SEARCH · PubMed Health

Results for “Experimental validation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41Linked to original sources

PubMed2004

Direct measurement of dynamic frequency shift induced by cross-correlations in 15N-enriched proteins.

We describe a new NMR experimental scheme that allows the direct determination of the dynamic frequency shift induced by chemical shift anisotropy/dipolar interaction (CSA/DD) cross-correlations in 15N-enriched proteins. Its principle consists of comparing two rates of polarisation transfer between the amide proton and nitrogen. The first rate, which is independent of the dynamic frequency shift, is based on a selective Hartmann-Hahn coherence transfer. The second rate, which depends on the dynamic frequency shift, is based on a free evolution of the transverse magnetisation. We report experimental validation of this approach by measuring the average dynamic frequency shift due to CSA/DD cross-correlations in the calcium-binding protein D9k. The method may also be applicable to the measurement of dynamic frequency shift induced by cross-correlations between the Curie spin and dipolar interactions.

Magnetic Resonance Spectroscopy↗

PubMed2003

A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal image stacks.

BACKGROUND: Automated segmentation of fluorescently-labeled cell nuclei in 3D confocal microscope images is essential to many studies involving morphological and functional analysis. A common source of segmentation error is tight clustering of nuclei. There is a compelling need to minimize these errors for constructing highly automated scoring systems. METHODS: A combination of two approaches is presented. First, an improved distance transform combining intensity gradients and geometric distance is used for the watershed step. Second, an explicit mathematical model for the anatomic characteristics of cell nuclei such as size and shape measures is incorporated. This model is constructed automatically from the data. Deliberate initial over-segmentation of the image data is performed, followed by statistical model-based merging. A confidence score is computed for each detected nucleus, measuring how well the nucleus fits the model. This is used in combination with the intensity gradient to control the merge decisions. RESULTS: Experimental validation on a set of rodent brain cell images showed 97% concordance with the human observer and significant improvement over prior methods. CONCLUSIONS: Combining a gradient-weighted distance transform with a richer morphometric model significantly improves the accuracy of automated segmentation and FISH analysis.

Algorithms↗

PubMed2004

Pathologic fear conditioning and anorexia nervosa: on the search for novel paradigms.

Although eating disorders have been the focus of an unprecedented explosion of clinical interest in recent years, the etiology of anorexia nervosa remains elusive. It is hypothesized that an underlying causative mechanism involves a propensity to extreme fear conditioning and greater than normal resistance to its extinction. Knowledge accrued from recent behavioral, genetic, and neuroanatomic research on anxiety may yield further insight into the pathogenesis of anorexia nervosa, which can be subjected to experimental validation using objective measures of classical fear conditioning and functional neuroimaging of brain structures mediating fear behavior.

Adolescent↗

PubMed2005

Anger and bulimic psychopathology: gender differences in a nonclinical group.

OBJECTIVE: The current study addressed the link between anger and bulimic psychopathology between young adult men and women. METHOD: Volunteers (125 males and 125 females) completed two self-report questionnaires measuring anger (State Trait Anger Inventory [STAXI]) and bulimic attitudes and behaviors (Bulimic Investigatory Test, Edinburgh [BITE]). RESULTS: Although overall levels of anger did not differ broadly across genders, bulimic attitudes were associated with state anger in men but with anger suppression in women. DISCUSSION: Men appear to engage in bulimic behaviors to reduce anger states, whereas women appear to use such behaviors to reduce the likelihood of anger states from arising. Further experimental validation of these findings is required in both clinical and nonclinical groups.

Adolescent↗

PubMed2004

Exploring interactions between rat hepatocytes and nonparenchymal cells using gene expression profiling.

Cocultivation of primary hepatocytes with a plethora of nonparenchymal cells (from within and outside the liver) has been shown to support hepatic functions in vitro. Despite significant investigation into this phenomenon, the molecular mechanism underlying epithelial-nonparenchymal interactions in hepatocyte cocultures remains poorly understood. In this study, we present a functional genomic approach utilizing gene expression profiling to isolate molecular mediators potentially involved in induction of liver-specific functions by nonparenchymal cells. Specifically, primary rat hepatocytes were cocultivated with closely related murine fibroblast cell types (3T3-J2, NIH-3T3, mouse embryonic fibroblasts) to allow their classification as "high," "medium," or "low" inducers of hepatic functions. These functional responses were correlated with fibroblast gene expression profiles obtained using Affymetrix GeneChips. Microarray data analysis provided us with 17 functionally characterized candidate genes in the cell communication category (cell surface, extracellular matrix, secreted factors) that may be involved in induction of hepatic functions. Further analysis using various databases (i.e., PubMed, GenBank) facilitated prioritization of the candidates for functional characterization. We experimentally validated the potential role of two candidates in our coculture model. The cell surface protein, neural cadherin (N-cadherin), was localized to hepatocyte-fibroblast junctions, while adsorbed decorin up-regulated hepatic functions in pure cultures as well as cocultures with low-inducing fibroblasts. In the future, identifying mediators of hepatocyte differentiation may have implications for both fundamental hepatology and cell-based therapies (e.g., bioartificial liver devices). In conclusion, the functional genomic approach presented in this study may be utilized to investigate mechanisms of cell-cell interaction in a variety of tissues and disease states.

Animals↗

PubMed2004

Non-self-discrimination as a driving concept in the identification of an immunodominant HMW-MAA epitopic peptide sequence by autoantibodies from melanoma cancer patients.

We analyzed the sera of patients with melanoma to define the human humoral autoantibody profile towards HMW-MAA. Computational proteome scanning using the non-self-discrimination principle as a guide led to the individuation of the low-similarity HMW-MAA781-789RATVWMLRL peptide fragment as an immunodominant B-cell epitope. Linear B-cell determinant individuation was experimentally validated by dot blot immunoassay and NMR spectroscopy analysis. Regulation of physiologic self-reactivity by the non-self-discrimination principle is discussed.

Antigens, Neoplasm↗

PubMed2005

A computational approach to predicting cell growth on polymeric biomaterials.

A predictive model that can correlate the chemical composition of a biomaterial with the biological response of cells that are in contact with that biomaterial would represent a major advance and would facilitate the rational design of new biomaterials. As a first step toward this goal, we report here on the use of Logical Analysis of Data (LAD) to model the effect of selected polymer properties on the growth of two different cell types, rat lung fibroblasts (RLF, a transformed cell line), and normal foreskin fibroblasts (NFF, nontransformed human cells), on 112 surfaces obtained from a combinatorially designed library of polymers. LAD is a knowledge extraction methodology, based on using combinatorics, optimization, and Boolean logic. LAD was trained on a subset of 62 polymers and was then used to predict cell growth on 50 previously untested polymers. Experimental validation indicated that LAD correctly predicted the high and low cell growth polymers and found optimal ranges for polymer chemical composition, surface chemistry, and bulk properties. Particularly noteworthy is that LAD correctly identified high-performing polymer surfaces, which surpassed commercial tissue culture polystyrene as growth substratum for normal foreskin fibroblasts. Our results establish the feasibility of using computational modeling of cell growth on flat polymeric surfaces to identify promising "lead" polymers for applications that require either high or low cell growth.

Animals↗

PubMed1989

Preparation and characterization of plasma membrane vesicles from human polymorphonuclear leukocytes.

It would be advantageous to prepare models of the neutrophil plasma membrane in order to examine the role of the plasma membrane in transmembrane signal transduction in the human neutrophil and to dissect ligand-receptor interactions and structural changes in the cell surface upon stimulation. A number of investigators have prepared neutrophil membrane vesicles by homogenization, sonication, or centrifugation--techniques that can result in the loss of substantial amounts of surface membrane material, disruption of lysosomes causing proteolysis of membrane proteins, and contamination of the plasma membrane fraction by internal membranes. These limitations have been overcome in the present studies by employing a modification of the method previously developed in this laboratory. Human neutrophils were suspended in a buffer simulating cytoplasmic ionic and osmotic conditions and disrupted by nitrogen cavitation. The resultant cavitate was freed of undisrupted cells and nuclei and then centrifuged through discontinuous isotonic/isoosmotic Percoll gradients, which resolved four fractions: alpha (intact azurophilic granules), beta (intact specific granules), gamma (membrane vesicles), and delta (cytosol). The gamma fraction was highly enriched in alkaline phosphatase, a marker of the plasma membrane. In addition, this fraction contained less than 5% of the amounts of lysosomes (indicated by lysozyme activity) and nuclei (indicated by DNA content) found in intact cells or in unfractionated cavitate. Furthermore, the gamma fraction contained less than 10% of the levels of endoplasmic reticulum, Golgi, mitochondrial, and lysosomal membranes in cells or cavitates, as determined by assays for glucose 6-phosphatase, galactosyl transferase, monoamine oxidase, and Mo1 (CD11b/CD18; Mac-1), respectively. Finally, 75% of the membrane vesicles were sealed, as indicated by assay of ouabain-sensitive (Na+,K+) ATPase activity, and 55% were oriented right-side-out, as determined by exposure of concanavalin A (ConA) receptors and sialic acid residues on the surfaces of the vesicles. These heterogeneous preparations could be enriched for right-side-out vesicles by their selective adherence to ConA-coated plates and subsequent detachment by rinsing the surfaces of the plates with alpha-methylmannoside. This enrichment protocol did not affect the integrity of the vesicles and resulted in populations in which greater than 85% of the vesicles were oriented right-side-out. This procedure thus permits the preparation of sealed, right-side-out membrane vesicles that may be used as valid experimental models of the neutrophil plasma membrane in a variety of functional studies.

Biomarkers↗

PubMed1990

Transient response of a solid-liquid model biological fluidised bed to a step change in fluid superficial velocity.

The evolution of a solid-liquid model biological fluidised bed under a step change in fluid superficial velocity is described. During a transient step change, the fluidised bed divides into a top zone which remains at the initial porosity and a bottom zone which settles at the final porosity. The interface of discontinuity in porosity moves progressively upwards through the fluidised bed. The velocity at which the top of the fluidised bed expands or contracts and the upward velocity of the porosity transition interface depend only upon the initial and final states of the bed porosity and the fluid superficial velocity. This results in a linear evolution with time of the total bed height and the height of porosity transition interface. The proposed model is well suited to describe the transient response of low-density particles in a fluidised bed, such as encountered in biological systems, to a sudden change of liquid superficial velocity. The model was validated experimentally.

Biomedical Engineering↗

PubMed2001

Precision of magnetic resonance velocity and acceleration measurements: theoretical issues and phantom experiments.

Magnetic resonance (MR) sequences have been developed for acquiring multiple components of velocity and/or acceleration in a reasonable time and with a single acquisition. They have many parameters that influence the precision of measurements: NS, the number of flow-encoding steps; NEX, the number of signal accumulations; and ND, the number of dimensions. Our aims were to establish a general relationship revealing the precision of these measurements as a function of NS, ND, and NEX and to validate it by experiments using phantoms. Previous work on precision has been restricted to two-step (NS = 2) or 1D (ND = 1) MR velocity measurements. We describe a comprehensive approach that encompasses both multistep and multidimensional strategies. Our theoretical formula gives the precision of velocity and acceleration measurements. It was validated experimentally with measurements on a rotating disk phantom. This phantom was much easier to handle than fluid-based phantoms. It could be used to assess both velocity and acceleration sequences and provided accurate and precise assessments over a wide, adjustable range of values within a single experiment. Increasing each of the three parameters, NS, ND, and NEX, improves the precision but makes the acquisition time longer. However, if only one parameter is to be assessed, maximizing the number of steps (NS) is the most efficient way of improving the precision of measurements; if several parameters are of interest, they should be measured simultaneously. By contrast, increasing the number of signals accumulated (NEX) is the least efficient strategy.

Acceleration↗

PubMedDate not supplied

MR measurements of pulsatile pressure gradients.

A magnetic resonance (MR) imaging method for evaluating pulsatile pressure gradients in laminar blood flow is presented. The technique is based on an evaluation of fluid shear and inertial forces from cardiac-gated phase-contrast velocity measurements. The technique was experimentally validated by comparing MR and manometer pressure gradient measurements performed in a pulsatile flow phantom. Analyses of random noise propagation and sampling error were performed to determine the precision and accuracy of the method. The results indicate that a precision of 0.01-0.03 mmHg/cm and an accuracy of better than 8% can be achieved by using standard clinical pulse sequences in tubes exceeding 6 mm in diameter. The authors conclude that MR measurement of pressure gradients is feasible and that additional hemodynamic information may be derived from conventional phase-contrast imaging studies.

Algorithms↗

PubMed2006

Controlling diffusion of 3He by buffer gases: a structural contrast agent in lung MRI.

PURPOSE: To study the influence of admixing inert buffer gases to laser-polarized (3)He in terms of resulting diffusion coefficients and the consequences for image contrast and resolution. MATERIALS AND METHODS: The diffusion coefficient of (3)He was altered by admixing buffer gases of various molecular weights ((4)He, N(2), and SF(6)). The influence of the pulse sequence and the diffusion coefficient on the appearance of MRI of (laser-polarized) gases was analyzed by comparison of basic theoretical concepts with demonstrative experiments. RESULTS: Excellent agreement between theoretical description and observed signal in simple gradient echoes was observed. A maximum signal gain can be predicted and was experimentally validated. Images acquired under such conditions revealed improved resolution. The nature and concentration of the admixed gas defines a structural threshold for the observed apparent diffusion coefficient (ADC) as demonstrated with diffusion-weighted MRI on a pig's lung flooded with suitable gas mixtures. CONCLUSION: A novel procedure is proposed to control the diffusion coefficient of gases in MRI by admixture of inert buffer gases. Their molecular mass and concentration enter as additional parameters into the equations that describe structural contrast. This allows for setting a structural threshold up to which structures contribute to the image. For MRI of the lung this enables images of very small structural elements (alveoli) only, or in the other extreme, all airways can be displayed with minimal signal loss due to diffusion.

Contrast Media↗

PubMed1995

Studies in phlebitis. VII: In vitro and in vivo evaluation of pH-solubilized levemopamil.

We describe a computational model and an in vitro experiment for assessing whether or not a pH-solubilized drug has the potential to precipitate upon dilution with blood. The computational model enables an efficient means of selecting buffer concentration and pH, and the in vitro test provides a simple experimental validation. Both means of screening are applied to the formulation of the weakly basic drug levemopamil-HCI. A buffered formulation of levemopamil is chosen from the computational model and shown to be free of precipitation upon dilution in vitro and to not produce phlebitis in the rabbit ear model. In comparison, an unbuffered formulation at the same pH and drug concentration precipitates in vitro and causes significant phlebitis in vivo. The results of this study reinforce the importance of buffering parenteral formulations instead of simply adjusting the pH of the formulation.

Animals↗

PubMed2006

Determination of calibration function in thermal field flow fractionation under thermal field programming.

A new procedure for determining the calibration function able to relate retention and operative parameters to molecular weight of the species in thermal field flow (ThFFF) under thermal field programming (TFP) conditions is presented. The procedure involves determining the average values of retention parameters under TFP and determining a numerical function related to the temperature variations that occur during TFP. The calibration parameters are obtained by a procedure fitting the retention and operative parameters that hold true at the beginning of the TFP. The procedure is closely related to the one previously developed to calibrate the retention time axis under TFP ThFFF and, together, they constitute a full calibration procedure. Experimental validation was performed with reference to polystyrene (PS)-decalin and PS-THF systems. The calibration functions here obtained were compared to those derived by the classical procedure at constant thermal field ThFFF to obtain the calibration function at variable cold wall temperatures. Excellent agreement was found in all cases proving "universality" of the ThFFF calibration concept, i.e. it is independent of the particular system on which it was determined and can thus be extended to ThFFF operating under TFP. The new procedure is simpler than the classical one since it requires less precision in setting the instrumentation and can be obtained with fewer experiments. The potential applications for the method are discussed.

Journal Article↗

PubMed2004

Arterialization of the portal stump by right renal artery after portocaval shunt in the rat.

Portosystemic shunts cause severe secondary effects, so that arterializations of the portal stump are planned to increase the blood supply to the liver. The aim of this study was to verify the technical feasibility of arterialization of the portal stump with the right renal artery in order to obtain a valid experimental model to study the pathophysiology of arterial revascularization of the liver. Twenty rats underwent end-to-side portocaval shunt + end-to-end anastomosis between the right renal artery and portal stump; another 20 rats were subjected to the same surgical procedure, but the portal stump underwent a reduction in size. In our study, both techniques gave good results, but the use of an operating microscope and good microsurgical training were essential in achieving a good patency rate (78.3%).

Anastomosis, Surgical↗

PubMed2002

k-space filtering in 2D gradient-echo breath-hold hyperpolarized 3He MRI: spatial resolution and signal-to-noise ratio considerations.

In this work some of the factors that can influence the signal-to-noise ratio (SNR) and spatial resolution in MR images of inhaled hyperpolarized gases are systematically addressed. In particular, the effects of RF depletion of longitudinal polarization and image gradient diffusion dephasing were assessed in terms of their contribution to a k-space filter. By means of theoretical simulations and a novel method of experimental validation using a variable transverse magnetization of the 1H signal, systematic quantitative and qualitative investigations of the effects of k-space filtering intrinsic to imaging of hyperpolarized gas were made. A 2D gradient-echo image is considered for a range of flip angles with centric, sequential, and half-Fourier Cartesian phase-encoding strategies, and the results are assessed in terms of SNR and spatial resolution in the reconstructed images. Centric phase encoding was found to give the best SNR at higher flip angles, with a trade-off in spatial resolution compared to sequential phase encoding. A half-Fourier approach potentially offers increased SNR through the use of higher flip angles without compromising the spatial resolution, which is comparable to that achieved with sequential encoding.

Fourier Analysis↗

PubMed2003

Arterial transit time imaging with flow encoding arterial spin tagging (FEAST).

Arterial spin labeling (ASL) perfusion imaging provides direct and absolute measurement of cerebral blood flow (CBF). Arterial transit time is a related physiological parameter reflecting the duration for the labeled spins to reach the brain region of interest. Most of the existing ASL approaches to assess arterial transit time rely on multiple measurements at various postlabeling delay times, and thus are vulnerable to motion artifact as well as computational error. We describe the use of flow encoding arterial spin tagging (FEAST) technique to measure tissue transit time, which can be derived from the ratio between the ASL signals measured with and without appropriate bipolar gradients. In the present study, we provided a theoretical framework and carried out an experimental validation during steady-state imaging. The global mean tissue transit time was approximately 1100 and 1400 ms for two conditions of bipolar gradients with specific encoding velocity (Venc) of 29 and 8 mm/sec, respectively. The mean tissue transit time measured within cerebral vascular territories was shortest in the deep middle cerebral artery (MCA) territory. Application of the FEAST technique in two patients with cerebrovascular disease demonstrated prolonged tissue transit times in the affected vascular territories which were consistent with results from other MR imaging modalities.

Adult↗

PubMed2001

Quantitative imaging of magnetization transfer exchange and relaxation properties in vivo using MRI.

We describe a novel imaging technique that yields all of the observable properties of the binary spin-bath model for magnetization transfer (MT) and demonstrate this method for in vivo studies of the human head. Based on a new model of the steady-state behavior of the magnetization during a pulsed MT-weighted imaging sequence, this approach yields parametric images of the fractional size of the restricted pool, the magnetization exchange rate, the T(2) of the restricted pool, as well as the relaxation times in the free pool. Validated experimentally on agar gels and samples of uncooked beef, we demonstrate the method's application on two normal subjects and a patient with multiple sclerosis.

Animals↗