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 1,081 records · Page 60Linked to original sources
PubMed2004

Use of three-dimensional basement membrane cultures to model oncogene-induced changes in mammary epithelial morphogenesis.

The development of breast carcinomas involves a complex set of phenotypic alterations in breast epithelial cells and the surrounding microenvironment. While traditional transformation assays provide models for investigating certain aspects of the cellular processes associated with tumor initiation and progression, they do not model alterations in tissue architecture that are critically involved in tumor development. In this review, we provide examples of how three-dimensional (3D) cell culture models can be utilized to dissect the pathways involved in the development of mammary epithelial structures and to elucidate the mechanisms responsible for oncogene-induced phenotypic alterations in epithelial behavior and architecture. Many normal mammary epithelial cell lines undergo a stereotypic morphogenetic process when grown in the presence of exogenous matrix proteins. This 3D morphogenesis culminates in the formation of well-organized, polarized spheroids, and/or tubules that are highly reminiscent of normal glandular architecture. In contrast, transformed cell lines isolated from mammary tumors exhibit significant deviations from normal epithelial behavior in 3D culture. We describe the use of 3D models as a method for both reconstructing and deconstructing the cell biological and biochemical events involved in mammary neoplasia.

Animals↗
PubMed2006

Development of a parallel demodulation system used for extrinsic Fabry-Perot interferometer and fiber Bragg grating sensors.

A parallel demodulation system for extrinsic Fabry-Perot interferometer (EFPI) and fiber Bragg grating (FBG) sensors is presented, which is based on a Michelson interferometer and combines the methods of low-coherence interference and a Fourier-transform spectrum. The parallel demodulation theory is modeled with Fourier-transform spectrum technology, and a signal separation method with an EFPI and FBG is proposed. The design of an optical path difference scanning and sampling method without a reference light is described. Experiments show that the parallel demodulation system has good spectrum demodulation and low-coherence interference demodulation performance. It can realize simultaneous strain and temperature measurements while keeping the whole system configuration less complex.

Journal Article↗
PubMed2026

AI-driven diagnostic and prognostic models for metabolic dysfunction-associated steatotic liver disease: insights from clinical, imaging, and multi-omics studies-a scoping review.

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is the most common chronic liver disease around the world, affecting 33.6% of the adult population (95% CI: 28.1%-39.5%; I 2 = 99.9%), or roughly one in three. The extent of the liver damage is variable, from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH, formerly NASH), cirrhosis and hepatocellular carcinoma (HCC). Early diagnosis is essential to prevent serious liver damage. Traditional diagnostic techniques such as liver biopsy, imaging, and biomarker testing are all invasive, costly, reduced sensitive to early-stage disease, and they also have variability among observers. Modern diagnostic and prognostic approaches based on the principles of Artificial Intelligence (AI) and specifically on machine learning (ML) and deep learning (DL) have enabled multimodal approaches integrating clinical, imaging and molecular data. This scoping review conducted per PRISMA-ScR guidelines, synthesizes findings from 73 studies (search window 2020-2026) across three dimensions: clinical data driven models, imaging-based classifiers (ultrasound, CT and MRI), and multi-omics (genomics, transcriptomics and proteomics) techniques. Moreover, emergence of models such as U-Net and LiverNet 2.x, classification models like DeepLiverNet and BiLSTM models, as well as transformer frameworks and the identification of biomarkers models are also described. This study also investigates challenges such as data heterogeneity, data interpretability, fairness and real-world clinical application. Finally, important areas of research opportunities and future directions are highlighted to present a developing clinically applicable, explainable and ethical AI solutions to manage MASLD.

MASLD↗
PubMed1986

Phenotype, frequency, and EBV responsiveness of human marrow B and pre-B cells.

We have purified subpopulations of B lineage cells from human adult (rib) bone marrow by cell sorting and panning. Limiting dilution analysis was then used for a clonal analysis of cells able to secrete IgG, IgA, or IgM spontaneously or after infection with EBV. Nonproliferating, high rate IgG or IgA producers occurred at frequencies of about one per 1000 marrow mononuclear cells. Their frequency and Ig production was unaffected by EBV, and they appeared not to express EBNA after exposure to EBV. These cells were Ia+, B1+, and over 85% expressed sIg of the IgM/D (up to 75%) and/or IgG/A isotypes (40 to 60%). B cells committed to the secretion of IgM represent 2 to 10% of marrow B lymphocytes. They were found to be Ia+/B1+/B2+/CALLA- and C3b receptor (CR3)-cells, and most (greater than 90%) required infection with EBV and proliferation to develop into IgM-producing lymphocytes. Thirty to 40% of these cells did not express Ig (H or L chain) on their surface, and therefore resembled pre-B cells at the beginning of the 4- to 5-wk culture period. Proliferating pre-B cells from adult human marrow have been described, but their conversion into IgM-producing cells has not been formally demonstrated. Although EBV induces IgM production, the expression of EBNA, and several rounds of cell division in these cells, the induction of stable (greater than 5 wk) growth transformation represents a rare event in these pre-B cells: in several thousand limiting dilution wells, not a single culture of sIg-cells showed stable growth transformation. The dichotomy between EBV-induced high-rate IgM responses and absent growth transformation discriminates activation and transformation as distinct aspects of EBV-induced B cell "responses", and suggests that cellular properties play critical roles for viral transformation. We propose a model in which cellular target genes for transforming sequences in the EBV genome are transiently expressed during B cell differentiation.

Adult↗
PubMed1994

TGF-beta 1 post-treatment in a rabbit model of cerebral ischaemia.

Transforming growth factor-beta 1 (TGF-beta 1), suggested in some studies to suppress astrocyte and neutrophil function, has also reduced ischaemic brain injury when administered immediately prior to clot embolization in models of thromboembolic stroke. The effect of TGF-beta 1 as a post-treatment paradigm was investigated in a rabbit model of thromboembolic stroke. Following clot embolization, regional cerebral blood flow fell to < 10 cc 100 g-1 min-1 in all animals. TGF-beta 1 (10 micrograms) or vehicle (n = 5 each group) was infused via the contralateral carotid artery. TGF-beta 1 administration resulted in a rapid and selective reduction in the peripheral neutrophil count as compared to a significant (p < 0.05) increase in control values (2336 +/- 817 vs 4320 +/- 928 neutrophils mm3, mean +/- SEM). Neutrophil aggregation was increased within 30 min of TGF-beta 1 infusion when compared to control (2.07 +/- 0.70 vs 1.09 +/- 0.17 ohms, p < 0.05); neutrophil chemiluminescence, an index of the oxygen respiratory burst was not significantly affected by TGF-beta 1 administration. No difference in platelet counts or aggregation was noted. There was no significant difference between the two groups regarding brain infarct size (47.5 +/- 10.9 vs 56.5 +/- 10.4, n = 4, TGF-beta vs control, mean +/- SEM), intracranial pressure, or brain excitatory amino acid levels (aspartate and glutamate) within ischaemic regions.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of Variance↗
PubMed1987

Relationship between tumour size and uptake of radiolabelled anti-CEA in a colon tumour xenograft.

The relationship between tumour size and the uptake of three radiolabelled anti-CEA localising antibodies (A5B7, 1H12 and PK2G) into a human colon tumour xenograft (MaWi) has been examined. For tumour weights greater than 100 mg (109-873 mg) there was a strong positive correlation between absolute uptake and tumour weight with mean uptakes per gram of 9.8 (r = 0.92), 5.0 (r = 0.93) and 5.3 (r = 0.94) for A5B7, 1H12 and PK2G respectively. For tumour weights below 100 mg (17-99 mg) the percentage uptake per gram (specific uptake) increased markedly reaching 80% of the injected dose for A5B7. The above phenomena could be modelled by representing uptake by the surface area of a sphere and tumour weight by its volume. Transformation of this model produced a linear relationship suitable for regression analysis of the experimental data. The slopes of the regression lines for the three antibodies were very close to that predicted by the model suggesting that their uptake into MaWi xenografts is proportional to surface area. The main discrepancy of the actual data was shown by the intercepts which relate to the variation in uptake between different antibodies. This model provides a possible means of correcting for the effect of tumour size when investigating the uptake of antibodies into xenografts.

Adenocarcinoma, Mucinous↗
PubMed1998

Transformation of a liposomal dispersion containing ibuprofen lysinate and phospholipids into mixed micelles - physico-chemical characterization and influence on drug permeation through excised human stratum corneum.

Our study is meant as a contribution to the investigation of molecular association of phospholipids and amphiphilic substances like, e.g. non-steroidal anti-inflammatory drugs. Our research focused on physico-chemical characterization of ternary systems containing ibuprofen lysinate, lecithin and water. The influence of the resulting microstructures on drug release and permeation through excised human stratum corneum was also investigated. Depending on the mixing ratio different physical states (lamellar and hexagonal liquid crystals, micellar solutions, liposomal dispersions and biphasic systems) were determined by gross, polarizing microscopic and small angle-X-ray analysis. A special emphasis was laid upon the storage-induced transformation of liposomal dispersions into mixed micellar solutions and its influence on drug release and permeation. A model for the transformation process is presented. Drug release of the liposomal dispersion (Da=1.1x10-5 cm2/s) and of the identically composed mixed micellar solution (Da=2.9x10-5 cm2/s) was delayed compared with the data of the aqueous drug solution (Da=4.7x10-5 cm2/s). Because of the association of ibuprofen lysinate molecules with phospholipid molecules within the liposomal and the mixed micellar system the share of free ibuprofen lysinate monomers, which can pass through the dialysis membrane in the release experiment, is markedly reduced. The results of permeation experiments of these systems, however, did not correspond to the release data. The permeability of the mixed micellar solution rose after 6 weeks of storage (P=4.2x10-8 cm/s), and almost reached the permeation of the aqueous solution (P=3.9x10-8 cm/s), whereas the permeation of the liposomal dispersion was very slow (P=1.5x10-8 cm/s). The different colloidal microstructures of the formulations obviously resulted in divergent interactions with the permeation barrier - the stratum corneum - and subsequently in different permeation behavior.

Cell Membrane Permeability↗
PubMed1974

The stochastic properties of spontaneous quantal release of transmitter at the frog neuromuscular junction.

1. Earlier results showed that it is unlikely that spontaneous quantal release of transmitter at the frog neuromuscular junction is produced by a Poisson process.2. Data sets were tested, by using the u statistic, to see whether if they are assumed to be generated by a Poisson process, the mean interval is changing monotonically with time. By this critieria, some of the data sets are stationary, others are not.3. A variety of mathematical transforms are employed on empirical data sets to characterize the properties of the spontaneous quantal release.(a) The intensity function, which calculates the frequency distribution of all possible combinations of intervals, shows an excess of short intervals, without any sign of periodicity.(b) The variance-time curve, which estimates the accumulated variance of the series as a function of time into the series, lies significantly above the Poisson prediction.(c) The power spectrum, whether calculated on the intervals or on the number of intervals in time bins, deviates significantly from the Poisson prediction at the low frequencies.(d) The ln-survivor curve has two phases: a concave section for the short intervals, and a roughly linear section for the intervals of greater length.These transforms indicate that the min.e.p.p.s are clustered.4. A series of models for spontaneous quantal release were considered.(a) A Poisson model. Rejected because of consistent failure to fit the data.(b) A periodic model. Rejected because the intervals should be ordered rather than clustered.(c) A time-dependent model, in which quantal release is governed by a Poisson process with a mean interval that is oscillating in time. This model will generate clustering; by the transforms the model can be shown to closely fit the data. However, an autocorrelation of min.e.p.p. amplitudes shows that there is a relationship between the amplitudes and their position in the series. This is not predicted by the time-dependent oscillating model.(d) A branching Poisson model, in which a primary release, generated by a Poisson process, is likely to be followed by one or more subsidiary releases from the same site. The parameters of the branching model can be determined from ln-survivor curves. Theoretical curves, created with these parameters, give power spectra, variance-time curves, and ln-survivor curves that strongly resemble those calculated from the data. The model also predicts a significant autocorrelation of amplitudes.5. Min.e.p.p.s recorded with an extracellular electrode also fit well to a branching Poisson model.6. The effects of raised [Ca(2+)](o) on the intervals between min.e.p.p.s were studied. In our experiments the change in extracellular solution did not produce any notable change in release statistics.7. The effects of elevated [K(+)](o) on the intervals between spontaneous releases were studied. Depolarization of the nerve terminal increases the frequency of primary releases and decreases the chance of having subsidiary releases.8. Possible physical mechanisms by which quantal release of transmitter from a nerve terminal would fit a branching Poisson model are described.

Journal Article↗
PubMed1997

Malignant lymphoma induction of rabbits with oral spray of Epstein-Barr virus-related herpesvirus from Si-IIA cells (HTLV-II-transformed Cynomolgus cell line): a possible animal model for Epstein-Barr virus infection and subsequent virus-related tumors in humans.

Malignant lymphoma (ML) was induced in eight of nine rabbits inoculated by oral spray of the cell-free pellets from Si-IIA culture (HTLV-II-transformed leukocyte cell line of the Cynomolgus-producing Epstein-Barr virus (EBV)-related herpesvirus) after 64-141 days. None of the rabbits inoculated with EBV from B-95-8 cells or HTLV-II from MOT cells developed ML. Malignant lymphomas were usually of diffuse, large-cell or mixed type. HTLV-II infection was excluded by the polymerase chain reaction (PCR) and the particle agglutination test. EBV-encoded RNA-1 and EBV-related DNA were detected in the tumor tissues by in situ hybridization and PCR, respectively. Anti-viral capsid antigen of EBV antibody (anti-VCA) was observed 3 weeks after oral inoculation of Si-IIA cell-free pellets. Polymerase chain reaction revealed continuous detection of EBV-related virus DNA in the peripheral blood leukocytes from 3 days after oral inoculation. These results show that ML induced orally with Si-IIA cell-free pellets was caused by EBV-related herpesvirus harbored by Si-IIA cells. Oral spray of EBV from B-95-8 also induced EBV infection in rabbits, which was confirmed both by the presence of anti-VCA and by PCR. These oral infection and malignant lymphoma induction systems of rabbit using EBV-related virus from Si-IIA or human EBV are useful animal models for the study of EBV infection and EBV-related lymphomas in humans.

Administration, Oral↗
PubMed1999

PKCdelta acts as a growth and tumor suppressor in rat colonic epithelial cells.

We have analysed the expression of three calcium-independent isoforms of protein kinase C (PKC), PKCdelta, PKCepsilon and PKCzeta, in an in vitro model of colon carcinogenesis consisting of the nontumorigenic rat colonic epithelial cell line D/WT, and a derivative src-transformed line D/src. While PKCzeta and PKCepsilon showed similar protein levels, PKCdelta was markedly decreased in D/src cells when compared to the D/WT line. To assess whether down-regulation of PKCdelta was causally involved in the neoplastic phenotype in D/src cells, we prepared a kinase-defective mutant of PKCdelta. Stable transfection of this sequence caused morphological and growth changes characteristic of partial transformation in D/WT cells. Moreover, to test whether PKCdelta was involved in growth control and transformation in this model, we overexpressed PKCdelta in D/src cells. Transfected cells underwent marked growth and morphological modifications toward the D/WT phenotype. In a late stage in culture, transfected cells ceased to proliferate, rounded up and degenerated into multinucleated, giant-like cells. We conclude that PKCdelta can reverse the transformed phenotype and act as a suppressor of cell growth in D/src cells. Moreover, our data show that downregulation of this isoenzyme of PKC may cooperate in the neoplastic transformation induced by the src oncogene in D/WT cells.

Animals↗
PubMed2002

Anaerobic transformations of wastewater organic matter and sulfide production--investigations in a pilot plant pressure sewer.

Anaerobic transformations of wastewater organic matter and sulfide production rate were studied using a pilot plant pressure sewer (inner diameter: 102 mm, length: 47 m). Furthermore, a process model description including carbon and sulfur cycle was presented. Wastewater characterization based on oxygen utilization rate (OUR) measurement and VFA analysis was employed. Under anaerobic conditions, a net production of readily biodegradable substrate was observed, which fact is important for biological removal of nitrogen and phosphorus at subsequent wastewater treatment plants. Model parameters were determined on the basis of experimental findings. The model simulation of transformations of organic matter in sewers can be used as input to the model simulation and evaluation of the processes in wastewater treatment plants. The model is also useful to evaluate the problems in both sewers themselves and treatment plants caused by hydrogen sulfide.

Bacteria, Anaerobic↗
PubMed1982

Intramolecular recombination during plasmid transformation of Bacillus subtilis competent cells.

We have constructed plasmids carrying direct internal repeats 260-2000 bp long. Monomers of such plasmids transformed Bacillus subtilis competent cells. The efficiency of transformation varied with the square of the length of repeats. The transformed clones harbored either the entire transforming plasmid and the plasmid arising by recombination between the repeats, or only the latter plasmid. Internally-repeated plasmids linearized by in vitro cleavage with restriction endonuclease could transform, yielding clones which exclusively harbored a plasmid resulting from recombination between the repeats. When the transforming plasmid carried repeats which differed slightly, conversion of one repeat into the other could occur. The following model of plasmid transformation accounts for these data: (1) plasmid DNA is cleaved and rendered linear in contact with competent cells; (2) a linear, at least partially double-stranded plasmid molecule is introduced or formed by repair within the cell; (3) a circular viable plasmid is produced by recombination between repeats carried on this molecule; (4) alternatively, a viable plasmid is produced by repairing the cut within one of the repeats by DNA synthesis which uses the other repeat as a template.

Bacillus subtilis↗
PubMed2001

Important ECG diagnosis-aiding indices of ventricular septal defect children with or without congestive heart failure.

In this paper we perform a statistical study of the conventional RR intervals and two newly defined PR' and RT intervals of ECG data. A quadratic classification rule is applied to extract several important ECG diagnosis-aiding indices among normal children and children with ventricular septal defect (VSD) with or without congestive heart failure (CHF). The results show that certain statistics computed from PR', RR and RT intervals are important diagnosis-aiding indices. Best classification vectors are searched for pairwise classification. Two methods, minimum distance criterion and a two-stage classification procedure, are considered for three-way classification. Furthermore, logistic regression models based on transformations of these important diagnosis-aiding indices are proposed. The receiver operating characteristic curves of the proposed models show better performance than those of linear and quadratic logistic models. In order to proceed with this study, a computer algorithm to automatically detect the three intervals is developed and the related ECG data are collected and analysed. The algorithm is also enhanced with an outlier detection procedure for the automatic measurements of the PR' and RT intervals.

Algorithms↗
PubMed1988

"Hit and run" transformation of mouse C127 cells by bovine papillomavirus type 4: the viral DNA is required for the initiation but not for maintenance of the transformed phenotype.

Morphological transformation of C127 mouse fibroblasts by bovine papillomavirus type 4 (BPV-4) DNA depends on additional factors, including cell density, the presence of TPA, the concentration of fetal calf serum, and the physical state of the input DNA. Low cell density or the presence of TPA allows the achievement of full transformation, suggesting that disturbance of cell-to-cell contact may be necessary for the expression of the malignant phenotype. TPA also induces a burst of viral DNA synthesis and transcription. The frequency of focus formation is fivefold higher in the presence of high serum than in low serum, indicating that growth factors are required during the early stages of transformation. Although the same number of foci is obtained with either circular or linear DNA, the cells transfected with linear DNA are at a more advanced stage of transformation, being capable of anchorage-independent growth and tumorigenic in nude mice; only 5 out of 21 of these cell lines contain viral DNA in integrated and rearranged forms. In contrast cells transfected with circular DNA are anchorage-dependent but tumorigenic in mice, and do not contain any viral DNA. The linear DNA has an interrupted E1 ORF and fully transformed cells are obtained also with a subgenomic viral DNA fragment containing part of the L1 ORF, the complete E6, E7, and E8 ORFs, and the truncated E1 ORF under the control of the BPV-4 regulatory region; viral DNA is not maintained in any of these cell lines. In total, only 15% of the transformed cell lines contains viral DNA. These results are discussed in the light of the "hit and run" model of cell transformation.

Animals↗
PubMed1999

Defects in transforming growth factor-beta signaling cooperate with a Ras oncogene to cause rapid aneuploidy and malignant transformation of mouse keratinocytes.

Genetic inactivation of the transforming growth factor-beta (TGF-beta) signaling pathway can accelerate tumor progression in the mouse epidermal model of multistage carcinogenesis. By using an in vitro model of keratinocyte transformation that parallels in vivo malignant conversion to squamous cell carcinoma, we show that v-ras(Ha) transduced primary TGF-beta1-/- keratinocytes and keratinocytes expressing a TGF-beta type II dominant-negative receptor transgene have significantly higher frequencies of spontaneous transformation than control genotypes. Malignant transformation in the TGF-beta1-/- keratinocytes is preceded by aneuploidy and accumulation of chromosomal aberrations. Similarly, transient inactivation of TGF-beta signaling with a type II dominant-negative receptor adenovirus causes rapid changes in ploidy. Exogenous TGF-beta1 can suppress aneuploidy, chromosome breaks, and malignant transformation of the TGF-beta1-/- keratinocytes at concentrations that do not significantly arrest cell proliferation. These results point to genomic instability as a mechanism by which defects in TGF-beta signaling could accelerate tumor progression in mouse multistage carcinogenesis.

Aneuploidy↗
PubMed2004

[The establishment of 3D-FE model libraries for the elements of the RPD].

PURPOSE: To establish the 3D-FE model libraries for the elements of the RPD. METHODS: Based on the 3D geometric model libraries of the RPD and normal stomatognathic system, using the software, such as Powershape,Pro/E and Ansys5.5, transformed data, trimmed models, or rebuilt it, established many kinds of FE model elements, then combine these elements in the whole model, connected and trimmed, at last created several kinds of FE model libraries. RESULTS: This study established eight kinds of FE model libraries, including the occlusal rests, clasps, bases, artificial teeth, and connectors, etc, nearly two hundreds FE model elements. CONCLUSION: The established models have a satisfied geometric configuration; these elements combined well in the whole model, and can be easily call-in and edit.

Denture, Partial, Removable↗
PubMed1993

SIDS--a developmental neurological perspective.

Most SIDS deaths occur between 2 and 4 months of age. Neural transformations may be important in SIDS. Evidence of delayed myelination has been found in SIDS victims. However a simple neuro-developmental model is insufficient to explain SIDS. The age of death profile is reportedly similar for pre-term and full-term SIDS victims. Another developmental change is that IgG levels are lowest when SIDS risk peaks, and there is data linking SIDS and infections. Prone position may also increase risk. While a developmental model emphasizing neural transformation is useful, other factors affect risk also.

Aging↗
PubMed2004

Effects of transforming growth factor-beta 1 on the early stages of healing of the Achilles tendon in a rat model.

We studied the effects of transforming growth factor-beta 1 (TGF-beta 1) on the genetic expression of procollagen type I and III and its effects on structural properties in the early stages of healing in rat Achilles tendon. The Achilles tendons in 90 rats were transsected and repaired immediately. TGF-beta 1 dissolved in phosphate-buffered saline was injected locally at the repair site using two different doses, and outcomes in both groups were compared to that in the control group given phosphate-buffered saline only. Five animals in each group were killed at one, two, and four weeks postoperatively, and the healing tendon was evaluated. A dose-dependent increase in the expression of procollagen type I and III mRNA was found one week postoperatively. The failure load and stiffness of the healing tendon were increased by TGF-beta 1 at two and four weeks.

Achilles Tendon↗