical coverage of the tumour, compared to other electrode configurations. However, in some cases the hexagonal 2 × 2 geometry can ablate the entire tumour with less damage to normal tissue. We found that the deeper insertion of 2- and 4-electrode geometries can lead to more damage to healthy tissue. The results also indicate that the insertion of the electrodes into tumour tissue can increase thermal damage dramatically due to existing large electrical conductivity. These findings suggest that needle electrodes should not be placed within the tumour tissue if the goal is to prevent thermal damage. This method can be used as a trade-off between electric field coverage in tumour tissue and thermal damage to both tumour and normal tissue.

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.

Dynamic contrast-enhanced CT of head and neck tumors: perfusion measurements using a distributed-parameter tracer kinetic model. Initial results and comparison with deconvolution-based analysis

NASA Astrophysics Data System (ADS)

Bisdas, Sotirios; Konstantinou, George N.; Sherng Lee, Puor; Thng, Choon Hua; Wagenblast, Jens; Baghi, Mehran; San Koh, Tong

2007-10-01

The objective of this work was to evaluate the feasibility of a two-compartment distributed-parameter (DP) tracer kinetic model to generate functional images of several physiologic parameters from dynamic contrast-enhanced CT data obtained of patients with extracranial head and neck tumors and to compare the DP functional images to those obtained by deconvolution-based DCE-CT data analysis. We performed post-processing of DCE-CT studies, obtained from 15 patients with benign and malignant head and neck cancer. We introduced a DP model of the impulse residue function for a capillary-tissue exchange unit, which accounts for the processes of convective transport and capillary-tissue exchange. The calculated parametric maps represented blood flow (F), intravascular blood volume (v1), extravascular extracellular blood volume (v2), vascular transit time (t1), permeability-surface area product (PS), transfer ratios k12 and k21, and the fraction of extracted tracer (E). Based on the same regions of interest (ROI) analysis, we calculated the tumor blood flow (BF), blood volume (BV) and mean transit time (MTT) by using a modified deconvolution-based analysis taking into account the extravasation of the contrast agent for PS imaging. We compared the corresponding values by using Bland-Altman plot analysis. We outlined 73 ROIs including tumor sites, lymph nodes and normal tissue. The Bland-Altman plot analysis revealed that the two methods showed an accepted degree of agreement for blood flow, and, thus, can be used interchangeably for measuring this parameter. Slightly worse agreement was observed between v1 in the DP model and BV but even here the two tracer kinetic analyses can be used interchangeably. Under consideration of whether both techniques may be used interchangeably was the case of t1 and MTT, as well as for measurements of the PS values. The application of the proposed DP model is feasible in the clinical routine and it can be used interchangeably for measuring blood flow and vascular volume with the commercially available reference standard of the deconvolution-based approach. The lack of substantial agreement between the measurements of vascular transit time and permeability-surface area product may be attributed to the different tracer kinetic principles employed by both models and the detailed capillary tissue exchange physiological modeling of the DP technique.

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.

[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.

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.

High-power picosecond fiber source for coherent Raman microscopy

PubMed Central

Kieu, Khanh; Saar, Brian G.; Holtom, Gary R.; Xie, X. Sunney; Wise, Frank W.

2011-01-01

We report a high-power picosecond fiber pump laser system for coherent Raman microscopy (CRM). The fiber laser system generates 3.5 ps pulses with 6 W average power at 1030 nm. Frequency doubling yields more than 2 W of green light, which can be used to pump an optical parametric oscillator to produce the pump and the Stokes beams for CRM. Detailed performance data on the laser and the various wavelength conversion steps are discussed, together with representative CRM images of fresh animal tissue obtained with the new source. PMID:19571996

Track structure model for damage to mammalian cell cultures during solar proton events

NASA Technical Reports Server (NTRS)

Cucinotta, F. A.; Wilson, J. W.; Townsend, L. W.; Shinn, J. L.; Katz, R.

1992-01-01

Solar proton events (SPEs) occur infrequently and unpredictably, thus representing a potential hazard to interplanetary space missions. Biological damage from SPEs will be produced principally through secondary electron production in tissue, including important contributions due to delta rays from nuclear reaction products. We review methods for estimating the biological effectiveness of SPEs using a high energy proton model and the parametric cellular track model. Results of the model are presented for several of the historically largest flares using typical levels and body shielding.

Assessment of three different software systems in the evaluation of dynamic MRI of the breast.

PubMed

Kurz, K D; Steinhaus, D; Klar, V; Cohnen, M; Wittsack, H J; Saleh, A; Mödder, U; Blondin, D

2009-02-01

The aim was to compare the diagnostic performance and handling of dynamic contrast-enhanced MRI of the breast with two commercial software solutions ("CADstream" and "3TP") and one self-developed software system ("Mammatool"). Identical data sets of dynamic breast MRI from 21 patients were evaluated retrospectively with all three software systems. The exams were classified according to the BI-RADS classification. The number of lesions in the parametric mapping was compared to histology or follow-up of more than 2 years. In addition, 25 quality criteria were judged by 3 independent investigators with a score from 0 to 5. Statistical analysis was performed to document the quality ranking of the different software systems. There were 9 invasive carcinomas, one pure DCIS, one papilloma, one radial scar, three histologically proven changes due to mastopathy, one adenosis and two fibroadenomas. Additionally two patients with enhancing parenchyma followed with MRI for more than 3 years and one scar after breast conserving therapy were included. All malignant lesions were classified as BI-RADS 4 or 5 using all software systems and showed significant enhancement in the parametric mapping. "CADstream" showed the best score on subjective quality criteria. "3TP" showed the lowest number of false-positive results. "Mammatool" produced the lowest number of benign tissues indicated with parametric overlay. All three software programs tested were adequate for sensitive and efficient assessment of dynamic MRI of the breast. Improvements in specificity may be achievable.

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 ...

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

Model of dissolution in the framework of tissue engineering and drug delivery.

PubMed

Sanz-Herrera, J A; Soria, L; Reina-Romo, E; Torres, Y; Boccaccini, A R

2018-05-22

Dissolution phenomena are ubiquitously present in biomaterials in many different fields. Despite the advantages of simulation-based design of biomaterials in medical applications, additional efforts are needed to derive reliable models which describe the process of dissolution. A phenomenologically based model, available for simulation of dissolution in biomaterials, is introduced in this paper. The model turns into a set of reaction-diffusion equations implemented in a finite element numerical framework. First, a parametric analysis is conducted in order to explore the role of model parameters on the overall dissolution process. Then, the model is calibrated and validated versus a straightforward but rigorous experimental setup. Results show that the mathematical model macroscopically reproduces the main physicochemical phenomena that take place in the tests, corroborating its usefulness for design of biomaterials in the tissue engineering and drug delivery research areas.

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

PubMed

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

2009-05-01

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

Design and Parametric Sizing of Deep Space Habitats Supporting NASA'S Human Space Flight Architecture Team

NASA Technical Reports Server (NTRS)

Toups, Larry; Simon, Matthew; Smitherman, David; Spexarth, Gary

2012-01-01

NASA's Human Space Flight Architecture Team (HAT) is a multi-disciplinary, cross-agency study team that conducts strategic analysis of integrated development approaches for human and robotic space exploration architectures. During each analysis cycle, HAT iterates and refines the definition of design reference missions (DRMs), which inform the definition of a set of integrated capabilities required to explore multiple destinations. An important capability identified in this capability-driven approach is habitation, which is necessary for crewmembers to live and work effectively during long duration transits to and operations at exploration destinations beyond Low Earth Orbit (LEO). This capability is captured by an element referred to as the Deep Space Habitat (DSH), which provides all equipment and resources for the functions required to support crew safety, health, and work including: life support, food preparation, waste management, sleep quarters, and housekeeping.The purpose of this paper is to describe the design of the DSH capable of supporting crew during exploration missions. First, the paper describes the functionality required in a DSH to support the HAT defined exploration missions, the parameters affecting its design, and the assumptions used in the sizing of the habitat. Then, the process used for arriving at parametric sizing estimates to support additional HAT analyses is detailed. Finally, results from the HAT Cycle C DSH sizing are presented followed by a brief description of the remaining design trades and technological advancements necessary to enable the exploration habitation capability.

Nonparametric Analyses of Log-Periodic Precursors to Financial Crashes

NASA Astrophysics Data System (ADS)

Zhou, Wei-Xing; Sornette, Didier

We apply two nonparametric methods to further test the hypothesis that log-periodicity characterizes the detrended price trajectory of large financial indices prior to financial crashes or strong corrections. The term "parametric" refers here to the use of the log-periodic power law formula to fit the data; in contrast, "nonparametric" refers to the use of general tools such as Fourier transform, and in the present case the Hilbert transform and the so-called (H, q)-analysis. The analysis using the (H, q)-derivative is applied to seven time series ending with the October 1987 crash, the October 1997 correction and the April 2000 crash of the Dow Jones Industrial Average (DJIA), the Standard & Poor 500 and Nasdaq indices. The Hilbert transform is applied to two detrended price time series in terms of the ln(tc-t) variable, where tc is the time of the crash. Taking all results together, we find strong evidence for a universal fundamental log-frequency f=1.02±0.05 corresponding to the scaling ratio λ=2.67±0.12. These values are in very good agreement with those obtained in earlier works with different parametric techniques. This note is extracted from a long unpublished report with 58 figures available at , which extensively describes the evidence we have accumulated on these seven time series, in particular by presenting all relevant details so that the reader can judge for himself or herself the validity and robustness of the results.

Optical-thermal light-tissue interactions during photoacoustic imaging

NASA Astrophysics Data System (ADS)

Gould, Taylor; Wang, Quanzeng; Pfefer, T. Joshua

2014-03-01

Photoacoustic imaging (PAI) has grown rapidly as a biomedical imaging technique in recent years, with key applications in cancer diagnosis and oximetry. In spite of these advances, the literature provides little insight into thermal tissue interactions involved in PAI. To elucidate these basic phenomena, we have developed, validated, and implemented a three-dimensional numerical model of tissue photothermal (PT) response to repetitive laser pulses. The model calculates energy deposition, fluence distributions, transient temperature and damage profiles in breast tissue with blood vessels and generalized perfusion. A parametric evaluation of these outputs vs. vessel diameter and depth, optical beam diameter, wavelength, and irradiance, was performed. For a constant radiant exposure level, increasing beam diameter led to a significant increase in subsurface heat generation rate. Increasing vessel diameter resulted in two competing effects - reduced mean energy deposition in the vessel due to light attenuation and greater thermal superpositioning due to reduced thermal relaxation. Maximum temperatures occurred either at the surface or in subsurface regions of the dermis, depending on vessel geometry and position. Results are discussed in terms of established exposure limits and levels used in prior studies. While additional experimental and numerical study is needed, numerical modeling represents a powerful tool for elucidating the effect of PA imaging devices on biological tissue.

[Expression and clinical significance of 5hmC in bladder urothelial carcinoma].

PubMed

Li, Jie; Xu, Yuqiao; Zhang, Zhiwen; Zhang, Ming; Zhang, Zhekai; Zhang, Feng; Li, Qing

2016-02-01

To investigate the expression of 5-hydroxymethylcytosine (5hmC) in bladder urothelial carcinoma (UC) and its clinical significance. The expression of 5hmC in 21 cases of UC tissues and pericarcinous urinary tract epithelium was detected by immunohistochemical staining. Then the expression of 5hmC in the surgical resection of UC tissues in 92 cases was also surveyed. Non parametric U Mann-Whitney test was used to analyze the correlation between 5hmC expression and clinical data. Single factor survival analysis was performed by Kaplan-Meier test. The expression of 5hmC in normal urinary tract epithelium and UC tissues was significantly different, but there was no significant difference in the expression of 5hmC between low and high grades of UC tissues as well as between different TNM grades. Kaplan-Meier single factor survival analysis showed that there was no significant correlation between the 5hmC expression level and the survival rate or the recurrence-free survival of UC patients. The expression level of 5hmC in UC tissues is significantly lower than that in pericarcinous urinary tract epithelium. There is no correlation between the 5hmC expression and the progression, prognosis and recurrence of UC.

Numerical investigation of oxygen transport by hemoglobin-based carriers through microvessels.

PubMed

Hyakutake, Toru; Kishimoto, Takumi

2017-12-01

The small size of hemoglobin-based oxygen carriers (HBOCs) may expand the realm of new treatment possibilities for various circulatory diseases. The parametric evaluation of HBOC performance for oxygen transport within tissue is essential for effectively characterizing its performance for each circulatory disease assessed. Thus, the overarching objective of this present study was to numerically investigate the reaction-diffusion phenomenon of oxygenated HBOCs and oxygen on tissues through microvessels. We considered dissociation rate coefficients, oxygen affinity, and diffusion coefficients due to Brownian motion as the biophysical parameters for estimating HBOC performance for oxygen transport. A two-dimensional computational domain, including vessel and tissue regions, was, therefore, accordingly assumed. It was observed that HBOC flows in a microvessel with a diameter of 25 μm and a length of 1 mm, and that the dissociated oxygen diffuses to the tissue region. The results indicated that oxyhemoglobin saturation and partial oxygen tension in a downstream region changed according to each biophysical parameter of HBOC. Moreover, the change in oxygen consumption rate in the tissue region had considerable influence on the oxyhemoglobin saturation level within the vessel. Comparison between simulation results and existing in vitro experimental data of actual HBOCs and RBC showed qualitatively good agreement. These results provide important information for the effective design of robust HBOCs in future.

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

PubMed

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

2009-06-01

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

Infrared laser damage thresholds in corneal tissue phantoms using femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Boretsky, Adam R.; Clary, Joseph E.; Noojin, Gary D.; Rockwell, Benjamin A.

2018-02-01

Ultrafast lasers have become a fixture in many biomedical, industrial, telecommunications, and defense applications in recent years. These sources are capable of generating extremely high peak power that can cause laser-induced tissue breakdown through the formation of a plasma upon exposure. Despite the increasing prevalence of such lasers, current safety standards (ANSI Z136.1-2014) do not include maximum permissible exposure (MPE) values for the cornea with pulse durations less than one nanosecond. This study was designed to measure damage thresholds in corneal tissue phantoms in the near-infrared and mid-infrared to identify the wavelength dependence of laser damage thresholds from 1200-2500 nm. A high-energy regenerative amplifier and optical parametric amplifier outputting 100 femtosecond pulses with pulse energies up to 2 mJ were used to perform exposures and determine damage thresholds in transparent collagen gel tissue phantoms. Three-dimensional imaging, primarily optical coherence tomography, was used to evaluate tissue phantoms following exposure to determine ablation characteristics at the surface and within the bulk material. The determination of laser damage thresholds in the near-IR and mid-IR for ultrafast lasers will help to guide safety standards and establish the appropriate MPE levels for exposure sensitive ocular tissue such as the cornea. These data will help promote the safe use of ultrafast lasers for a wide range of applications.

Nationwide Multicenter Reference Interval Study for 28 Common Biochemical Analytes in China.

PubMed

Xia, Liangyu; Chen, Ming; Liu, Min; Tao, Zhihua; Li, Shijun; Wang, Liang; Cheng, Xinqi; Qin, Xuzhen; Han, Jianhua; Li, Pengchang; Hou, Li'an; Yu, Songlin; Ichihara, Kiyoshi; Qiu, Ling

2016-03-01

A nationwide multicenter study was conducted in the China to explore sources of variation of reference values and establish reference intervals for 28 common biochemical analytes, as a part of the International Federation of Clinical Chemistry and Laboratory Medicine, Committee on Reference Intervals and Decision Limits (IFCC/C-RIDL) global study on reference values. A total of 3148 apparently healthy volunteers were recruited in 6 cities covering a wide area in China. Blood samples were tested in 2 central laboratories using Beckman Coulter AU5800 chemistry analyzers. Certified reference materials and value-assigned serum panel were used for standardization of test results. Multiple regression analysis was performed to explore sources of variation. Need for partition of reference intervals was evaluated based on 3-level nested ANOVA. After secondary exclusion using the latent abnormal values exclusion method, reference intervals were derived by a parametric method using the modified Box-Cox formula. Test results of 20 analytes were made traceable to reference measurement procedures. By the ANOVA, significant sex-related and age-related differences were observed in 12 and 12 analytes, respectively. A small regional difference was observed in the results for albumin, glucose, and sodium. Multiple regression analysis revealed BMI-related changes in results of 9 analytes for man and 6 for woman. Reference intervals of 28 analytes were computed with 17 analytes partitioned by sex and/or age. In conclusion, reference intervals of 28 common chemistry analytes applicable to Chinese Han population were established by use of the latest methodology. Reference intervals of 20 analytes traceable to reference measurement procedures can be used as common reference intervals, whereas others can be used as the assay system-specific reference intervals in China.

Nationwide Multicenter Reference Interval Study for 28 Common Biochemical Analytes in China

PubMed Central

Xia, Liangyu; Chen, Ming; Liu, Min; Tao, Zhihua; Li, Shijun; Wang, Liang; Cheng, Xinqi; Qin, Xuzhen; Han, Jianhua; Li, Pengchang; Hou, Li’an; Yu, Songlin; Ichihara, Kiyoshi; Qiu, Ling

2016-01-01

Abstract A nationwide multicenter study was conducted in the China to explore sources of variation of reference values and establish reference intervals for 28 common biochemical analytes, as a part of the International Federation of Clinical Chemistry and Laboratory Medicine, Committee on Reference Intervals and Decision Limits (IFCC/C-RIDL) global study on reference values. A total of 3148 apparently healthy volunteers were recruited in 6 cities covering a wide area in China. Blood samples were tested in 2 central laboratories using Beckman Coulter AU5800 chemistry analyzers. Certified reference materials and value-assigned serum panel were used for standardization of test results. Multiple regression analysis was performed to explore sources of variation. Need for partition of reference intervals was evaluated based on 3-level nested ANOVA. After secondary exclusion using the latent abnormal values exclusion method, reference intervals were derived by a parametric method using the modified Box–Cox formula. Test results of 20 analytes were made traceable to reference measurement procedures. By the ANOVA, significant sex-related and age-related differences were observed in 12 and 12 analytes, respectively. A small regional difference was observed in the results for albumin, glucose, and sodium. Multiple regression analysis revealed BMI-related changes in results of 9 analytes for man and 6 for woman. Reference intervals of 28 analytes were computed with 17 analytes partitioned by sex and/or age. In conclusion, reference intervals of 28 common chemistry analytes applicable to Chinese Han population were established by use of the latest methodology. Reference intervals of 20 analytes traceable to reference measurement procedures can be used as common reference intervals, whereas others can be used as the assay system-specific reference intervals in China. PMID:26945390

Characterization of tissue response to radiofrequency ablation using 3D model-based analysis of interventional MR images

NASA Astrophysics Data System (ADS)

Weinberg, Brent D.; Lazebnik, Roee S.; Breen, Michael S.; Lewin, Jonathan S.; Wilson, David L.

2003-05-01

Using magnetic resonance imaging (MRI), real-time guidance is feasible for radiofrequency (RF) current ablation of pathologic tissue. Lesions have a characteristic two-zone appearance: an inner core (Zone I) surrounded by a hyper-intense rim (Zone II). A better understanding of both the immediate (hyper-acute) and delayed (sub-acute) physiological response of the target tissue will aid development of minimally invasive tumor treatment strategies. We performed in vivo RF ablations in a rabbit thigh model and characterized the tissue response to treatment through contrast enhanced (CE) T1 and T2 weighted MR images at two time points. We measured zonal grayscale changes as well as zone volume changes using a 3D computationally fitted globally deformable parametric model. Comparison over time demonstrated an increase in the volume of both the inner necrotic core (mean 56.5% increase) and outer rim (mean 16.8% increase) of the lesion. Additionally, T2 images of the lesion exhibited contrast greater than or equal to CE T1 (mean 35% improvement). This work establishes a foundation for the clinical use of T2 MR images coupled with a geometric model of the ablation for noninvasive lesion monitoring and characterization.

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.

Development of the 1.6μm OPG/OPA system wavelength-controlled precisely for CO2 DIAL

NASA Astrophysics Data System (ADS)

Abo, M.; Shibata, Y.; Nagasawa, C.

2010-12-01

We developed an optical parametric oscillator (OPO) laser system for 1.6μm CO2 DIAL1). In order to improve the measurement accuracy of CO2 profiles, development of high power and wavelength stabilized laser system has been conducted. We report a new high-power 1.6μm laser transmitter based on a parametric master oscillator-power amplifier (MOPA) system pumped by a LD-pumped Q-switched Nd:YAG laser which has the injection seed laser locked to the iodine absorption line. The master oscillator is an optical parametric generator (OPG), based on an MgO-doped periodically poled LiTaO3 (PPMgLT) crystal. The OPOs require either active control of the cavity length or slight misalignment of the cavity. On the other hand, the OPGs do not require a cavity and instead rely on sufficient conversion efficiency to be obtained with a single pass through the crystal. The single-frequency oscillation of the OPG was achieved by injection seeding. The 1.6μm emission of the OPG is amplified by two-stage optical parametric amplifiers (OPAs). The each PPMgLT crystal was mounted on the copper holder, and the temperature control of the each holder was carried out within 0.01 K. The wavelength feedback system of the Nd:YAG seed laser is performed with the side locking of the iodine absorption spectrum (line No.1107) and the frequency stability is realized within 10 MHz rms. Stabilization of the 1.6μm DFB seed laser is estimated to within 4 MHz rms at the CO2 absorption line center and within 1.8 MHz rms at the CO2 absorption line slope using the wavelength control unit. We demonstrated single-longitudinal-mode emission with the OPG and two OPAs. The beam quality was TEM00 mode, the pulse energy was 12 mJ at 500 Hz repetition rate and the frequency stability was less than 10MHz rms. The unique performances of this optical parametric system make a relevant transmitter for CO2 DIAL. This work was financially supported by the System Development Program for Advanced Measurement and Analysis of the Japan Science and Technology Agency. Reference (1) D. Sakaisawa, C. Nagasawa, T. Nagai, M. Abo, Y. Shibata, H. Nagai, M. Nakazato, and T. Sakai, Development of a 1.6μm differential absorption lidar with a quasi-phase-matching optical parametric oscillator and photon-counting detector for the vertical CO2 profile, Applied Optics, Vol.48, No.4, pp.748-757, 2009.

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

Historical earthquakes studies in Eastern Siberia: State-of-the-art and plans for future

NASA Astrophysics Data System (ADS)

Radziminovich, Ya. B.; Shchetnikov, A. A.

2013-01-01

Many problems in investigating historical seismicity of East Siberia remain unsolved. A list of these problems may refer particularly to the quality and reliability of data sources, completeness of parametric earthquake catalogues, and precision and transparency of estimates for the main parameters of historical earthquakes. The main purpose of this paper is to highlight the current status of the studies of historical seismicity in Eastern Siberia, as well as analysis of existing macroseismic and parametric earthquake catalogues. We also made an attempt to identify the main shortcomings of existing catalogues and to clarify the reasons for their appearance in the light of the history of seismic observations in Eastern Siberia. Contentious issues in the catalogues of earthquakes are considered by the example of three strong historical earthquakes, important for assessing seismic hazard in the region. In particular, it was found that due to technical error the parameters of large M = 7.7 earthquakes of 1742 were transferred from the regional catalogue to the worldwide database with incorrect epicenter coordinates. The way some stereotypes concerning active tectonics influences on the localization of the epicenter is shown by the example of a strong М = 6.4 earthquake of 1814. Effect of insufficient use of the primary data source on completeness of earthquake catalogues is illustrated by the example of a strong M = 7.0 event of 1859. Analysis of the state-of-the-art of historical earthquakes studies in Eastern Siberia allows us to propose the following activities in the near future: (1) database compilation including initial descriptions of macroseismic effects with reference to their place and time of occurrence; (2) parameterization of the maximum possible (magnitude-unlimited) number of historical earthquakes on the basis of all the data available; (3) compilation of an improved version of the parametric historical earthquake catalogue for East Siberia with detailed consideration of each event and distinct logic schemes for data interpretation. Thus, we can make the conclusion regarding the necessity of a large-scale revision in historical earthquakes catalogues for the area of study.

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

Kinetic evaluation and test-retest reproducibility of [11C]UCB-J, a novel radioligand for positron emission tomography imaging of synaptic vesicle glycoprotein 2A in humans.

PubMed

Finnema, Sjoerd J; Nabulsi, Nabeel B; Mercier, Joël; Lin, Shu-Fei; Chen, Ming-Kai; Matuskey, David; Gallezot, Jean-Dominique; Henry, Shannan; Hannestad, Jonas; Huang, Yiyun; Carson, Richard E

2017-01-01

Synaptic vesicle glycoprotein 2A (SV2A) is ubiquitously present in presynaptic terminals. Here we report kinetic modeling and test-retest reproducibility assessment of the SV2A positron emission tomography (PET) radioligand [ 11 C]UCB-J in humans. Five volunteers were examined twice on the HRRT after bolus injection of [ 11 C]UCB-J. Arterial blood samples were collected for measurements of radiometabolites and free fraction. Regional time-activity curves were analyzed with 1-tissue (1T) and 2-tissue (2T) compartment models to estimate volumes of distribution ( V T ). Parametric maps were generated using the 1T model. [ 11 C]UCB-J metabolized fairly quickly, with parent fraction of 36 ± 13% at 15 min after injection. Plasma free fraction was 32 ± 1%. Regional time-activity curves displayed rapid kinetics and were well described by the 1T model, except for the cerebellum and hippocampus. V T values estimated with the 2T model were similar to 1T values. Parametric maps were of high quality and V T values correlated well with time activity curve (TAC)-based estimates. Shortening of acquisition time from 120 min to 60 min had a negligible effect on V T values. The mean absolute test-retest reproducibility for V T was 3-9% across regions. In conclusion, [ 11 C]UCB-J exhibited excellent PET tracer characteristics and has potential as a general purpose tool for measuring synaptic density in neurodegenerative disorders.

Breast tumour visualization using 3D quantitative ultrasound methods

NASA Astrophysics Data System (ADS)

Gangeh, Mehrdad J.; Raheem, Abdul; Tadayyon, Hadi; Liu, Simon; Hadizad, Farnoosh; Czarnota, Gregory J.

2016-04-01

Breast cancer is one of the most common cancer types accounting for 29% of all cancer cases. Early detection and treatment has a crucial impact on improving the survival of affected patients. Ultrasound (US) is non-ionizing, portable, inexpensive, and real-time imaging modality for screening and quantifying breast cancer. Due to these attractive attributes, the last decade has witnessed many studies on using quantitative ultrasound (QUS) methods in tissue characterization. However, these studies have mainly been limited to 2-D QUS methods using hand-held US (HHUS) scanners. With the availability of automated breast ultrasound (ABUS) technology, this study is the first to develop 3-D QUS methods for the ABUS visualization of breast tumours. Using an ABUS system, unlike the manual 2-D HHUS device, the whole patient's breast was scanned in an automated manner. The acquired frames were subsequently examined and a region of interest (ROI) was selected in each frame where tumour was identified. Standard 2-D QUS methods were used to compute spectral and backscatter coefficient (BSC) parametric maps on the selected ROIs. Next, the computed 2-D parameters were mapped to a Cartesian 3-D space, interpolated, and rendered to provide a transparent color-coded visualization of the entire breast tumour. Such 3-D visualization can potentially be used for further analysis of the breast tumours in terms of their size and extension. Moreover, the 3-D volumetric scans can be used for tissue characterization and the categorization of breast tumours as benign or malignant by quantifying the computed parametric maps over the whole tumour volume.

Parametric and Non-Parametric Vibration-Based Structural Identification Under Earthquake Excitation

NASA Astrophysics Data System (ADS)

Pentaris, Fragkiskos P.; Fouskitakis, George N.

2014-05-01

The problem of modal identification in civil structures is of crucial importance, and thus has been receiving increasing attention in recent years. Vibration-based methods are quite promising as they are capable of identifying the structure's global characteristics, they are relatively easy to implement and they tend to be time effective and less expensive than most alternatives [1]. This paper focuses on the off-line structural/modal identification of civil (concrete) structures subjected to low-level earthquake excitations, under which, they remain within their linear operating regime. Earthquakes and their details are recorded and provided by the seismological network of Crete [2], which 'monitors' the broad region of south Hellenic arc, an active seismic region which functions as a natural laboratory for earthquake engineering of this kind. A sufficient number of seismic events are analyzed in order to reveal the modal characteristics of the structures under study, that consist of the two concrete buildings of the School of Applied Sciences, Technological Education Institute of Crete, located in Chania, Crete, Hellas. Both buildings are equipped with high-sensitivity and accuracy seismographs - providing acceleration measurements - established at the basement (structure's foundation) presently considered as the ground's acceleration (excitation) and at all levels (ground floor, 1st floor, 2nd floor and terrace). Further details regarding the instrumentation setup and data acquisition may be found in [3]. The present study invokes stochastic, both non-parametric (frequency-based) and parametric methods for structural/modal identification (natural frequencies and/or damping ratios). Non-parametric methods include Welch-based spectrum and Frequency response Function (FrF) estimation, while parametric methods, include AutoRegressive (AR), AutoRegressive with eXogeneous input (ARX) and Autoregressive Moving-Average with eXogeneous input (ARMAX) models[4, 5]. Preliminary results indicate that parametric methods are capable of sufficiently providing the structural/modal characteristics such as natural frequencies and damping ratios. The study also aims - at a further level of investigation - to provide a reliable statistically-based methodology for structural health monitoring after major seismic events which potentially cause harming consequences in structures. Acknowledgments This work was supported by the State Scholarships Foundation of Hellas. References [1] J. S. Sakellariou and S. D. Fassois, "Stochastic output error vibration-based damage detection and assessment in structures under earthquake excitation," Journal of Sound and Vibration, vol. 297, pp. 1048-1067, 2006. [2] G. Hloupis, I. Papadopoulos, J. P. Makris, and F. Vallianatos, "The South Aegean seismological network - HSNC," Adv. Geosci., vol. 34, pp. 15-21, 2013. [3] F. P. Pentaris, J. Stonham, and J. P. Makris, "A review of the state-of-the-art of wireless SHM systems and an experimental set-up towards an improved design," presented at the EUROCON, 2013 IEEE, Zagreb, 2013. [4] S. D. Fassois, "Parametric Identification of Vibrating Structures," in Encyclopedia of Vibration, S. G. Braun, D. J. Ewins, and S. S. Rao, Eds., ed London: Academic Press, London, 2001. [5] S. D. Fassois and J. S. Sakellariou, "Time-series methods for fault detection and identification in vibrating structures," Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 365, pp. 411-448, February 15 2007.

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

Parametric trade studies on a Shuttle 2 launch system architecture

NASA Technical Reports Server (NTRS)

Stanley, Douglas O.; Talay, Theodore A.; Lepsch, Roger A.; Morris, W. Douglas; Naftel, J. Christopher; Cruz, Christopher I.

1991-01-01

A series of trade studies are presented on a complementary architecture of launch vehicles as a part of a study often referred to as Shuttle-2. The results of the trade studies performed on the vehicles of a reference Shuttle-2 mixed fleet architecture have provided an increased understanding of the relative importance of each of the major vehicle parameters. As a result of trades on the reference booster-orbiter configuration with a methane booster, the study showed that 60 percent of the total liftoff thrust should be on the booster and 40 percent on the orbiter. It was also found that the liftoff thrust to weight ratio (T/W) on the booster-orbiter should be 1.3. This leads to a low dry weight and still provides enough thrust to allow the design of a heavy lift architecture. As a result of another trade study, the dry weight of the reference booster-orbiter was chosen for a variety of operational considerations. Other trade studies on the booster-orbiter demonstrate that the cross feeding of propellant during boost phase is desirable and that engine-out capability from launch to orbit is worth the performance penalty. Technology assumptions made during the Shuttle-2 design were shown to be approx. equivalent to a 25 percent across the board weight reduction over the Space Shuttle technology. The vehicles of the Shuttle-2 architecture were also sized for a wide variety of payloads and missions to different orbits. Many of these same parametric trades were also performed on completely liquid hydrogen fueled fully reusable concepts. If a booster-orbiter is designed using liquid hydrogen engines on both the booster and orbiter, the total vehicle dry weight is only 3.0 percent higher than the reference dual-fuel booster-orbiter, and the gross weight is 3.8 percent less. For this booster-orbiter vehicle, a liftoff T/W of 1.3, a thrust of about 60 percent on the booster, and a Mach staging number of 3 all proved to be desirable. This modest dry weight increase for a liquid hydrogen fueled Shuttle-2 system should be more than offset by the elimination of the entire hydrocarbon engine development program and the savings in operation cost realized by the elimination of an entire fuel type.

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.

Electron Energy Deposition in Atomic Oxygen

DTIC Science & Technology

1986-12-31

the parametric fits developed by Jackman et al^ where the cross section is expressed as ij -14 6.5x10 Cf ij ( 1 -¥~ n 4L ^ ’ij (7) and the...Res. 72, 3967 (1967). 4. H.S. Porter, C.H. Jackman and A.E.S. Green, J. Chem. Phys. 65, 154 (1976) and references therein. 5. P.M. Banks, C.R...1966). 28. S.P. Roundtree and R.J.W. Henry, Phys. Rev. A6, 2106 (1972). 29. T. Sawada and P.S. Ganas, Phys. Rev. A7, 617 (1973). 30. C.H. Jackman

Component pattern analysis of chemicals using multispectral THz imaging system

NASA Astrophysics Data System (ADS)

Kawase, Kodo; Ogawa, Yuichi; Watanabe, Yuki

2004-04-01

We have developed a novel basic technology for terahertz (THz) imaging, which allows detection and identification of chemicals by introducing the component spatial pattern analysis. The spatial distributions of the chemicals were obtained from terahertz multispectral transillumination images, using absorption spectra previously measured with a widely tunable THz-wave parametric oscillator. Further we have applied this technique to the detection and identification of illicit drugs concealed in envelopes. The samples we used were methamphetamine and MDMA, two of the most widely consumed illegal drugs in Japan, and aspirin as a reference.

Analysis of the uncertainties in the physical calculations of water-moderated power reactors of the VVER type by the parameters of models of preparing few-group constants

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

Bryukhin, V. V., E-mail: bryuhin@yandex.ru; Kurakin, K. Yu.; Uvakin, M. A.

The article covers the uncertainty analysis of the physical calculations of the VVER reactor core for different meshes of the reference values of the feedback parameters (FBP). Various numbers of nodes of the parametric axes of FBPs and different ranges between them are investigated. The uncertainties of the dynamic calculations are analyzed using RTS RCCA ejection as an example within the framework of the model with the boundary conditions at the core inlet and outlet.

Local Sampling of the Wigner Function at Telecom Wavelength with Loss-Tolerant Detection of Photon Statistics.

PubMed

Harder, G; Silberhorn, Ch; Rehacek, J; Hradil, Z; Motka, L; Stoklasa, B; Sánchez-Soto, L L

2016-04-01

We report the experimental point-by-point sampling of the Wigner function for nonclassical states created in an ultrafast pulsed type-II parametric down-conversion source. We use a loss-tolerant time-multiplexed detector based on a fiber-optical setup and a pair of photon-number-resolving avalanche photodiodes. By capitalizing on an expedient data-pattern tomography, we assess the properties of the light states with outstanding accuracy. The method allows us to reliably infer the squeezing of genuine two-mode states without any phase reference.

Sonic Boom Minimization Efforts on Boeing HSCT Baseline

NASA Technical Reports Server (NTRS)

Cheung, Samson H.; Fouladi, Kamran; Haglund, George; Tu, Eugene

1999-01-01

A team was formed to tackle the sonic boom softening issues of the current Boeing HSCT design. The team consisted of personnel from NASA Ames, NASA Langley, and Boeing company. The work described in this paper was done when the first author was at NASA Ames Research Center. This paper presents the sonic boom softening work on two Boeing High Speed Civil Transport (HSCT) baseline configurations, Reference-H and Boeing-1122. This presentation can be divided into two parts: parametric studies and sonic boom minimization by CFD optimization routines.

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.

Reference Value Advisor: a new freeware set of macroinstructions to calculate reference intervals with Microsoft Excel.

PubMed

Geffré, Anne; Concordet, Didier; Braun, Jean-Pierre; Trumel, Catherine

2011-03-01

International recommendations for determination of reference intervals have been recently updated, especially for small reference sample groups, and use of the robust method and Box-Cox transformation is now recommended. Unfortunately, these methods are not included in most software programs used for data analysis by clinical laboratories. We have created a set of macroinstructions, named Reference Value Advisor, for use in Microsoft Excel to calculate reference limits applying different methods. For any series of data, Reference Value Advisor calculates reference limits (with 90% confidence intervals [CI]) using a nonparametric method when n≥40 and by parametric and robust methods from native and Box-Cox transformed values; tests normality of distributions using the Anderson-Darling test and outliers using Tukey and Dixon-Reed tests; displays the distribution of values in dot plots and histograms and constructs Q-Q plots for visual inspection of normality; and provides minimal guidelines in the form of comments based on international recommendations. The critical steps in determination of reference intervals are correct selection of as many reference individuals as possible and analysis of specimens in controlled preanalytical and analytical conditions. Computing tools cannot compensate for flaws in selection and size of the reference sample group and handling and analysis of samples. However, if those steps are performed properly, Reference Value Advisor, available as freeware at http://www.biostat.envt.fr/spip/spip.php?article63, permits rapid assessment and comparison of results calculated using different methods, including currently unavailable methods. This allows for selection of the most appropriate method, especially as the program provides the CI of limits. It should be useful in veterinary clinical pathology when only small reference sample groups are available. ©2011 American Society for Veterinary Clinical Pathology.

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

Comparison of Kinetic Models for Dual-Tracer Receptor Concentration Imaging in Tumors

PubMed Central

Hamzei, Nazanin; Samkoe, Kimberley S; Elliott, Jonathan T; Holt, Robert W; Gunn, Jason R; Hasan, Tayyaba; Pogue, Brian W; Tichauer, Kenneth M

2014-01-01

Molecular differences between cancerous and healthy tissue have become key targets for novel therapeutics specific to tumor receptors. However, cancer cell receptor expression can vary within and amongst different tumors, making strategies that can quantify receptor concentration in vivo critical for the progression of targeted therapies. Recently a dual-tracer imaging approach capable of providing quantitative measures of receptor concentration in vivo was developed. It relies on the simultaneous injection and imaging of receptor-targeted tracer and an untargeted tracer (to account for non-specific uptake of the targeted tracer). Early implementations of this approach have been structured on existing “reference tissue” imaging methods that have not been optimized for or validated in dual-tracer imaging. Using simulations and mouse tumor model experimental data, the salient findings in this study were that all widely used reference tissue kinetic models can be used for dual-tracer imaging, with the linearized simplified reference tissue model offering a good balance of accuracy and computational efficiency. Moreover, an alternate version of the full two-compartment reference tissue model can be employed accurately by assuming that the K1s of the targeted and untargeted tracers are similar to avoid assuming an instantaneous equilibrium between bound and free states (made by all other models). PMID:25414912

Parametric and non-parametric modeling of short-term synaptic plasticity. Part I: computational study

PubMed Central

Marmarelis, Vasilis Z.; Berger, Theodore W.

2009-01-01

Parametric and non-parametric modeling methods are combined to study the short-term plasticity (STP) of synapses in the central nervous system (CNS). The nonlinear dynamics of STP are modeled by means: (1) previously proposed parametric models based on mechanistic hypotheses and/or specific dynamical processes, and (2) non-parametric models (in the form of Volterra kernels) that transforms the presynaptic signals into postsynaptic signals. In order to synergistically use the two approaches, we estimate the Volterra kernels of the parametric models of STP for four types of synapses using synthetic broadband input–output data. Results show that the non-parametric models accurately and efficiently replicate the input–output transformations of the parametric models. Volterra kernels provide a general and quantitative representation of the STP. PMID:18506609

Parametric analysis of parameters for electrical-load forecasting using artificial neural networks

NASA Astrophysics Data System (ADS)

Gerber, William J.; Gonzalez, Avelino J.; Georgiopoulos, Michael

1997-04-01

Accurate total system electrical load forecasting is a necessary part of resource management for power generation companies. The better the hourly load forecast, the more closely the power generation assets of the company can be configured to minimize the cost. Automating this process is a profitable goal and neural networks should provide an excellent means of doing the automation. However, prior to developing such a system, the optimal set of input parameters must be determined. The approach of this research was to determine what those inputs should be through a parametric study of potentially good inputs. Input parameters tested were ambient temperature, total electrical load, the day of the week, humidity, dew point temperature, daylight savings time, length of daylight, season, forecast light index and forecast wind velocity. For testing, a limited number of temperatures and total electrical loads were used as a basic reference input parameter set. Most parameters showed some forecasting improvement when added individually to the basic parameter set. Significantly, major improvements were exhibited with the day of the week, dew point temperatures, additional temperatures and loads, forecast light index and forecast wind velocity.

3-D Quantitative Dynamic Contrast Ultrasound for Prostate Cancer Localization.

PubMed

Schalk, Stefan G; Huang, Jing; Li, Jia; Demi, Libertario; Wijkstra, Hessel; Huang, Pintong; Mischi, Massimo

2018-04-01

To investigate quantitative 3-D dynamic contrast-enhanced ultrasound (DCE-US) and, in particular 3-D contrast-ultrasound dispersion imaging (CUDI), for prostate cancer detection and localization, 43 patients referred for 10-12-core systematic biopsy underwent 3-D DCE-US. For each 3-D DCE-US recording, parametric maps of CUDI-based and perfusion-based parameters were computed. The parametric maps were divided in regions, each corresponding to a biopsy core. The obtained parameters were validated per biopsy location and after combining two or more adjacent regions. For CUDI by correlation (r) and for the wash-in time (WIT), a significant difference in parameter values between benign and malignant biopsy cores was found (p < 0.001). In a per-prostate analysis, sensitivity and specificity were 94% and 50% for r, and 53% and 81% for WIT. Based on these results, it can be concluded that quantitative 3-D DCE-US could aid in localizing prostate cancer. Therefore, we recommend follow-up studies to investigate its value for targeting biopsies. Copyright © 2018 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

Distributed parametric amplifier for RZ-DPSK signal transmission system.

PubMed

Xu, Xing; Zhang, Chi; Yuk, T I; Wong, Kenneth K Y

2012-08-13

We have experimentally demonstrated a single pump distributed parametric amplification (DPA) system for differential phase shift keying (DPSK) signal in a spool of dispersion-shifted fiber (DSF). The gain spectrum of single pump DPA is thoroughly investigated by both simulation and experiment, and a possible reference for optimal input pump power and fiber length relationship is provided to DPA based applications. Furthermore, DPSK format is compared with on-off keying (OOK) within DPA scheme. Eight WDM signal channels at 10-Gb/s are utilized, and approximately 0.5-dB power penalties at the bit-error rate (BER) of 10(-9) are achieved for return-to-zero DPSK (RZ-DPSK), comparing to larger than 1.5-dB with OOK format. In order to improve the system power efficiency, at the receiver, the pump is recycled by a photovoltaic cell and the converted energy can be used by potential low-power-consuming devices, i.e sensors or small-scale electronic circuits. Additionally, with suitable components, the whole DPA concept could be directly applied to the 1.3-μm telecommunication window along the most commonly used single-mode fiber (SMF).

Gluon and Wilson loop TMDs for hadrons of spin ≤ 1

NASA Astrophysics Data System (ADS)

Boer, Daniël; Cotogno, Sabrina; van Daal, Tom; Mulders, Piet J.; Signori, Andrea; Zhou, Ya-Jin

2016-10-01

In this paper we consider the parametrizations of gluon transverse momentum dependent (TMD) correlators in terms of TMD parton distribution functions (PDFs). These functions, referred to as TMDs, are defined as the Fourier transforms of hadronic matrix elements of nonlocal combinations of gluon fields. The nonlocality is bridged by gauge links, which have characteristic paths (future or past pointing), giving rise to a process dependence that breaks universality. For gluons, the specific correlator with one future and one past pointing gauge link is, in the limit of small x, related to a correlator of a single Wilson loop. We present the parametrization of Wilson loop correlators in terms of Wilson loop TMDs and discuss the relation between these functions and the small- x `dipole' gluon TMDs. This analysis shows which gluon TMDs are leading or suppressed in the small- x limit. We discuss hadronic targets that are unpolarized, vector polarized (relevant for spin-1 /2 and spin-1 hadrons), and tensor polarized (relevant for spin-1 hadrons). The latter are of interest for studies with a future Electron-Ion Collider with polarized deuterons.

Reference Intervals of Hematology and Clinical Chemistry Analytes for 1-Year-Old Korean Children

PubMed Central

Lee, Hye Ryun; Roh, Eun Youn; Chang, Ju Young

2016-01-01

Background Reference intervals need to be established according to age. We established reference intervals of hematology and chemistry from community-based healthy 1-yr-old children and analyzed their iron status according to the feeding methods during the first six months after birth. Methods A total of 887 children who received a medical check-up between 2010 and 2014 at Boramae Hospital (Seoul, Korea) were enrolled. A total of 534 children (247 boys and 287 girls) were enrolled as reference individuals after the exclusion of data obtained from children with suspected iron deficiency. Hematology and clinical chemistry analytes were measured, and the reference value of each analyte was estimated by using parametric (mean±2 SD) or nonparametric methods (2.5-97.5th percentile). Iron, total iron-binding capacity, and ferritin were measured, and transferrin saturation was calculated. Results As there were no differences in the mean values between boys and girls, we established the reference intervals for 1-yr-old children regardless of sex. The analysis of serum iron status according to feeding methods during the first six months revealed higher iron, ferritin, and transferrin saturation levels in children exclusively or mainly fed formula than in children exclusively or mainly fed breast milk. Conclusions We established reference intervals of hematology and clinical chemistry analytes from community-based healthy children at one year of age. These reference intervals will be useful for interpreting results of medical check-ups at one year of age. PMID:27374715

Reference Intervals of Hematology and Clinical Chemistry Analytes for 1-Year-Old Korean Children.

PubMed

Lee, Hye Ryun; Shin, Sue; Yoon, Jong Hyun; Roh, Eun Youn; Chang, Ju Young

2016-09-01

Reference intervals need to be established according to age. We established reference intervals of hematology and chemistry from community-based healthy 1-yr-old children and analyzed their iron status according to the feeding methods during the first six months after birth. A total of 887 children who received a medical check-up between 2010 and 2014 at Boramae Hospital (Seoul, Korea) were enrolled. A total of 534 children (247 boys and 287 girls) were enrolled as reference individuals after the exclusion of data obtained from children with suspected iron deficiency. Hematology and clinical chemistry analytes were measured, and the reference value of each analyte was estimated by using parametric (mean±2 SD) or nonparametric methods (2.5-97.5th percentile). Iron, total iron-binding capacity, and ferritin were measured, and transferrin saturation was calculated. As there were no differences in the mean values between boys and girls, we established the reference intervals for 1-yr-old children regardless of sex. The analysis of serum iron status according to feeding methods during the first six months revealed higher iron, ferritin, and transferrin saturation levels in children exclusively or mainly fed formula than in children exclusively or mainly fed breast milk. We established reference intervals of hematology and clinical chemistry analytes from community-based healthy children at one year of age. These reference intervals will be useful for interpreting results of medical check-ups at one year of age.

Determination of Mechanical Properties of Spatially Heterogeneous Breast Tissue Specimens Using Contact Mode Atomic Force Microscopy (AFM)

PubMed Central

Roy, Rajarshi; Desai, Jaydev P.

2016-01-01

This paper outlines a comprehensive parametric approach for quantifying mechanical properties of spatially heterogeneous thin biological specimens such as human breast tissue using contact-mode Atomic Force Microscopy. Using inverse finite element (FE) analysis of spherical nanoindentation, the force response from hyperelastic material models is compared with the predicted force response from existing analytical contact models, and a sensitivity study is carried out to assess uniqueness of the inverse FE solution. Furthermore, an automation strategy is proposed to analyze AFM force curves with varying levels of material nonlinearity with minimal user intervention. Implementation of our approach on an elastic map acquired from raster AFM indentation of breast tissue specimens indicates that a judicious combination of analytical and numerical techniques allow more accurate interpretation of AFM indentation data compared to relying on purely analytical contact models, while keeping the computational cost associated an inverse FE solution with reasonable limits. The results reported in this study have several implications in performing unsupervised data analysis on AFM indentation measurements on a wide variety of heterogeneous biomaterials. PMID:25015130

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.

Parametric techniques for characterizing myocardial tissue by magnetic resonance imaging (part 1): T1 mapping.

PubMed

Perea Palazón, R J; Ortiz Pérez, J T; Prat González, S; de Caralt Robira, T M; Cibeira López, M T; Solé Arqués, M

2016-01-01

The development of myocardial fibrosis is a common process in the appearance of ventricular dysfunction in many heart diseases. Magnetic resonance imaging makes it possible to accurately evaluate the structure and function of the heart, and its role in the macroscopic characterization of myocardial fibrosis by late enhancement techniques has been widely validated clinically. Recent studies have demonstrated that T1-mapping techniques can quantify diffuse myocardial fibrosis and the expansion of the myocardial extracellular space in absolute terms. However, further studies are necessary to validate the usefulness of this technique in the early detection of tissue remodeling at a time when implementing early treatment would improve a patient's prognosis. This article reviews the state of the art for T1 mapping of the myocardium, its clinical applications, and its limitations. Copyright © 2016 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

Growth curves of preschool children in the northeast of iran: a population based study using quantile regression approach.

PubMed

Payande, Abolfazl; Tabesh, Hamed; Shakeri, Mohammad Taghi; Saki, Azadeh; Safarian, Mohammad

2013-01-14

Growth charts are widely used to assess children's growth status and can provide a trajectory of growth during early important months of life. The objectives of this study are going to construct growth charts and normal values of weight-for-age for children aged 0 to 5 years using a powerful and applicable methodology. The results compare with the World Health Organization (WHO) references and semi-parametric LMS method of Cole and Green. A total of 70737 apparently healthy boys and girls aged 0 to 5 years were recruited in July 2004 for 20 days from those attending community clinics for routine health checks as a part of a national survey. Anthropometric measurements were done by trained health staff using WHO methodology. The nonparametric quantile regression method obtained by local constant kernel estimation of conditional quantiles curves using for estimation of curves and normal values. The weight-for-age growth curves for boys and girls aged from 0 to 5 years were derived utilizing a population of children living in the northeast of Iran. The results were similar to the ones obtained by the semi-parametric LMS method in the same data. Among all age groups from 0 to 5 years, the median values of children's weight living in the northeast of Iran were lower than the corresponding values in WHO reference data. The weight curves of boys were higher than those of girls in all age groups. The differences between growth patterns of children living in the northeast of Iran versus international ones necessitate using local and regional growth charts. International normal values may not properly recognize the populations at risk for growth problems in Iranian children. Quantile regression (QR) as a flexible method which doesn't require restricted assumptions, proposed for estimation reference curves and normal values.

A new definition for an old entity: improved definition of mitral valve prolapse using three-dimensional echocardiography and color-coded parametric models.

PubMed

Addetia, Karima; Mor-Avi, Victor; Weinert, Lynn; Salgo, Ivan S; Lang, Roberto M

2014-01-01

Differentiating between mitral valve (MV) prolapse (MVP) and MV billowing (MVB) on two-dimensional echocardiography is challenging. The aim of this study was to test the hypothesis that color-coded models of maximal leaflet displacement from the annular plane into the atrium derived from three-dimensional transesophageal echocardiography would allow discrimination between these lesions. Three-dimensional transesophageal echocardiographic imaging of the MV was performed in 50 patients with (n = 38) and without (n = 12) degenerative MV disease. Definitive diagnosis of MVP versus MVB was made using inspection of dynamic three-dimensional renderings and multiple two-dimensional cut planes extracted from three-dimensional data sets. This was used as a reference standard to test an alternative approach, wherein the color-coded parametric models were inspected for integrity of the coaptation line and location of the maximally displaced portion of the leaflet. Diagnostic interpretations of these models by two independent readers were compared with the reference standard. In all cases of MVP, the color-coded models depicted loss of integrity of the coaptation line and maximal leaflet displacement extending to the coaptation line. MVB was depicted by preserved leaflet apposition with maximal displacement away from the coaptation line. Interpretation of the 50 color-coded models by novice readers took 5 to 10 min and resulted in good agreement with the reference technique (κ = 0.81 and κ = 0.73 for the two readers). Three-dimensional color-coded models provide a static display of MV leaflet displacement, allowing differentiation between MVP and MVB, without the need to inspect multiple planes and while taking into account the saddle shape of the mitral annulus. Copyright © 2014 American Society of Echocardiography. Published by Mosby, Inc. All rights reserved.

Growth Curves of Preschool Children in the Northeast of Iran: A Population Based Study Using Quantile Regression Approach

PubMed Central

Payande, Abolfazl; Tabesh, Hamed; Shakeri, Mohammad Taghi; Saki, Azadeh; Safarian, Mohammad

2013-01-01

Introduction: Growth charts are widely used to assess children’s growth status and can provide a trajectory of growth during early important months of life. The objectives of this study are going to construct growth charts and normal values of weight-for-age for children aged 0 to 5 years using a powerful and applicable methodology. The results compare with the World Health Organization (WHO) references and semi-parametric LMS method of Cole and Green. Methods: A total of 70737 apparently healthy boys and girls aged 0 to 5 years were recruited in July 2004 for 20 days from those attending community clinics for routine health checks as a part of a national survey. Anthropometric measurements were done by trained health staff using WHO methodology. The nonparametric quantile regression method obtained by local constant kernel estimation of conditional quantiles curves using for estimation of curves and normal values. Results: The weight-for-age growth curves for boys and girls aged from 0 to 5 years were derived utilizing a population of children living in the northeast of Iran. The results were similar to the ones obtained by the semi-parametric LMS method in the same data. Among all age groups from 0 to 5 years, the median values of children’s weight living in the northeast of Iran were lower than the corresponding values in WHO reference data. The weight curves of boys were higher than those of girls in all age groups. Conclusion: The differences between growth patterns of children living in the northeast of Iran versus international ones necessitate using local and regional growth charts. International normal values may not properly recognize the populations at risk for growth problems in Iranian children. Quantile regression (QR) as a flexible method which doesn’t require restricted assumptions, proposed for estimation reference curves and normal values. PMID:23618470

Estimation of reference intervals from small samples: an example using canine plasma creatinine.

PubMed

Geffré, A; Braun, J P; Trumel, C; Concordet, D

2009-12-01

According to international recommendations, reference intervals should be determined from at least 120 reference individuals, which often are impossible to achieve in veterinary clinical pathology, especially for wild animals. When only a small number of reference subjects is available, the possible bias cannot be known and the normality of the distribution cannot be evaluated. A comparison of reference intervals estimated by different methods could be helpful. The purpose of this study was to compare reference limits determined from a large set of canine plasma creatinine reference values, and large subsets of this data, with estimates obtained from small samples selected randomly. Twenty sets each of 120 and 27 samples were randomly selected from a set of 1439 plasma creatinine results obtained from healthy dogs in another study. Reference intervals for the whole sample and for the large samples were determined by a nonparametric method. The estimated reference limits for the small samples were minimum and maximum, mean +/- 2 SD of native and Box-Cox-transformed values, 2.5th and 97.5th percentiles by a robust method on native and Box-Cox-transformed values, and estimates from diagrams of cumulative distribution functions. The whole sample had a heavily skewed distribution, which approached Gaussian after Box-Cox transformation. The reference limits estimated from small samples were highly variable. The closest estimates to the 1439-result reference interval for 27-result subsamples were obtained by both parametric and robust methods after Box-Cox transformation but were grossly erroneous in some cases. For small samples, it is recommended that all values be reported graphically in a dot plot or histogram and that estimates of the reference limits be compared using different methods.

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

PubMed

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

2015-05-01

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

Integrated transrectal probe for translational ultrasound-photoacoustic imaging

NASA Astrophysics Data System (ADS)

Bell, Kevan L.; Harrison, Tyler; Usmani, Nawaid; Zemp, Roger J.

2016-03-01

A compact photoacoustic transrectal probe is constructed for improved imaging in brachytherapy treatment. A 192 element 5 MHz linear transducer array is mounted inside a small 3D printed casing along with an array of optical fibers. The device is fed by a pump laser and tunable NIR-optical parametric oscillator with data collected by a Verasonics ultrasound platform. This assembly demonstrates improved imaging of brachytherapy seeds in phantoms with depths up to 5 cm. The tuneable excitation in combination with standard US integration provides adjustable contrast between the brachytherapy seeds, blood filled tubes and background tissue.

Laser-induced fluorescence spectroscopy of the secondary cataract

NASA Astrophysics Data System (ADS)

Maslov, N. A.; Larionov, P. M.; Rozhin, I. A.; Druzhinin, I. B.; Chernykh, V. V.

2016-06-01

Excitation-emission matrices of laser-induced fluorescence of lens capsule epithelium, the lens nucleus, and the lens capsule are investigated. A solid-state laser in combination with an optical parametric generator tunable in the range from 210 to 350 nm was used for excitation of fluorescence. The spectra of fluorescence of all three types of tissues exhibit typical features that are specific to them and drastically differ from one another. This effect can be used for intrasurgical control of presence of residual lens capsule epithelium cells in the capsular bag after surgical treatment of a cataract.

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.

A review of parametric approaches specific to aerodynamic design process

NASA Astrophysics Data System (ADS)

Zhang, Tian-tian; Wang, Zhen-guo; Huang, Wei; Yan, Li

2018-04-01

Parametric modeling of aircrafts plays a crucial role in the aerodynamic design process. Effective parametric approaches have large design space with a few variables. Parametric methods that commonly used nowadays are summarized in this paper, and their principles have been introduced briefly. Two-dimensional parametric methods include B-Spline method, Class/Shape function transformation method, Parametric Section method, Hicks-Henne method and Singular Value Decomposition method, and all of them have wide application in the design of the airfoil. This survey made a comparison among them to find out their abilities in the design of the airfoil, and the results show that the Singular Value Decomposition method has the best parametric accuracy. The development of three-dimensional parametric methods is limited, and the most popular one is the Free-form deformation method. Those methods extended from two-dimensional parametric methods have promising prospect in aircraft modeling. Since different parametric methods differ in their characteristics, real design process needs flexible choice among them to adapt to subsequent optimization procedure.

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

Mechanics of oriented electrospun nanofibrous scaffolds for annulus fibrosus tissue engineering.

PubMed

Nerurkar, Nandan L; Elliott, Dawn M; Mauck, Robert L

2007-08-01

Engineering a functional replacement for the annulus fibrosus (AF) of the intervertebral disc is contingent upon recapitulation of AF structure, composition, and mechanical properties. In this study, we propose a new paradigm for AF tissue engineering that focuses on the reconstitution of anatomic fiber architecture and uses constitutive modeling to evaluate construct function. A modified electrospinning technique was utilized to generate aligned nanofibrous polymer scaffolds for engineering the basic functional unit of the AF, a single lamella. Scaffolds were tested in uniaxial tension at multiple fiber orientations, demonstrating a nonlinear dependence of modulus on fiber angle that mimicked the nonlinearity and anisotropy of native AF. A homogenization model previously applied to native AF successfully described scaffold mechanical response, and parametric studies demonstrated that nonfibrillar matrix, along with fiber connectivity, are key contributors to tensile mechanics for engineered AF. We demonstrated that AF cells orient themselves along the aligned scaffolds and deposit matrix that contributes to construct mechanics under loading conditions relevant to the in vivo environment. The homogenization model was applied to cell-seeded constructs and provided quantitative measures for the evolution of matrix and interfibrillar interactions. Finally, the model demonstrated that at fiber angles of the AF (28 degrees -44 degrees ), engineered material behaved much like native tissue, suggesting that engineered constructs replicate the physiologic behavior of the single AF lamella. Constitutive modeling provides a powerful tool for analysis of engineered AF neo-tissue and native AF tissue alike, highlighting key mechanical design criteria for functional AF tissue engineering.

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

PubMed

Trnka, Tomáš; Tvaroška, Igor; Koča, Jaroslav

2018-01-09

Computational studies of the reaction mechanisms of various enzymes are nowadays based almost exclusively on hybrid QM/MM models. Unfortunately, the success of this approach strongly depends on the selection of the QM region, and computational cost is a crucial limiting factor. An interesting alternative is offered by empirical reactive molecular force fields, especially the ReaxFF potential developed by van Duin and co-workers. However, even though an initial parametrization of ReaxFF for biomolecules already exists, it does not provide the desired level of accuracy. We have conducted a thorough refitting of the ReaxFF force field to improve the description of reaction energetics. To minimize the human effort required, we propose a fully automated approach to generate an extensive training set comprised of thousands of different geometries and molecular fragments starting from a few model molecules. Electrostatic parameters were optimized with QM electrostatic potentials as the main target quantity, avoiding excessive dependence on the choice of reference atomic charges and improving robustness and transferability. The remaining force field parameters were optimized using the VD-CMA-ES variant of the CMA-ES optimization algorithm. This method is able to optimize hundreds of parameters simultaneously with unprecedented speed and reliability. The resulting force field was validated on a real enzymatic system, ppGalNAcT2 glycosyltransferase. The new force field offers excellent qualitative agreement with the reference QM/MM reaction energy profile, matches the relative energies of intermediate and product minima almost exactly, and reduces the overestimation of transition state energies by 27-48% compared with the previous parametrization.

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.

Chromium content in the human hip joint tissues.

PubMed

Brodziak-Dopierała, Barbara; Kwapuliński, Jerzy; Sobczyk, Krzysztof; Wiechuła, Danuta

2015-02-01

Chromium has many important functions in the human body. For the osseous tissue, its role has not been clearly defined. This study was aimed at determining chromium content in hip joint tissues. A total of 91 hip joint samples were taken in this study, including 66 from females and 25 from males. The sample tissues were separated according to their anatomical parts. The chromium content was determined by the AAS method. The statistical analysis was performed with U Mann-Whitney's non-parametric test, P≤0.05. The overall chromium content in tissues of the hip joint in the study subjects was as follows: 5.73 µg/g in the articular cartilage, 5.33 µg/g in the cortical bone, 17.86 µg/g in the cancellous bone, 5.95 µg/g in the fragment of the cancellous bone from the intertrochanteric region, and 1.28 µg/g in the joint capsule. The chromium contents were observed in 2 group patients, it was 7.04 µg/g in people with osteoarthritis and 12.59 µg/g in people with fractures. The observed chromium content was highest in the cancellous bone and the lowest in the joint capsule. Chromium content was significantly different between the people with hip joint osteoarthritis and the people with femoral neck fractures. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Assessment of tissue oxygenation of periodontal inflammation in smokers using optical spectroscopy.

PubMed

Liu, Kan-Zhi; Duarte, Poliana Mendes; Santos, Vanessa Renata; Xiang, Xiaoming; Xu, Minqi; Miranda, Tamires Szeremeske; Fermiano, Daiane; Gonçalves, Tiago Eduardo Dias; Sowa, Micheal G

2014-04-01

We have recently developed a periodontal diagnostic tool that was validated in non-smokers with periodontitis. Tobacco smoking is a recognized risk factor for periodontal diseases that can mask gingival bleeding and lead to a false negative diagnosis. Therefore, the purpose of current study is to further validate this instrument in smokers with periodontal diseases. Using a portable optical near-infrared spectrometer, optical spectra were obtained, processed and evaluated from healthy (n = 108), gingivitis (n = 100), and periodontitis (n = 79) sites of 54 systemically healthy smokers. A modified Beer-Lambert unmixing model that incorporates a non-parametric scattering loss function was used to determine the relative contribution of deoxygenated haemoglobin (Hb) and oxygenated haemoglobin (HbO2 ) to the overall spectrum. The balance between tissue oxygen delivery and utilization in periodontal tissues was then assessed. Tissue oxygen saturation was significantly decreased in the gingivitis (p = 0.016) and periodontitis (p = 0.007) sites, compared to the healthy sites. There was a trend towards increased concentration of Hb and decreased concentration of HbO2 from healthy to diseased sites, without statistical significance (p > 0.05). Optical spectroscopy can determine tissue oxygenation profiles of healthy and diseased sites in smokers. The spectral profile of periodontal sites in smokers generally resembles those from non-smoking patients. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

BRIDGING GAPS BETWEEN ZOO AND WILDLIFE MEDICINE: ESTABLISHING REFERENCE INTERVALS FOR FREE-RANGING AFRICAN LIONS (PANTHERA LEO).

PubMed

Broughton, Heather M; Govender, Danny; Shikwambana, Purvance; Chappell, Patrick; Jolles, Anna

2017-06-01

The International Species Information System has set forth an extensive database of reference intervals for zoologic species, allowing veterinarians and game park officials to distinguish normal health parameters from underlying disease processes in captive wildlife. However, several recent studies comparing reference values from captive and free-ranging animals have found significant variation between populations, necessitating the development of separate reference intervals in free-ranging wildlife to aid in the interpretation of health data. Thus, this study characterizes reference intervals for six biochemical analytes, eleven hematologic or immune parameters, and three hormones using samples from 219 free-ranging African lions ( Panthera leo ) captured in Kruger National Park, South Africa. Using the original sample population, exclusion criteria based on physical examination were applied to yield a final reference population of 52 clinically normal lions. Reference intervals were then generated via 90% confidence intervals on log-transformed data using parametric bootstrapping techniques. In addition to the generation of reference intervals, linear mixed-effect models and generalized linear mixed-effect models were used to model associations of each focal parameter with the following independent variables: age, sex, and body condition score. Age and sex were statistically significant drivers for changes in hepatic enzymes, renal values, hematologic parameters, and leptin, a hormone related to body fat stores. Body condition was positively correlated with changes in monocyte counts. Given the large variation in reference values taken from captive versus free-ranging lions, it is our hope that this study will serve as a baseline for future clinical evaluations and biomedical research targeting free-ranging African lions.

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.

Collaborative derivation of reference intervals for major clinical laboratory tests in Japan.

PubMed

Ichihara, Kiyoshi; Yomamoto, Yoshikazu; Hotta, Taeko; Hosogaya, Shigemi; Miyachi, Hayato; Itoh, Yoshihisa; Ishibashi, Midori; Kang, Dongchon

2016-05-01

Three multicentre studies of reference intervals were conducted recently in Japan. The Committee on Common Reference Intervals of the Japan Society of Clinical Chemistry sought to establish common reference intervals for 40 laboratory tests which were measured in common in the three studies and regarded as well harmonized in Japan. The study protocols were comparable with recruitment mostly from hospital workers with body mass index ≤28 and no medications. Age and sex distributions were made equal to obtain a final data size of 6345 individuals. Between-subgroup differences were expressed as the SD ratio (between-subgroup SD divided by SD representing the reference interval). Between-study differences were all within acceptable levels, and thus the three datasets were merged. By adopting SD ratio ≥0.50 as a guide, sex-specific reference intervals were necessary for 12 assays. Age-specific reference intervals for females partitioned at age 45 were required for five analytes. The reference intervals derived by the parametric method resulted in appreciable narrowing of the ranges by applying the latent abnormal values exclusion method in 10 items which were closely associated with prevalent disorders among healthy individuals. Sex- and age-related profiles of reference values, derived from individuals with no abnormal results in major tests, showed peculiar patterns specific to each analyte. Common reference intervals for nationwide use were developed for 40 major tests, based on three multicentre studies by advanced statistical methods. Sex- and age-related profiles of reference values are of great relevance not only for interpreting test results, but for applying clinical decision limits specified in various clinical guidelines. © The Author(s) 2015.

Rephasing invariant parametrization of flavor mixing

NASA Astrophysics Data System (ADS)

Lee, Tae-Hun

A new rephasing invariant parametrization for the 3 x 3 CKM matrix, called (x, y) parametrization, is introduced and the properties and applications of the parametrization are discussed. The overall phase condition leads this parametrization to have only six rephsing invariant parameters and two constraints. Its simplicity and regularity become apparent when it is applied to the one-loop RGE (renormalization group equations) for the Yukawa couplings. The implications of this parametrization for unification of the Yukawa couplings are also explored.

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

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.

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

NASA Tech Briefs, October 2007

NASA Technical Reports Server (NTRS)

2007-01-01

Topics covered include; Wirelessly Interrogated Position or Displacement Sensors; Ka-Band Radar Terminal Descent Sensor; Metal/Metal Oxide Differential Electrode pH Sensors; Improved Sensing Coils for SQUIDs; Inductive Linear-Position Sensor/Limit-Sensor Units; Hilbert-Curve Fractal Antenna With Radiation- Pattern Diversity; Single-Camera Panoramic-Imaging Systems; Interface Electronic Circuitry for an Electronic Tongue; Inexpensive Clock for Displaying Planetary or Sidereal Time; Efficient Switching Arrangement for (N + 1)/N Redundancy; Lightweight Reflectarray Antenna for 7.115 and 32 GHz; Opto-Electronic Oscillator Using Suppressed Phase Modulation; Alternative Controller for a Fiber-Optic Switch; Strong, Lightweight, Porous Materials; Nanowicks; Lightweight Thermal Protection System for Atmospheric Entry; Rapid and Quiet Drill; Hydrogen Peroxide Concentrator; MMIC Amplifiers for 90 to 130 GHz; Robot Would Climb Steep Terrain; Measuring Dynamic Transfer Functions of Cavitating Pumps; Advanced Resistive Exercise Device; Rapid Engineering of Three-Dimensional, Multicellular Tissues With Polymeric Scaffolds; Resonant Tunneling Spin Pump; Enhancing Spin Filters by Use of Bulk Inversion Asymmetry; Optical Magnetometer Incorporating Photonic Crystals; WGM-Resonator/Tapered-Waveguide White-Light Sensor Optics; Raman-Suppressing Coupling for Optical Parametric Oscillator; CO2-Reduction Primary Cell for Use on Venus; Cold Atom Source Containing Multiple Magneto- Optical Traps; POD Model Reconstruction for Gray-Box Fault Detection; System for Estimating Horizontal Velocity During Descent; Software Framework for Peer Data-Management Services; Autogen Version 2.0; Tracking-Data-Conversion Tool; NASA Enterprise Visual Analysis; Advanced Reference Counting Pointers for Better Performance; C Namelist Facility; and Efficient Mosaicking of Spitzer Space Telescope Images.

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.

Distributed capillary adiabatic tissue homogeneity model in parametric multi-channel blind AIF estimation using DCE-MRI.

PubMed

Kratochvíla, Jiří; Jiřík, Radovan; Bartoš, Michal; Standara, Michal; Starčuk, Zenon; Taxt, Torfinn

2016-03-01

One of the main challenges in quantitative dynamic contrast-enhanced (DCE) MRI is estimation of the arterial input function (AIF). Usually, the signal from a single artery (ignoring contrast dispersion, partial volume effects and flow artifacts) or a population average of such signals (also ignoring variability between patients) is used. Multi-channel blind deconvolution is an alternative approach avoiding most of these problems. The AIF is estimated directly from the measured tracer concentration curves in several tissues. This contribution extends the published methods of multi-channel blind deconvolution by applying a more realistic model of the impulse residue function, the distributed capillary adiabatic tissue homogeneity model (DCATH). In addition, an alternative AIF model is used and several AIF-scaling methods are tested. The proposed method is evaluated on synthetic data with respect to the number of tissue regions and to the signal-to-noise ratio. Evaluation on clinical data (renal cell carcinoma patients before and after the beginning of the treatment) gave consistent results. An initial evaluation on clinical data indicates more reliable and less noise sensitive perfusion parameter estimates. Blind multi-channel deconvolution using the DCATH model might be a method of choice for AIF estimation in a clinical setup. © 2015 Wiley Periodicals, Inc.

A parametric approach for simultaneous bias correction and high-resolution downscaling of climate model rainfall

NASA Astrophysics Data System (ADS)

Mamalakis, Antonios; Langousis, Andreas; Deidda, Roberto; Marrocu, Marino

2017-03-01

Distribution mapping has been identified as the most efficient approach to bias-correct climate model rainfall, while reproducing its statistics at spatial and temporal resolutions suitable to run hydrologic models. Yet its implementation based on empirical distributions derived from control samples (referred to as nonparametric distribution mapping) makes the method's performance sensitive to sample length variations, the presence of outliers, the spatial resolution of climate model results, and may lead to biases, especially in extreme rainfall estimation. To address these shortcomings, we propose a methodology for simultaneous bias correction and high-resolution downscaling of climate model rainfall products that uses: (a) a two-component theoretical distribution model (i.e., a generalized Pareto (GP) model for rainfall intensities above a specified threshold u*, and an exponential model for lower rainrates), and (b) proper interpolation of the corresponding distribution parameters on a user-defined high-resolution grid, using kriging for uncertain data. We assess the performance of the suggested parametric approach relative to the nonparametric one, using daily raingauge measurements from a dense network in the island of Sardinia (Italy), and rainfall data from four GCM/RCM model chains of the ENSEMBLES project. The obtained results shed light on the competitive advantages of the parametric approach, which is proved more accurate and considerably less sensitive to the characteristics of the calibration period, independent of the GCM/RCM combination used. This is especially the case for extreme rainfall estimation, where the GP assumption allows for more accurate and robust estimates, also beyond the range of the available data.

The extension of the parametrization of the radio source coordinates in geodetic VLBI and its impact on the time series analysis

NASA Astrophysics Data System (ADS)

Karbon, Maria; Heinkelmann, Robert; Mora-Diaz, Julian; Xu, Minghui; Nilsson, Tobias; Schuh, Harald

2017-07-01

The radio sources within the most recent celestial reference frame (CRF) catalog ICRF2 are represented by a single, time-invariant coordinate pair. The datum sources were chosen mainly according to certain statistical properties of their position time series. Yet, such statistics are not applicable unconditionally, and also ambiguous. However, ignoring systematics in the source positions of the datum sources inevitably leads to a degradation of the quality of the frame and, therefore, also of the derived quantities such as the Earth orientation parameters. One possible approach to overcome these deficiencies is to extend the parametrization of the source positions, similarly to what is done for the station positions. We decided to use the multivariate adaptive regression splines algorithm to parametrize the source coordinates. It allows a great deal of automation, by combining recursive partitioning and spline fitting in an optimal way. The algorithm finds the ideal knot positions for the splines and, thus, the best number of polynomial pieces to fit the data autonomously. With that we can correct the ICRF2 a priori coordinates for our analysis and eliminate the systematics in the position estimates. This allows us to introduce also special handling sources into the datum definition, leading to on average 30 % more sources in the datum. We find that not only the CPO can be improved by more than 10 % due to the improved geometry, but also the station positions, especially in the early years of VLBI, can benefit greatly.

Parametric Method to Define Area of Allowable Configurations while Changing Position of Restricted Zones

NASA Astrophysics Data System (ADS)

Pritykin, F. N.; Nefedov, D. I.; Rogoza, Yu A.; Zinchenko, Yu V.

2018-03-01

The article presents the findings related to the development of the module for automatic collision detection of the manipulator with restricted zones for virtual motion modeling. It proposes the parametric method for specifying the area of allowable joint configurations. The authors study the cases when restricted zones are specified using the horizontal plane or front-projection planes. The joint coordinate space is specified by rectangular axes in the direction of which the angles defining the displacements in turning pairs are laid off. The authors present the results of modeling which enabled to develop a parametric method for specifying a set of cross-sections defining the shape and position of allowable configurations in different positions of a restricted zone. All joint points that define allowable configurations refer to the indicated sections. The area of allowable configurations is specified analytically by using several kinematic surfaces that limit it. A geometric analysis is developed based on the use of the area of allowable configurations characterizing the position of the manipulator and reported restricted zones. The paper presents numerical calculations related to virtual simulation of the manipulator path performed by the mobile robot Varan when using the developed algorithm and restricted zones. The obtained analytical dependencies allow us to define the area of allowable configurations, which is a knowledge pool to ensure the intelligent control of the manipulator path in a predefined environment. The use of the obtained region to synthesize a joint trajectory makes it possible to correct the manipulator path to foresee and eliminate deadlocks when synthesizing motions along the velocity vector.

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.

Effect of sample size on multi-parametric prediction of tissue outcome in acute ischemic stroke using a random forest classifier

NASA Astrophysics Data System (ADS)

Forkert, Nils Daniel; Fiehler, Jens

2015-03-01

The tissue outcome prediction in acute ischemic stroke patients is highly relevant for clinical and research purposes. It has been shown that the combined analysis of diffusion and perfusion MRI datasets using high-level machine learning techniques leads to an improved prediction of final infarction compared to single perfusion parameter thresholding. However, most high-level classifiers require a previous training and, until now, it is ambiguous how many subjects are required for this, which is the focus of this work. 23 MRI datasets of acute stroke patients with known tissue outcome were used in this work. Relative values of diffusion and perfusion parameters as well as the binary tissue outcome were extracted on a voxel-by- voxel level for all patients and used for training of a random forest classifier. The number of patients used for training set definition was iteratively and randomly reduced from using all 22 other patients to only one other patient. Thus, 22 tissue outcome predictions were generated for each patient using the trained random forest classifiers and compared to the known tissue outcome using the Dice coefficient. Overall, a logarithmic relation between the number of patients used for training set definition and tissue outcome prediction accuracy was found. Quantitatively, a mean Dice coefficient of 0.45 was found for the prediction using the training set consisting of the voxel information from only one other patient, which increases to 0.53 if using all other patients (n=22). Based on extrapolation, 50-100 patients appear to be a reasonable tradeoff between tissue outcome prediction accuracy and effort required for data acquisition and preparation.

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

PubMed

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

2002-03-01

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

Whole-body diffusion kurtosis imaging: initial experience on non-Gaussian diffusion in various organs.

PubMed

Filli, Lukas; Wurnig, Moritz; Nanz, Daniel; Luechinger, Roger; Kenkel, David; Boss, Andreas

2014-12-01

Diffusion kurtosis imaging (DKI) is based on a non-Gaussian diffusion model that should inherently better account for restricted water diffusion within the complex microstructure of most tissues than the conventional diffusion-weighted imaging (DWI), which presumes Gaussian distributed water molecule displacement probability. The aim of this investigation was to test the technical feasibility of in vivo whole-body DKI, probe for organ-specific differences, and compare whole-body DKI and DWI results. Eight healthy subjects underwent whole-body DWI on a clinical 3.0 T magnetic resonance imaging system. Echo-planar images in the axial orientation were acquired at b-values of 0, 150, 300, 500, and 800 mm²/s. Parametrical whole-body maps of the diffusion coefficient (D), the kurtosis (K), and the traditional apparent diffusion coefficient (ADC) were generated. Goodness of fit was compared between DKI and DWI fits using the sums of squared residuals. Data groups were tested for significant differences of the mean by paired Student t tests. Good-quality parametrical whole-body maps of D, K, and ADC could be computed. Compared with ADC values, D values were significantly higher in the cerebral gray matter (by 30%) and white matter (27%), renal cortex (23%) and medulla (21%), spleen (101%), as well as erector spinae muscle (34%) (each P value <0.001). No significant differences between D and ADC were found in the cerebrospinal fluid (P = 0.08) and in the liver (P = 0.13). Curves of DKI fitted the measurement points significantly better than DWI curves did in most organs. Whole-body DKI is technically feasible and may reflect tissue microstructure more meaningfully than whole-body DWI.

Simulation model of converging-diverging (CD) nozzle to improve particle delivery system of deoxyribonucleic acid (DNA)

NASA Astrophysics Data System (ADS)

Sumarsono, Danardono A.; Ibrahim, Fera; Santoso, Satria P.; Sari, Gema P.

2018-02-01

Gene gun is a mechanical device which has been used to deliver DNA vaccine into the cells and tissues by increasing the uptake of DNA plasmid so it can generate a high immune response with less amount of DNA. Nozzle is an important part of the gene gun which used to accelerate DNA in particle form with a gas flow to reach adequate momentum to enter the epidermis of human skin and elicit immune response. We developed new designs of nozzle for gene gun to make DNA uptake more efficient in vaccination. We used Computational Fluid Dynamics (CFD) by Autodesk® Simulation 2015 to simulate static fluid pressure and velocity contour of supersonic wave and parametric distance to predict the accuracy of the new nozzle. The result showed that the nozzle could create a shockwave at the distance parametric to the object from 4 to 5 cm using fluid pressure varied between 0.8-1.2 MPa. This is indication a possibility that the DNA particle could penetrate under the mammalian skin. For the future research step, this new nozzle model could be considered for development the main component of the DNA delivery system in vaccination in vivo

Do dual-thread orthodontic mini-implants improve bone/tissue mechanical retention?

PubMed

Lin, Yang-Sung; Chang, Yau-Zen; Yu, Jian-Hong; Lin, Chun-Li

2014-12-01

The aim of this study was to understand whether the pitch relationship between micro and macro thread designs with a parametrical relationship in a dual-thread mini-implant can improve primary stability. Three types of mini-implants consisting of single-thread (ST) (0.75 mm pitch in whole length), dual-thread A (DTA) with double-start 0.375 mm pitch, and dual-thread B (DTB) with single-start 0.2 mm pitch in upper 2-mm micro thread region for performing insertion and pull-out testing. Histomorphometric analysis was performed in these specimens in evaluating peri-implant bone defects using a non-contact vision measuring system. The maximum inserted torque (Tmax) in type DTA was found to be the smallest significantly, but corresponding values found no significant difference between ST and DTB. The largest pull-out strength (Fmax) in the DTA mini-implant was found significantly greater than that for the ST mini-implant regardless of implant insertion orientation. Mini-implant engaged the cortical bone well as observed in ST and DTA types. Dual-thread mini-implant with correct micro thread pitch (parametrical relationship with macro thread pitch) in the cortical bone region can improve primary stability and enhanced mechanical retention.

A Comparative Study of Average, Linked Mastoid, and REST References for ERP Components Acquired during fMRI

PubMed Central

Yang, Ping; Fan, Chenggui; Wang, Min; Li, Ling

2017-01-01

In simultaneous electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) studies, average reference (AR), and digitally linked mastoid (LM) are popular re-referencing techniques in event-related potential (ERP) analyses. However, they may introduce their own physiological signals and alter the EEG/ERP outcome. A reference electrode standardization technique (REST) that calculated a reference point at infinity was proposed to solve this problem. To confirm the advantage of REST in ERP analyses of synchronous EEG-fMRI studies, we compared the reference effect of AR, LM, and REST on task-related ERP results of a working memory task during an fMRI scan. As we hypothesized, we found that the adopted reference did not change the topography map of ERP components (N1 and P300 in the present study), but it did alter the task-related effect on ERP components. LM decreased or eliminated the visual working memory (VWM) load effect on P300, and the AR distorted the distribution of VWM location-related effect at left posterior electrodes as shown in the statistical parametric scalp mapping (SPSM) of N1. ERP cortical source estimates, which are independent of the EEG reference choice, were used as the golden standard to infer the relative utility of different references on the ERP task-related effect. By comparison, REST reference provided a more integrated and reasonable result. These results were further confirmed by the results of fMRI activations and a corresponding EEG-only study. Thus, we recommend the REST, especially with a realistic head model, as the optimal reference method for ERP data analysis in simultaneous EEG-fMRI studies. PMID:28529472

Statistical considerations for harmonization of the global multicenter study on reference values.

PubMed

Ichihara, Kiyoshi

2014-05-15

The global multicenter study on reference values coordinated by the Committee on Reference Intervals and Decision Limits (C-RIDL) of the IFCC was launched in December 2011, targeting 45 commonly tested analytes with the following objectives: 1) to derive reference intervals (RIs) country by country using a common protocol, and 2) to explore regionality/ethnicity of reference values by aligning test results among the countries. To achieve these objectives, it is crucial to harmonize 1) the protocol for recruitment and sampling, 2) statistical procedures for deriving the RI, and 3) test results through measurement of a panel of sera in common. For harmonized recruitment, very lenient inclusion/exclusion criteria were adopted in view of differences in interpretation of what constitutes healthiness by different cultures and investigators. This policy may require secondary exclusion of individuals according to the standard of each country at the time of deriving RIs. An iterative optimization procedure, called the latent abnormal values exclusion (LAVE) method, can be applied to automate the process of refining the choice of reference individuals. For global comparison of reference values, test results must be harmonized, based on the among-country, pair-wise linear relationships of test values for the panel. Traceability of reference values can be ensured based on values assigned indirectly to the panel through collaborative measurement of certified reference materials. The validity of the adopted strategies is discussed in this article, based on interim results obtained to date from five countries. Special considerations are made for dissociation of RIs by parametric and nonparametric methods and between-country difference in the effect of body mass index on reference values. Copyright © 2014 Elsevier B.V. All rights reserved.

A Comparative Study of Average, Linked Mastoid, and REST References for ERP Components Acquired during fMRI.

PubMed

Yang, Ping; Fan, Chenggui; Wang, Min; Li, Ling

2017-01-01

In simultaneous electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) studies, average reference (AR), and digitally linked mastoid (LM) are popular re-referencing techniques in event-related potential (ERP) analyses. However, they may introduce their own physiological signals and alter the EEG/ERP outcome. A reference electrode standardization technique (REST) that calculated a reference point at infinity was proposed to solve this problem. To confirm the advantage of REST in ERP analyses of synchronous EEG-fMRI studies, we compared the reference effect of AR, LM, and REST on task-related ERP results of a working memory task during an fMRI scan. As we hypothesized, we found that the adopted reference did not change the topography map of ERP components (N1 and P300 in the present study), but it did alter the task-related effect on ERP components. LM decreased or eliminated the visual working memory (VWM) load effect on P300, and the AR distorted the distribution of VWM location-related effect at left posterior electrodes as shown in the statistical parametric scalp mapping (SPSM) of N1. ERP cortical source estimates, which are independent of the EEG reference choice, were used as the golden standard to infer the relative utility of different references on the ERP task-related effect. By comparison, REST reference provided a more integrated and reasonable result. These results were further confirmed by the results of fMRI activations and a corresponding EEG-only study. Thus, we recommend the REST, especially with a realistic head model, as the optimal reference method for ERP data analysis in simultaneous EEG-fMRI studies.

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.

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.

[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.

Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

NASA Astrophysics Data System (ADS)

Endres, Christopher J.; Hammoud, Dima A.; Pomper, Martin G.

2011-04-01

When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [11C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (kr2) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BPND). Compared with standard SRTM, either coupling of kr2 across regions or constraining kr2 to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BPND between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining kr2 to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the variance of parameter estimates and may better discriminate between-group differences in specific binding.

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

R-parametrization and its role in classification of linear multivariable feedback systems

NASA Technical Reports Server (NTRS)

Chen, Robert T. N.

1988-01-01

A classification of all the compensators that stabilize a given general plant in a linear, time-invariant multi-input, multi-output feedback system is developed. This classification, along with the associated necessary and sufficient conditions for stability of the feedback system, is achieved through the introduction of a new parameterization, referred to as R-Parameterization, which is a dual of the familiar Q-Parameterization. The classification is made to the stability conditions of the compensators and the plant by themselves; and necessary and sufficient conditions are based on the stability of Q and R themselves.

Advanced propulsion system concept for hybrid vehicles

NASA Technical Reports Server (NTRS)

Bhate, S.; Chen, H.; Dochat, G.

1980-01-01

A series hybrid system, utilizing a free piston Stirling engine with a linear alternator, and a parallel hybrid system, incorporating a kinematic Stirling engine, are analyzed for various specified reference missions/vehicles ranging from a small two passenger commuter vehicle to a van. Parametric studies for each configuration, detail tradeoff studies to determine engine, battery and system definition, short term energy storage evaluation, and detail life cycle cost studies were performed. Results indicate that the selection of a parallel Stirling engine/electric, hybrid propulsion system can significantly reduce petroleum consumption by 70 percent over present conventional vehicles.

Navigation analysis for Viking 1979, option B

NASA Technical Reports Server (NTRS)

Mitchell, P. H.

1971-01-01

A parametric study performed for 48 trans-Mars reference missions in support of the Viking program is reported. The launch dates cover several months in the year 1979, and each launch date has multiple arrival dates in 1980. A plot of launch versus arrival dates with case numbers designated for reference purposes is included. The analysis consists of the computation of statistical covariance matrices based on certain assumptions about the ground-based tracking systems. The error model statistics are listed in tables. Tracking systems were assumed at three sites: Goldstone, California; Canberra, Australia; and Madrid, Spain. The tracking data consisted of range and Doppler measurements taken during the tracking intervals starting at E-30(d) and ending at E-10(d) for the control data and ending at E-18(h) for the knowledge data. The control and knowledge covariance matrices were delivered to the Planetary Mission Analysis Branch for inputs into a delta V dispersion analysis.

It's time to move on from the bell curve.

PubMed

Robinson, Lawrence R

2017-11-01

The bell curve was first described in the 18th century by de Moivre and Gauss to depict the distribution of binomial events, such as coin tossing, or repeated measures of physical objects. In the 19th and 20th centuries, the bell curve was appropriated, or perhaps misappropriated, to apply to biologic and social measures across people. For many years we used it to derive reference values for our electrophysiologic studies. There is, however, no reason to believe that electrophysiologic measures should approximate a bell-curve distribution, and empiric evidence suggests they do not. The concept of using mean ± 2 standard deviations should be abandoned. Reference values are best derived by using non-parametric analyses, such as percentile values. This proposal aligns with the recommendation of the recent normative data task force of the American Association of Neuromuscular & Electrodiagnostic Medicine and follows sound statistical principles. Muscle Nerve 56: 859-860, 2017. © 2017 Wiley Periodicals, Inc.

On-Line Tracking Controller for Brushless DC Motor Drives Using Artificial Neural Networks

NASA Technical Reports Server (NTRS)

Rubaai, Ahmed

1996-01-01

A real-time control architecture is developed for time-varying nonlinear brushless dc motors operating in a high performance drives environment. The developed control architecture possesses the capabilities of simultaneous on-line identification and control. The dynamics of the motor are modeled on-line and controlled using an artificial neural network, as the system runs. The control architecture combines the experience and dependability of adaptive tracking systems with potential and promise of the neural computing technology. The sensitivity of real-time controller to parametric changes that occur during training is investigated. Such changes are usually manifested by rapid changes in the load of the brushless motor drives. This sudden change in the external load is simulated for the sigmoidal and sinusoidal reference tracks. The ability of the neuro-controller to maintain reasonable tracking accuracy in the presence of external noise is also verified for a number of desired reference trajectories.

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.

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.

Demonstration of optical parametric gain generation in the 1 μm regime based on a photonic crystal fiber pumped by a picosecond mode-locked ytterbium-doped fiber laser

NASA Astrophysics Data System (ADS)

Zhang, Lei; Yang, Si-Gang; Wang, Xiao-Jian; Gou, Dou-Dou; Chen, Hong-Wei; Chen, Ming-Hua; Xie, Shi-Zhong

2014-01-01

We report the experimental demonstration of the optical parametric gain generation in the 1 μm regime based on a photonic crystal fiber (PCF) with a zero group velocity dispersion (GVD) wavelength of 1062 nm pumped by a homemade tunable picosecond mode-locked ytterbium-doped fiber laser. A broad parametric gain band is obtained by pumping the PCF in the anomalous GVD regime with a relatively low power. Two separated narrow parametric gain bands are observed by pumping the PCF in the normal GVD regime. The peak of the parametric gain profile can be tuned from 927 to 1038 nm and from 1099 to 1228 nm. This widely tunable parametric gain band can be used for a broad band optical parametric amplifier, large span wavelength conversion or a tunable optical parametric oscillator.

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.

Development, Evaluation, and Sensitivity Analysis of Parametric Finite Element Whole-Body Human Models in Side Impacts.

PubMed

Hwang, Eunjoo; Hu, Jingwen; Chen, Cong; Klein, Katelyn F; Miller, Carl S; Reed, Matthew P; Rupp, Jonathan D; Hallman, Jason J

2016-11-01

Occupant stature and body shape may have significant effects on injury risks in motor vehicle crashes, but the current finite element (FE) human body models (HBMs) only represent occupants with a few sizes and shapes. Our recent studies have demonstrated that, by using a mesh morphing method, parametric FE HBMs can be rapidly developed for representing a diverse population. However, the biofidelity of those models across a wide range of human attributes has not been established. Therefore, the objectives of this study are 1) to evaluate the accuracy of HBMs considering subject-specific geometry information, and 2) to apply the parametric HBMs in a sensitivity analysis for identifying the specific parameters affecting body responses in side impact conditions. Four side-impact tests with two male post-mortem human subjects (PMHSs) were selected to evaluate the accuracy of the geometry and impact responses of the morphed HBMs. For each PMHS test, three HBMs were simulated to compare with the test results: the original Total Human Model for Safety (THUMS) v4.01 (O-THUMS), a parametric THUMS (P-THUMS), and a subject-specific THUMS (S-THUMS). The P-THUMS geometry was predicted from only age, sex, stature, and BMI using our statistical geometry models of skeleton and body shape, while the S-THUMS geometry was based on each PMHS's CT data. The simulation results showed a preliminary trend that the correlations between the PTHUMS- predicted impact responses and the four PMHS tests (mean-CORA: 0.84, 0.78, 0.69, 0.70) were better than those between the O-THUMS and the normalized PMHS responses (mean-CORA: 0.74, 0.72, 0.55, 0.63), while they are similar to the correlations between S-THUMS and the PMHS tests (mean-CORA: 0.85, 0.85, 0.67, 0.72). The sensitivity analysis using the PTHUMS showed that, in side impact conditions, the HBM skeleton and body shape geometries as well as the body posture were more important in modeling the occupant impact responses than the bone and soft tissue material properties and the padding stiffness with the given parameter ranges. More investigations are needed to further support these findings.

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

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

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

Analysis of Parasite and Other Skewed Counts

PubMed Central

Alexander, Neal

2012-01-01

Objective To review methods for the statistical analysis of parasite and other skewed count data. Methods Statistical methods for skewed count data are described and compared, with reference to those used over a ten year period of Tropical Medicine and International Health. Two parasitological datasets are used for illustration. Results Ninety papers were identified, 89 with descriptive and 60 with inferential analysis. A lack of clarity is noted in identifying measures of location, in particular the Williams and geometric mean. The different measures are compared, emphasizing the legitimacy of the arithmetic mean for skewed data. In the published papers, the t test and related methods were often used on untransformed data, which is likely to be invalid. Several approaches to inferential analysis are described, emphasizing 1) non-parametric methods, while noting that they are not simply comparisons of medians, and 2) generalized linear modelling, in particular with the negative binomial distribution. Additional methods, such as the bootstrap, with potential for greater use are described. Conclusions Clarity is recommended when describing transformations and measures of location. It is suggested that non-parametric methods and generalized linear models are likely to be sufficient for most analyses. PMID:22943299

Mediation analysis with time varying exposures and mediators

PubMed Central

VanderWeele, Tyler J.; Tchetgen Tchetgen, Eric J.

2016-01-01

Summary In this paper we consider causal mediation analysis when exposures and mediators vary over time. We give non-parametric identification results, discuss parametric implementation, and also provide a weighting approach to direct and indirect effects based on combining the results of two marginal structural models. We also discuss how our results give rise to a causal interpretation of the effect estimates produced from longitudinal structural equation models. When there are time-varying confounders affected by prior exposure and mediator, natural direct and indirect effects are not identified. However, we define a randomized interventional analogue of natural direct and indirect effects that are identified in this setting. The formula that identifies these effects we refer to as the “mediational g-formula.” When there is no mediation, the mediational g-formula reduces to Robins’ regular g-formula for longitudinal data. When there are no time-varying confounders affected by prior exposure and mediator values, then the mediational g-formula reduces to a longitudinal version of Pearl’s mediation formula. However, the mediational g-formula itself can accommodate both mediation and time-varying confounders and constitutes a general approach to mediation analysis with time-varying exposures and mediators. PMID:28824285

Layout design-based research on optimization and assessment method for shipbuilding workshop

NASA Astrophysics Data System (ADS)

Liu, Yang; Meng, Mei; Liu, Shuang

2013-06-01

The research study proposes to examine a three-dimensional visualization program, emphasizing on improving genetic algorithms through the optimization of a layout design-based standard and discrete shipbuilding workshop. By utilizing a steel processing workshop as an example, the principle of minimum logistic costs will be implemented to obtain an ideological equipment layout, and a mathematical model. The objectiveness is to minimize the total necessary distance traveled between machines. An improved control operator is implemented to improve the iterative efficiency of the genetic algorithm, and yield relevant parameters. The Computer Aided Tri-Dimensional Interface Application (CATIA) software is applied to establish the manufacturing resource base and parametric model of the steel processing workshop. Based on the results of optimized planar logistics, a visual parametric model of the steel processing workshop is constructed, and qualitative and quantitative adjustments then are applied to the model. The method for evaluating the results of the layout is subsequently established through the utilization of AHP. In order to provide a mode of reference to the optimization and layout of the digitalized production workshop, the optimized discrete production workshop will possess a certain level of practical significance.

Multivariable control of the Space Shuttle remote manipulator system using H2 and H(infinity) optimization. M.S. Thesis - Massachusetts Inst. of Tech.

NASA Technical Reports Server (NTRS)

Prakash, OM, II

1991-01-01

Three linear controllers are desiged to regulate the end effector of the Space Shuttle Remote Manipulator System (SRMS) operating in Position Hold Mode. In this mode of operation, jet firings of the Orbiter can be treated as disturbances while the controller tries to keep the end effector stationary in an orbiter-fixed reference frame. The three design techniques used include: the Linear Quadratic Regulator (LQR), H2 optimization, and H-infinity optimization. The nonlinear SRMS is linearized by modelling the effects of the significant nonlinearities as uncertain parameters. Each regulator design is evaluated for robust stability in light of the parametric uncertanties using both the small gain theorem with an H-infinity norm and the less conservative micro-analysis test. All three regulator designs offer significant improvement over the current system on the nominal plant. Unfortunately, even after dropping performance requirements and designing exclusively for robust stability, robust stability cannot be achieved. The SRMS suffers from lightly damped poles with real parametric uncertainties. Such a system renders the micro-analysis test, which allows for complex peturbations, too conservative.

Forensic discrimination of copper wire using trace element concentrations.

PubMed

Dettman, Joshua R; Cassabaum, Alyssa A; Saunders, Christopher P; Snyder, Deanna L; Buscaglia, JoAnn

2014-08-19

Copper may be recovered as evidence in high-profile cases such as thefts and improvised explosive device incidents; comparison of copper samples from the crime scene and those associated with the subject of an investigation can provide probative associative evidence and investigative support. A solution-based inductively coupled plasma mass spectrometry method for measuring trace element concentrations in high-purity copper was developed using standard reference materials. The method was evaluated for its ability to use trace element profiles to statistically discriminate between copper samples considering the precision of the measurement and manufacturing processes. The discriminating power was estimated by comparing samples chosen on the basis of the copper refining and production process to represent the within-source (samples expected to be similar) and between-source (samples expected to be different) variability using multivariate parametric- and empirical-based data simulation models with bootstrap resampling. If the false exclusion rate is set to 5%, >90% of the copper samples can be correctly determined to originate from different sources using a parametric-based model and >87% with an empirical-based approach. These results demonstrate the potential utility of the developed method for the comparison of copper samples encountered as forensic evidence.

Mediation analysis with time varying exposures and mediators.

PubMed

VanderWeele, Tyler J; Tchetgen Tchetgen, Eric J

2017-06-01

In this paper we consider causal mediation analysis when exposures and mediators vary over time. We give non-parametric identification results, discuss parametric implementation, and also provide a weighting approach to direct and indirect effects based on combining the results of two marginal structural models. We also discuss how our results give rise to a causal interpretation of the effect estimates produced from longitudinal structural equation models. When there are time-varying confounders affected by prior exposure and mediator, natural direct and indirect effects are not identified. However, we define a randomized interventional analogue of natural direct and indirect effects that are identified in this setting. The formula that identifies these effects we refer to as the "mediational g-formula." When there is no mediation, the mediational g-formula reduces to Robins' regular g-formula for longitudinal data. When there are no time-varying confounders affected by prior exposure and mediator values, then the mediational g-formula reduces to a longitudinal version of Pearl's mediation formula. However, the mediational g-formula itself can accommodate both mediation and time-varying confounders and constitutes a general approach to mediation analysis with time-varying exposures and mediators.

Visual to Parametric Interaction (V2PI)

PubMed Central

Maiti, Dipayan; Endert, Alex; North, Chris

2013-01-01

Typical data visualizations result from linear pipelines that start by characterizing data using a model or algorithm to reduce the dimension and summarize structure, and end by displaying the data in a reduced dimensional form. Sensemaking may take place at the end of the pipeline when users have an opportunity to observe, digest, and internalize any information displayed. However, some visualizations mask meaningful data structures when model or algorithm constraints (e.g., parameter specifications) contradict information in the data. Yet, due to the linearity of the pipeline, users do not have a natural means to adjust the displays. In this paper, we present a framework for creating dynamic data displays that rely on both mechanistic data summaries and expert judgement. The key is that we develop both the theory and methods of a new human-data interaction to which we refer as “ Visual to Parametric Interaction” (V2PI). With V2PI, the pipeline becomes bi-directional in that users are embedded in the pipeline; users learn from visualizations and the visualizations adjust to expert judgement. We demonstrate the utility of V2PI and a bi-directional pipeline with two examples. PMID:23555552

Comparison of System Identification Techniques for the Hydraulic Manipulator Test Bed (HMTB)

NASA Technical Reports Server (NTRS)

Morris, A. Terry

1996-01-01

In this thesis linear, dynamic, multivariable state-space models for three joints of the ground-based Hydraulic Manipulator Test Bed (HMTB) are identified. HMTB, housed at the NASA Langley Research Center, is a ground-based version of the Dexterous Orbital Servicing System (DOSS), a representative space station manipulator. The dynamic models of the HMTB manipulator will first be estimated by applying nonparametric identification methods to determine each joint's response characteristics using various input excitations. These excitations include sum of sinusoids, pseudorandom binary sequences (PRBS), bipolar ramping pulses, and chirp input signals. Next, two different parametric system identification techniques will be applied to identify the best dynamical description of the joints. The manipulator is localized about a representative space station orbital replacement unit (ORU) task allowing the use of linear system identification methods. Comparisons, observations, and results of both parametric system identification techniques are discussed. The thesis concludes by proposing a model reference control system to aid in astronaut ground tests. This approach would allow the identified models to mimic on-orbit dynamic characteristics of the actual flight manipulator thus providing astronauts with realistic on-orbit responses to perform space station tasks in a ground-based environment.

Hyperbolic and semi-parametric models in finance

NASA Astrophysics Data System (ADS)

Bingham, N. H.; Kiesel, Rüdiger

2001-02-01

The benchmark Black-Scholes-Merton model of mathematical finance is parametric, based on the normal/Gaussian distribution. Its principal parametric competitor, the hyperbolic model of Barndorff-Nielsen, Eberlein and others, is briefly discussed. Our main theme is the use of semi-parametric models, incorporating the mean vector and covariance matrix as in the Markowitz approach, plus a non-parametric part, a scalar function incorporating features such as tail-decay. Implementation is also briefly discussed.

Comparison of classification methods for voxel-based prediction of acute ischemic stroke outcome following intra-arterial intervention

NASA Astrophysics Data System (ADS)

Winder, Anthony J.; Siemonsen, Susanne; Flottmann, Fabian; Fiehler, Jens; Forkert, Nils D.

2017-03-01

Voxel-based tissue outcome prediction in acute ischemic stroke patients is highly relevant for both clinical routine and research. Previous research has shown that features extracted from baseline multi-parametric MRI datasets have a high predictive value and can be used for the training of classifiers, which can generate tissue outcome predictions for both intravenous and conservative treatments. However, with the recent advent and popularization of intra-arterial thrombectomy treatment, novel research specifically addressing the utility of predictive classi- fiers for thrombectomy intervention is necessary for a holistic understanding of current stroke treatment options. The aim of this work was to develop three clinically viable tissue outcome prediction models using approximate nearest-neighbor, generalized linear model, and random decision forest approaches and to evaluate the accuracy of predicting tissue outcome after intra-arterial treatment. Therefore, the three machine learning models were trained, evaluated, and compared using datasets of 42 acute ischemic stroke patients treated with intra-arterial thrombectomy. Classifier training utilized eight voxel-based features extracted from baseline MRI datasets and five global features. Evaluation of classifier-based predictions was performed via comparison to the known tissue outcome, which was determined in follow-up imaging, using the Dice coefficient and leave-on-patient-out cross validation. The random decision forest prediction model led to the best tissue outcome predictions with a mean Dice coefficient of 0.37. The approximate nearest-neighbor and generalized linear model performed equally suboptimally with average Dice coefficients of 0.28 and 0.27 respectively, suggesting that both non-linearity and machine learning are desirable properties of a classifier well-suited to the intra-arterial tissue outcome prediction problem.

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.

Polarization image segmentation of radiofrequency ablated porcine myocardial tissue

PubMed Central

Ahmad, Iftikhar; Gribble, Adam; Murtza, Iqbal; Ikram, Masroor; Pop, Mihaela; Vitkin, Alex

2017-01-01

Optical polarimetry has previously imaged the spatial extent of a typical radiofrequency ablated (RFA) lesion in myocardial tissue, exhibiting significantly lower total depolarization at the necrotic core compared to healthy tissue, and intermediate values at the RFA rim region. Here, total depolarization in ablated myocardium was used to segment the total depolarization image into three (core, rim and healthy) zones. A local fuzzy thresholding algorithm was used for this multi-region segmentation, and then compared with a ground truth segmentation obtained from manual demarcation of RFA core and rim regions on the histopathology image. Quantitative comparison of the algorithm segmentation results was performed with evaluation metrics such as dice similarity coefficient (DSC = 0.78 ± 0.02 and 0.80 ± 0.02), sensitivity (Sn = 0.83 ± 0.10 and 0.91 ± 0.08), specificity (Sp = 0.76 ± 0.17 and 0.72 ± 0.17) and accuracy (Acc = 0.81 ± 0.09 and 0.71 ± 0.10) for RFA core and rim regions, respectively. This automatic segmentation of parametric depolarization images suggests a novel application of optical polarimetry, namely its use in objective RFA image quantification. PMID:28380013

Multi-atlas-based CT synthesis from conventional MRI with patch-based refinement for MRI-based radiotherapy planning

NASA Astrophysics Data System (ADS)

Lee, Junghoon; Carass, Aaron; Jog, Amod; Zhao, Can; Prince, Jerry L.

2017-02-01

Accurate CT synthesis, sometimes called electron density estimation, from MRI is crucial for successful MRI-based radiotherapy planning and dose computation. Existing CT synthesis methods are able to synthesize normal tissues but are unable to accurately synthesize abnormal tissues (i.e., tumor), thus providing a suboptimal solution. We propose a multiatlas- based hybrid synthesis approach that combines multi-atlas registration and patch-based synthesis to accurately synthesize both normal and abnormal tissues. Multi-parametric atlas MR images are registered to the target MR images by multi-channel deformable registration, from which the atlas CT images are deformed and fused by locally-weighted averaging using a structural similarity measure (SSIM). Synthetic MR images are also computed from the registered atlas MRIs by using the same weights used for the CT synthesis; these are compared to the target patient MRIs allowing for the assessment of the CT synthesis fidelity. Poor synthesis regions are automatically detected based on the fidelity measure and refined by a patch-based synthesis. The proposed approach was tested on brain cancer patient data, and showed a noticeable improvement for the tumor region.

Bubble dynamics in viscoelastic soft tissue in high-intensity focal ultrasound thermal therapy.

PubMed

Zilonova, E; Solovchuk, M; Sheu, T W H

2018-01-01

The present study is aimed to investigate bubble dynamics in a soft tissue, to which HIFU's continuous harmonic pulse is applied by introducing a viscoelastic cavitation model. After a comparison of some existing cavitation models, we decided to employ Gilmore-Akulichev model. This chosen cavitation model should be coupled with the Zener viscoelastic model in order to be able to simulate soft tissue features such as elasticity and relaxation time. The proposed Gilmore-Akulichev-Zener model was investigated for exploring cavitation dynamics. The parametric study led us to the conclusion that the elasticity and viscosity both damp bubble oscillations, whereas the relaxation effect depends mainly on the period of the ultrasound wave. The similar influence of elasticity, viscosity and relaxation time on the temperature inside the bubble can be observed. Cavitation heat source terms (corresponding to viscous damping and pressure wave radiated by bubble collapse) were obtained based on the proposed model to examine the cavitation significance during the treatment process. Their maximum values both overdominate the acoustic ultrasound term in HIFU applications. Elasticity was revealed to damp a certain amount of deposited heat for both cavitation terms. Copyright © 2017 Elsevier B.V. All rights reserved.

Coupled B-snake grids and constrained thin-plate splines for analysis of 2-D tissue deformations from tagged MRI.

PubMed

Amini, A A; Chen, Y; Curwen, R W; Mani, V; Sun, J

1998-06-01

Magnetic resonance imaging (MRI) is unique in its ability to noninvasively and selectively alter tissue magnetization and create tagged patterns within a deforming body such as the heart muscle. The resulting patterns define a time-varying curvilinear coordinate system on the tissue, which we track with coupled B-snake grids. B-spline bases provide local control of shape, compact representation, and parametric continuity. Efficient spline warps are proposed which warp an area in the plane such that two embedded snake grids obtained from two tagged frames are brought into registration, interpolating a dense displacement vector field. The reconstructed vector field adheres to the known displacement information at the intersections, forces corresponding snakes to be warped into one another, and for all other points in the plane, where no information is available, a C1 continuous vector field is interpolated. The implementation proposed in this paper improves on our previous variational-based implementation and generalizes warp methods to include biologically relevant contiguous open curves, in addition to standard landmark points. The methods are validated with a cardiac motion simulator, in addition to in-vivo tagging data sets.

Multi-atlas-based CT synthesis from conventional MRI with patch-based refinement for MRI-based radiotherapy planning.

PubMed

Lee, Junghoon; Carass, Aaron; Jog, Amod; Zhao, Can; Prince, Jerry L

2017-02-01

Accurate CT synthesis, sometimes called electron density estimation, from MRI is crucial for successful MRI-based radiotherapy planning and dose computation. Existing CT synthesis methods are able to synthesize normal tissues but are unable to accurately synthesize abnormal tissues (i.e., tumor), thus providing a suboptimal solution. We propose a multi-atlas-based hybrid synthesis approach that combines multi-atlas registration and patch-based synthesis to accurately synthesize both normal and abnormal tissues. Multi-parametric atlas MR images are registered to the target MR images by multi-channel deformable registration, from which the atlas CT images are deformed and fused by locally-weighted averaging using a structural similarity measure (SSIM). Synthetic MR images are also computed from the registered atlas MRIs by using the same weights used for the CT synthesis; these are compared to the target patient MRIs allowing for the assessment of the CT synthesis fidelity. Poor synthesis regions are automatically detected based on the fidelity measure and refined by a patch-based synthesis. The proposed approach was tested on brain cancer patient data, and showed a noticeable improvement for the tumor region.

Simulation of long-term fatigue damage in bioprosthetic heart valves: effects of leaflet and stent elastic properties

PubMed Central

Martin, Caitlin

2014-01-01

One of the major failure modes of bioprosthetic heart valves (BHVs) is noncalcific structural deterioration due to fatigue of the tissue leaflets; yet, the mechanisms of fatigue are not well understood. BHV durability is primarily assessed based on visual inspection of the leaflets following accelerated wear testing. In this study, we developed a computational framework to simulate BHV leaflet fatigue, which is both efficient and quantitative, making it an attractive alternative to traditional accelerated wear testing. We utilize a phenomenological soft tissue fatigue damage model developed previously to describe the stress softening and permanent set of the glutaraldehyde-treated bovine pericardium leaflets in BHVs subjected to cyclic loading. A parametric study was conducted to determine the effects of altered leaflet and stent elastic properties on the fatigue of the leaflets. The simulation results show that heterogeneity of the leaflet elastic properties, poor leaflet coaptation, and little stent-tip deflection may accelerate leaflet fatigue, which agrees with clinical findings. Therefore, the developed framework may be an invaluable tool for evaluating leaflet durability in new tissue valve designs, including traditional BHVs as well as new transcatheter valves. PMID:24092257

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

PubMed Central

2011-01-01

With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set. PMID:21836824

An ISRU Propellant Production System to Fully Fuel a Mars Ascent Vehicle

NASA Technical Reports Server (NTRS)

Kleinhenz, Julie; Paz, Aaron

2017-01-01

ISRU of Mars resources was base lined in 2009 Design Reference Architecture (DRA) 5.0, but only for Oxygen production using atmospheric CO2The Methane (LCH4) needed for ascent propulsion of the Mars Ascent Vehicle (MAV) would need to be brought from Earth. HOWEVER: Extracting water from the Martian Regolith enables the production of both Oxygen and Methane from Mars resources Water resources could also be used for other applications including: Life support, radiation shielding, plant growth, etc. Water extraction was not base lined in DRA5.0 due to perceived difficulties and complexity in processing regolith. The NASA Evolvable Mars Campaign (EMC) requested studies to look at the quantitative benefits and trades of using Mars water ISRU Phase 1: Examined architecture scenarios for regolith water retrieval. Completed October 2015Phase 2: Deep dive of one architecture concept to look at end-to-end system size, mass, power of a LCH4LO2 ISRU production system.Evolvable Mars CampaignPre-deployed Mars ascent vehicle (MAV)4 crew membersPropellants: Oxygen MethaneGenerate a system model to roll up mass power of a full ISRU system and enable parametric trade studies. Leverage models from previous studies and technology development programs Anchor with mass power performance from existing hardware. Whenever possible used reference-able (published) numbers for traceability.Modular approach to allow subsystem trades and parametric studies. Propellant mass needs taken from most recently published MAV study:Polsgrove, T. et al. (2015), AIAA2015-4416MAV engines operate at mixture ratios (oxygen: methane) between 3:1 and 3.5:1, whereas the Sabatier reactor produces at a 4:1 ratio. Therefore:Methane production is the driving requirement-Excess Oxygen will be produced.

Post traumatic brain perfusion SPECT analysis using reconstructed ROI maps of radioactive microsphere derived cerebral blood flow and statistical parametric mapping

PubMed Central

McGoron, Anthony J; Capille, Michael; Georgiou, Michael F; Sanchez, Pablo; Solano, Juan; Gonzalez-Brito, Manuel; Kuluz, John W

2008-01-01

Background Assessment of cerebral blood flow (CBF) by SPECT could be important in the management of patients with severe traumatic brain injury (TBI) because changes in regional CBF can affect outcome by promoting edema formation and intracranial pressure elevation (with cerebral hyperemia), or by causing secondary ischemic injury including post-traumatic stroke. The purpose of this study was to establish an improved method for evaluating regional CBF changes after TBI in piglets. Methods The focal effects of moderate traumatic brain injury (TBI) on cerebral blood flow (CBF) by SPECT cerebral blood perfusion (CBP) imaging in an animal model were investigated by parallelized statistical techniques. Regional CBF was measured by radioactive microspheres and by SPECT 2 hours after injury in sham-operated piglets versus those receiving severe TBI by fluid-percussion injury to the left parietal lobe. Qualitative SPECT CBP accuracy was assessed against reference radioactive microsphere regional CBF measurements by map reconstruction, registration and smoothing. Cerebral hypoperfusion in the test group was identified at the voxel level using statistical parametric mapping (SPM). Results A significant area of hypoperfusion (P < 0.01) was found as a response to the TBI. Statistical mapping of the reference microsphere CBF data confirms a focal decrease found with SPECT and SPM. Conclusion The suitability of SPM for application to the experimental model and ability to provide insight into CBF changes in response to traumatic injury was validated by the SPECT SPM result of a decrease in CBP at the left parietal region injury area of the test group. Further study and correlation of this characteristic lesion with long-term outcomes and auxiliary diagnostic modalities is critical to developing more effective critical care treatment guidelines and automated medical imaging processing techniques. PMID:18312639

Post traumatic brain perfusion SPECT analysis using reconstructed ROI maps of radioactive microsphere derived cerebral blood flow and statistical parametric mapping.

PubMed

McGoron, Anthony J; Capille, Michael; Georgiou, Michael F; Sanchez, Pablo; Solano, Juan; Gonzalez-Brito, Manuel; Kuluz, John W

2008-02-29

Assessment of cerebral blood flow (CBF) by SPECT could be important in the management of patients with severe traumatic brain injury (TBI) because changes in regional CBF can affect outcome by promoting edema formation and intracranial pressure elevation (with cerebral hyperemia), or by causing secondary ischemic injury including post-traumatic stroke. The purpose of this study was to establish an improved method for evaluating regional CBF changes after TBI in piglets. The focal effects of moderate traumatic brain injury (TBI) on cerebral blood flow (CBF) by SPECT cerebral blood perfusion (CBP) imaging in an animal model were investigated by parallelized statistical techniques. Regional CBF was measured by radioactive microspheres and by SPECT 2 hours after injury in sham-operated piglets versus those receiving severe TBI by fluid-percussion injury to the left parietal lobe. Qualitative SPECT CBP accuracy was assessed against reference radioactive microsphere regional CBF measurements by map reconstruction, registration and smoothing. Cerebral hypoperfusion in the test group was identified at the voxel level using statistical parametric mapping (SPM). A significant area of hypoperfusion (P < 0.01) was found as a response to the TBI. Statistical mapping of the reference microsphere CBF data confirms a focal decrease found with SPECT and SPM. The suitability of SPM for application to the experimental model and ability to provide insight into CBF changes in response to traumatic injury was validated by the SPECT SPM result of a decrease in CBP at the left parietal region injury area of the test group. Further study and correlation of this characteristic lesion with long-term outcomes and auxiliary diagnostic modalities is critical to developing more effective critical care treatment guidelines and automated medical imaging processing techniques.

Pediatric Reference Intervals for Free Thyroxine and Free Triiodothyronine by Equilibrium Dialysis-Liquid Chromatography-Tandem Mass Spectrometry.

PubMed

La'ulu, Sonia L; Rasmussen, Kyle J; Straseski, Joely A

2016-03-05

Thyroid hormone concentrations fluctuate during growth and development. To accurately diagnose thyroid disease in pediatric patients, reference intervals (RIs) should be established with appropriate age groups from an adequate number of healthy subjects using the most exact methods possible. Obtaining statistically useful numbers of healthy patients is particularly challenging for pediatric populations. The objective of this study was to determine non-parametric RIs for free thyroxine (fT4) and free triiodothyronine (fT3) using equilibrium dialysis-high performance liquid chromatography-tandem mass spectrometry with over 2200 healthy children 6 months-17 years of age. Subjects were negative for both thyroglobulin and thyroid peroxidase autoantibodies and had normal thyrotropin concentrations. The study included 2213 children (1129 boys and 1084 girls), with at least 120 subjects (average of 125) from each year of life, except for the 6 month to 1 year age group (n=96). Non-parametric RIs (95th percentile) for fT4 were: 18.0-34.7 pmol/L (boys and girls, 6 months-6 years) and 14.2-25.7 pmol/L (boys and girls, 7-17 years). RIs for fT3 were: 5.8-13.1 pmol/L (girls, 6 months-6 years); 5.7-11.8 pmol/L (boys, 6 months-6 years); 5.7-10.0 pmol/L (boys and girls, 7-12 years); 4.5-8.6 pmol/L (girls, 13-17 years); and 5.2-9.4 pmol/L (boys, 13-17 years). Numerous significant differences were observed between pediatric age groups and previously established adult ranges. This emphasizes the need for well-characterized RIs for thyroid hormones in the pediatric population.

Pediatric Reference Intervals for Free Thyroxine and Free Triiodothyronine by Equilibrium Dialysis-Liquid Chromatography-Tandem Mass Spectrometry

PubMed Central

La’ulu, Sonia L.; Rasmussen, Kyle J.; Straseski, Joely A.

2016-01-01

Objective: Thyroid hormone concentrations fluctuate during growth and development. To accurately diagnose thyroid disease in pediatric patients, reference intervals (RIs) should be established with appropriate age groups from an adequate number of healthy subjects using the most exact methods possible. Obtaining statistically useful numbers of healthy patients is particularly challenging for pediatric populations. The objective of this study was to determine non-parametric RIs for free thyroxine (fT4) and free triiodothyronine (fT3) using equilibrium dialysis-high performance liquid chromatography-tandem mass spectrometry with over 2200 healthy children 6 months-17 years of age. Methods: Subjects were negative for both thyroglobulin and thyroid peroxidase autoantibodies and had normal thyrotropin concentrations. The study included 2213 children (1129 boys and 1084 girls), with at least 120 subjects (average of 125) from each year of life, except for the 6 month to 1 year age group (n=96). Results: Non-parametric RIs (95th percentile) for fT4 were: 18.0-34.7 pmol/L (boys and girls, 6 months-6 years) and 14.2-25.7 pmol/L (boys and girls, 7-17 years). RIs for fT3 were: 5.8-13.1 pmol/L (girls, 6 months-6 years); 5.7-11.8 pmol/L (boys, 6 months-6 years); 5.7-10.0 pmol/L (boys and girls, 7-12 years); 4.5-8.6 pmol/L (girls, 13-17 years); and 5.2-9.4 pmol/L (boys, 13-17 years). Conclusion: Numerous significant differences were observed between pediatric age groups and previously established adult ranges. This emphasizes the need for well-characterized RIs for thyroid hormones in the pediatric population. PMID:26758817

Bioequivalence assessment of ambroxol tablet after a single oral dose administration to healthy male volunteers.

PubMed

Lee, Hee Joo; Joung, Sun Koung; Kim, Yoon Gyoon; Yoo, Jeong-Yeon; Han, Sang Beom

2004-01-01

A bioequivalence study of the ambroxol hydrochloride tablets was conducted. Twenty-four healthy male Korean volunteers received each medicine at the ambroxol hydrochloride dose of 30 mg in a 2 x 2 cross-over study. There was a 1-week washout period between the doses. Plasma concentrations of ambroxol were monitored by a high-performance liquid chromatography (HPLC) for over a period of 24h after the administration. AUC(t) (the area under the plasma concentration-time curve from time 0 to last sampling time, 24h) was calculated by the linear-log trapezoidal rule method. C(max) (maximum plasma drug concentration) and T(max) (time to reach C(max)) were compiled from the plasma concentration-time data. Analysis of variance was carried out using logarithmically transformed AUC(t) and C(max), and untransformed T(max). The geometric mean of AUC(t) was 495.8 ng ml(-1)h(-1) (test medication) and 468.3 ng ml(-1)h(-1) (reference medication). C(max) of 61.5 and 57.3 ng ml(-1) were achieved for the test and the reference medication, respectively. The point estimates and 90% confidence intervals for AUC(t) (parametric) and C(max) (parametric) were, in point estimate (90% confidence interval), 1.058 (0.989-1.134) and 1.073 (1.007-1.142), respectively, satisfying the bioequivalence criteria of the European Committee for Proprietary Medicinal Products and the US Food and Drug Administration Guidelines. The corresponding value of T(max) was 0.229 (0.015-0.444). These results indicate that the two medications of ambroxol hydrochloride are bioequivalent and, thus, may be prescribed interchangeably.

Vers une Theorie de l'Education/Apprentissage

NASA Astrophysics Data System (ADS)

Goulet, Georges

1986-12-01

The author has attempted to clarify the idea of the curriculum as a distinct area of knowledge which is characteristic of educational science within the wider framework of educational sciences. Inspired by the method of a comparative analysis which was developed by George Z. Bereday, the author analyzes the data which are used referring to a typology of definitions based on the Aristotelian idea of causality. In the article a meta-theory of the curriculum is proposed and defined based on the consensus discovered among the authors whose views are analyzed. The present curriculum is examined with respect to its original meaning as proposed by John Dewey in order to establish the process of organized and intentional education/learning. However, the plan or programme of education/learning which is often identified as the notion of the curriculum, is presented here as being only one of the parametres determining the nature of the whole process of organized education/learning. The convergence of the remaining four parametres constitutes a special process of education/learning realized to suit each learner as the beneficiary agent (learner), the initiating agent (intervener), the physical and social environment as well as the knowledge or the culture to be transmitted. The theory goes on to deal with the paradigmatic nature of the process and the four levels of intentionality characterizing the planning and actualization of each process. The theory presents the curriculum as if it were a phenomenon which functions like an open system, i.e. where the total or the `Gestalt' constitutes the realized learning by each learner, referring to the laws of equifinality and homeostasis. The article closes by presenting a spiral model which seeks to represent the web of real and perceptual influences which contribute to the learning aimed at by the whole institution of education/learning.

RCSED—A Value-added Reference Catalog of Spectral Energy Distributions of 800,299 Galaxies in 11 Ultraviolet, Optical, and Near-infrared Bands: Morphologies, Colors, Ionized Gas, and Stellar Population Properties

NASA Astrophysics Data System (ADS)

Chilingarian, Igor V.; Zolotukhin, Ivan Yu.; Katkov, Ivan Yu.; Melchior, Anne-Laure; Rubtsov, Evgeniy V.; Grishin, Kirill A.

2017-02-01

We present RCSED, the value-added Reference Catalog of Spectral Energy Distributions of galaxies, which contains homogenized spectrophotometric data for 800,299 low- and intermediate-redshift galaxies (0.007< z< 0.6) selected from the Sloan Digital Sky Survey spectroscopic sample. Accessible from the Virtual Observatory (VO) and complemented with detailed information on galaxy properties obtained with state-of-the-art data analysis, RCSED enables direct studies of galaxy formation and evolution over the last 5 Gyr. We provide tabulated color transformations for galaxies of different morphologies and luminosities, and analytic expressions for the red sequence shape in different colors. RCSED comprises integrated k-corrected photometry in up to 11 ultraviolet, optical, and near-infrared bands published by the GALEX, SDSS, and UKIDSS wide-field imaging surveys; results of the stellar population fitting of SDSS spectra including best-fitting templates, velocity dispersions, parameterized star formation histories, and stellar metallicities computed for instantaneous starburst and exponentially declining star formation models; parametric and non-parametric emission line fluxes and profiles; and gas phase metallicities. We link RCSED to the Galaxy Zoo morphological classification and galaxy bulge+disk decomposition results of Simard et al. We construct the color-magnitude, Faber-Jackson, and mass-metallicity relations; compare them with the literature; and discuss systematic errors of the galaxy properties presented in our catalog. RCSED is accessible from the project web site and via VO simple spectrum access and table access services using VO-compliant applications. We describe several examples of SQL queries to the database. Finally, we briefly discuss existing and future scientific applications of RCSED and prospective catalog extensions to higher redshifts and different wavelengths. .

ISC-GEM: Global Instrumental Earthquake Catalogue (1900-2009), I. Data collection from early instrumental seismological bulletins

NASA Astrophysics Data System (ADS)

Di Giacomo, Domenico; Harris, James; Villaseñor, Antonio; Storchak, Dmitry A.; Engdahl, E. Robert; Lee, William H. K.

2015-02-01

In order to produce a new global reference earthquake catalogue based on instrumental data covering the last 100+ years of global earthquakes, we collected, digitized and processed an unprecedented amount of printed early instrumental seismological bulletins with fundamental parametric data for relocating and reassessing the magnitude of earthquakes that occurred in the period between 1904 and 1970. This effort was necessary in order to produce an earthquake catalogue with locations and magnitudes as homogeneous as possible. The parametric data obtained and processed during this work fills a large gap in electronic bulletin data availability. This new dataset complements the data publicly available in the International Seismological Centre (ISC) Bulletin starting in 1964. With respect to the amplitude-period data necessary to re-compute magnitude, we searched through the global collection of printed bulletins stored at the ISC and entered relevant station parametric data into the database. As a result, over 110,000 surface and body-wave amplitude-period pairs for re-computing standard magnitudes MS and mb were added to the ISC database. To facilitate earthquake relocation, different sources have been used to retrieve body-wave arrival times. These were entered into the database using optical character recognition methods (International Seismological Summary, 1918-1959) or manually (e.g., British Association for the Advancement of Science, 1913-1917). In total, ∼1,000,000 phase arrival times were added to the ISC database for large earthquakes that occurred in the time interval 1904-1970. The selection of earthquakes for which data was added depends on time period and magnitude: for the early years of last century (until 1917) only very large earthquakes were selected for processing (M ⩾ 7.5), whereas in the periods 1918-1959 and 1960-2009 the magnitude thresholds are 6.25 and 5.5, respectively. Such a selection was mainly dictated by limitations in time and funding. Although the newly available parametric data is only a subset of the station data available in the printed bulletins, its electronic availability will be important for any future study of earthquakes that occurred during the early instrumental period.

Parametric Cost Deployment

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1995-01-01

Parametric cost analysis is a mathematical approach to estimating cost. Parametric cost analysis uses non-cost parameters, such as quality characteristics, to estimate the cost to bring forth, sustain, and retire a product. This paper reviews parametric cost analysis and shows how it can be used within the cost deployment process.

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.

Investigation of the photon statistics of parametric fluorescence in a traveling-wave parametric amplifier by means of self-homodyne tomography.

PubMed

Vasilyev, M; Choi, S K; Kumar, P; D'Ariano, G M

1998-09-01

Photon-number distributions for parametric fluorescence from a nondegenerate optical parametric amplifier are measured with a novel self-homodyne technique. These distributions exhibit the thermal-state character predicted by theory. However, a difference between the fluorescence gain and the signal gain of the parametric amplifier is observed. We attribute this difference to a change in the signal-beam profile during the traveling-wave pulsed amplification process.

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.

A Cartesian parametrization for the numerical analysis of material instability

DOE PAGES

Mota, Alejandro; Chen, Qiushi; Foulk, III, James W.; ...

2016-02-25

We examine four parametrizations of the unit sphere in the context of material stability analysis by means of the singularity of the acoustic tensor. We then propose a Cartesian parametrization for vectors that lie a cube of side length two and use these vectors in lieu of unit normals to test for the loss of the ellipticity condition. This parametrization is then used to construct a tensor akin to the acoustic tensor. It is shown that both of these tensors become singular at the same time and in the same planes in the presence of a material instability. Furthermore, themore » performance of the Cartesian parametrization is compared against the other parametrizations, with the results of these comparisons showing that in general, the Cartesian parametrization is more robust and more numerically efficient than the others.« less

A Cartesian parametrization for the numerical analysis of material instability

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

Mota, Alejandro; Chen, Qiushi; Foulk, III, James W.

We examine four parametrizations of the unit sphere in the context of material stability analysis by means of the singularity of the acoustic tensor. We then propose a Cartesian parametrization for vectors that lie a cube of side length two and use these vectors in lieu of unit normals to test for the loss of the ellipticity condition. This parametrization is then used to construct a tensor akin to the acoustic tensor. It is shown that both of these tensors become singular at the same time and in the same planes in the presence of a material instability. Furthermore, themore » performance of the Cartesian parametrization is compared against the other parametrizations, with the results of these comparisons showing that in general, the Cartesian parametrization is more robust and more numerically efficient than the others.« less

Multicentre physiological reference intervals for serum concentrations of immunoglobulins A, G and M, complement C3c and C4 measured with Tina-Quant reagents systems.

PubMed

Fuentes-Arderiu, Xavier; Alonso-Gregorio, Eduardo; Alvarez-Funes, Virtudes; Ambrós-Marigómez, Carmen; Coca-Fábregas, Lluís; Cruz-Placer, Marta; Díaz-Fernández, Julián; Pinel-Julián, María Pilar; Gutiérrez-Cecchini, Beatriz; Herrero-Bernal, Pilar; Sempere-Alcocer, Marcos; García-Caballero, Francisca; Del Mar Larrea-Ortiz-Quintana, María; La-Torre-Marcellán, Pedro; Del Señor López-Vélez, María; Mar-Medina, Carmen; Martín-Oncina, Javier; Rodríguez-Hernández, María Victoria; Romero-Sotomayor, María Victoria; Serrano-López, Cándido; Sicilia-Enríquez-de-Salamanca, Adolfo; Velasco-Romero, Ana María; Juvé-Cuxart, Santiago

2007-01-01

Clinical laboratories seeking accreditation for compliance with ISO 15189:2003 need to demonstrate that the physiological reference intervals communicated to all users of the laboratory service are appropriate for the patient population served and for the measurement systems used. In the case of immunological quantities, few articles have been published in peer-reviewed journals. A total of 21 clinical laboratories in different regions of Spain collaborated in identifying reference individuals and determining adult reference intervals for some immunological quantities measured using RD/Hitachi Modular Analytics analysers and Tina-Quant reagent systems. These immunological quantities are the mass concentrations of immunoglobulin A, immunoglobulin G, immunoglobulin M, complement C3c and complement C4 in serum. All the logistic work was carried out in co-operation with the supplier of the reagents and analysers (Roche Diagnostics España, S.L., Sant Cugat del Vallès, Catalonia, Spain). From the set of reference values obtained by each laboratory, multicentre reference limits were estimated non-parametrically. The reference intervals estimated in this study for concentrations of serum components under consideration are: complement C3c, 0.62-1.64 g/L for women and men; complement C4, 0.14-0.72 g/L for women and men; immunoglobulin A, 0.89-4.80 g/L for women and men; immunoglobulin G, 6.5-14.3 g/L for women and men; and immunoglobulin M, 0.48-3.38 g/L for women and 0.41-2.46 g/L for men.

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 ...

Testing Neuronal Accounts of Anisotropic Motion Perception with Computational Modelling

PubMed Central

Wong, William; Chiang Price, Nicholas Seow

2014-01-01

There is an over-representation of neurons in early visual cortical areas that respond most strongly to cardinal (horizontal and vertical) orientations and directions of visual stimuli, and cardinal- and oblique-preferring neurons are reported to have different tuning curves. Collectively, these neuronal anisotropies can explain two commonly-reported phenomena of motion perception – the oblique effect and reference repulsion – but it remains unclear whether neuronal anisotropies can simultaneously account for both perceptual effects. We show in psychophysical experiments that reference repulsion and the oblique effect do not depend on the duration of a moving stimulus, and that brief adaptation to a single direction simultaneously causes a reference repulsion in the orientation domain, and the inverse of the oblique effect in the direction domain. We attempted to link these results to underlying neuronal anisotropies by implementing a large family of neuronal decoding models with parametrically varied levels of anisotropy in neuronal direction-tuning preferences, tuning bandwidths and spiking rates. Surprisingly, no model instantiation was able to satisfactorily explain our perceptual data. We argue that the oblique effect arises from the anisotropic distribution of preferred directions evident in V1 and MT, but that reference repulsion occurs separately, perhaps reflecting a process of categorisation occurring in higher-order cortical areas. PMID:25409518

Parametric binary dissection

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.; Crockett, Thomas W.; Nicol, David M.

1993-01-01

Binary dissection is widely used to partition non-uniform domains over parallel computers. This algorithm does not consider the perimeter, surface area, or aspect ratio of the regions being generated and can yield decompositions that have poor communication to computation ratio. Parametric Binary Dissection (PBD) is a new algorithm in which each cut is chosen to minimize load + lambda x(shape). In a 2 (or 3) dimensional problem, load is the amount of computation to be performed in a subregion and shape could refer to the perimeter (respectively surface) of that subregion. Shape is a measure of communication overhead and the parameter permits us to trade off load imbalance against communication overhead. When A is zero, the algorithm reduces to plain binary dissection. This algorithm can be used to partition graphs embedded in 2 or 3-d. Load is the number of nodes in a subregion, shape the number of edges that leave that subregion, and lambda the ratio of time to communicate over an edge to the time to compute at a node. An algorithm is presented that finds the depth d parametric dissection of an embedded graph with n vertices and e edges in O(max(n log n, de)) time, which is an improvement over the O(dn log n) time of plain binary dissection. Parallel versions of this algorithm are also presented; the best of these requires O((n/p) log(sup 3)p) time on a p processor hypercube, assuming graphs of bounded degree. How PBD is applied to 3-d unstructured meshes and yields partitions that are better than those obtained by plain dissection is described. Its application to the color image quantization problem is also discussed, in which samples in a high-resolution color space are mapped onto a lower resolution space in a way that minimizes the color error.

Monitoring glucose, calcium, and magnesium levels in saliva as a non-invasive analysis by sequential injection multi-parametric determination.

PubMed

Machado, Ana; Maneiras, Rui; Bordalo, Adriano A; Mesquita, Raquel B R

2018-08-15

The use of saliva for diagnose and surveillance of systemic illnesses, and general health has been arousing great interest worldwide, emerging as a highly desirable goal in healthcare. The collection is non-invasive, stress-free, inexpensive, and simple representing a major asset. Glucose, calcium, and magnesium concentration are three major parameters evaluated in clinical context due to their essential role in a wide range of biochemical reactions, and consequently many health disorders. In this work, a spectrophotometric sequential injection method is described for the fast screening of glucose, calcium, and magnesium in saliva samples. The glucose determination reaction involves the oxidation of the aldehyde functional group present in glucose with simultaneous reduction of 3,5-dinitrosalicylic acid (DNS) to 3-amino, 5-nitrosalicylic acid under alkaline conditions, followed by the development of colour. The determination of both metals is based on their reaction with cresolphtalein complexone (CPC), and the interference of calcium in the magnesium determination minimized by ethylene glycol-bis[β-aminoethyl ether]-N,N,N',N'-tetraacetic acid (EGTA). The developed multi-parametric method enabled dynamic ranges of 50 - 300 mg/dL for glucose, 0.1 - 2 mg/dL for calcium, and 0.1 - 0.5 mg/dL for magnesium. Determination rates of 28, 60, 52 h -1 were achieved for glucose, calcium, and magnesium, respectively. Less than 300 µL of saliva is required for the multi-parametric determination due to saliva viscosity and inherent necessity of dilution prior to analysis. RSDs lower than 5% were obtained, and the results agreed with those obtained by reference methods, while recovery tests confirmed its accuracy. Copyright © 2018 Elsevier B.V. All rights reserved.

Modelling Pollutant Dispersion in a Street Network

NASA Astrophysics Data System (ADS)

Salem, N. Ben; Garbero, V.; Salizzoni, P.; Lamaison, G.; Soulhac, L.

2015-04-01

This study constitutes a further step in the analysis of the performances of a street network model to simulate atmospheric pollutant dispersion in urban areas. The model, named SIRANE, is based on the decomposition of the urban atmosphere into two sub-domains: the urban boundary layer, whose dynamics is assumed to be well established, and the urban canopy, represented as a series of interconnected boxes. Parametric laws govern the mass exchanges between the boxes under the assumption that the pollutant dispersion within the canopy can be fully simulated by modelling three main bulk transfer phenomena: channelling along street axes, transfers at street intersections, and vertical exchange between street canyons and the overlying atmosphere. Here, we aim to evaluate the reliability of the parametrizations adopted to simulate these phenomena, by focusing on their possible dependence on the external wind direction. To this end, we test the model against concentration measurements within an idealized urban district whose geometrical layout closely matches the street network represented in SIRANE. The analysis is performed for an urban array with a fixed geometry and a varying wind incidence angle. The results show that the model provides generally good results with the reference parametrizations adopted in SIRANE and that its performances are quite robust for a wide range of the model parameters. This proves the reliability of the street network approach in simulating pollutant dispersion in densely built city districts. The results also show that the model performances may be improved by considering a dependence of the wind fluctuations at street intersections and of the vertical exchange velocity on the direction of the incident wind. This opens the way for further investigations to clarify the dependence of these parameters on wind direction and street aspect ratios.

Constellation Program Life-cycle Cost Analysis Model (LCAM)

NASA Technical Reports Server (NTRS)

Prince, Andy; Rose, Heidi; Wood, James

2008-01-01

The Constellation Program (CxP) is NASA's effort to replace the Space Shuttle, return humans to the moon, and prepare for a human mission to Mars. The major elements of the Constellation Lunar sortie design reference mission architecture are shown. Unlike the Apollo Program of the 1960's, affordability is a major concern of United States policy makers and NASA management. To measure Constellation affordability, a total ownership cost life-cycle parametric cost estimating capability is required. This capability is being developed by the Constellation Systems Engineering and Integration (SE&I) Directorate, and is called the Lifecycle Cost Analysis Model (LCAM). The requirements for LCAM are based on the need to have a parametric estimating capability in order to do top-level program analysis, evaluate design alternatives, and explore options for future systems. By estimating the total cost of ownership within the context of the planned Constellation budget, LCAM can provide Program and NASA management with the cost data necessary to identify the most affordable alternatives. LCAM is also a key component of the Integrated Program Model (IPM), an SE&I developed capability that combines parametric sizing tools with cost, schedule, and risk models to perform program analysis. LCAM is used in the generation of cost estimates for system level trades and analyses. It draws upon the legacy of previous architecture level cost models, such as the Exploration Systems Mission Directorate (ESMD) Architecture Cost Model (ARCOM) developed for Simulation Based Acquisition (SBA), and ATLAS. LCAM is used to support requirements and design trade studies by calculating changes in cost relative to a baseline option cost. Estimated costs are generally low fidelity to accommodate available input data and available cost estimating relationships (CERs). LCAM is capable of interfacing with the Integrated Program Model to provide the cost estimating capability for that suite of tools.

Task-based detectability comparison of exponential transformation of free-response operating characteristic (EFROC) curve and channelized Hotelling observer (CHO)

NASA Astrophysics Data System (ADS)

Khobragade, P.; Fan, Jiahua; Rupcich, Franco; Crotty, Dominic J.; Gilat Schmidt, Taly

2016-03-01

This study quantitatively evaluated the performance of the exponential transformation of the free-response operating characteristic curve (EFROC) metric, with the Channelized Hotelling Observer (CHO) as a reference. The CHO has been used for image quality assessment of reconstruction algorithms and imaging systems and often it is applied to study the signal-location-known cases. The CHO also requires a large set of images to estimate the covariance matrix. In terms of clinical applications, this assumption and requirement may be unrealistic. The newly developed location-unknown EFROC detectability metric is estimated from the confidence scores reported by a model observer. Unlike the CHO, EFROC does not require a channelization step and is a non-parametric detectability metric. There are few quantitative studies available on application of the EFROC metric, most of which are based on simulation data. This study investigated the EFROC metric using experimental CT data. A phantom with four low contrast objects: 3mm (14 HU), 5mm (7HU), 7mm (5 HU) and 10 mm (3 HU) was scanned at dose levels ranging from 25 mAs to 270 mAs and reconstructed using filtered backprojection. The area under the curve values for CHO (AUC) and EFROC (AFE) were plotted with respect to different dose levels. The number of images required to estimate the non-parametric AFE metric was calculated for varying tasks and found to be less than the number of images required for parametric CHO estimation. The AFE metric was found to be more sensitive to changes in dose than the CHO metric. This increased sensitivity and the assumption of unknown signal location may be useful for investigating and optimizing CT imaging methods. Future work is required to validate the AFE metric against human observers.

Neuroscience imaging enabled by new highly tunable and high peak power femtosecond lasers

NASA Astrophysics Data System (ADS)

Hakulinen, T.; Klein, J.

2017-02-01

Neuroscience applications benefit from recent developments in industrial femtosecond laser technology. New laser sources provide several megawatts of peak power at wavelength of 1040 nm, which enables simultaneous optogenetics photoactivation of tens or even hundreds of neurons using red shifted opsins. Another recent imaging trend is to move towards longer wavelengths, which would enable access to deeper layers of tissue due to lower scattering and lower absorption in the tissue. Femtosecond lasers pumping a non-collinear optical parametric amplifier (NOPA) enable the access to longer wavelengths with high peak powers. High peak powers of >10 MW at 1300 nm and 1700 nm allow effective 3-photon excitation of green and red shifted calcium indicators respectively and access to deeper, sub-cortex layers of the brain. Early results include in vivo detection of spontaneous activity in hippocampus within an intact mouse brain, where neurons express GCaMP6 activated in a 3-photon process at 1320 nm.

Adaptive plasticity in mammalian masticatory joints

NASA Astrophysics Data System (ADS)

Ravosa, Matthew J.; Kunwar, Ravinder; Nicholson, Elisabeth K.; Klopp, Emily B.; Pinchoff, Jessie; Stock, Stuart R.; Stack, M. Sharon; Hamrick, Mark W.

2006-08-01

Genetically similar white rabbits raised on diets of different mechanical properties, as well as wild-type and myostatin-deficient mice raised on similar diets, were compared to assess the postweaning effects of elevated masticatory loads due to increased jaw-adductor muscle and bite forces on the proportions and properties of the mandibular symphysis and temporomandibular joint (TMJ). Microcomputed tomography (microCT) was used to quantify bone structure at a series of equidistant external and internal sites in coronal sections for a series of joint locations. Discriminant function analyses and non-parametric ANOVAs were used to characterize variation in biomineralization within and between loading cohorts. In both species, long-term excessive loading results in larger joint proportions, thicker articular and cortical bone, and increased biomineralization of hard tissues. Such adaptive plasticity appears designed to maintain the postnatal integrity of masticatory joint systems for a primary loading environment(s). This behavioral signal may be increasingly mitigated in older organisms by the interplay between adaptive and degradative joint tissue responses.

Parametric convergence sensitivity and validation of a finite element model of the human lumbar spine.

PubMed

Ayturk, Ugur M; Puttlitz, Christian M

2011-08-01

The primary objective of this study was to generate a finite element model of the human lumbar spine (L1-L5), verify mesh convergence for each tissue constituent and perform an extensive validation using both kinematic/kinetic and stress/strain data. Mesh refinement was accomplished via convergence of strain energy density (SED) predictions for each spinal tissue. The converged model was validated based on range of motion, intradiscal pressure, facet force transmission, anterolateral cortical bone strain and anterior longitudinal ligament deformation predictions. Changes in mesh resolution had the biggest impact on SED predictions under axial rotation loading. Nonlinearity of the moment-rotation curves was accurately simulated and the model predictions on the aforementioned parameters were in good agreement with experimental data. The validated and converged model will be utilised to study the effects of degeneration on the lumbar spine biomechanics, as well as to investigate the mechanical underpinning of the contemporary treatment strategies.

Novel cardiac magnetic resonance biomarkers: native T1 and extracellular volume myocardial mapping.

PubMed

Cannaò, Paola Maria; Altabella, Luisa; Petrini, Marcello; Alì, Marco; Secchi, Francesco; Sardanelli, Francesco

2016-04-28

Cardiac magnetic resonance (CMR) is a non-invasive diagnostic tool playing a key role in the assessment of cardiac morphology and function as well as in tissue characterization. Late gadolinium enhancement is a fundamental CMR technique for detecting focal or regional abnormalities such as scar tissue, replacement fibrosis, or inflammation using qualitative, semi-quantitative, or quantitative methods, but not allowing for evaluating the whole myocardium in the presence of diffuse disease. The novel T1 mapping approach permits a quantitative assessment of the entire myocardium providing a voxel-by-voxel map of native T1 relaxation time, obtained before the intravenous administration of gadolinium-based contrast material. Combining T1 data obtained before and after contrast injection, it is also possible to calculate the voxel-by-voxel extracellular volume (ECV), resulting in another myocardial parametric map. This article describes technical challenges and clinical perspectives of these two novel CMR biomarkers: myocardial native T1 and ECV mapping.

The role of fractional calculus in modeling biological phenomena: A review

NASA Astrophysics Data System (ADS)

Ionescu, C.; Lopes, A.; Copot, D.; Machado, J. A. T.; Bates, J. H. T.

2017-10-01

This review provides the latest developments and trends in the application of fractional calculus (FC) in biomedicine and biology. Nature has often showed to follow rather simple rules that lead to the emergence of complex phenomena as a result. Of these, the paper addresses the properties in respiratory lung tissue, whose natural solutions arise from the midst of FC in the form of non-integer differ-integral solutions and non-integer parametric models. Diffusion of substances in human body, e.g. drug diffusion, is also a phenomena well known to be captured with such mathematical models. FC has been employed in neuroscience to characterize the generation of action potentials and spiking patters but also in characterizing bio-systems (e.g. vegetable tissues). Despite the natural complexity, biological systems belong as well to this class of systems, where FC has offered parsimonious yet accurate models. This review paper is a collection of results and literature reports who are essential to any versed engineer with multidisciplinary applications and bio-medical in particular.

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...

Inverse finite element methods for extracting elastic-poroviscoelastic properties of cartilage and other soft tissues from indentation

NASA Astrophysics Data System (ADS)

Namani, Ravi

Mechanical properties are essential for understanding diseases that afflict various soft tissues, such as osteoarthritic cartilage and hypertension which alters cardiovascular arteries. Although the linear elastic modulus is routinely measured for hard materials, standard methods are not available for extracting the nonlinear elastic, linear elastic and time-dependent properties of soft tissues. Consequently, the focus of this work is to develop indentation methods for soft biological tissues; since analytical solutions are not available for the general context, finite element simulations are used. First, parametric studies of finite indentation of hyperelastic layers are performed to examine if indentation has the potential to identify nonlinear elastic behavior. To answer this, spherical, flat-ended conical and cylindrical tips are examined and the influence of thickness is exploited. Also the influence of the specimen/substrate boundary condition (slip or non-slip) is clarified. Second, a new inverse method---the hyperelastic extraction algorithm (HPE)---was developed to extract two nonlinear elastic parameters from the indentation force-depth data, which is the basic measurement in an indentation test. The accuracy of the extracted parameters and the influence of noise in measurements on this accuracy were obtained. This showed that the standard Berkovitch tip could only extract one parameter with sufficient accuracy, since the indentation force-depth curve has limited sensitivity to both nonlinear elastic parameters. Third, indentation methods for testing tissues from small animals were explored. New methods for flat-ended conical tips are derived. These account for practical test issues like the difficulty in locating the surface or soft specimens. Also, finite element simulations are explored to elucidate the influence of specimen curvature on the indentation force-depth curve. Fourth, the influence of inhomogeneity and material anisotropy on the extracted "average" linear elastic modulus was studied. The focus here is on murine tibial cartilage, since recent experiments have shown that the modulus measured by a 15 mum tip is considerably larger than that obtained from a 90 mum tip. It is shown that a depth-dependent modulus could give rise to such a size effect. Lastly, parametric studies were performed within the small strain setting to understand the influence of permeability and viscoelastic properties on the indentation stress-relaxation response. The focus here is on cartilage, and specific test protocols (single-step vs. multi-step stress relaxation) are explored. An inverse algorithm was developed to extract the poroviscoelastic parameters. A sensitivity study using this algorithm shows that the instantaneous elastic modulus (which is a measure of the viscous relaxation) can be extracted with very good accuracy, but the permeability and long-time relaxation constant cannot be extracted with good accuracy. The thesis concludes with implications of these studies. The potential and limitations of indentation tests for studying cartilage and other soft tissues is discussed.

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.

Parameter variation effects on temperature elevation in a steady-state, one-dimensional thermal model for millimeter wave exposure of one- and three-layer human tissue.

PubMed

Kanezaki, Akio; Hirata, Akimasa; Watanabe, Soichi; Shirai, Hiroshi

2010-08-21

The present study describes theoretical parametric analysis of the steady-state temperature elevation in one-dimensional three-layer (skin, fat and muscle) and one-layer (skin only) models due to millimeter-wave exposure. The motivation of this fundamental investigation is that some variability of warmth sensation in the human skin has been reported. An analytical solution for a bioheat equation was derived by using the Laplace transform for the one-dimensional human models. Approximate expressions were obtained to investigate the dependence of temperature elevation on different thermal and tissue thickness parameters. It was shown that the temperature elevation on the body surface decreases monotonically with the blood perfusion rate, heat conductivity and heat transfer from the body to air. Also revealed were the conditions where maximum and minimum surface temperature elevations were observed for different thermal and tissue thickness parameters. The surface temperature elevation in the three-layer model is 1.3-2.8 times greater than that in the one-layer model. The main reason for this difference is attributed to the adiabatic nature of the fat layer. By considering the variation range of thermal and tissue thickness parameters which causes the maximum and minimum temperature elevations, the dominant parameter influencing the surface temperature elevation was found to be the heat transfer coefficient between the body surface and air.

Parametric nanomechanical amplification at very high frequency.

PubMed

Karabalin, R B; Feng, X L; Roukes, M L

2009-09-01

Parametric resonance and amplification are important in both fundamental physics and technological applications. Here we report very high frequency (VHF) parametric resonators and mechanical-domain amplifiers based on nanoelectromechanical systems (NEMS). Compound mechanical nanostructures patterned by multilayer, top-down nanofabrication are read out by a novel scheme that parametrically modulates longitudinal stress in doubly clamped beam NEMS resonators. Parametric pumping and signal amplification are demonstrated for VHF resonators up to approximately 130 MHz and provide useful enhancement of both resonance signal amplitude and quality factor. We find that Joule heating and reduced thermal conductance in these nanostructures ultimately impose an upper limit to device performance. We develop a theoretical model to account for both the parametric response and nonequilibrium thermal transport in these composite nanostructures. The results closely conform to our experimental observations, elucidate the frequency and threshold-voltage scaling in parametric VHF NEMS resonators and sensors, and establish the ultimate sensitivity limits of this approach.

Parametric amplification in MoS2 drum resonator.

PubMed

Prasad, Parmeshwar; Arora, Nishta; Naik, A K

2017-11-30

Parametric amplification is widely used in diverse areas from optics to electronic circuits to enhance low level signals by varying relevant system parameters. Parametric amplification has also been performed in several micro-nano resonators including nano-electromechanical system (NEMS) resonators based on a two-dimensional (2D) material. Here, we report the enhancement of mechanical response in a MoS 2 drum resonator using degenerate parametric amplification. We use parametric pumping to modulate the spring constant of the MoS 2 resonator and achieve a 10 dB amplitude gain. We also demonstrate quality factor enhancement in the resonator with parametric amplification. We investigate the effect of cubic nonlinearity on parametric amplification and show that it limits the gain of the mechanical resonator. Amplifying ultra-small displacements at room temperature and understanding the limitations of the amplification in these devices is key for using these devices for practical applications.

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.

Problems of the design of low-noise input devices. [parametric amplifiers

NASA Technical Reports Server (NTRS)

Manokhin, V. M.; Nemlikher, Y. A.; Strukov, I. A.; Sharfov, Y. A.

1974-01-01

An analysis is given of the requirements placed on the elements of parametric centimeter waveband amplifiers for achievement of minimal noise temperatures. A low-noise semiconductor parametric amplifier using germanium parametric diodes for a receiver operating in the 4 GHz band was developed and tested confirming the possibility of satisfying all requirements.

Acceleration of the direct reconstruction of linear parametric images using nested algorithms.

PubMed

Wang, Guobao; Qi, Jinyi

2010-03-07

Parametric imaging using dynamic positron emission tomography (PET) provides important information for biological research and clinical diagnosis. Indirect and direct methods have been developed for reconstructing linear parametric images from dynamic PET data. Indirect methods are relatively simple and easy to implement because the image reconstruction and kinetic modeling are performed in two separate steps. Direct methods estimate parametric images directly from raw PET data and are statistically more efficient. However, the convergence rate of direct algorithms can be slow due to the coupling between the reconstruction and kinetic modeling. Here we present two fast gradient-type algorithms for direct reconstruction of linear parametric images. The new algorithms decouple the reconstruction and linear parametric modeling at each iteration by employing the principle of optimization transfer. Convergence speed is accelerated by running more sub-iterations of linear parametric estimation because the computation cost of the linear parametric modeling is much less than that of the image reconstruction. Computer simulation studies demonstrated that the new algorithms converge much faster than the traditional expectation maximization (EM) and the preconditioned conjugate gradient algorithms for dynamic PET.

Sensitivity enhancement in swept-source optical coherence tomography by parametric balanced detector and amplifier

PubMed Central

Kang, Jiqiang; Wei, Xiaoming; Li, Bowen; Wang, Xie; Yu, Luoqin; Tan, Sisi; Jinata, Chandra; Wong, Kenneth K. Y.

2016-01-01

We proposed a sensitivity enhancement method of the interference-based signal detection approach and applied it on a swept-source optical coherence tomography (SS-OCT) system through all-fiber optical parametric amplifier (FOPA) and parametric balanced detector (BD). The parametric BD was realized by combining the signal and phase conjugated idler band that was newly-generated through FOPA, and specifically by superimposing these two bands at a photodetector. The sensitivity enhancement by FOPA and parametric BD in SS-OCT were demonstrated experimentally. The results show that SS-OCT with FOPA and SS-OCT with parametric BD can provide more than 9 dB and 12 dB sensitivity improvement, respectively, when compared with the conventional SS-OCT in a spectral bandwidth spanning over 76 nm. To further verify and elaborate their sensitivity enhancement, a bio-sample imaging experiment was conducted on loach eyes by conventional SS-OCT setup, SS-OCT with FOPA and parametric BD at different illumination power levels. All these results proved that using FOPA and parametric BD could improve the sensitivity significantly in SS-OCT systems. PMID:27446655

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.

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.

Zero- vs. one-dimensional, parametric vs. non-parametric, and confidence interval vs. hypothesis testing procedures in one-dimensional biomechanical trajectory analysis.

PubMed

Pataky, Todd C; Vanrenterghem, Jos; Robinson, Mark A

2015-05-01

Biomechanical processes are often manifested as one-dimensional (1D) trajectories. It has been shown that 1D confidence intervals (CIs) are biased when based on 0D statistical procedures, and the non-parametric 1D bootstrap CI has emerged in the Biomechanics literature as a viable solution. The primary purpose of this paper was to clarify that, for 1D biomechanics datasets, the distinction between 0D and 1D methods is much more important than the distinction between parametric and non-parametric procedures. A secondary purpose was to demonstrate that a parametric equivalent to the 1D bootstrap exists in the form of a random field theory (RFT) correction for multiple comparisons. To emphasize these points we analyzed six datasets consisting of force and kinematic trajectories in one-sample, paired, two-sample and regression designs. Results showed, first, that the 1D bootstrap and other 1D non-parametric CIs were qualitatively identical to RFT CIs, and all were very different from 0D CIs. Second, 1D parametric and 1D non-parametric hypothesis testing results were qualitatively identical for all six datasets. Last, we highlight the limitations of 1D CIs by demonstrating that they are complex, design-dependent, and thus non-generalizable. These results suggest that (i) analyses of 1D data based on 0D models of randomness are generally biased unless one explicitly identifies 0D variables before the experiment, and (ii) parametric and non-parametric 1D hypothesis testing provide an unambiguous framework for analysis when one׳s hypothesis explicitly or implicitly pertains to whole 1D trajectories. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Randomized controlled clinical study evaluating effectiveness and safety of a volume-stable collagen matrix compared to autogenous connective tissue grafts for soft tissue augmentation at implant sites.

PubMed

Thoma, Daniel S; Zeltner, Marco; Hilbe, Monika; Hämmerle, Christoph H F; Hüsler, Jürg; Jung, Ronald E

2016-10-01

To test whether or not the use of a collagen matrix (VCMX) results in short-term soft tissue volume increase at implant sites non-inferior to an autogenous subepithelial connective tissue graft (SCTG), and to evaluate safety and tissue integration of VCMX and SCTG. In 20 patients with a volume deficiency at single-tooth implant sites, soft tissue volume augmentation was performed randomly allocating VCMX or SCTG. Soft tissue thickness, patient-reported outcome measures (PROMs), and safety were assessed up to 90 days (FU-90). At FU-90 (abutment connection), tissue samples were obtained for histological analysis. Descriptive analysis was computed for both groups. Non-parametric tests were applied to test non-inferiority for the gain in soft tissue thickness at the occlusal site. Median soft tissue thickness increased between BL and FU-90 by 1.8 mm (Q1:0.5; Q3:2.0) (VCMX) (p = 0.018) and 0.5 mm (-1.0; 2.0) (SCTG) (p = 0.395) (occlusal) and by 1.0 mm (0.5; 2.0) (VCMX) (p = 0.074) and 1.5 mm (-2.0; 2.0) (SCTG) (p = 0.563) (buccal). Non-inferiority with a non-inferiority margin of 1 mm could be demonstrated (p = 0.020); the difference between the two group medians (1.3 mm) for occlusal sites indicated no relevant, but not significant superiority of VCMX versus SCTG (primary endpoint). Pain medication consumption and pain perceived were non-significantly higher in group SCTG up to day 3. Median physical pain (OHIP-14) at day 7 was 100% higher for SCTG than for VCMX. The histological analysis revealed well-integrated grafts. Soft tissue augmentation at implant sites resulted in a similar or higher soft tissue volume increase after 90 days for VCMX versus SCTG. PROMs did not reveal relevant differences between the two groups. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Long term effects of below-the-knee angioplasty in diabetic patients with critical ischemia of lower limbs referred to Sina Hospital during 2010-2011.

PubMed

Zafarghandi, Mohammad-Reza; Nazari, Iraj; Taghavi, Morteza; Rashidi, Abbas; Dardashti, Sanaz Karimi; Sadid, Donya; Esmaili, Leyli; Mahmoodi, Seyed Mostafa; Mousavi, Masood

2015-03-01

Despite significant advances in the treatment of diabetic foot ulcers and below-the-knee critical ischemia, there are ongoing efforts to achieve a method with low complication, high success rate and persistence of long-term effects. The aim of the study was to examine the outcome of angioplasty in patients with below-the-knee critical ischemia referred to Hospital. This semi-experimental study conducted on diabetics patients treated with PTA (Percutaneous transluminal angioplasty) with critical ischemia of lower limbs referred to Sina Hospital. After discharge, the patients were followed weekly for the first month and then monthly up to 12 months. The procedure short-term effects were examined through evaluation of wound healing as well as patients' recovery and pain relief, after one month. Given the distribution type, parametric and non-parametric test were used to compare the results before and after treatment. Pearson's correlation coefficient was used to determine the correlation between variables. Twenty four patients participated in this study. The mean ankle-brachial index (ABI) at baseline was 0.55 ± 0.17. A month after angioplasty, the index increased statistically significant to 0.93 ± 0.16. The mean health score expressed by the patients at baseline was 5.48 ± 1.39. A month after angioplasty, it was significantly increased (6.32 ± 1.24). The mean pain score before enrollment was 6.68 ± 2.52 (according to VAS scale). There was a significant decrease over time (3.45 ± 1.13). The overall mean score of all patients at Rutherford Classification was 3.88 ± 0.63 at baseline. During the 1st month and 6th month follow-up, it was changed to Class 0 that was statistically significant in the first month. This study represents the mid-term outcomes of PTA. Although PTA treatment was associated with improved pain scores, satisfaction with health, classification of limb ischemia and diabetic foot ulcers, the effects only remain short-term and mid-term. However, long-term efficacy of PTA needs to be investigated further.

Commercial D-T FRC Power Plant Systems Analysis

NASA Astrophysics Data System (ADS)

Nguyen, Canh; Santarius, John; Emmert, Gilbert; Steinhauer, Loren; Stubna, Michael

1998-11-01

Results of an engineering issues scoping study of a Field-Reversed Configuration (FRC) burning D-T fuel will be presented. The study primarily focuses on engineering issues, such as tritium-breeding blanket design, radiation shielding, neutron damage, activation, safety, and environment. This presentation will concentrate on plasma physics, current drive, economics, and systems integration, which are important for the overall systems analysis. A systems code serves as the key tool in defining a reference point for detailed physics and engineering calculations plus parametric variations, and typical cases will be presented. Advantages of the cylindrical geometry and high beta (plasma pressure/magnetic-field pressure) are evident.

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.

Multiple Frequency Parametric Sonar

DTIC Science & Technology

2015-09-28

300003 1 MULTIPLE FREQUENCY PARAMETRIC SONAR STATEMENT OF GOVERNMENT INTEREST [0001] The invention described herein may be manufactured and...a method for increasing the bandwidth of a parametric sonar system by using multiple primary frequencies rather than only two primary frequencies...2) Description of Prior Art [0004] Parametric sonar generates narrow beams at low frequencies by projecting sound at two distinct primary

Parametric instabilities of rotor-support systems with application to industrial ventilators

NASA Technical Reports Server (NTRS)

Parszewski, Z.; Krodkiemski, T.; Marynowski, K.

1980-01-01

Rotor support systems interaction with parametric excitation is considered for both unequal principal shaft stiffness (generators) and offset disc rotors (ventilators). Instability regions and types of instability are computed in the first case, and parametric resonances in the second case. Computed and experimental results are compared for laboratory machine models. A field case study of parametric vibrations in industrial ventilators is reported. Computed parametric resonances are confirmed in field measurements, and some industrial failures are explained. Also the dynamic influence and gyroscopic effect of supporting structures are shown and computed.

Parametric robust control and system identification: Unified approach

NASA Technical Reports Server (NTRS)

Keel, Leehyun

1994-01-01

Despite significant advancement in the area of robust parametric control, the problem of synthesizing such a controller is still a wide open problem. Thus, we attempt to give a solution to this important problem. Our approach captures the parametric uncertainty as an H(sub infinity) unstructured uncertainty so that H(sub infinity) synthesis techniques are applicable. Although the techniques cannot cope with the exact parametric uncertainty, they give a reasonable guideline to model the unstructured uncertainty that contains the parametric uncertainty. An additional loop shaping technique is also introduced to relax its conservatism.

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 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

Direct parametric reconstruction in dynamic PET myocardial perfusion imaging: in vivo studies.

PubMed

Petibon, Yoann; Rakvongthai, Yothin; El Fakhri, Georges; Ouyang, Jinsong

2017-05-07

Dynamic PET myocardial perfusion imaging (MPI) used in conjunction with tracer kinetic modeling enables the quantification of absolute myocardial blood flow (MBF). However, MBF maps computed using the traditional indirect method (i.e. post-reconstruction voxel-wise fitting of kinetic model to PET time-activity-curves-TACs) suffer from poor signal-to-noise ratio (SNR). Direct reconstruction of kinetic parameters from raw PET projection data has been shown to offer parametric images with higher SNR compared to the indirect method. The aim of this study was to extend and evaluate the performance of a direct parametric reconstruction method using in vivo dynamic PET MPI data for the purpose of quantifying MBF. Dynamic PET MPI studies were performed on two healthy pigs using a Siemens Biograph mMR scanner. List-mode PET data for each animal were acquired following a bolus injection of ~7-8 mCi of 18 F-flurpiridaz, a myocardial perfusion agent. Fully-3D dynamic PET sinograms were obtained by sorting the coincidence events into 16 temporal frames covering ~5 min after radiotracer administration. Additionally, eight independent noise realizations of both scans-each containing 1/8th of the total number of events-were generated from the original list-mode data. Dynamic sinograms were then used to compute parametric maps using the conventional indirect method and the proposed direct method. For both methods, a one-tissue compartment model accounting for spillover from the left and right ventricle blood-pools was used to describe the kinetics of 18 F-flurpiridaz. An image-derived arterial input function obtained from a TAC taken in the left ventricle cavity was used for tracer kinetic analysis. For the indirect method, frame-by-frame images were estimated using two fully-3D reconstruction techniques: the standard ordered subset expectation maximization (OSEM) reconstruction algorithm on one side, and the one-step late maximum a posteriori (OSL-MAP) algorithm on the other side, which incorporates a quadratic penalty function. The parametric images were then calculated using voxel-wise weighted least-square fitting of the reconstructed myocardial PET TACs. For the direct method, parametric images were estimated directly from the dynamic PET sinograms using a maximum a posteriori (MAP) parametric reconstruction algorithm which optimizes an objective function comprised of the Poisson log-likelihood term, the kinetic model and a quadratic penalty function. Maximization of the objective function with respect to each set of parameters was achieved using a preconditioned conjugate gradient algorithm with a specifically developed pre-conditioner. The performance of the direct method was evaluated by comparing voxel- and segment-wise estimates of [Formula: see text], the tracer transport rate (ml · min -1 · ml -1 ), to those obtained using the indirect method applied to both OSEM and OSL-MAP dynamic reconstructions. The proposed direct reconstruction method produced [Formula: see text] maps with visibly lower noise than the indirect method based on OSEM and OSL-MAP reconstructions. At normal count levels, the direct method was shown to outperform the indirect method based on OSL-MAP in the sense that at matched level of bias, reduced regional noise levels were obtained. At lower count levels, the direct method produced [Formula: see text] estimates with significantly lower standard deviation across noise realizations than the indirect method based on OSL-MAP at matched bias level. In all cases, the direct method yielded lower noise and standard deviation than the indirect method based on OSEM. Overall, the proposed direct reconstruction offered a better bias-variance tradeoff than the indirect method applied to either OSEM and OSL-MAP. Direct parametric reconstruction as applied to in vivo dynamic PET MPI data is therefore a promising method for producing MBF maps with lower variance.

Direct parametric reconstruction in dynamic PET myocardial perfusion imaging: in-vivo studies

PubMed Central

Petibon, Yoann; Rakvongthai, Yothin; Fakhri, Georges El; Ouyang, Jinsong

2017-01-01

Dynamic PET myocardial perfusion imaging (MPI) used in conjunction with tracer kinetic modeling enables the quantification of absolute myocardial blood flow (MBF). However, MBF maps computed using the traditional indirect method (i.e. post-reconstruction voxel-wise fitting of kinetic model to PET time-activity-curves -TACs) suffer from poor signal-to-noise ratio (SNR). Direct reconstruction of kinetic parameters from raw PET projection data has been shown to offer parametric images with higher SNR compared to the indirect method. The aim of this study was to extend and evaluate the performance of a direct parametric reconstruction method using in-vivo dynamic PET MPI data for the purpose of quantifying MBF. Dynamic PET MPI studies were performed on two healthy pigs using a Siemens Biograph mMR scanner. List-mode PET data for each animal were acquired following a bolus injection of ~7-8 mCi of 18F-flurpiridaz, a myocardial perfusion agent. Fully-3D dynamic PET sinograms were obtained by sorting the coincidence events into 16 temporal frames covering ~5 min after radiotracer administration. Additionally, eight independent noise realizations of both scans - each containing 1/8th of the total number of events - were generated from the original list-mode data. Dynamic sinograms were then used to compute parametric maps using the conventional indirect method and the proposed direct method. For both methods, a one-tissue compartment model accounting for spillover from the left and right ventricle blood-pools was used to describe the kinetics of 18F-flurpiridaz. An image-derived arterial input function obtained from a TAC taken in the left ventricle cavity was used for tracer kinetic analysis. For the indirect method, frame-by-frame images were estimated using two fully-3D reconstruction techniques: the standard Ordered Subset Expectation Maximization (OSEM) reconstruction algorithm on one side, and the One-Step Late Maximum a Posteriori (OSL-MAP) algorithm on the other side, which incorporates a quadratic penalty function. The parametric images were then calculated using voxel-wise weighted least-square fitting of the reconstructed myocardial PET TACs. For the direct method, parametric images were estimated directly from the dynamic PET sinograms using a maximum a posteriori (MAP) parametric reconstruction algorithm which optimizes an objective function comprised of the Poisson log-likelihood term, the kinetic model and a quadratic penalty function. Maximization of the objective function with respect to each set of parameters was achieved using a preconditioned conjugate gradient algorithm with a specifically developed pre-conditioner. The performance of the direct method was evaluated by comparing voxel- and segment-wise estimates of K1, the tracer transport rate (mL.min−1.mL−1), to those obtained using the indirect method applied to both OSEM and OSL-MAP dynamic reconstructions. The proposed direct reconstruction method produced K1 maps with visibly lower noise than the indirect method based on OSEM and OSL-MAP reconstructions. At normal count levels, the direct method was shown to outperform the indirect method based on OSL-MAP in the sense that at matched level of bias, reduced regional noise levels were obtained. At lower count levels, the direct method produced K1 estimates with significantly lower standard deviation across noise realizations than the indirect method based on OSL-MAP at matched bias level. In all cases, the direct method yielded lower noise and standard deviation than the indirect method based on OSEM. Overall, the proposed direct reconstruction offered a better bias-variance tradeoff than the indirect method applied to either OSEM and OSL-MAP. Direct parametric reconstruction as applied to in-vivo dynamic PET MPI data is therefore a promising method for producing MBF maps with lower variance. PMID:28379843

Direct parametric reconstruction in dynamic PET myocardial perfusion imaging: in vivo studies

NASA Astrophysics Data System (ADS)

Petibon, Yoann; Rakvongthai, Yothin; El Fakhri, Georges; Ouyang, Jinsong

2017-05-01

Dynamic PET myocardial perfusion imaging (MPI) used in conjunction with tracer kinetic modeling enables the quantification of absolute myocardial blood flow (MBF). However, MBF maps computed using the traditional indirect method (i.e. post-reconstruction voxel-wise fitting of kinetic model to PET time-activity-curves-TACs) suffer from poor signal-to-noise ratio (SNR). Direct reconstruction of kinetic parameters from raw PET projection data has been shown to offer parametric images with higher SNR compared to the indirect method. The aim of this study was to extend and evaluate the performance of a direct parametric reconstruction method using in vivo dynamic PET MPI data for the purpose of quantifying MBF. Dynamic PET MPI studies were performed on two healthy pigs using a Siemens Biograph mMR scanner. List-mode PET data for each animal were acquired following a bolus injection of ~7-8 mCi of 18F-flurpiridaz, a myocardial perfusion agent. Fully-3D dynamic PET sinograms were obtained by sorting the coincidence events into 16 temporal frames covering ~5 min after radiotracer administration. Additionally, eight independent noise realizations of both scans—each containing 1/8th of the total number of events—were generated from the original list-mode data. Dynamic sinograms were then used to compute parametric maps using the conventional indirect method and the proposed direct method. For both methods, a one-tissue compartment model accounting for spillover from the left and right ventricle blood-pools was used to describe the kinetics of 18F-flurpiridaz. An image-derived arterial input function obtained from a TAC taken in the left ventricle cavity was used for tracer kinetic analysis. For the indirect method, frame-by-frame images were estimated using two fully-3D reconstruction techniques: the standard ordered subset expectation maximization (OSEM) reconstruction algorithm on one side, and the one-step late maximum a posteriori (OSL-MAP) algorithm on the other side, which incorporates a quadratic penalty function. The parametric images were then calculated using voxel-wise weighted least-square fitting of the reconstructed myocardial PET TACs. For the direct method, parametric images were estimated directly from the dynamic PET sinograms using a maximum a posteriori (MAP) parametric reconstruction algorithm which optimizes an objective function comprised of the Poisson log-likelihood term, the kinetic model and a quadratic penalty function. Maximization of the objective function with respect to each set of parameters was achieved using a preconditioned conjugate gradient algorithm with a specifically developed pre-conditioner. The performance of the direct method was evaluated by comparing voxel- and segment-wise estimates of {{K}1} , the tracer transport rate (ml · min-1 · ml-1), to those obtained using the indirect method applied to both OSEM and OSL-MAP dynamic reconstructions. The proposed direct reconstruction method produced {{K}1} maps with visibly lower noise than the indirect method based on OSEM and OSL-MAP reconstructions. At normal count levels, the direct method was shown to outperform the indirect method based on OSL-MAP in the sense that at matched level of bias, reduced regional noise levels were obtained. At lower count levels, the direct method produced {{K}1} estimates with significantly lower standard deviation across noise realizations than the indirect method based on OSL-MAP at matched bias level. In all cases, the direct method yielded lower noise and standard deviation than the indirect method based on OSEM. Overall, the proposed direct reconstruction offered a better bias-variance tradeoff than the indirect method applied to either OSEM and OSL-MAP. Direct parametric reconstruction as applied to in vivo dynamic PET MPI data is therefore a promising method for producing MBF maps with lower variance.

Separation of β-amyloid binding and white matter uptake of 18F-flutemetamol using spectral analysis

PubMed Central

Heurling, Kerstin; Buckley, Christopher; Vandenberghe, Rik; Laere, Koen Van; Lubberink, Mark

2015-01-01

The kinetic components of the β-amyloid ligand 18F-flutemetamol binding in grey and white matter were investigated through spectral analysis, and a method developed for creation of parametric images separating grey and white matter uptake. Tracer uptake in grey and white matter and cerebellar cortex was analyzed through spectral analysis in six subjects, with (n=4) or without (n=2) apparent β-amyloid deposition, having undergone dynamic 18F-flutemetamol scanning with arterial blood sampling. The spectra were divided into three components: slow, intermediate and fast basis function rates. The contribution of each of the components to total volume of distribution (VT) was assessed for different tissue types. The slow component dominated in white matter (average 90%), had a higher contribution to grey matter VT in subjects with β-amyloid deposition (average 44%) than without (average 6%) and was absent in cerebellar cortex, attributing the slow component of 18F-flutemetamol uptake in grey matter to β-amyloid binding. Parametric images of voxel-based spectral analysis were created for VT, the slow component and images segmented based on the slow component contribution; confirming that grey matter and white matter uptake can be discriminated on voxel-level using a threshold for the contribution from the slow component to VT. PMID:26550542

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.

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.

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.

Quantification of 18F-JNJ-42259152, a novel phosphodiesterase 10A PET tracer: kinetic modeling and test-retest study in human brain.

PubMed

Van Laere, Koen; Ahmad, Rawaha U; Hudyana, Hendra; Dubois, Kristof; Schmidt, Mark E; Celen, Sofie; Bormans, Guy; Koole, Michel

2013-08-01

Phosphodiesterase 10A (PDE10A) plays a central role in striatal signaling and is implicated in several neuropsychiatric disorders, such as movement disorders and schizophrenia. We performed initial brain kinetic modeling of the novel PDE10A tracer (18)F-JNJ-42259152 (2-[[4-[1-(2-(18)F-fluoroethyl)-4-(4-pyridinyl)-1H-pyrazol-3-yl]phenoxy]methyl]-3,5-dimethyl-pyridine) and studied test-retest reproducibility in healthy volunteers. Twelve healthy volunteers (5 men, 7 women; age range, 42-77 y) were scanned dynamically up to 135 min after bolus injection of 172.5 ± 10.3 MBq of (18)F-JNJ42259152. Four volunteers (2 men, 2 women) underwent retest scanning, with a mean interscan interval of 37 d. Input functions and tracer parent fractions were determined using arterial sampling and high-performance liquid chromatography analysis. Volumes of interest for the putamen, caudate nucleus, ventral striatum, substantia nigra, thalamus, frontal cortex, and cerebellum were delineated using individual volumetric T1 MR imaging scans. One-tissue (1T) and 2-tissue (2T) models were evaluated to calculate total distribution volume (VT). Simplified models were also tested to calculate binding potential (BPND), including the simplified reference tissue model (SRTM) and multilinear reference tissue model, using the frontal cortex as the optimal reference tissue. The stability of VT and BPND was assessed down to a 60-min scan time. The average intact tracer half-life in blood was 90 min. The 2T model VT values for the putamen, caudate nucleus, ventral striatum, substantia nigra, thalamus, frontal cortex, and cerebellum were 1.54 ± 0.37, 0.90 ± 0.24, 0.64 ± 0.18, 0.42 ± 0.09, 0.35 ± 0.09, 0.30 ± 0.07, and 0.36 ± 0.12, respectively. The 1T model provided significantly lower VT values, which were well correlated to the 2T VT. SRTM BPND values referenced to the frontal cortex were 3.45 ± 0.43, 1.78 ± 0.35, 1.10 ± 0.31, and 0.44 ± 0.09 for the respective target regions putamen, caudate nucleus, ventral striatum, and substantia nigra, with similar values for the multilinear reference tissue model. Good correlations were found for the target regions putamen, caudate nucleus, ventral striatum, and substantia nigra between the 2T-compartment model BPND and the SRTM BPND (r = 0.57, 0.82, 0.70, and 0.64, respectively). SRTM BPND using a 90- and 60-min acquisition interval showed low bias. Test-retest variability was 5%-19% for 2T VT and 5%-12% for BPND SRTM. Kinetic modeling of (18)F-JNJ-42259152 shows that PDE10A activity can be reliably quantified and simplified using a reference tissue model with the frontal cortex as reference and a 60-min acquisition period.

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