Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Transformer model”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 685 records · Page 38Linked to original sources
PubMed2004

Alterations in apoptosis and epithelial-mesenchymal transformation in an in vitro cleft palate model.

The processes of apoptosis and epithelial-mesenchymal transformation have been identified as two major mechanisms by which secondary palatal shelves achieve fusion. The aim of this study was to investigate alterations in these mechanisms by changing the physical distance between paired palatal shelves in an in vitro model of palatogenesis. Wild-type palatal pairs were dissected from E13.5 CD1 mouse embryos and allowed to grow in tissue culture for 48 hours at various intershelf distances. During the fusion process, medial edge epithelial cell fate was assessed using terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) staining, to evaluate apoptosis, and carboxyfluorescence (carboxy-2,7'-dichlorofluorescein diacetate succinimidyl ester) labeling, to measure transformation to mesenchymal cells. Palatal pairs separated in culture greater than or equal to 0.4 mm failed to fuse. TUNEL staining showed that the number of apoptotic cells in the palatal shelves increased as the intershelf distance increased, becoming marked in shelves that did not achieve fusion. The amount of epithelial-mesenchymal transformation, however, decreased with increasing intershelf distance. These results suggest that the contribution of epithelial-mesenchymal transformation and apoptosis to palatal shelf development and fusion can be altered by physical proximity. Therefore, one mechanism behind clefting in utero may result from an imbalance in epithelial-mesenchymal transformation and apoptosis as observed in vitro where palatal shelves are challenged to fuse by physical separation. This effect could be significant in the understanding and treatment of developmental palatal abnormalities. Perhaps in utero manipulation of intershelf spacing or epithelial-mesenchymal transformation and/or apoptosis could reverse the clefting paradigm.

Animals↗
PubMed2000

Culture models of human mammary epithelial cell transformation.

Human pre-malignant breast diseases, particularly ductal carcinoma in situ (DCIS) already display several of the aberrant phenotypes found in primary breast cancers, including chromosomal abnormalities, telomerase activity, inactivation of the p53 gene, and overexpression of some oncogenes. Efforts to model early breast carcinogenesis in human cell cultures have largely involved studies of in vitro transformation of normal finite lifespan human mammary epithelial cells (HMEC) to immortality and malignancy. We present a model of HMEC immortal transformation consistent with the known in vivo data. This model includes a recently described, presumably epigenetic process, termed conversion, which occurs in cells that have overcome stringent replicative senescence and are thus able to maintain proliferation with critically short telomeres. The conversion process involves reactivation of telomerase activity, and acquisition of good uniform growth in the absence and presence of TGFbeta. We propose that overcoming the proliferative constraints set by senescence, and undergoing conversion, represent key rate-limiting steps in human breast carcinogenesis, and occur during early stage breast cancer progression.

Breast Neoplasms↗
PubMed2001

Simple model of a random walk with arbitrarily long memory.

We present a generalization of the persistent random-walk model in which the step at time n depends on the state of the step at time n-T, for arbitrary T. This gives rise to arbitrarily long memory effects, yet by an appropriate transformation the model is tractable by essentially the same techniques applicable to the usual persistent random-walk problem. We apply our results to the specific case of delayed "step" persistence, and analyze its asymptotic statistical properties.

Journal Article↗
PubMed2003

Pressure ulcer prevention and treatment: transforming research findings into consensus based clinical guidelines.

The translation of research findings into practice guidelines is an important aspect in maintaining the currency of practice and adding value to research. While there has been a large amount of published literature regarding the treatment and prevention of pressure ulcers, very few studies have attempted to provide clear clinical guidelines. The present study proposes a model to transform research into clinical guidelines whilst developing a series of guidelines that can be applied to a variety of clinical settings.

Australia↗
PubMed1984

A continuum model for a red blood cell transformation: sphere to crenated sphere.

The evolution of crenations on the spherical red blood cell, which is part of the reversible disc-sphere transformation of these cells, is considered here. A continuum model is developed where the cell is treated as a small viscous droplet encapsulated by a viscoelastic solid membrane. When a small amount of material is deposited into the membrane, the drop responds by increasing its surface area as manifested by the appearance of ripples. A preferred number of crenations form and they are sustained for long time periods. The inception of crenations is due to a dynamic instability in the governing set of nonlinear equations, and depends on the rheological properties of the droplets' interior and membrane.

Elasticity↗
PubMed1999

Pretreatment evaluation of adnexal tumors predicting ovarian cancer.

Kobal B, Rakar S, Ribic-Pucelj M, Tomazevie T, Zaletel-Kragelj L. Pretreatment evaluation of adnexal tumors predicting ovarian cancer. The objective of this study was to determine the ability of tumor marker assessment, gray-scale transvaginal with color Doppler ultrasonography to predict ovarian malignancy. One hundred thirty-four subjects with ovarian masses who entered the study prospectively underwent pelvic examination, tumor marker assessment and gray-scale transvaginal with color flow Doppler ultrasonography preoperatively. Malignancy predictors were statistically evaluated with stepwise multiple logistic regression, and the scores from the model were transformed to probability for having a malignant disease. The presence of neovascularization, intracystic papillary projections, elevated serum CA 125, and age over 45 years were significant predictors for malignancy. Positive predictive value (PPV) for the regression model was 89.0%, and negative predictive value (NPV) was 96.8%. Probability for malignancy ranged from 0.004 to 0.991 depending on which covariates were included. Logistic regression analysis of pretreatment diagnostic gray-scale and color Doppler ultrasonographic characteristics, together with CA 125 enabled a creation of probability assessment scale for individual estimation of ovarian mass, which may contribute to final clinical decision.

Journal Article↗
PubMed1996

Telomerase activation in normal B lymphocytes and non-Hodgkin's lymphomas.

Activation of telomerase seems to be a prerequisite for immortalization and is found in permanent cell lines and most malignant tumors. Normal somatic cells are generally telomerase negative, except for bone marrow stem cells. Weak activity is also present in peripheral blood cells. In the present study strong telomerase activity was demonstrated in vivo in normal mature cells of the immune system, as well as in malignant lymphomas. Benign lymph nodes had lower telomerase activity than benign tonsils, which exhibited intermediate to high activity comparable with findings in malignant lymphomas. In benign tonsils the activity seemed to be restricted to germinal center B cells. In benign lymphoid tissues telomerase activity correlated with B-cell numbers and cell proliferation, but this was not observed in the lymphoma group. High-grade lymphomas exhibited higher levels of telomerase compared with low-grade cases. The data showed that in vivo activation of telomerase is a characteristic feature of germinal center B cells. Different signals for activation of telomerase are likely to exist, one of them being immune stimulation. The data suggest that telomerase activity in malignant lymphomas can be explained by an "induction and retention" model, ie, transformation occurs in a normal, mature B cell with reactivated telomerase, which is retained in the neoplastic clone.

B-Lymphocytes↗
PubMed2004

Internal models and contextual cues: encoding serial order and direction of movement.

During reaching, the brain may rely on internal models to transform desired sensory outcomes into motor commands. This transformation depends on both the state of the limb and the cues that can identify the context of the movement. How are contextual cues and information about state of the limb combined in the computations of internal models? We considered a reaching task where forces on the hand depended on both the direction of movement (state of the limb) and order of that movement in a predefined sequence (contextual cue). When the cue was available, the motor system formed an internal model that used both serial order and target direction to program motor commands. Assuming that the internal model was formed by a population code through a combination of unknown basis elements, the sensitivity of the bases with respect to state of the limb and contextual cue should dictate how error in one type of movement affected all other movement types. Using a state-space theory, we estimated this generalization function and identified the adaptive system from trial-by-trial changes in performance. The results implied that the basis elements were tuned to direction of movement but output of each basis at its preferred direction was multiplicatively modulated by a weak tuning with respect to the contextual cue. Activity fields that multiplicatively encode diverse sources of information may serve as a general mechanism for a single network to produce context-dependent motor output.

Cues↗
PubMed1994

Principal component analysis of Fourier transform infrared and/or circular dichroism spectra of proteins applied in a calibration of protein secondary structure.

Gaining information on the secondary structure of a protein from its spectra is presented as a calibration problem. The secondary structures known from X-ray studies and the spectra of 21 proteins are represented by a linear model. Fourier transform infrared (FTIR) spectra from 1700 to 1600 cm-1, circular dichroism (CD) spectra from 178 to 260 nm, and combined spectra are used; the secondary structure classes of interest are alpha-helices, antiparallel beta-sheets, parallel beta-sheets, beta-turns, and "other." The calibration is solved in two steps: (i) the dependencies between the structures and the spectra of reference proteins are found using the least-squares estimator, and (ii) the secondary structure of a protein is predicted from its spectra using the information gained in the first step and principal component analysis. The problem of information content of the reference spectra is analyzed using the linearly independent pieces of information, the so-called principal components, provided by singular value decomposition. Attention is paid to a number of the principal components sufficient for the prediction, which may be less than the total number. A relative estimable parameter is used to determine unambiguously the number of the components corresponding to the minimum mean square error of the predictor. The analysis gives the solutions to this linear calibration relevant to the underlying protein problem, thus reducing subjective assessments as well as computations.

Calibration↗
PubMed1995

Production evaluation techniques based on lactation curves.

Test day data on milk yield for individual cows were generated using Monte Carlo simulation consisting of 1000 herds. Each herd contained 30 second lactation cows for each of 2 yr. Three scenarios were simulated with increasing effects of test day and seasonality. For each test day, several statistics were calculated for each cow: test day data on yield deviated from expectations, deviated test day data on yield transformed to account for correlation of consecutive test day data on yields, 305-d mature equivalent estimates, and changes in these values from the previous test day. A probability value for each herd was calculated for test of month of lactation effects using ANOVA models with and without cows in the model. No month of lactation effects were simulated. The distribution of generated probability values were tested for uniformity using a chi-square test. The distribution of probability values associated with the change in test day deviations were most nearly uniform, and results for these variables were similar when the cow effect was removed from the analysis model. The transformed variables also provided a fairly uniform set of probability values, although interpretation of these statistical tests was more difficult. Tests based on mature equivalent, 305-d records were oversensitive.

Animals↗
PubMed2000

Physical model-based non-rigid registration incorporating statistical shape information.

This paper describes two new atlas-based methods of 2D single modality non-rigid registration using the combined power of physical and statistical shape models. The transformations are constrained to be consistent with the physical properties of deformable elastic solids in the first method and those of viscous fluids in the second, to maintain smoothness and continuity. A Bayesian formulation, based on each physical model, an intensity similarity measure, and statistical shape information embedded in corresponding boundary points, is employed to derive more accurate and robust approaches to non-rigid registration. A dense set of forces arises from the intensity similarity measure to accommodate complex anatomical details. A sparse set of forces constrains consistency with statistical shape models derived from a training set. A number of experiments were performed on both synthetic and real medical images of the brain and heart to evaluate the approaches. It is shown that statistical boundary shape information significantly augments and improves physical model-based non-rigid registration and the two methods we present each have advantages under different conditions.

Brain↗
PubMed2005

Enhancement of transformed foci and induction of prostaglandins in Balb/c 3T3 cells by palytoxin: in vitro model reproduces carcinogenic responses in animal models regarding the inhibitory effect of indomethacin and reversal of indomethacin's effect by exogenous prostaglandins.

Cell transforming activity of palytoxin, a non-TPA type tumor-promoter, was investigated with the two-stage transformation assay using Balb/c 3T3 cells. Palytoxin showed potent promoting activity; treatment at 1.9 pM or more increased the number of transformed foci after initiation by 3-methylcholanthrene (MCA). Determination of prostaglandin (PG) E2 and PGF(2alpha) concentrations in the culture medium revealed that palytoxin (1.9-3.7 pM for 24 h) stimulated the production of PG in Balb/c 3T3 cells (the concentration reached 3-4 microM), and treatment with PGE2 or PGF(2alpha) itself increased the number of transformed foci of Balb/c 3T3 cells after initiation by MCA. Neither palytoxin nor PGs showed initiating activity. Indomethacin suppressed the promoting activity of palytoxin, but not that of PGE2 and PGF(2alpha). Interestingly, concomitant treatment with PGE2 or PGF(2alpha) in addition to indomethacin markedly reversed the suppressive effect of indomethacin. These findings indicated that the in vitro transformation model could reproduce experiments that have been performed in animal models regarding the inhibitory effect of indomethacin on carcinogenic responses and reversal of indomethacin's effect by exogenous prostaglandin and, therefore, may provide insight into molecular modes of action of palytoxin. In the present study, palytoxin also induced prostaglandin synthesis, and therefore, the Balb/c 3T3 cell model should provide insight into the molecular mechanism by which palytoxin regulates prostaglandin biosynthesis.

Acrylamides↗
PubMed1997

A model for learning human reaching movements.

Reaching movement is a fast movement towards a given target. The main characteristics of such a movement are straight path and a bell-shaped speed profile. In this work a mathematical model for the control of the human arm during ballistic reaching movements is presented. The model of the arm contains a 2 degrees of freedom planar manipulator, and a Hill-type, non-linear mechanical model of six muscles. The arm model is taken from the literature with minor changes. The nervous system is modeled as an adjustable pattern generator that creates the control signals to the muscles. The control signals in this model are rectangular pulses activated at various amplitudes and timings, that are determined according to the given target. These amplitudes and timings are the parameters that should be related to each target and initial conditions in the work-space. The model of the nervous system consists of an artificial neural net that maps any given target to the parameter space of the pattern generator. In order to train this net, the nervous system model includes a sensitivity model that transforms the error from the arm end-point coordinates to the parameter coordinates. The error is assessed only at the termination of the movement from knowledge of the results. The role of the non-linearity in the muscle model and the performance of the learning scheme are analysed, illustrated in simulations and discussed. The results of the present study demonstrate the central nervous system's (CNS) ability to generate typical reaching movements with a simple feedforward controller that controls only the timing and amplitude of rectangular excitation pulses to the muscles and adjusts these parameters based on knowledge of the results. In this scheme, which is based on the adjustment of only a few parameters instead of the whole trajectory, the dimension of the control problem is reduced significantly. It is shown that the non-linear properties of the muscles are essential to achieve this simple control. This conclusion agrees with the general concept that motor control is the result of an interaction between the nervous system and the musculoskeletal dynamics.

Algorithms↗
PubMed1986

Induction of c-sis mRNA and activity similar to platelet-derived growth factor by transforming growth factor beta: a proposed model for indirect mitogenesis involving autocrine activity.

Treatment of quiescent cultures of mouse embryo-derived AKR-2B cells with transforming growth factor beta resulted in an early induction of c-sis mRNA. The increase in c-sis mRNA was followed by a corresponding increase in protein similar to platelet-derived growth factor (PDGF) in the culture medium. In addition, PDGF-regulated genes (c-fos and c-myc) were stimulated by transforming growth factor beta with delayed kinetics relative to that seen in other cell systems with direct PDGF stimulation. A model is proposed in which the monolayer mitogenicity of transforming growth factor beta is mediated by the induction of c-sis and PDGF and the subsequent autocrine stimulation of c-fos, c-myc, and other PDGF-inducible genes.

Animals↗
PubMed2000

Copper accumulation by Aspergillus awamori.

Aspergillus awamori accumulated Cu2+ from aqueous solutions. The level of copper uptake was dependent on the ambient metal concentration. The process consisted of two phases: a fast initial phase and a slower secondary phase. Chelation of these ions occurs by chemical, equilibrated and saturable mechanism, following the mathematical models of Langmuir and Freundlich, with better performance on the Langmuir model. Data transformation allowed us to calculate the kinetic constants of the sorption reaction.

Adsorption↗
PubMedDate not supplied

Proper folding of the antifungal protein PAF is required for optimal activity.

The Penicillium chrysogenumantifungal protein PAF is secreted into the supernatant after elimination of a preprosequence. PAF is actively internalized into the hyphae of sensitive molds and provokes growth retardation as well as changes in morphology. Thus far, no information is available on the exact mode of action of PAF, nor on the function of its prosequence in protein activity. Therefore, we sought to investigate the effects of secreted PAF as well as of intracellularly retained pro-PAF and mature PAF on the sensitive ascomycete Aspergillus nidulans, and transformed this model organism by expression vectors containing 5'-sequentially truncated paf-coding sequences under the control of the inducible P. chrysogenum-derived xylanase promoter. Indirect immunofluorescence staining revealed the localization of recombinant PAF predominantly in the hyphal tips of the transformant Xylpaf1 which expressed prepro-PAF, whereas the protein was found to be distributed intracellularly within all segments of hyphae of the transformants Xylpaf2 and Xylpaf3 which expressed pro-PAF and mature PAF, respectively. Growth retardation of Xylpaf1 and Xylpaf3 hyphae was detected by proliferation assays and by light microscopy analysis. Using transmission electron microscopy of ultrathin hyphal sections a marked alteration of the mitochondrial ultrastructure in Xylpaf1 was observed and an elevated amount of carbonylated proteins pointed to severe oxidative stress in this strain. The effects induced by secreted recombinant PAF resembled those evoked by native PAF. The results give evidence that properly folded PAF is a prerequisite for its activity.

Antifungal Agents↗
PubMedDate not supplied

Mechanical properties of model membranes studied from shape transformations of giant vesicles.

Membrane deformations occur frequently in cell functioning. From the physical point of view, the understanding of such shape changes requires the introduction of mechanical parameters like bending elasticity. In this article it is shown how this physical property can be obtained from the analysis of small or large shape transformations from giant vesicles. Then it is demonstrated that the bending modulus is strongly dependent on the membrane composition and environmental conditions. This is the case for one-component bilayers (dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidylcholine and stearoyloleoyl-phosphatidylcholine (SOPC) and for two-component lipid mixtures (DMPC/cholesterol, DLPC/dilauroylphosphatidic acid). Further it is shown that the bending elasticity of natural lipid extracts (egg phosphatidylcholine, digalactosyl diglyceride and red blood cell lipid extracts) is generally smaller than that of comparable synthetic model membranes. The role of transmembrane proteins is examined by measuring the bending elasticity of SOPC/gramicidin mixtures. Finally, larger scale shape transformations of giant vesicles under an alternative electric field are discussed.

Elasticity↗