Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “classifier”

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 1,063 records · Page 59Linked to original sources
PubMed2000

Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties.

Recent efforts at the proteomic level were employed to describe the protein equipment of the plasma membrane of the model plant Arabidopsis thaliana. These studies had revealed that the plasma membrane is rich in extrinsic proteins but came up against two major problems: (i) few hydrophobic proteins were recovered in two-dimensional electrophoresis gels, and (ii) many plasma membrane proteins had no known function or were unknown in the database despite extensive sequencing of the Arabidopsis genome. In this paper, several methods expected to enrich a membrane sample in hydrophobic proteins were compared. The optimization of solubilization procedures revealed that the detergent to be used depends on the lipid content of the sample. The corresponding proteomes were compared with the statistical model AMMI (additive main effects with multiplicative interaction) that aimed at regrouping proteins according to their solubility and electrophoretic properties. Distinct groups emerged from this analysis and the identification of proteins in each group allowed us to assign specific features to several of them. For instance, two of these groups regrouped very hydrophobic proteins, one group contained V-ATPase subunits, another group contained proteins with one transmembrane domain as well as proteins known to interact with membrane proteins. This study provides methodological tools to study particular classes of plasma membrane proteins and should be applicable to other cellular membranes.

Amino Acid Sequence↗
PubMed2000

Proteomics approach in classifying the biochemical basis of the anticancer activity of the new olomoucine-derived synthetic cyclin-dependent kinase inhibitor, bohemine.

The aim of this study was to use two-dimensional electrophoresis (2-DE) coupled with multivariate principal component analysis (PCA) to characterize the quantitative changes in the protein composition of the CEM T-lymphoblastic leukemia cell line after treatment with bohemine (BOH), a synthetic olomoucin-derived cyclin-dependent kinase inhibitor (CDKI). Cell classification, reflecting protein patterns, clearly distinguished two main groups: one group consists of 9, 12 and 24 h treated BOH cells while the second is represented by the 0 and 24 h control untreated cells and the 6 h BOH-exposed CEM lymphoblasts. Discriminant protein spots differentially expressed in the BOH-treated CEM cells were selected for identification by matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS) or electrospray ionization-tandem MS (ESI-MS/MS). Five of the selected protein spots were unequivocally identified as alpha-enolase, triosephosphate isomerase, eukaryotic initiation factor 5A, and alpha- and beta-subunits of Rho GDP-dissociation inhibitor 1. These proteins, all significantly downregulated in CEM T-lymphoblast leukemia in the course of BOH treatment, are known to play an important role in cellular functions such as glycolysis, protein biosynthesis, and cytoskeleton rearrangement. These results indicate that the cellular effects of olomoucine-derived CDKIs are not dependent on their ability to inhibit CDKs and could be mediated by several factors such as a decrease in protein synthesis and/or glycolysis which in turn diminishes the ability of cancer cells to function.

Antineoplastic Agents↗
PubMed1986

Intra- and interobserver concordance in classifying dental morphology.

A sample of 50 Kodiak Island Eskimo dental casts were observed, using standard reference plaques, three times by one observer and once by a second observer, for 47 graded and discrete morphological characters of the dentition and jaws. Although the frequency of both intra- and interobserver scoring differences between observation sessions are relatively high for some characters, statistical analysis reveals that differences are largely random in direction and cancel out. Most dental morphological variants can be observed in a ranked fashion with adequate within- and between-observer reliability. However, four traits present both within- and between-observer difficulties: the tuberculum dentale, the canine distal accessory ridge, marginal accessory cusps of the upper first premolar, and the anterior fovea on the lower first molar.

Alaska↗
PubMed2005

Classifying "kinase inhibitor-likeness" by using machine-learning methods.

By using an in-house data set of small-molecule structures, encoded by Ghose-Crippen parameters, several machine learning techniques were applied to distinguish between kinase inhibitors and other molecules with no reported activity on any protein kinase. All four approaches pursued--support-vector machines (SVM), artificial neural networks (ANN), k nearest neighbor classification with GA-optimized feature selection (GA/kNN), and recursive partitioning (RP)--proved capable of providing a reasonable discrimination. Nevertheless, substantial differences in performance among the methods were observed. For all techniques tested, the use of a consensus vote of the 13 different models derived improved the quality of the predictions in terms of accuracy, precision, recall, and F1 value. Support-vector machines, followed by the GA/kNN combination, outperformed the other techniques when comparing the average of individual models. By using the respective majority votes, the prediction of neural networks yielded the highest F1 value, followed by SVMs.

Algorithms↗
PubMed2002

Real-time, high-definition, three-dimensional microscopy for evaluating problematic cervical Papanicolaou smears classified as atypical squamous cells of undetermined significance.

BACKGROUND: The perceived inadequacies of the cervical Papanicolaou (Pap) smear have been attributed to sampling, screening, or interpretive errors. Within this type of cytologic preparation, there are thick cell clusters in which the cells are obscured. It may not possible to evaluate these areas by conventional microscopy. The authors clinically tested the hypothesis that high-definition, three-dimensional (3-D) microscopy based on multiple oblique illumination (MOI), with its ability to penetrate into thick areas, would be useful in evaluating problematic cervical Pap smears, particularly those diagnosed as atypical squamous cells of undetermined significance (ASCUS). METHODS: ASCUS Pap smears and corresponding surgical biopsy specimens were evaluated prospectively using standard, axially illuminated microscopes and a new high-definition, 3-D microscope employing MOI. The Pap smears were reviewed in a blinded fashion with both types of microscopy. The rendered diagnoses were then compared with the subsequent tissue biopsies, which also were blinded, as the definitive end point. RESULTS: It was immediately apparent that the high-definition, 3-D MOI microscope had better resolution compared with the standard microscopes. Pap smears and biopsy diagnoses were correlated significantly for MOI (P < 0.001), and there were significant improvements (P = 0.0108) in accuracy when 3-D, high-definition microscopy was compared with conventional microscopy. The authors found no statistically significant correlation between ASCUS diagnoses that were rendered by using standard microscopes compared with the subsequent biopsy. CONCLUSIONS: Due to enhanced visualization through thick cell clusters, an increased depth of field, light penetration, and resolution, high-definition, 3-D microscopy based on MOI produced superior accuracy compared with conventional light microscopy in evaluating cervical Pap smears.

Adolescent↗
PubMed2006

Distribution of human papillomavirus types in ThinPrep Papanicolaou tests classified according to the Bethesda 2001 terminology and correlations with patient age and biopsy outcomes.

BACKGROUND: A survey of the distribution of human papillomavirus (HPV) types across the spectrum of cervical cytologic categories defined by the Bethesda 2001 guidelines was conducted with the objective of examining how HPV detection by polymerase chain reaction (PCR) analysis may benefit the management of patients who have abnormal Papanicolaou (Pap) test results. METHODS: DNA samples from women with no intraepithelial lesion or malignancy (NLM) (n = 300 samples); atypical squamous cells of undetermined significance (ASC-US) (n = 200 samples); low-grade squamous intraepithelial lesion (LSIL) (n = 200 samples); atypical squamous cells, cannot rule out high-grade squamous intraepithelial lesion (ASC-H) (n = 200 samples); and high-grade squamous intraepithelial lesion (HSIL) (n = 200 samples) were tested for HPV using a modified general primer (GP)5+/GP6+ PCR assay and dot-blot hybridization with type-specific oligonucleotide probes (PCR assay analytical sensitivity: 1-100 copies of HPV, depending on the HPV type, in a background of 100 ng human DNA). RESULTS: HPV was detected in 27% of NLM samples, in 89.5% of ASC-US samples, in 97.5% of LSIL samples, in 93% of ASC-H samples, and in 96.5% of HSIL samples. Thirty-seven different HPV types were identified in total. One or more of 13 high-risk (HR) HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68) were detected in 53% of samples that were diagnosed as ASC-US (59.0% of patients younger than age 30 yrs; 45.5% of patients age 30 yrs and older), in 55.5% of samples that were diagnosed as LSIL (60.0% of patients younger than age 30 yrs; 44.0% of patients age 30 yrs and older), in 80% of samples that were diagnosed as ASC-H, and in 87.5% of samples that were diagnosed as HSIL (P < 0.001). HPV-16 was detected in 17.5% of ASC-US samples, in 15.5% of LSIL samples, in 48.5% of ASC-H samples, and in 49.0% of HSIL samples (P < 0.001). Among abnormal smears, HR HPV was significantly more common in women younger than age 30 years compared with women age 30 years and older (P < 0.002). Follow-up biopsy data were obtained for 359 patients. A "benign" biopsy result was recorded for 47 of 64 women (73.5%) with ASC-US, 30 of 66 women (45.5%) with LSIL, 39 of 87 women (45.0%) with ASC-H, and 26 of 142 women (18.0%) with HSIL and was most common in women age 30 years and older (P < 0.0001). Cervical intraepithelial neoplasia (CIN) Grade I (CIN-I) was found in 14.0% of women with ASC-US, in 39.5% of women with LSIL, in 8.0% of women with ASC-H, and in 7.0% of women with HSIL. CIN-II was diagnosed in 9.5% of women with ASC-US, in 13.5% of women with LSIL, in 19.5% of women with ASC-H, and in 24.0% of women with HSIL. CIN-III was identified in 2 women (3.0%) with ASC-US, in 1 woman (1.5%) with LSIL, in 24 women (27.5%) with ASC-H, and in 71 women (50.0%) with HSIL. CONCLUSIONS: HR HPV testing by PCR of samples diagnosed according to the Bethesda 2001 guidelines may benefit the management of patients with ASC-US or patients with LSIL, especially among women age 30 years and older, by allowing exclusion from referral for biopsy of women who are negative for HR HPV types. However, the small numbers of women who had CIN-III detected after a diagnosis of ASC-US or LSIL limited the assessment of test sensitivity.

Adult↗
PubMed1984

Classifying breast carcinomas with DNA measurements and morphometry.

The relation between the DNA distribution pattern and the variables DNA content and nuclear area was investigated in 73 breast carcinomas. According to the DNA patterns, the tumors were subclassified into groups I, II, III, and IV (Auer's classification). The Auer's classes correlate with prognosis. In this investigation it was shown that Auer's classes strongly correlate with the standard deviation of DNA content and mean nuclear area. The carcinomas were subclassified using data of DNA content and nuclear area. For the establishment of this subclassification, multivariate analysis was applied. It was evident that Auer's group III was a hybrid group. Therefore a second classification rule was calculated without the data of Auer's group III. This second classification rule was even more successful in determining the Auer's group of each individual case. Our investigation shows that it is possible to subclassify breast carcinomas objectively using DNA content and nuclear area of the tumor cells.

Breast Neoplasms↗
PubMed2022

Insights on the pathogenesis of type 2 diabetes as revealed by signature genomic classifiers in an African American population in the Washington, DC area.

AIMS: African Americans (AA) in the United States have a high risk of type 2 diabetes mellitus (T2DM) and suffer from disparities in the prevalence, mortality, and comorbidities of the disease compared to other Americans. The present study aimed to shed light on the molecular mechanisms of disease pathogenesis of T2DM among AA in the Washington, DC region. METHODS: We performed TaqMan Low Density Arrays (TLDA) on 24 genes of interest that belong to three categories: metabolic disease and disorders, cancer-related genes, and neurobehavioural disorders genes. The 18 genes, viz. ARNT, CYP2D6, IL6, INSR, RRAD, SLC2A2 (metabolic disease and disorders), APC, BCL2, CSNK1D, MYC, SOD2, TP53 (Cancer-related), APBA1, APBB2, APOC1, APOE, GSK3B, and NAE1 (neurobehavioural disorders), were differentially expressed in T2DM participants compared to controls. RESULTS: Our results suggest that factors including gender, smoking habits, and the severity or lack of control of T2DM (as indicated by HbA1c levels) were significantly associated with differential gene expression. APBA1 was significantly (p-value <0.05) downregulated in all diabetes participants. Upregulation of APOE and CYP2D6 genes and downregulation of the INSR gene were observed in the majority of diabetes patients. CONCLUSIONS: Tobacco smoking and gender were significantly associated with case-control differences in expression of the APBA1 and APOE genes (connected with Alzheimer's disease) and the INSR and CYP2D6 (associated with metabolic disorders). The results highlight the need for more effective management of T2DM and for tobacco smoking cessation interventions in this community, and further research on the associations of T2DM with other disease processes, including cancer and neurobehavioral pathways.

Humans↗
PubMed1986

Classifying mutagens as to their specificity in causing the six possible transitions and transversions: a simple analysis using the Salmonella mutagenicity assay.

The standard Salmonella tester strains used to detect base substitution mutations carry the hisG428 ochre mutation (TA102 and TA104) and the hisG46 missense mutation (TA100). These mutations can be reverted by base changes at their mutant his loci or at extragenic suppressor loci. The base changes resulting in each class of revertants of these mutations have been identified, and simple phenotypic screens have been developed to distinguish among them. Revertants at extragenic suppressor loci are distinguished from those at the his loci by their sensitivity to inhibitory histidine analogs. The four ochre suppressor loci of hisG428 are distinguished by their ability to support growth of nonsense mutants of phage P22. These screens are the basis for a rapid and simple system for determining the base substitution specificity of mutagens using hisG428- and hisG46-containing tester strains. Diagnostic mutagens specific for each of the six possible base changes (transitions and transversions) have been identified. Using these diagnostic mutagens, two additional strains, each specifically reverted by a single base substitution mutation, have been developed to provide a minimum of two loci at which to detect each type of base change. The ability of this system to provide detailed information about mutational specificity in a variety of DNA repair backgrounds will allow further elucidation of the mechanisms of mutagenesis and DNA repair.

Azacitidine↗
PubMed2004

Classifying disease chromosomes arising from multiple founders, with application to fine-scale haplotype mapping.

The availability of high-density haplotype data has motivated several fine-scale linkage disequilibrium mapping methods for locating disease-causing mutations. These methods identify loci around which haplotypes of case chromosomes exhibit greater similarity than do those of control chromosomes. A difficulty arising in such mapping is the possibility that case chromosomes have inherited disease-causing mutations from different ancestral chromosomes (founder heterogeneity). Such heterogeneity dilutes measures of case haplotype similarity. This dilution can be mitigated by separating case chromosomes into subsets according to their putative mutation origin, and searching for an area with excessive haplotype similarity within each subset. We propose a nonparametric method for identifying subsets of case chromosomes likely to share a common ancestral progenitor. By simulation studies and application to published data, we show that the method accurately identifies relatively large subsets of chromosomes that share a common founder. We also show that the method allows more precise estimates of the disease mutation loci than obtained by other fine-scale mapping methods.

Algorithms↗
PubMed1989

Attempt to classify glial cells by means of their process specialization using the rabbit retinal Müller cell as an example of cytotopographic specialization of glial cells.

The rabbit retinal Müller cell is one of the most widely studied glial cell types, and it has all forms of contacts that a glial cell can express, viz. 1) to a (ventricular) fluid space, 2) to a mesenchymal borderline (basal lamina), and 3) to neuronal compartments. This cell demonstrates the local adaptation of cell processes to the microenvironment with which they are in contact. Summarizing available data on Müller cells and other glial cell types, it is concluded that the structure with which the process is in contact determines the type of glial cell process that develops. The type I process has microvilli, desmosome-like junctions, and high Na+,K+-ATPase activity; this type of process is in direct contact with a fluid such as cerebrospinal fluid. The type II endfoot-bearing process contains gliofilaments and has a high K+ conductivity; this type of process is covered by a basal lamina and is in contact with mesenchyme. The type III sheath-bearing process insulates neuronal compartments and expresses suitable membrane properties for glia-neuronal communication. Since structurally similar processes have been shown to have similar physiological properties, a new systematic classification of glial cells is proposed, based on the presence or absence of defined types of cell processes. This approach is believed to provide new insights into the function of neuroglia in both the central and peripheral nervous systems, in vertebrates and invertebrates, and even during ontogenetic development.

Animals↗