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Results for “Pathway informed transformer”

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PubMed1989

[Central infantile hypotonia syndrome].

Czechoslovak child neurologists devoted much attention to central infantile hypotonic syndrome (CIHS) in a series of investigations conducted in 1959-1986. They found that it is a developmental syndrome caused by affection of the immature brain, and later, at the age of 3-5 years, it disappears or transforms into other syndromes: most frequently cerebellar syndromes and developmental disintegrations (disintegration of the development of the CNS and medium-grade mental retardation). These groups overlap only little. From the hypotonic syndrome also the spastic syndrome or minor cerebral syndromes may develop. CIHS has, similarly as some other manifestations of CNS affections, multiple causes. One of them is most probably a defect of or lack of development of facilitating pathways of gamma fibres from the cerebellum or possibly from the reticular formation of the brain stem to the spinal cord; another probable cause is longer immaturity of the afferent system (which leads finally to developmental disintegration). It may be assumed that the facilitating systems of pathways develop later and are thus more immature and therefore more vulnerable. According to the latest information it seems that in CIHS also the muscular component participates as prenatal cerebral affections can cause myopathy with hypotonia.

Cerebral Palsy↗

PubMed2002

[Hematopoietic stem cells and hematopoietic neoplasias].

Pluripotent hematopoietic stem cells have been defined as cells with extensive self-renewal capacity and lympho-hematopoietic differentiation potential. Clonal selection of a stem cell as a first step in the progression to neoplasia can be achieved by an alteration of this self-renewal potency. Our current understanding of the pathogenesis of the myeloproliferative disorders including acute myeloid leukemias, chronic myeloproliferative disorders (CMPD) and myelodysplastic syndromes (MDS), is based on the assumption that they represent a clonal disorder resulting from transformation of a hematopoietic stem cell. However, when performing methods for determining X-chromosome inactivation in female patients as a clonality marker, a significant minority of the patients with Philadelphia chromosome negative (Ph(-)) CMPD and MDS exhibit polyclonal proliferation. The implications of these results are not yet clarified and the lack of a proven target cell impairs the understanding of the underlying molecular defect. In this context, altered response to cytokine stimulation in vitro provides indirect information concerning molecular dysregulation. A subset of patients with MPD present with translocations that facilitate molecular investigation and clonality proof. They nearly always result in rearrangements of at least one transcription factor gene. Most of these fusion genes are constitutively active, sending out continuous proliferative and antiapoptotic signals or activate an overlapping set of signalling pathways. The classical example for a balanced translocation is the t(9;22) bcr-abl aberration in chronic myelogeneous leukemia. Many other karyotypic abnormalities have also been associated with CMPD and MDS and involve deletions of chromosomes 20q, 13q, 1q, 7q and 5q as well as trisomy of 8 and 9. Our increased understanding of the hematopoietic stem cell compartment and the molecular basis of regulation of its self-renewal and differentiation bears a direct impact on our understanding of leukemia evolution and progression.

Cell Differentiation↗

PubMed2000

Biomarkers and molecular epidemiology and chemoprevention of oral carcinogenesis.

Chemopreventives are chemicals that prevent the formation of cancers such as oral cancer. They can take the form of nutrients or synthetic molecules, and their fundamental characteristic is that they do not produce disease processes that would result in debilitating symptoms. Current evidence indicates that they function by modifying the oxidative state of transforming cells. Biomarkers can take the form of genetic and molecular indicators, which characterize the function of chemopreventives and cancer processes such as oral carcinogenesis. Biomarkers cannot provide all the required information for risk assessment or possible activity of the chemopreventives. Other methods, such as epidemiological analyses and techniques, must be used to enhance our understanding of the risk for oral cancer in human populations. One common epidemiologic method, the questionnaire, helps to determine the use and carcinogenic potential of tobacco and alcohol during oral carcinogenesis. Genetic and molecular changes in human patient populations may result in a reduction in the number and function of tumor suppressor genes. If these changes are to be assessed, the tissues (e.g., buccal mucosa) must be accessible and harvested in a reliable and consistent manner for the acquisition of DNA, mRNA, and protein. Oral tissues provide sufficient quantities of these molecules and, under stringent conditions, the quality required for the isolation of these molecular constituents. In conjunction with epidemiologic techniques, various genotypic polymorphisms, such as glutathione-S-transferase (GSTM1) or cytochrome P450 (CYP450A1), have indicated a loss in carcinogen detoxification or the processing of internal growth control signals. Biomarkers are composed of a large diverse group of genetic and molecular structures. Some of these biomarkers are indicators for programmed cell death (PCD), while others describe malignant tumor growth. Many of these classes of molecules are oxidative-responsive (e.g., tumor suppressor p53, Bcl-2, growth factors, immune-derived proteins, and death-inducing molecules) and induce PCD by triggering a cascade of cysteine proteases and regulators (e.g., caspases, death receptors). This pathway results in cell-cycle alterations and DNA fragmentation. It is hoped that a detailed knowledge of the processes involved in malignant transformation will better define the biomarker-screening tools for oral cancer. These tools will enhance our ability to predict the incidence of cancer, detect early malignant change, and quantitate chemoprevention during oral carcinogenesis. Chemopreventives such as the retinoids have already demonstrated their ability to suppress potential malignant changes in pre-malignant oral leukoplakias and decrease the incidence of second head-and-neck cancer primaries. It is our hope that this review will increase investigators' interest in developing new screening and detection systems for oral cancer.

Anticarcinogenic Agents↗

PubMed1995

A common neural code for frequency- and amplitude-modulated sounds.

Most naturally occurring sounds are modulated in amplitude or frequency; important examples include animal vocalizations and species-specific communication signals in mammals, insects, reptiles, birds and amphibians. Deciphering the information from amplitude-modulated (AM) sounds is a well-understood process, requiring a phase locking of primary auditory afferents to the modulation envelopes. The mechanism for decoding frequency modulation (FM) is not as clear because the FM envelope is flat (Fig. 1). One biological solution is to monitor amplitude fluctuations in frequency-tuned cochlear filters as the instantaneous frequency of the FM sweeps through the passband of these filters. This view postulates an FM-to-AM transduction whereby a change in frequency is transmitted as a change in amplitude. This is an appealing idea because, if such transduction occurs early in the auditory pathway, it provides a neurally economical solution to how the auditory system encodes these important sounds. Here we illustrate that an FM and AM sound must be transformed into a common neural code in the brain stem. Observers can accurately determine if the phase of an FM presented to one ear is leading or lagging, by only a fraction of a millisecond, the phase of an AM presented to the other ear. A single intracranial image is perceived, the spatial position of which is a function of this phase difference.

Brain Stem↗

PubMed2005

Engineering HlyA hypersecretion in Escherichia coli based on proteomic and microarray analyses.

Escherichia coli is a common host for recombinant protein production for biotechnology applications. Secretion to the extracellular media has the potential to reduce protein aggregation and to simplify downstream purification. However, the complexity of the mechanisms of protein secretion has confounded prior attempts to engineer enhanced secretion phenotypes. Here, mutagenesis was used to perturb E. coli W3110 cells secreting HlyA via a Type I pathway. An activity assay identified a mutant secreting fourfold more active alpha-hemolysin than the parent strain. The mutant was characterized using both high-density microarrays for mRNA profiling and a proteomics strategy for protein expression. The relative mRNA and protein expression levels of tRNA-synthetases were decreased in the mutant compared to the parent. A mathematical model of prokaryotic translation was used to design a variant of the hlyA gene that encodes the same amino acid sequence but uses rare codons to slow the rate of translation by altering five bases. Analysis of the parent strain transformed with a plasmid containing this variant gene resulted in the recovery of, and further improvement upon, the selected hypersecretion phenotype. These results present one of the first successful metabolic engineering attempts based on molecular information provided by mRNA and protein expression profiling approaches and resulting in a phenotype useful to the biotechnology community.

Computer Simulation↗

PubMedDate not supplied

Foundations of vectorial metabolism and osmochemistry.

Chemical transformations, like osmotic translocations, are transport processes when looked at in detail. In chemiosmotic systems, the pathways of specific ligand conduction are spatially orientated through osmoenzymes and porters in which the actions of chemical group, electron and solute transfer occur as vectorial (or higher tensorial order) diffusion processes down gradients of total potential energy that represent real spatially directed fields of force. Thus, it has been possible to describe classical bag-of-enzymes biochemistry as well as membrane biochemistry in terms of transport. But it would not have been possible to explain biological transport in terms of classical transformational biochemistry or chemistry. The recognition of this conceptual asymmetry in favour of transport has seemed to be upsetting to some biochemists and chemists; and they have resisted the shift towards thinking primarily in terms of the vectorial forces and co-linear displacements of ligands in place of their much less informative scalar products that correspond to the conventional scalar energies. Nevertheless, considerable progress has been made in establishing vectorial metabolism and osmochemistry as acceptable biochemical disciplines embracing transport and metabolism, and bioenergetics has been fundamentally transformed as a result.

Biochemistry↗

PubMed2026

Advancing cancer detection and treatment using longitudinal routine clinical data.

Cancer management remains fragmented across its continuum, from late-stage diagnosis and salvage therapies to non-personalized surveillance. Here, we present Oncoformer, a unified multimodal transformer model trained on the China Oncology Multimodal Prediction and Surveillance Study (COMPASS) cohort (3.67 million individuals, 17.7 million clinical visits) and validated on independent external cohorts, including the UK Biobank. Oncoformer integrates longitudinal electronic health records with chest X-ray imaging to address multiple clinical tasks: pan-cancer diagnosis (area under the receiver operating characteristic curve [AUROC] = 0.956), future cancer prediction up to 1 year before diagnosis (AUROC = 0.869), tumor stage inference (mean AUROC > 0.90), patient-specific treatment-response forecasting, and recurrence-free survival stratification across ten cancer types (all p < 0.01). Staging predictions were independently validated against postoperative pathological endpoints and shown to converge on core cancer genomic pathways. By translating routine clinical data into a dynamic view of cancer evolution, Oncoformer provides a framework for risk-informed cancer prediction and treatment stratification using routine clinical data.

Humans↗

PubMed2002

Cytosolic NADP(+)-dependent isocitrate dehydrogenase status modulates oxidative damage to cells.

NADPH is an important cofactor in many biosynthesis pathways and the regeneration of reduced glutathione, critically important in cellular defense against oxidative damage. It is mainly produced by glucose 6-phosphate dehydrogenase (G6PD), malic enzyme, and the cytosolic form of NADP(+)-dependent isocitrate dehydrogenase (IDPc). Little information is available about the role of IDPc in antioxidant defense. In this study we investigated the role of IDPc against cytotoxicity induced by oxidative stress by comparing the relative degree of cellular responses in three different NIH3T3 cells with stable transfection with the cDNA for mouse IDPc in sense and antisense orientations, where IDPc activities were 3-4-fold higher and 35% lower, respectively, than that in the parental cells carrying the vector alone. Although the activities of other antioxidant enzymes, such as superoxide dismutase, catalase, glutathione reductase, glutathione peroxidase, and G6PD, were comparable in all transformed cells, the ratio of GSSG to total glutathione was significantly higher in the cells expressing the lower level of IDPc. This finding indicates that IDPc is essential for the efficient glutathione recycling. Upon transient exposure to increasing concentrations of H(2)O(2) or menadione, an intracellular source of free radicals and reactive oxygen species, the cells with low levels of IDPc became more sensitive to oxidative damage by H(2)O(2) or menadione. Lipid peroxidation, oxidative DNA damage, and intracellular peroxide generation were higher in the cell-line expressing the lower level of IDPc. However, the cells with the highly over-expressed IDPc exhibited enhanced resistance against oxidative stress, compared to the control cells. This study provides direct evidence correlating the activities of IDPc and the maintenance of the cellular redox state, suggesting that IDPc plays an important role in cellular defense against oxidative stress.

3T3 Cells↗

PubMed1989

Visual responses of neurons in somatosensory cortex of hamsters with experimentally induced retinal projections to somatosensory thalamus.

These experiments investigate the capacity of thalamic and cortical structures in a sensory system to process information of a modality normally associated with another system. Retinal ganglion cells in newborn Syrian hamsters were made to project permanently to the main thalamic somatosensory (ventrobasal) nucleus. When the animals were adults, single unit recordings were made in the somatosensory cortices, the principal targets of the ventrobasal nucleus. The somatosensory neurons responded to visual stimulation of distinct receptive fields, and their response properties resembled, in several characteristic features, those of normal visual cortical neurons. In the visual cortex of normal animals and the somatosensory cortex of operated animals, the same functional categories of neurons occurred in similar proportions, and the neurons' selectivity for the orientation or direction of movement of visual stimuli was comparable. These results suggest that thalamic nuclei or cortical areas at corresponding levels in the visual and somatosensory pathways perform similar transformations on their inputs.

Animals↗

PubMed2006

Behavioral analysis of olfactory coding and computation in rodents.

Behavioral analysis is essential to understand how the olfactory system transforms chemosensory signals into information that can be used to guide actions. Recent studies in rodents have begun to address the behavioral relevance of putative olfactory codes and computations including spatial maps, oscillatory synchrony, and evolving temporal codes. To date, these studies have failed to find support for a role of any of these mechanisms in odor discrimination. Progress calls for experiments using precise psychophysical methods in conjunction with neural recording or perturbation, in addition to ethologically minded exploration of more complex forms of odor-guided behavior.

Action Potentials↗

PubMed1991

Foundations of vectorial metabolism and osmochemistry.

Chemical transformations, like osmotic translocations, are transport processes when looked at in detail. In chemiosmotic systems, the pathways of specific ligand conduction are spatially orientated through osmoenzymes and porters in which the actions of chemical group, electron and solute transfer occur as vectorial (or higher tensorial order) diffusion processes down gradients of total potential energy that represent real spatially-directed fields of force. Thus, it has been possible to describe classical bag-of-enzymes biochemistry as well as membrane biochemistry in terms of transport. But it would not have been possible to explain biological transport in terms of classical transformational biochemistry or chemistry. The recognition of this conceptual asymmetry in favour of transport has seemed to be upsetting to some biochemists and chemists; and they have resisted the shift towards thinking primarily in terms of the vectorial forces and co-linear displacements of ligands in place of their much less informative scalar products that correspond to the conventional scalar energies. Nevertheless, considerable progress has been made in establishing vectorial metabolism and osmochemistry as acceptable biochemical disciplines embracing transport and metabolism, and bioenergetics has been fundamentally transformed as a result.

Biological Transport, Active↗

PubMed2006

The role of residue Thr249 in modulating the catalytic efficiency and substrate specificity of catechol-2,3-dioxygenase from Pseudomonas stutzeri OX1.

Bioremediation strategies use microorganisms to remove hazardous substances, such as aromatic molecules, from polluted sites. The applicability of these techniques would greatly benefit from the expansion of the catabolic ability of these bacteria in transforming a variety of aromatic compounds. Catechol-2,3-dioxygenase (C2,3O) from Pseudomonas stutzeri OX1 is a key enzyme in the catabolic pathway for aromatic molecules. Its specificity and regioselectivity control the range of molecules degraded through the catabolic pathway of the microorganism that is able to use aromatic hydrocarbons as growth substrates. We have used in silico substrate docking procedures to investigate the molecular determinants that direct the enzyme substrate specificity. In particular, we looked for a possible molecular explanation of the inability of catechol-2,3-dioxygenase to cleave 3,5-dimethylcatechol and 3,6-dimethylcatechol and of the efficient cleavage of 3,4-dimethylcatechol. The docking study suggested that reduction in the volume of the side chain of residue 249 could allow the binding of 3,5-dimethylcatechol and 3,6-dimethylcatechol. This information was used to prepare and characterize mutants at position 249. The kinetic and regiospecificity parameters of the mutants confirm the docking predictions, and indicate that this position controls the substrate specificity of catechol-2,3-dioxygenase. Moreover, our results suggest that Thr249 also plays a previously unsuspected role in the catalytic mechanism of substrate cleavage. The hypothesis is advanced that a water molecule bound between one of the hydroxyl groups of the substrate and the side chain of Thr249 favors the deprotonation/protonation of this hydroxyl group, thus assisting the final steps of the cleavage reaction.

Binding Sites↗

PubMed2001

TGFbeta1 allele association with asthma severity.

Transforming growth factor beta1 (TGFbeta1) is a multifunctional cytokine involved in pro- and anti-inflammatory pathways and is expressed in several cell types. Subepithelial fibrosis is one of the principle features of airway remodelling in asthma and is increased in severe patients. TGFbeta1 is implicated in fibrosis, including the deposition of extracellular matrix proteins. TGFbeta1 mRNA levels in eosinophils are increased in severe asthmatics relative to mild asthmatics. Therefore, TGFbeta1 is a promising candidate gene for contributing to asthma severity. Four polymorphisms located in the promoter region and signal peptide (C-509T, 72insC, T869C and G915C) were genotyped in groups of severe asthmatic, mild asthmatic or control individuals defined by steroid usage and pulmonary function. Significant differences ( P=0.016) were found between the groups for the genotype frequencies at C-509T, attributable mainly to a greater relative frequency of homozygosity for the -509T allele in the severe group compared to the mild and control groups. Individuals homozygous for -509T were also homozygous at the other variant sites for the 72C, 869C and 915G alleles (haplotype 1). The T allele creates a putative YY1 transcription factor binding site, but binding between YY1 and the DNA sequence of the T allele was not detected in vitro. In this study, we show that the -509T variant on haplotype 1 is the most informative marker of the TGFbeta1 contribution to asthma severity.

Adrenal Cortex Hormones↗

PubMed2003

Skin permeability enhancement by low frequency sonophoresis: lipid extraction and transport pathways.

The objective of this study was to shed light on the mechanism(s) by which low-frequency ultrasound (20 KHz) enhances the permeability of the skin. The physical effects on the barrier and the transport pathway, in particular, were examined. The amount of lipid removed from the intercellular domains of the stratum corneum following sonophoresis was determined by infrared spectroscopy. Transport of the fluorescent probes nile red and calcein, under the influence of ultrasound, was evaluated by laser-scanning confocal microscopy. The results were compared with the appropriate passive control data and with data obtained from experiments in which the skin was exposed simply to the thermal effects induced by ultrasound treatment. A significant fraction ( approximately 30%) of the intercellular lipids of the stratum corneum, which are principally responsible for skin barrier function, were removed during the application of low-frequency sonophoresis. Although the confocal images from the nile red experiments were not particularly informative, ultrasound clearly and significantly (again, relative to the corresponding controls) facilitated transport of the hydrophilic calcein via discrete permeabilized regions, whereas other areas of the barrier were apparently unaffected. Lipid removal from the stratum corneum is implicated as a factor contributing the observed permeation enhancement effects of low-frequency ultrasound. However, microscopic observations imply that sonophoresis induces localized (aqueous?) permeation pathways at discrete sites.

Administration, Cutaneous↗

PubMed1991

ras proteins and the ras-related signal transduction pathway.

Mammalian ras genes may naturally acquire oncogenic transformation potential through some point mutations which result in the impairment of the normal ras protein functions, and which are localised in codons 12, 13 or 61. Mutationally activated ras alleles were found in a wide variety of human and carcinogen (including radiation)-induced animal malignancies. In man, myeloid leukemias are often associated with the presence of a mutationally activated ras gene (for review, see Bos JL (1989), Cancer Res 49:4682-4689). However, we failed till now in our attempts to detect oncogenic ras mutations in radiation-induced mouse myeloid leukemias. We thus have the feeling that ras might perhaps participate to tumorigenesis through another mechanism provoking a deregulation of the ras protein functions. In order to help evaluate such a possibility, we give here a very concise overview of the properties of the ras proteins and of their regulation by a variety of still hypothetical molecular switches. This overview does not include bibliographic references. Indeed, we gathered much of the information described below at the Cold Spring Harbor Symposium on "Function and Evolution of ras Proteins", May 9-13, 1990. Communications presented at Cold Spring Harbor Symposia may contain preliminary data and should not be cited in bibliographies. Another voluntary omission in this overview is that, for the sake of simplicity, we do not mention whether the data were obtained from experiments performed on H-, K- or N-ras. Details can be found in the published book of abstracts.

Animals↗

PubMed1991

Tumour progression and the nature of cancer.

The nature of neoplasia and its sometime end result, cancer, has been studied by exposition and explanation of the sequential lesions of tumour progression. Neoplastic lesions were divided into four classes on the basis of growth characteristics and whether lesional growth is confined to one or more tissue compartments. Class IA, the initial lesion, an orderly, probably clonal growth, usually differentiates and disappears. Class IB: Failure to differentiate accompanied by disorderly growth. Class IC: Randomly dispersed atypical cells, constituting a precursor state. Class II, intermediate lesions, apparently arising from the atypical cells, show temporally unrestricted growth within the tissue compartment of origin. Class III lesions, primary invasive cancers, show temporally unrestricted growth in two or more tissue compartments and metastasise along different paths, a property associated with extracellular matrix interaction. The metastatic pathways may result from different subsets of cells in the primary cancer. Class IV lesions are the metastases. It was concluded that, all neoplasms develop in the same way, have the same general behavioural characteristics, and, when malignant, all interact with the extracellular matrix of the primary and the secondary sites. The origins and development of cancer are considered to be pluralistic and not due to a discrete change in a cell, whose progeny, as a result of that discrete change, carries all of the information required to explain the almost limitless events of a neoplastic system.

Cell Division↗

PubMed2002

GCR1, the putative Arabidopsis G protein-coupled receptor gene is cell cycle-regulated, and its overexpression abolishes seed dormancy and shortens time to flowering.

Although signaling through heterotrimeric G proteins has been extensively studied in eukaryotes, there is little information about this important signaling pathway in plants. We observed that expression of GCR1, the gene encoding the only known (but still putative) G protein-coupled receptor of Arabidopsis thaliana, is modulated during the cell cycle and during plant development. Overexpression of GCR1 in tobacco (Nicotiana tabacum) BY-2 cells caused an increase in thymidine incorporation and in the mitotic index of aphidicolin synchronized cells. Overexpression of GCR1 in Arabidopsis caused two remarkable phenotypes: seed dormancy was abolished and time to flowering was reduced. Molecular markers of these two developmental processes (phosphatase PP2A and MYB65 in germination; LFY during flowering) were up-regulated in GCR1 overexpressors. These data are consistent with the hypothesis that GCR1 may be a regulator of the cell cycle and that this regulation underlies the developmental changes observed in the GCR1 transformants.

Arabidopsis↗

PubMedDate not supplied

Genetics of colorectal cancer.

The multistep nature of cancer has been well-documented through molecular genetic studies of colorectal cancer. The information provided by basic, translational and clinical science highlighted several genes associated with different hereditary syndromes predisposing to colorectal cancer. Due to these and other findings, the molecular pathogenesis of this cancer has been clarified also with respect to genetic pathways which can lead to an otherwise undistinguishable disease. As a result of both the available and continuously added data, our knowledge and understanding of colorectal cancer is subject to constant changes. Ultimately, these are expected to result in multiple and strategical managements based on molecular genetics which will likely change our approach to this cancer in the incoming millennium.

Cell Transformation, Neoplastic↗