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 415 records · Page 23Linked to original sources
PubMed2001

Arthropod touch reception: stimulus transformation and finite element model of spider tactile hairs.

Striving towards an in depth understanding of stimulus transformation in arthropod tactile hairs, we studied the mechanical events associated with tactile stimulation. A finite element model was developed taking a tarsal tactile hair of the spider Cupiennius salei as an example. Considering hair diameter, wall thickness, and curvature, the hair is subdivided into six regions each with its specific mechanical properties. When the hair is touched from above with a flat surface oriented parallel to the tarsus the point of stimulus contact moves towards the hair base with increasing load and hair deflection. Thereby the effective lever arm is reduced protecting the hair against breaking near its base. At the same time the mechanical working range of the hair increases implying higher mechanical sensitivity for small deflections (about 5x10(-5) N/degrees) than for large deflections (about 1x10(-4) N/degrees). The major stresses within the hair shaft are axial stresses due to bending. The position of stress maxima moves along the shaft with the movement of the stimulus contact point. Remarkably, the amplitude of this maximum (about 1x10(5) N/m2) hardly changes with increasing loading force due to the way the hair shaft is deflected by the stimulus.

Animals↗
PubMed2004

Agrobacterium T-DNA integration: molecules and models.

Genetic transformation mediated by Agrobacterium involves the transfer of a DNA molecule (T-DNA) from the bacterium to the eukaryotic host cell, and its integration into the host genome. Whereas extensive work has revealed the biological mechanisms governing the production, Agrobacterium-to-plant cell transport and nuclear import of the Agrobacterium T-DNA, the integration step remains largely unexplored, although several different T-DNA integration mechanisms have been suggested. Recent genetic and functional studies have revealed the importance of host proteins involved in DNA repair and maintenance for T-DNA integration. In this article, we review our understanding of the specific function of these proteins and propose a detailed model for integration.

Active Transport, Cell Nucleus↗
PubMed2003

Sustained activation of fibroblast transforming growth factor-beta/Smad signaling in a murine model of scleroderma.

Transforming growth factor-beta is responsible for triggering a cascade of events leading to fibrosis in scleroderma. The Smads are intracellular signal transducers recently shown to mediate fibroblast activation and other profibrotic responses elicited by transforming growth factor-betain vitro. To understand better the involvement of Smads in the pathogenesis of fibrosis, we examined Smad expression and activation in situ in a murine model of scleroderma. Bleomycin injections induced striking dermal infiltration with macrophages by 3 d, and progressive fibrosis by 2 wk. Infiltrating macrophages and resident fibroblasts expressed Smad3, the positive mediator for transforming growth factor-beta responses. Importantly, in bleomycin-injected skin, fibroblasts showed predominantly nuclear localization of Smad3 and intense staining for phospho-Smad2/3. Furthermore, phosphorylated Smad2/3 in fibroblasts was detected even after the resolution of inflammation. Expression of Smad7, the endogenous inhibitor of transforming growth factor-beta/Smad signaling, was strongly induced in dermal cells by transforming growth factor-beta, but not by bleomycin injections. Collectively, these results indicate that bleomycin-induced murine scleroderma is associated with rapid and sustained induction of transforming growth factor-beta/Smad signaling in resident dermal fibroblasts. Despite apparent activation of the intracellular transforming growth factor-beta signaling pathway in the lesional dermis, the expression of transforming growth factor-beta-inducible Smad7 was not upregulated. In light of the critical function of Smad7 as an endogenous inhibitor of Smad signaling that restricts the duration and magnitude of transforming growth factor-beta responses, and as a mediator of apoptosis, relative Smad7 deficiency observed in the present studies may account for sustained activation of transforming growth factor-beta/Smad signaling in lesional tissues. These findings raise the possibility that Smads plays an important part in the pathogenesis of fibrosis, and may therefore represent targets for selective anti-fibrotic interventions.

Animals↗
PubMed2004

Functional mapping of quantitative trait loci underlying growth trajectories using a transform-both-sides logistic model.

The incorporation of developmental control mechanisms of growth has proven to be a powerful tool in mapping quantitative trait loci (QTL) underlying growth trajectories. A theoretical framework for implementing a QTL mapping strategy with growth laws has been established. This framework can be generalized to an arbitrary number of time points, where growth is measured, and becomes computationally more tractable, when the assumption of variance stationarity is made. In practice, however, this assumption is likely to be violated for age-specific growth traits due to a scale effect. In this article, we present a new statistical model for mapping growth QTL, which also addresses the problem of variance stationarity, by using a transform-both-sides (TBS) model advocated by Carroll and Ruppert (1984, Journal of the American Statistical Association 79, 321-328). The TBS-based model for mapping growth QTL cannot only maintain the original biological properties of a growth model, but also can increase the accuracy and precision of parameter estimation and the power to detect a QTL responsible for growth differentiation. Using the TBS-based model, we successfully map a QTL governing growth trajectories to a linkage group in an example of forest trees. The statistical and biological properties of the estimates of this growth QTL position and effect are investigated using Monte Carlo simulation studies. The implications of our model for understanding the genetic architecture of growth are discussed.

Biometry↗
PubMed2001

The role of selection in progressive neoplastic transformation.

Mathematical modeling indicates that selective growth of cells with biallelic mutations in tumor suppressor genes is the driving force in the development of most human tumors, and that increased mutation rate is not required. Spontaneous neoplastic transformation of cells in culture offers the opportunity for quantitative analysis of all stages of neoplastic progression, the cellular variation that underlies it, and the selective conditions that promote it. Most of the early work on spontaneous transformation was done in primary cultures of mouse embryo cells, but established mouse cell lines have been used more in recent years. The main criteria for transformation have been tumorigenesis in mice, increase in saturation density, and production of discrete, multilayered foci in confluent cell cultures. Spontaneous transformation in NIH 3T3 mouse fibroblasts is efficiently evoked by progressive selection under prolonged contact inhibition at high population density or during multiplication at low population density in suboptimal concentrations or types of serum. In general, it is a multistep process with some stages of progression occurring before there is any visible sign of transformed foci. There is a high degree of heritable heterogeneity in the original NIH 3T3 cell population for susceptibility to transformation. Isolation and expansion of minority susceptible clones from a relatively refractory population exhibit transformation long before the polyclonal parental population does because of the increased proportion of susceptible cells in these clones. There are indications that the selective conditions induce selectable variants. Tumor development in animals and man shares important characteristics with spontaneous transformation in culture, including a major role for selection, but the selective conditions for clonal expansion probably vary with the dynamics of differentiation in each tissue. These considerations support a role for an altered microenvironment (as in the aging process) in selective growth of rogue clones.

Animals↗
PubMed2007

Transformation of 3DP gypsum model to HA by treating in ammonium phosphate solution.

Three-dimensional printing (3DP) is a CAD/CAM built-up using ink-jet printing technique. Commercially available 3DP system can form only gypsum model and not for bioceramics. On the other hand, transformation of hardened gypsum into hydroxyapatite (HA) by treatment in ammonium phosphate solution was found lately. In the present study, transformation of the 3DP gypsum block to HA was attempted. However, the fabricated 3DP block was soluble in water. To insolubilize, it was heated at 300 degrees C for 10 min, and then, gypsum was transformed to calcium sulfate hemihydrate, CaSO(4) x 0.5H(2)O. The 3D block was immersed in 1M (NH(4))(3)PO(4) x 3H(2)O solution at 80 degrees C for 1-24 h, and the transformation into HA within 4 h was ascertained. A heat-treated plaster of Paris (POP) block was also investigated for comparison. The unheated POP block consisting of gypsum dihydrate took 24 h to complete the transformation, while the heat-treated POP consisting calcium sulfate hemihydrate promoted the transformation into HA; but the transformed thickness in the block was less than the 3DP block. This is probably due to higher solubility of the hemihydrate than gypsum dihydrate. Accelerated transformation of the 3DP block was also caused by its porous structure, which enabled an easy penetration of the phosphate solution. With the present method, it is possible to transform the fabricated gypsum by 3D printing that is adaptive to the osseous defect into HA prostheses or scaffold.

Bone Substitutes↗
PubMed1999

Coupled modified baker's transformations for the Ising model.

An invertible coupled map lattice is proposed for the Ising model. Each elemental map is a modified baker's transformation, which is a two-dimensional map of X and Y. The time evolution of the spin variable is memorized in the binary representation of the Y variable. The temporal entropy and time correlation of the spin variable are calculated from the snapshot configuration of the Y variables.

Journal Article↗
PubMed1997

Multiresolution EEG comparison of rat ischemia models.

Fourier transform of Electroencephalography (EEG) restricts EEG analysis due to its stationary properties with time change. It makes analysis difficult to ascertain the global effects of transient change in EEG signals. This study tested that multi-resolution analysis distinguishes different depths of ischemic insult related to the degree of residual blood flow in animal models. The results suggest that multi-resolution analysis demonstrate that little blood flowing to the brain has more detrimental effect to the EEG properties than no blood flowing, which is contrary to the common sense.

Animals↗
PubMed1986

Transformations of arylpropane lignin model compounds by a lignin peroxidase of the white-rot fungus Phanerochaete chrysosporium.

Various lignin model compounds of the O-arylpropane type were oxidized with purified lignin peroxidase from the white-rot fungus Phanerochaete chrysosporium, and oxidation products were identified by gas-chromatography/mass-spectroscopy procedures. Our results are in accord with the theory that lignin peroxidase catalyzes one-electron oxidations of its substrates with formation of cation radicals, and that these radicals undergo degradative reactions that are predictable from a knowledge of cation radical and oxygen chemistry. Cation radicals formed from O-arylpropane model compounds appeared to undergo the following types of degradative transformations: addition of water to ring-centered radicals, followed by proton loss yielding quinones and alcohols; nucleophilic attack by hydroxy functions on propanoid moieties giving cyclic ketals as intermediates which decompose to yield side chain migration products; transfer of the charge of a radical from a ring to the associated alkyl moiety through an ether bond, with loss of a proton from the latter, forming a new carbon-centered radical. The new alkyl-centered radicals apparently were able to abduct dioxygen to form peroxyl radicals which decomposed giving a variety of oxidation products and probably superoxide anion. Specific examples of the above transformations are presented, and their relevance to lignin degradation is discussed.

Basidiomycota↗
PubMed2002

Multiple stages of malignant transformation of human endothelial cells modelled by co-expression of telomerase reverse transcriptase, SV40 T antigen and oncogenic N-ras.

We have modelled multiple stages of malignant transformation of human endothelial cells (ECs) by overexpressing the catalytic subunit of human telomerase (hTERT), together with SV40 T antigen (SV40T) and oncogenic N-ras. Transfection with hTERT alone, led to the immortalization of two out of three cultures of bone marrow-derived ECs (BMECs). One hTERT transduced BMEC culture underwent a long proliferative lag before resuming proliferation. BMECs transfected with hTERT alone were functionally and phenotypically normal. BMECs transfected with SV40T (BMSVTs) had an extended lifespan, but eventually succumbed to crisis. BMSVTs exhibited a partially transformed phenotype, demonstrating growth factor independence, altered antigen expression and forming tiny, infrequent colonies in vitro. Transduction of BMSVTs with hTERT resulted in immortalization of 4 out of 4 cultures. BMSVTs immortalized with hTERT formed large colonies in vitro and small transient tumours in vivo. BMECs co-expressing SV40T, hTERT and N-ras exhibited an overtly transformed phenotype; forming very large colonies with an altered morphology and generating rapidly growing tumours in vivo. These investigations demonstrate transformation of human ECs to an overtly malignant phenotype. This model will be useful for understanding mechanisms underlying vascular and angiogenic neoplasias, as well as for testing drugs designed to curtail aberrant EC growth.

Adult↗
PubMed1985

Processing of donor DNA during Haemophilus influenzae transformation: analysis using a model plasmid system.

A plasmid system was used to investigate the processing of donor DNA during transformation of competent Haemophilus influenzae. Using biochemical and genetic methods, we have determined that portion of a donor plasmid molecule that, on average, can become integrated into a homologous recipient plasmid during transformation. Our results show that (i) transformation efficiency decreases linearly with donor DNA length over the range of 11 to 3.5 kilobase pairs, (ii) transformation efficiency decreases exponentially with size for donor molecules less than 3.5 kilobase pairs in length, and (iii) 5'-end label, but not 3'-end label, can be specifically incorporated into the resident homologous region. We present a model for donor processing during entry that encompasses and explains these observations.

DNA Restriction Enzymes↗
PubMed1993

Transforming growth factor-beta accelerates osteoinduction in a craniofacial onlay model.

Recombinant human transforming growth factor beta 1 was added to a demineralized bone matrix (DBM) paste, formed into cylinders and implanted onto the cranial periosteum of New Zealand White rabbits. The TGF-beta was added at doses of 0, 0.3, 3, 30 and 75 micrograms per implant. When the implants were removed after six weeks, histomorphometric analysis of the implants showed that TGF-beta induced significantly higher levels of trabecular bone formation than in the controls (mineralized bone area 6.0 +/- 0.8, 6.0 +/- 1.2, 5.6 +/- 1.0, 10.1 +/- 1.5, and 10.8 +/- 1.4 mm2, respectively, P < 0.05), TGF-beta also caused greater resorption of the demineralized bone matrix carrier (matrix area 7.2 +/- 0.9, 6.8 +/- 1.4, 3.7 +/- 0.9, 2.7 +/- 1.2, 0.9 +/- 0.5 mm2, respectively, P < 0.02). Measurements of the osteoid demonstrated a more active bone surface and there was evidence of rapid bone remodeling. Similar results were obtained using TGF-5 beta, a new hybrid molecule. These results demonstrate the capacity of transforming growth factor beta in accelerating osteoinduction.

Analysis of Variance↗
PubMed1991

Oncogene-mediated transformation. An in vitro model for colon carcinogenesis.

Evaluation of molecular events in human colon polyps and tumors has revealed constitutive elevated expression of c-myc, activation of both ras and src proto-oncogenes, and allelic deletion events involving inactivation of putative regulatory genes, including p53. To evaluate the contribution of each of these events to colon carcinogenesis, it is desirable to establish epithelial cell lines representing different stages of neoplastic progression. Such in vitro models can be used to establish a primary role for different genes implicated in neoplastic transformation, identifying events involved in multistep carcinogenesis and delineating the factors modulating cellular transformation. We present herein a summary of such an in vitro model for colon carcinogenesis using the introduction of relevant genetic elements into normal mucosa to identify the molecular steps and accompanying cellular events underlying neoplastic progression in the colon.

Animals↗
PubMed2004

Transforming growth factor-{beta} regulates susceptibility of epithelial apoptosis in murine model of colitis.

Transforming growth factor (TGF)-beta has a key role in intestinal homeostasis. Our present data suggest that TGF-beta, which was constitutively expressed by lamina propria mononuclear cells and epithelium, affected epithelial cells. Abnormal suppression of TGF-beta could enhance the sensitivity of epithelial cells to apoptosis associated with interferon-gamma in DSS-induced colitis.

Animals↗
PubMed2006

Bone sialoprotein mediates the tumor cell-targeted prometastatic activity of transforming growth factor beta in a mouse model of breast cancer.

Transforming growth factor betas (TGF-beta) play a dual role in carcinogenesis, functioning as tumor suppressors early in the process, and then switching to act as prometastatic factors in late-stage disease. We have previously shown that high molecular weight TGF-beta antagonists can suppress metastasis without the predicted toxicities. To address the underlying mechanisms, we have used the 4T1 syngeneic mouse model of metastatic breast cancer. Treatment of mice with a monoclonal anti-TGF-beta antibody (1D11) significantly suppressed metastasis of 4T1 cells to the lungs. When metastatic 4T1 cells were recovered from lungs of 1D11-treated and control mice, the most differentially expressed gene was found to be bone sialoprotein (Bsp). Immunostaining confirmed the loss of Bsp protein in 1D11-treated lung metastases, and TGF-beta was shown to regulate and correlate with Bsp expression in vitro. Functionally, knockdown of Bsp in 4T1 cells reduced the ability of TGF-beta to induce local collagen degradation and invasion in vitro, and treatment with recombinant Bsp protected 4T1 cells from complement-mediated lysis. Finally, suppression of Bsp in 4T1 cells reduced metastasis in vivo. We conclude that Bsp is a plausible mediator of at least some of the tumor cell-targeted prometastatic activity of TGF-beta in this model and that Bsp expression in metastases can be successfully suppressed by systemic treatment with anti-TGF-beta antibodies.

Animals↗
PubMed1998

Expression of TGF-beta-1 mRNA and ultrastructural alterations in pharmacologically induced prolonged penile erection in a canine model.

PURPOSE: Transforming growth factor beta (TGF-beta) is known to induce fibrosis. Our objective was to study the role of TGF-beta as a possible mediator of fibrosis that may follow prolonged penile erection. MATERIALS AND METHODS: Prolonged penile erection was induced in seven adult male mongrel dogs by intracavernosal injection of papaverine into one of the corpora cavernosa while the other was used as a control. Intracavernosal pressure measurements were carried out prior to administration of papaverine and at the end of the procedure. Penile tissue was collected from anesthetized animals prior to euthanasia for histological and electron microscopic (EM) studies. RT-PCR was carried out for detection of mRNA on same tissue samples. RESULTS: The light microscopy showed stasis of blood in the cavernosal sinusoids. EM studies revealed sporadic endothelial defects, loss of plasma membrane integrity and cytoplasmic condensation. There was expression of TGF-beta1 mRNA in 66.7% of the experimental group compared with 16.7% of the control group. CONCLUSIONS: Pharmacologically induced low flow prolonged penile erection in canine models is associated with histomorphological changes in relatively short periods of time, suggesting that early therapeutic intervention is desirable. The gene expression for TGF-beta1 may be a mediator of fibrosis; therefore the use of anti-TGF-beta agents presents a possible tool for therapeutic intervention.

Animals↗
PubMed2002

Cucumber: a model angiosperm for mitochondrial transformation?

Plants possess three major genomes, carried in the chloroplast, mitochondrion, and nucleus. The chloroplast genomes of higher plants tend to be of similar sizes and structure. In contrast both the nuclear and mitochondrial genomes show great size differences, even among closely related species. The largest plant mitochondrial genomes exist in the genus Cucumis at 1500 to 2300 kilobases, over 100 times the sizes of the yeast or human mitochondrial genomes. Biochemical and molecular analyses have established that the huge Cucumis mitochondrial genomes are due to extensive duplication of short repetitive DNA motifs. The organellar genomes of almost all organisms are maternally transmitted and few methods exist to manipulate these important genomes. Although chloroplast transformation has been achieved, no routine method exists to transform the mitochondrial genome of higher plants. A mitochondrial-transformation system for a higher plant would allow geneticists to use reverse genetics to study mitochondrial gene expression and to establish the efficacy of engineered mitochondrial genes for the genetic improvement of the mitochondrial genome. Cucumber possesses three unique attributes that make it a potential model system for mitochondrial transformation of a higher plant. Firstly, its mitochondria show paternal transmission. Secondly, microspores possess relatively few, huge mitochondria. Finally, there exists in cucumber unique mitochondrial mutations conditioning strongly mosaic (msc) phenotypes. The msc phenotypes appear after regeneration of plants from cell culture and sort with specific rearranged and deleted regions in the mitochondrial genome. These mitochondrial deletions may be a useful genetic tool to develop selectable markers for mitochondrial transformation of higher plants.

Cucumis sativus↗
PubMed1991

Mechanical coupling of the rib cage, abdomen, and diaphragm through their area of apposition.

Although volumetric displacements of the chest wall are often analyzed in terms of two independent parallel pathways (rib cage and abdomen), Loring and Mead have argued that these pathways are not mechanically independent (J. Appl. Physiol. 53: 756-760, 1982). Because of its apposition with the diaphragm, the rib cage is exposed to two distinct pressure differences, one of which depends on abdominal pressure. Using the analysis of Loring and Mead as a point of departure, we developed a complementary analysis in which mechanical coupling of the rib cage, abdomen, and diaphragm is modeled by a linear translational transformer. This model has the advantage that it possesses a precise electrical analogue. Pressure differences and compartmental displacements are related by the transformation ratio (n), which is the mechanical advantage of abdominal over pleural pressure changes in displacing the rib cage. In the limiting case of very high lung volume, n----0 and the pathways uncouple. In the limit of very small lung volume, n----infinity and the pathways remain coupled; both rib cage and abdomen are driven by abdominal pressure alone, in accord with the Goldman-Mead hypothesis. A good fit was obtained between the model and the previously reported data for the human chest wall from 0.5 to 4 Hz (J. Appl. Physiol. 66:350-359, 1989). The model was then used to estimate rib cage, diaphragm, and abdominal elastance, resistance, and inertance. The abdomen was a high-elastance high-inertance highly damped compartment, and the rib cage a low-elastance low-inertance more lightly damped compartment. Our estimate that n = 1.9 is consistent with the findings of Loring and Mead and suggests substantial pathway coupling.

Abdomen↗