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Results for “Pathway informed transformer”

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At least 649 records · Page 36Linked to original sources

PubMed2003

Src in human carcinogenesis.

The signaling machinery in cells is a complex, multi-factorial network of cross-talking proteins that enables dynamic communication between upstream causal factors and downstream effectors. Non-receptor tyrosine kinases, including Src, are the intermediates of information transfer, controlling pathways as diverse as cell growth, migration, death, and genome maintenance. When expressed as viral genes these proteins are potent carcinogens, yet analogous genetic alterations are rarely observed in human tumors. In seeking to characterize the role of the non-receptor tyrosine kinase Src in neoplasia, arguments can be made that the consequences of mutation, or perturbations in the activity or expression of this protein is a determinative factor in clinical prognosis and pathogenicity. In a variety of tumor types including those derived from the colon and breast, the Src non-receptor tyrosine kinase is either overexpressed or constitutively active in a large percentage of the tumors. Increased expression or activity of Src correlates with the stage and metastatic potential of some neoplasia.

Animals↗

PubMed1981

Inhibition of the platelet-aggregating activity of two human adenocarcinomas of the colon and an anaplastic murine tumor with a specific thrombin inhibitor, dansylarginine N-(3-ethyl-1,5-pentanediyl)amide.

Platelets are required for certain experimental metastases. Several lines of animal tumor cells aggregate platelets in vitro and in vivo. Previous studies with one of these lines, an SV40-transformed 3T3 mouse fibroblast (SV3T3) have revealed that the platelet-aggregating material is an extractable membrane-associated sialolipoprotein which requires divalent cation, complement, and a heat-stable plasma component for activity. Little information is available on the interaction of human tumors with platelets. We now report on the ability of two human adenocarcinomas of the colon (LoVo and HCT-8) and an anaplastic mouse tumor (Hut-20) to aggregate platelets by a different mechanism, the generation of thrombin. These spontaneous cell lines aggregate human or rabbit platelet-rich plasma after a 1- to 2-min lag period. This is often followed by a visible clot. Unlike SV3T3 cells, aggregation by LoVo, HCT-8, and Hut-20 cells is not inhibited by neuraminidase, trypsin, or cobra venom factor. These three cell lines markedly shorten the recalcification time of citrated plasma, whereas SV3T3 cells do not. Phospholipase A2 treatment inhibits the shortening of the recalcification time for the three tumors; this parallels its inhibitory effect on platelet aggregation. LoVo, HCT-8, and Hut-20 cells generate thrombin via the "tissue factor" coagulation pathway (using coagulation factor-deficient substrates). Dansylarginine-N-(3-ethyl-1,5-pentanediyl)amide, a highly specific, potent antithrombin antagonist, inhibits LoVo-, HCT-8-, and Hut-20-induced platelet aggregation at 4 to 15 microM, whereas its effect on SV3T3 cells is negligible. If platelets are required for certain human tumor metastases, dansylarginine-N-(3-ethyl-1, 5-pentanediyl)amide, or other antithrombin agents, may prove to be valuable therapeutic agents.

Adenocarcinoma↗

PubMed1995

Signaling pathways that establish the dorsal-ventral pattern of the Drosophila embryo.

The dorsal-ventral pattern of the Drosophila embryo is established by three sequential signaling pathways. Each pathway transmits spatial information by localizing the activity of an extracellular signal, which acts as a ligand for a broadly distributed transmembrane receptor. The components of the first two pathways are encoded by maternal effect genes, while the third pathway is specified by genes expressed in the zygote. During oogenesis, the oocyte transmits a signal to the surrounding follicle cells by the gurken-torpedo pathway. After fertilization, the initial asymmetry of the egg chamber is used by the spätzle-Toll pathway to generate within the embryo a nuclear gradient of the transcription factor Dorsal, which regulates the regional expression of a set of zygotic genes. On the dorsal side of the embryo, the decapentaplegic-punt/thick veins pathway then establishes patterning of the amnioserosa and dorsal ectoderm. Each pathway uses a distinct strategy to achieve spatial localization of signaling activity.

Animals↗

PubMed1995

Transient transfection of murine B lymphocyte blasts as a method for examining gene regulation in primary B cells.

Studies of the biochemical and genetic processes associated with activation of B lymphocytes have contributed much to the understanding of the regulation of the B cell response to antigen. Primary, non-transformed B cells from the spleen in mice and the tonsils or peripheral blood in humans have proven to be informative models for dissection of the biochemical events leading to B cell activation. In contrast, genetic studies of this process have relied on transformed cell lines grown in culture. The influence of the transformed state on the results obtained using these models may limit their physiological relevance. This report describes a method whereby non-transformed B lymphocytes in primary culture can be transfected for use in studies of gene regulation in response to antigen receptor signals. Transfection was accomplished after only a 72 h exposure to LPS. The cells obtained after LPS treatment were greater than 97% pure, and more importantly, remained responsive to antigen-receptor generated signals. Responsiveness was confirmed by demonstrating induction of mRNA for the primary response gene egr-1, as well as induction of specific transcription factor binding activity in nuclear extracts from these cells. DEAE-dextran-mediated transient transfection was utilized to introduce an egr-1 promoter/reporter construct into these cells. This analysis of promoter activity yielded results which were indistinguishable from the pattern of expression of the endogenous egr-1 gene. Potential applications for dissection of transcriptional regulatory pathways in B lymphocytes are discussed.

Animals↗

PubMed2005

Dynamic properties of thalamic neurons for vision.

A striking property of neurons in the lateral geniculate nucleus (LGN) of the thalamus is the ability to dynamically filter and transform the temporal structure of their retinal spike input. In particular, LGN neurons respond to visual stimuli with either burst spike responses or tonic spike responses. While much is known from in vitro studies about the cellular mechanisms that underlie burst and tonic spikes, relatively little is known about the sensory stimuli that evoke these two categories of spikes. This review examines recent progress that has been made towards understanding the spatiotemporal properties of visual stimuli that evoke burst and tonic spikes. Using white-noise stimuli and reverse-correlation analysis, results show that burst and tonic spikes carry similar, but distinct, information to cortex. Compared to tonic spikes, burst spikes (1) occur with a shorter latency between stimulus and response, (2) have a greater dependence on stimuli with transitions from suppressive to preferred states, and (3) prefer stimuli that provide increased drive to the receptive field center and even greater increased drive to the receptive field surround. These results are discussed with an emphasis placed on relating the cellular constraints for burst and tonic activity with the functional properties of the early visual pathway during sensory processing.

Action Potentials↗

PubMed2002

Temporally graded requirement for protein synthesis following memory reactivation.

Learning of new information is transformed into long-lasting memory through a process known as consolidation, which requires protein synthesis. Classical theory held that once consolidated, memory was insensitive to disruption. However, old memories that are insensitive to protein synthesis inhibitors can become vulnerable if they are recalled (reactivated). These findings led to a new hypothesis that when an old memory is reactivated, it again becomes labile and, similar to a newly formed memory, requires a process of reconsolidation in order to be maintained. Here, we show that the requirement for protein synthesis of a reactivated memory is evident only when the memory is recent. In fact, memory vulnerability decreases as the time between the original training and the recall increases.

Amygdala↗

PubMed2026

Genomic Profiling of Epidermal Growth Factor Receptor Mutation-Positive Non-Small Cell Lung Cancer after Progression on First-line Osimertinib: Phase II ORCHARD Study.

PURPOSE: Osimertinib is the standard of care for first-line treatment for epidermal growth factor receptor-mutated (EGFRm) non-small cell lung cancer (NSCLC). Understanding the tumor molecular profile of patients following progression on osimertinib could help inform optimal second-line treatment. PATIENTS AND METHODS: ORCHARD (NCT03944772), a phase II biomarker-directed study, enrolled patients with EGFRm NSCLC who progressed on first-line osimertinib to receive treatment based on their tumor molecular profile after progression. The study comprised three groups into which patients were allocated based on the molecular profile of their tumor, determined via next-generation sequencing (NGS) of a tumor biopsy. We report results from a prespecified, exploratory analysis of baseline tumor tissue and plasma samples to evaluate mechanisms of resistance to first-line osimertinib identified by tissue and plasma NGS. Agreement between tissue and plasma NGS data was also assessed. RESULTS: This study provided a comprehensive dataset exploring tissue (n = 400) and plasma (n = 191) genomics, enabling characterization of the histogenomic landscape after first-line osimertinib treatment. TP53 and MDM2/4 alterations were mutually exclusive and occurred in 86% of tumors. When combining tissue and plasma genomics, resistance alterations were detected in 87% of samples, with multiple resistance alterations in 46%. Alterations in the PI3K pathway, SOX2, and MYC were frequently detected in histologically transformed tumors. Additionally, differential patterns of co-occurring EGFR mutations in tumors with L858R versus exon 19 deletion were observed. CONCLUSIONS: This comprehensive analysis highlights potential heterogeneous resistance to first-line osimertinib treatment, providing a rationale for combining treatments with broad activity to improve patient outcomes. See related commentary by Gupta et al., p. 3718.

Humans↗

PubMed2007

Pathways as "signatures in landscape": towards an ethnography of mobility among the Mbya-Guaraní (Northeastern Argentina).

Processes of spatial mobility among the Mbya are of interest in anthropological and ethnobiological studies, as these processes are related to transformations in the landscape and the environment. Despite this, ethnographic literature usually focuses itself on the mobility of Guaraní communities from the perspective of population dynamics on a regional scale. Our research among two Mbya-Guaraní communities in the Argentinean province of Misiones has enabled us to recognize patterns of mobility on a micro-scale. Certainly, the mobility of adult members of these communities as they perform hunting and gathering activities delimit spaces of individual use. We consider the different pathways as "signatures in landscape", resulting from processes of spatial mobility inherent to those activities. Taking into account the gathering and circulation of medicinal plants for treatment of gastrointestinal illnesses, we have been able to identify different pathways inherent in their search, towards the monte or other spaces away from de settlement. The design and construction of the pathways is determined by the specific personal knowledge of individuals who search for these valuable resources. Using both strategies of direct observation--as members of the community manipulate different resources during these search and gathering trips--and interviews, we have been able to gather and interpret significant information on the strategies used by the Mbya to domesticate the monte areas. As a consequence of our approach we suggest that the landscape design resulting from these trips should not be considered a consensual or collective strategy of the whole community; it is rather the result of the daily strategies of individuals, which involves the selection of resources mainly based on each individual's knowledge and interests.

Adult↗

PubMed1995

A molecular pathway determining left-right asymmetry in chick embryogenesis.

While significant progress has been made in understanding the molecular events underlying the early specification of the antero-posterior and dorso-ventral axes, little information is available regarding the cellular or molecular basis for left-right (LR) differences in animal morphogenesis. We describe the expression patterns of three genes involved in LR determination in chick embryos: activin receptor IIa, Sonic hedgehog (Shh), and cNR-1 (related to the mouse gene nodal). These genes are expressed asymmetrically during and after gastrulation and regulate the expression of one another in a sequential pathway. Moreover, manipulation of the sidedness of either activin protein or Shh expression alters heart situs. Together, these observations identify a cascade of molecular asymmetry in that determines morphological LR asymmetry in the chick embryo.

Activins↗

PubMed2004

Laminin-2 stimulates the proliferation of epithelial cells in a conjunctival epithelial cell line.

Laminin-2 (LN-2, alpha2beta1gamma1) is a basement membrane-associated laminin isoform usually considered in the context of muscle and nerve tissues. To test the hypothesis that LN-2 can additionally modulate epithelial cell biology, an analysis of the role of LN-2 in cell adhesion, activation of signalling intermediates and proliferation was undertaken. A virally transformed human conjunctival epithelial cell line (HC0597) was utilized in this study. Adhesion assays using function-inhibiting antibodies demonstrated that alpha3beta1 integrin is essential for the rapid attachment of conjunctival epithelial cells to LN-2. Bromodeoxyuridine (BrdU) incorporation analyses revealed that, compared with LN-1 or LN-10, LN-2 significantly promotes epithelial proliferation. Phosphorylation of the signalling intermediates Erk1/2 and Akt-1 was observed within 15 min of cell adhesion to LN-2. Inhibiting alpha3beta1 integrin function decreased total cellular phosphotyrosine levels, specifically inhibited phosphorylation of Erk1/2 and Akt-1, and dampened the proliferation response of epithelial cells adherent to LN-2. Inhibition of Erk or Akt activation inhibited cell proliferation in a dose-dependent manner. However, the inhibition of Erk resulted in a stronger suppression of proliferation compared with Akt inhibition. From these results, it is concluded that human conjunctival epithelial cells adhere to immobilized LN-2 using alpha3beta1 integrin. alpha3beta1 integrin/LN-2 signalling, transduced primarily through an Erk pathway, enhances epithelial cell proliferation. These results demonstrate that LN-2 can impact on epithelial cell biology in addition to nerve and muscle, and provide information regarding the role of this isoform in ocular surface epithelial cells.

Cell Adhesion↗

PubMed2003

PPARalpha agonist-induced rodent tumors: modes of action and human relevance.

Widely varied chemicals--including certain herbicides, plasticizers, drugs, and natural products--induce peroxisome proliferation in rodent liver and other tissues. This phenomenon is characterized by increases in the volume density and fatty acid oxidation of these organelles, which contain hydrogen peroxide and fatty acid oxidation systems important in lipid metabolism. Research showing that some peroxisome proliferating chemicals are nongenotoxic animal carcinogens stimulated interest in developing mode of action (MOA) information to understand and explain the human relevance of animal tumors associated with these chemicals. Studies have demonstrated that a nuclear hormone receptor implicated in energy homeostasis, designated peroxisome proliferator-activated receptor alpha (PPARalpha), is an obligatory factor in peroxisome proliferation in rodent hepatocytes. This report provides an in-depth analysis of the state of the science on several topics critical to evaluating the relationship between the MOA for PPARalpha agonists and the human relevance of related animal tumors. Topics include a review of existing tumor bioassay data, data from animal and human sources relating to the MOA for PPARalpha agonists in several different tissues, and case studies on the potential human relevance of the animal MOA data. The summary of existing bioassay data discloses substantial species differences in response to peroxisome proliferators in vivo, with rodents more responsive than primates. Among the rat and mouse strains tested, both males and females develop tumors in response to exposure to a wide range of chemicals including DEHP and other phthalates, chlorinated paraffins, chlorinated solvents such as trichloroethylene and perchloroethylene, and certain pesticides and hypolipidemic pharmaceuticals. MOA data from three different rodent tissues--rat and mouse liver, rat pancreas, and rat testis--lead to several different postulated MOAs, some beginning with PPARalpha activation as a causal first step. For example, studies in rodent liver identified seven "key events," including three "causal events"--activation of PPARalpha, perturbation of cell proliferation and apoptosis, and selective clonal expansion--and a series of associative events involving peroxisome proliferation, hepatocyte oxidative stress, and Kupffer-cell-mediated events. Similar in-depth analysis for rat Leydig-cell tumors (LCTs) posits one MOA that begins with PPARalpha activation in the liver, but two possible pathways, one secondary to liver induction and the other direct inhibition of testicular testosterone biosynthesis. For this tumor, both proposed pathways involve changes in the metabolism and quantity of related hormones and hormone precursors. Key events in the postulated MOA for the third tumor type, pancreatic acinar-cell tumors (PACTs) in rats, also begin with PPARalpha activation in the liver, followed by changes in bile synthesis and composition. Using the new human relevance framework (HRF) (see companion article), case studies involving PPARalpha-related tumors in each of these three tissues produced a range of outcomes, depending partly on the quality and quantity of MOA data available from laboratory animals and related information from human data sources.

Animals↗

PubMed2004

Early visual evoked potentials are modulated by eye position in humans induced by whole body rotations.

BACKGROUND: To reach and grasp an object in space on the basis of its image cast on the retina requires different coordinate transformations that take into account gaze and limb positioning. Eye position in the orbit influences the image's conversion from retinotopic (eye-centered) coordinates to an egocentric frame necessary for guiding action. Neuroimaging studies have revealed eye position-dependent activity in extrastriate visual, parietal and frontal areas that is along the visuo-motor pathway. At the earliest vision stage, the role of the primary visual area (V1) in this process remains unclear. We used an experimental design based on pattern-onset visual evoked potentials (VEP) recordings to study the effect of eye position on V1 activity in humans. RESULTS: We showed that the amplitude of the initial C1 component of VEP, acknowledged to originate in V1, was modulated by the eye position. We also established that putative spontaneous small saccades related to eccentric fixation, as well as retinal disparity cannot explain the effects of changing C1 amplitude of VEP in the present study. CONCLUSIONS: The present modulation of the early component of VEP suggests an eye position-dependent activity of the human primary visual area. Our findings also evidence that cortical processes combine information about the position of the stimulus on the retinae with information about the location of the eyes in their orbit as early as the stage of primary visual area.

Adult↗

PubMed1987

The role of lipid-derived second messengers in cell growth and transformation.

Recent information on the structure of growth factor receptors and oncogenes has advanced our understanding of the biochemical mechanism of growth control. Several peptide growth factor receptors have now been purified and, with a few notable exceptions, they fall into a family of homologous proteins with growth factor-stimulated protein-tyrosine kinase (PTK) activity. Mutations in the genes encoding for both the growth factors and the growth factor receptors of this family have been shown to cause cell transformation. Thus, PTKs have been implicated both in normal growth control and in cell transformation. The critical targets for these PTKs have not been determined. Several but not all growth factors stimulate production of the phosphatidylinositol (PI)-derived second messengers, diacylglycerol and inositol-1,4,5-trisphosphate. By purifying and characterizing the enzymes involved in PI turnover we are attempting to determine how this system is regulated by growth factors and oncogene products. We have found that fibroblasts contain two distinct PI kinases, and that one of these enzymes can be precipitated with antibodies against phosphotyrosine only after addition of platelet-derived growth factor. The relevance of the PI turnover pathway in propagation of growth signals is discussed.

Cell Division↗

PubMed1977

[Long term transformation of neuronal activity in the superior colliculus isolated from corticofugal influences].

Neuronal activity of the superior colliculus isolated from the corticofugal influences was studied in various periods of time (from 3 to 20 months) after unilateral dissection of cortico-subcortical projections. In 16 unanesthetized immobilized cats, after the surgery, spontaneous activity of collicular neurons became more regular and with less complex bursts during the postoperative period. Evoked activity was completely suppressed during early hours of the postoperative period. Only 31.5% of collicular cells were sensitive to light 3 months after the operation. Evoked responses to light of 90.4% cells reappeared in the isolated colliculus not earlier than 10-12 months after the isolation, while directional and movement sensitivity practically did not restore even within 20 months after the surgery. Corticocollicular influences are considered to be a necessary condition for effective visual information processing in the colliculi superiores.

Animals↗

PubMed2006

Multiscale white matter fiber tract coregistration: a new feature-based approach to align diffusion tensor data.

In this paper an automatic multiscale feature-based rigid-body coregistration technique for diffusion tensor imaging (DTI) based on the local curvature kappa and torsion tau of the white matter (WM) fiber pathways is presented. As a similarity measure, the mean squared difference (MSD) of corresponding fiber pathways in (kappa, tau)-space is chosen. After the MSD is minimized along the arc length of the curve, principal component analysis is applied to calculate the transformation parameters. In addition, a scale-space representation of the space curves is incorporated, resulting in a multiscale robust coregistration technique. This fully automatic technique inherently allows one to apply region of interest (ROI) coregistration, and is adequate for performing both global and local transformations. Simulations were performed on synthetic DT data to evaluate the coregistration accuracy and precision. An in vivo coregistration example is presented and compared with a voxel-based coregistration approach, demonstrating the feasibility and advantages of the proposed technique to align DT data of the human brain.

Adult↗

PubMed2005

Gene expression profiles in varicose veins using complementary DNA microarray.

BACKGROUND: There has been little information reported about the genetic event concerning the pathophysiology of varicose vein (VV). OBJECTIVES: The purpose of this study was to examine the differentiation of gene expression in the wall of VV using complementary deoxyribonucleic acid (cDNA) microarrays. METHODS: The study was performed with four pairs of VVs and control veins (CVs). cDNA specimens of VVs were prepared from the ribonucleic acid-isolated VVs of patients who underwent venous obliteration, using radiofrequency, as well as from CVs of those who underwent aortocoronary bypass grafting. Each set of VVs and CVs was hybridized with high-density microarray containing 3,063 human cDNAs. The finding of microarray hybridization were scanned, analyzed, and classified with the cluster program. RESULTS: Among 3,063 cDNA clones, 82 genes were up-regulated in VVs, and some of the up-regulated genes, which were detected by cDNA microarray, including transforming growth factor 3-induced gene (BIGH3), tubulin, lumican, actinin, collagen type I, versican, actin, and tropomyosin, belonged to extracelluar matrix molecules, cytoskeletal proteins, or myofibroblasts. CONCLUSIONS: Many up-regulated genes were found in Ws by applying cDNA microarray. These gene profiles suggested a pathway associated with fibrosis and that wound healing might be related to the pathophysiology of VVs.

DNA, Complementary↗

PubMed2004

Dynamics of water molecules in the bacteriorhodopsin trimer in explicit lipid/water environment.

Protonated networks of internal water molecules appear to be involved in proton transfer in various integral membrane proteins. High-resolution x-ray studies of protein crystals at low temperature deliver mean positions of most internal waters, but only limited information about fluctuations within such H-bonded networks formed by water and residues. The question arises as to how water molecules behave inside and on the surface of a fluctuating membrane protein under more physiological conditions. Therefore, as an example, long-time molecular dynamics simulations of bacteriorhodopsin were performed with explicit membrane/water environment. Based on a recent x-ray model the bacteriorhodopsin trimer was inserted in a fully solvated 16 x 16 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-bilayer patch, resulting in a system of approximately 84,000 atoms. Unrestrained molecular dynamics calculations of 5 ns were performed using the GROMACS package and force field. Mean water densities were computed to describe the anisotropic distribution of internal water molecules. In the whole protein two larger areas of higher water density are identified. They are located between the central proton binding site, the Schiff base, and the extracellular proton release site. Separated by Arg-82 these water clusters could provide a proton release pathway in a Grotthus-like mechanism as indicated by a continuum absorbance change observed during the photocycle by time-resolved Fourier transform infrared spectroscopy. Residues are identified which are H-bonded to the water clusters and are therefore facilitating proton conduction. Their influence on proton transfer via the H-bonded network as indicated by the continuum absorbance change is predicted. This may explain why several site-directed mutations alter the proton release kinetics without a direct involvement in proton transfer.

Amino Acids↗

PubMedDate not supplied

Central auditory system.

A biological view of the central auditory system seems to be replacing the older Galilean or physics-based view as the guide for research in the late 20th century. This emerging view is primarily Darwinian in origin and recognizes that the entire auditory system is an adaptation for extracting information from natural sounds and their sources, usually for the guidance of immediate behavioral action. The fact that natural sounds themselves are almost always transients, too brief in duration to have tonal quality, suggests that the ear is far more of a Fast Fourier Transformer (and less of a Fourier analyzer) than is usually explicitly stated. Since the brief sounds constituting most of the acoustical environment contain critical information for guiding behavioral activity, several further hypotheses regarding the cell-level and tissue-level contributions of the central auditory system also follow. For example, the new view suggests that the central auditory system's role is likely to include the extraction of the behaviorally most important features, aspects, or dimensions of the sources of sounds in addition to, or possibly instead of, the physical dimensions of the sounds themselves. Because this new view has already enjoyed some measure of success and has also suggested a number of new and unusual directions for future research, it may become the dominant theory for research in the 21st century.

Animals↗