SEARCH · Search PubMed

Results for “functional profiling”

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.

SourceResearch connectionFrom yearThrough year

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

At least 1,063 records · Page 59Linked to original sources

PubMed1993

Near-lifetime exposure of the rat to a simulated urban profile of nitrogen dioxide: pulmonary function evaluation.

To investigate the potential for up to a near-lifetime exposure to high-ambient levels of nitrogen dioxide (NO2) to induce functional lung damage, groups of rats were exposed to air or a simulated urban profile of NO2 (0.5 ppm background, 1.5 ppm peak) for 1, 3, 13, 52, or 78 weeks. The dynamic, static, and diffusional characteristics of the lung were evaluated postexposure in anesthetized rats. Furthermore, for the 13-, 52-, and 78-week groups, additional animals were tested after a 6-, 26-, or 17-week period in filtered air, respectively. No significant NO2 differences between exposed and control animals were found for the nitrogen washout, compliance, lung volume, or diffusion capacity of carbon monoxide measurements. At 78 weeks, however, a reduction in delta FEF25%, an estimate of convexity in the later portion of the forced expiratory flow volume curve, was observed. Breathing patterns and mechanisms were also assessed postexposure in a parallel group of similarly exposed unanesthetized rats. These rats were examined during a filtered air, 4 and 8% carbon dioxide (CO2) challenge. In the unanesthetized rat, frequency of breathing was significantly decreased and tidal volume, expiratory resistance, and inspiratory and expiratory times tended to increase. For several of these variables, the largest response also occurred at 78 weeks and seemed to be exacerbated by CO2 challenge.(ABSTRACT TRUNCATED AT 250 WORDS)

Air Pollutants↗

PubMed2002

Genomic functional annotation using co-evolution profiles of gene clusters.

BACKGROUND: The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains uncharacterized. Here we propose a new method for functional annotation using the conservation patterns of gene clusters. If several gene clusters show the same coevolution pattern across different genomes it is reasonable to infer they are functionally related. The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome. RESULTS: As a proof of concept, we applied our method to the genome of Escherichia coli K12 strain. Our method establishes functional relationships among 176 gene clusters, comprising 738 E. coli genes. The accuracy of pair phylogenetic profiles was compared with the single-gene phylogenetic profile and was shown to be higher. As a result, we are able to suggest functional roles for several previously unknown genes or unknown genomic regions in E. coli. We also examined the robustness of coevolution signals across a larger set of genomes and suggest a possible upper limit of accuracy for the phylogenetic profile methods. CONCLUSIONS: The higher-order phylogenetic profiles, such as the gene-pair phylogenetic profiles, can detect functional dependences that are missed by using conventional single-gene phylogenetic profile or the chromosomal proximity method only. We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles.

Alleles↗

PubMed2004

Pediatric physical functioning reference curves.

We developed normative profiles of physical functioning (mobility and self-care) in infancy up through 14 years of age with an expanded version of the Pediatric Evaluation of Disability Inventory. Mobility and self-care reference curves were based on the original Pediatric Evaluation of Disability Inventory standardization data (n = 412) and data from an additional cross-sectional, convenience sample (n = 373) via web-based survey, telephone or in-person interviews of parents. This new sample, which included children up through 14 years-of-age, was stratified for race, age, and sex, but was primarily limited geographically to the Northeast region of the United States. Goodness of fit of male, female, and combined sex (male and female) reference curves was examined. The mobility and self-care reference curves produced efficient and well-fitting estimates of conventional percentiles (3rd, 10th, 25th, 50th, 75th, 97th). Differences between males' and females' reference curves were negligible. This study highlights the use of these reference curves for determining the functional impact of Pompe disease, a lysosomal storage disorder that affects skeletal and cardiac muscle, restricting normal expression of mobility and self-care activities. This physical functioning instrument could also be used to evaluate the impact of muscle weakness in other neuromuscular disorders.

Activities of Daily Living↗

PubMed1996

In vivo and in vitro studies on the morphological change in the monkey epidermal Langerhans cells following exposure to dengue 2 (16681) virus.

A direct comparison of skin Langerhans cell (LC) morphologic change following in vivo and in vitro exposure to dengue-2 (DEN-2) virus (16681) was performed in the monkey to investigate any differences in functional activity profiles. Time-lapse study of skin biopsy at the intradermal (id) virus injection sites, and thin skin sheets removed from the monkey with exposure to virus in culture medium, revealed a highly active migration of epidermal LCs in both sets of experimental specimens. The migration led to a relatively higher number of dendritic cells (DC) which appeared in active migrational profiles, in the superficial dermis. Moreover, obvious cytoplasmic structural changes, corresponding to their immunologic function, were observed in these superficial dermal DCs 2 hours after exposure. Despite their similar changes, early and late endosomes with degraded virus-like particles could be seen in the skin sheets owing to lagging in cellular physiological process in vitro, but none in the skin biopsies. Existence of these endosomes, which was extremely difficult to visualize in vivo, highlighted the mode of antigen processing by the endocytic pathway. The present study showed that the epidermal LC was a potent antigen-presenting cell for eliciting the success of id immunization and carried out the immunological activity in vivo or in vitro in the like manner, in respect to the physiological conditions.

Animals↗

PubMed1999

A new schematic eye model incorporating accommodation.

PURPOSE: To create a schematic eye model with four refracting surfaces and with the new function describing the crystalline lens profile. METHODS: The new function describing the crystalline lens profile is a combination of hyperbolic cosine functions modulated by hyperbolic tangent functions. It ensures the continuity of the radius of curvature along the whole lens profile. Recent experimental results on cornea and lens shape measurements have been applied to the proposed model. The new function describing the lens profile has been used to model the eye during accommodation. RESULTS: Spherical aberration and modulation transfer function have been computed to test the eye model. Results of calculations are in agreement with experimental findings. CONCLUSIONS: The calculations show that spherical aberrations of the cornea and crystalline lens cancel each other. The new description of the crystalline lens offers a reduction of longitudinal spherical aberration. The image quality of the unaccommodated eye model is slightly better than that of the accommodated one.

Accommodation, Ocular↗

PubMed1992

Immunophenotyping and functional analysis of purified human uterine mast cells.

Human mast cells have been purified from uterine tissues, and their surface marker profile and function have been evaluated as part of ongoing studies of mast cell heterogeneity. Using a panel of antibodies, purified uterine mast cells (UMC; 81% +/- 7% purity, n = 10) were analyzed by immunofluorescence and flow cytometry for surface expression of various antigens. Consistent with previous analyses of mast cells from other tissues, UMC expressed HLA class I, IgE, c-kit receptor, CD9, CD33, CD43, CD45, and CD54, while CD11a, CD11b, CD14, CD16, CD23, and CD64 were not detected. Unlike other mast cells, UMC expressed CD11c/CD18 (p150,95) and CD32 (Fc gamma RII). Additional antigens not previously studied on mast cells included the selectin LECAM-1 (Leu-8) and several beta 1 and beta 3 integrins; expression of very late activation antigen-4 (VLA-4) (CD49d/CD29), VLA-5 (CD49e/CD29), and the vitronectin receptor (CD51/CD61) was seen. Functional studies showed that treatment of human umbilical vein endothelial cells with interleukin-1 (5 ng/mL for 4 hours) resulted in a twofold to threefold increase in adhesiveness for UMC. Purification procedures did not alter histamine release responses to anti-IgE or the calcium ionophore A23187, and treatment of UMC with an anti-CD32 monoclonal antibody (IV.3) did not induce histamine release or alter anti-IgE-induced release. These data suggest that UMC may possess unique phenotypic characteristics, and support the concept of mast cell heterogeneity.

Antibodies, Monoclonal↗

PubMed1991

The Life Skills Profile: psychometric properties of a measure assessing function and disability in schizophrenia.

The Life Skills Profile (LSP) was developed as a measure of function and disability in schizophrenia. We now report a number of studies assessing its psychometric properties, principally when completed by case workers, residential carers and parents. We demonstrate high test-retest reliability for all 3 rater groups. High interrater reliability was demonstrated between raters of the same background (such as parent vs parent) and when co-ratings by caseworkers and residential carers were examined. By contrast, parents rated differently to case workers and residential carers, a finding that could reflect different raters "knowing" subjects in different ways, or the effects of response biases. To pursue the latter possibility, the influences of rater "burden of care" and "optimism" were examined. A concurrent validity study is reported, offering additional support for the validity of the measure.

Activities of Daily Living↗

PubMed1994

Expression patterns of Fc gamma receptors, HLA-DR and selected adhesion molecules on monocytes from normal and HIV-infected individuals.

The expression and co-expression profiles of functionally important monocyte surface markers were compared between control and HIV+ individuals using combined physical gating and dim CD4 expression to delineate the monocytes. The Fc gamma RII (CD32), the MHC class II antigen HLA-DR and the adhesion molecules CD11a (LFA-1 alpha), CD18 and CD54 (ICAM-1) showed an unimodal distribution. Of these markers, CD11a and HLA-DR were up-regulated in the HIV+ subjects compared with controls. The expression levels of the adhesion molecules correlated with each other in both patients and controls. The CD11b (CR3-alpha), CD14, Fc gamma RI, and Fc gamma RIII markers were bimodally distributed. Compared with controls, monocytes from seropositives contained fewer CD14bright+ cells, an equal proportion of Fc gamma RIbright+ cells, but twice as many Fc gamma RIII+ cells. The expression level of Fc gamma RI and CD11b within their brightly positive subset increased as CD4 T cells decreased. Both in patients and controls, co-expression of bright CD11b, CD14 and Fc gamma RI was shown, whereas the Fc gamma RIII+ cells were negative or dim positive for the former triad. We conclude that the expression of two Fc gamma R (I and III), of the adhesion molecules CD11a and CD11b and of HLA-DR showed particular alterations on monocytes from HIV+ subjects. The relationship of these phenotypic observations with altered cytokine profiles and altered monocyte function is discussed.

Antigens, CD↗

PubMed2026

ORBIT: Oncogenic Representation Learning via Bi-Prototype Contrastive Learning in Hyperbolic Space for cancer driver gene identification.

Accurate identification of cancer driver genes is crucial for precision oncology but remains challenging due to the complexity of integrating heterogeneous data and modeling dynamic biological systems. To address these limitations, we propose ORBIT (Oncogenic Representation Learning via Bi-Prototype Contrastive Learning in Hyperbolic Space). Our framework synergistically fuses multi-omics profiles with functional network data using a context-adaptive graph reweighting mechanism to capture cancer-specific dynamics. The model employs a bi-prototype contrastive learning strategy within hyperbolic space, which aligns gene representations around distinct driver and non-driver semantic anchors while preserving the intrinsic hierarchy of biological networks. Comprehensive evaluations demonstrate that ORBIT achieves highly competitive stability in pan-cancer analysis while consistently outperforming state-of-the-art methods in cancer-specific predictions. Furthermore, functional enrichment analysis confirms that the model effectively segregates core cancer pathways, and drug sensitivity profiling validates the clinical relevance of the identified drivers. By integrating hyperbolic geometry with context-adaptive learning, ORBIT offers a robust and interpretable paradigm for precision medicine. The source codes and datasets are publicly accessible at https://github.com/spcho-dev/ORBIT.

Humans↗

PubMed2005

Dysfunction of simian immunodeficiency virus/simian human immunodeficiency virus-induced IL-2 expression by central memory CD4+ T lymphocytes.

Production of IL-2 and IFN-gamma by CD4+ T lymphocytes is important for the maintenance of a functional immune system in infected individuals. In the present study, we assessed the cytokine production profiles of functionally distinct subsets of CD4+ T lymphocytes in rhesus monkeys infected with pathogenic or attenuated SIV/simian human immunodeficiency virus (SHIV) isolates, and these responses were compared with those in vaccinated monkeys that were protected from immunodeficiency following pathogenic SHIV challenge. We observed that preserved central memory CD4+ T lymphocyte production of SIV/SHIV-induced IL-2 was associated with disease protection following primate lentivirus infection. Persisting clinical protection in vaccinated and challenged monkeys is thus correlated with a preserved capacity of the peripheral blood central memory CD4+ T cells to express this important immunomodulatory cytokine.

AIDS Vaccines↗

PubMedDate not supplied

[Diabetes mellitus in the aged. 4. Cardiovascular risk profile of aged long term diabetics from the viewpoint of their kidney function].

The cardiovasculary risk profile of 138 old grown long term diabetics (mean age 71,1 years, mean duration of the disease 19,9 years) was analysed in the frame of the so called metabolic syndrome and put in relation to the corresponding value of serum creatinine. With increasing concentration of creatinine the mean value of diabetes-associated cardiovasculary risk factors grew with old age, where only the frequency of hyperuricaemia correlated positively to the creatinine level. With comparable level of uric acid in serum the part of pathological increasing of creatinine in older age was more marked distinctly than with younger long term diabetics et respective time of disease (n = 112, mean age 45,7 years, mean duration of the disease 19,6 years). 42,0 per cent of the younger and 60.9 per cent of the older long term diabetics showed increased values of serum creatinine (p less than 0,01). The reduction of the cardiovasculary risk factors should also be forced with old grown long term diabetics.

Aged↗

PubMed2002

Cognitive profiles and social-communicative functioning in children with autism spectrum disorder.

BACKGROUND: Whether there is an unusual degree of unevenness in the cognitive abilities of children with autism spectrum disorder (ASD) and whether different cognitive profiles among children with ASD might index etiologically significant subgroups are questions of continued debate in autism research. METHOD: The Differential Ability Scales (DAS) and the Autism Diagnostic Observation Schedule (ADOS) were used to examine profiles of verbal and nonverbal abilities and their relationship to autistic symptomatology in 120 relatively high-functioning children with ADI-confirmed diagnoses of autism. RESULTS: Discrepancies between verbal and nonverbal ability scores occurred at a significantly higher rate than in the DAS normative sample (30%) in both a younger group of 73 children (56%) with a mean age of 5;5 and an older group of 47 children (62%) with a mean age of 8;11. Discrepancies were mainly in favor of nonverbal ability in the younger group, but occurred equally in favor of verbal and nonverbal abilities in the older group. Comparison of the two age groups suggested a growing dissociation between verbal and nonverbal (and particularly visual processing) skills with age. In the older group, children with discrepantly higher nonverbal abilities demonstrated significantly greater impairment in social functioning, as measured on the ADOS, independent of absolute level of verbal and overall ability. CONCLUSIONS: These findings demonstrate a high rate of uneven cognitive development in children with ASD. Indications of a dissociation between verbal and visual-perceptual skills among the older children, and the specific association of discrepantly high nonverbal skills with increased social symptoms suggest that the nonverbal > verbal profile may index an etiologically significant subtype of autism.

Adolescent↗

PubMed1992

Reconstruction of the acoustical impedance profile of a multilayer medium.

The recovery of the acoustical reflectivity function and impedance profile of a layered medium from bandlimited and noisy pulse-echo ultrasonic data is considered. The effects of the transducer and the noise are reduced using Wiener filtering. With further signal processing and a priori knowledge of the attenuation and the velocity profiles, the compensated coefficients of the reflectivity function and the impedance profile are recovered. The reconstruction techniques are presented analytically, and are also evaluated in an experimental setup composed of a conventional pulse echo system, a data acquisition and a data processing system. Under experimental conditions, the RMS errors in the estimation of the compensated acoustical discrete impedance profile were within 3% of the calculated values.

Algorithms↗

PubMed2006

SNPs3D: candidate gene and SNP selection for association studies.

BACKGROUND: The relationship between disease susceptibility and genetic variation is complex, and many different types of data are relevant. We describe a web resource and database that provides and integrates as much information as possible on disease/gene relationships at the molecular level. DESCRIPTION: The resource http://www.SNPs3D.org has three primary modules. One module identifies which genes are candidates for involvement in a specified disease. A second module provides information about the relationships between sets of candidate genes. The third module analyzes the likely impact of non-synonymous SNPs on protein function. Disease/candidate gene relationships and gene-gene relationships are derived from the literature using simple but effective text profiling. SNP/protein function relationships are derived by two methods, one using principles of protein structure and stability, the other based on sequence conservation. Entries for each gene include a number of links to other data, such as expression profiles, pathway context, mouse knockout information and papers. Gene-gene interactions are presented in an interactive graphical interface, providing rapid access to the underlying information, as well as convenient navigation through the network. Use of the resource is illustrated with aspects of the inflammatory response and hypertension. CONCLUSION: The combination of SNP impact analysis, a knowledge based network of gene relationships and candidate genes, and access to a wide range of data and literature allow a user to quickly assimilate available information, and so develop models of gene-pathway-disease interaction.

Databases, Genetic↗

PubMed2026

Integrative Transcriptomic and Proteomic Profiling Identifies S100P as a Potential Functional Biomarker for Sessile Serrated Lesions.

BACKGROUND: Sessile serrated lesions (SSLs) account for 15% of colorectal cancers (CRCs) but detection remains difficult due to flat morphology, mucinous features, and subtle histology. AIMS: This study aimed to identify novel and functionally relevant biomarkers of SSLs using transcriptomic screening and multi-omics validation. METHODS: Paired SSL and normal mucosa specimens (n = 6) underwent RNA sequencing. Differentially expressed genes (DEGs) were filtered for membrane or secretory proteins and validated across TCGA and adenoma transcriptomes. Functional significance was assessed using CRISPR dependency profiling, proteotranscriptomic concordance, pharmacogenomic sensitivity, and connectivity map analysis. RESULTS: We identified 216 upregulated genes in SSLs, including 68 encoding secretory/membrane proteins that better discriminated SSLs from controls and were enriched for adhesion and neuronal signaling while suppressing TNFα-NFκB inflammatory pathways. Cross-cohort comparison revealed five overlapping candidates between SSLs and TCGA CMS1 tumors. Among them, S100P emerged as the primary biomarker candidate, showing consistent upregulation in SSLs and CMS1 tumors while remaining low in normal mucosa and conventional adenomas. TFF1 also showed RNA-level upregulation but appeared more context-dependent. S100P demonstrated strong RNA-protein concordance in CRC cell-line profiling, supporting its detectability as a biomarker candidate. Pharmacogenomic profiling of LS411N cells revealed marked sensitivity to SN-38 and fluoropyrimidines, consistent with serrated CRC vulnerabilities. Connectivity map analysis identified perturbations, including MAPK1 and histone acetyltransferase suppression, that may reverse parts of the SSL transcriptional program. CONCLUSION: These findings prioritize S100P as a promising biomarker candidate for SSLs that warrants further validation in larger cohorts and clinically applicable platforms.

Humans↗

PubMed1990

Dysequilibrium and audiovestibular function in panic disorder: symptom profiles and test findings.

Patients with panic disorder commonly report symptoms of dizziness and imbalance. We studied the relationship between objective measures of audiovestibular function, phenomenologic, and self-report measures of dysequilibrium and related somatic symptoms in a sample of panic disorder patients with and without agoraphobia, unselected for the complaint of dysequilibrium. Of seventeen patients evaluated by electronystagmography, 71 percent exhibited abnormal vestibular test findings. These latter patients had higher total anxiety ratings than patients without vestibular abnormalities. We conclude that patients with panic disorder warrant evaluation of audiovestibular function.

Adult↗

PubMed2002

The consequences of volatile organic compound mediated bacterial and fungal interactions.

Microbial interactions via infochemicals are fundamental to the development of spatial distribution and activity variations in ecosystems. Microorganisms produce a wide range of infochemicals, frequently secondary metabolites, most of which are soluble and many volatile. Volatile organic compounds (VOCs) have been identified in soil atmospheres and related to community structure and function. VOC profiles produced by microorganisms are consistent, relating to cultural conditions, environment and inputs, and so to population and function dynamics. VOC-mediated interactions can result in functional responses by the organisms involved that result in selective advantage to some community members. Positive, negative or neutral interactions can occur between a very wide range of soil bacteria and fungi. These effects include both stimulation and inhibition of growth, by 40 and 60%, respectively, and enzyme production. These effects are usually transient, e.g. removal of an antagonist is followed by complete recovery. Up- and down-regulation of gene expression, by mRNA and protein profiling has been demonstrated. VOCs have played an important role during the evolution of microorganisms in the context of their communities.

Bacteria↗

PubMed2005

Negative acting HLH proteins Id 1, Id 2, Id 3, and Id 4 are expressed in prostate epithelial cells.

BACKGROUND: The four known Id proteins, Id 1, Id 2, Id 3, and Id 4 are largely considered as dominant negative helix-loop-helix (HLH) proteins. They can dimerize with basic helix loop proteins (bHLH) but the dimers fail to bind the consensus E box response element (CANNTG). Alternatively, members of the Id family, for example, Id 2 can also bind to non-bHLH proteins such as retinoblastoma (Rb) and ETS-TCF to modulate their activities. Consistent with their role as promoters of proliferation, subset of Id genes for example, Id 1 and Id 2 are expressed in many cancers including that of the prostate. However, their expression and function in the normal prostate is unknown. METHODS: The present study was designed to evaluate the expression profile and functional significance of all Id isoforms in normal rat prostate epithelial cells. The data suggests that all four Id isoforms are expressed in normal cells, albeit at different levels. RESULTS: Agents that promote growth, for example, serum increase the levels of Id 1, Id 2, and Id 3. The hormones and mitogens such as testosterone and hepatocyte growth factor (HGF) that promote prostate epithelial cell differentiation stimulate Id 4 and Id 2, respectively. CONCLUSIONS: In prostate epithelial cells, Id 1 may be specifically involved in promoting proliferation whereas Id 4 and Id 2 may have defined roles in regulating differentiated functions in response to androgens and local paracrine factors such as HGF.

Animals↗