Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Molecular Classification”

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 1,423 records · Page 79Linked to original sources

Molecular epidemiology of human rotaviruses: genogrouping by RNA-RNA hybridization.

RNA-RNA hybridization performed under high stringency conditions allows rotavirus isolates to be grouped together based on the overall similarity of their genomic RNA constellation. Classification by this scheme has been termed "genogrouping". Genogrouping has advanced molecular epidemiology of human rotaviruses. Major observations include (i) Interspecies transmission occurs in nature and (ii) Intergenogroup reassortment occurs in nature with or without exchange of serotype-determining genes. Genogrouping is a particularly valuable asset for determining the gene constellation of unusual rotavirus isolates.

Animals↗

Inference of the phylogenetic position of oxymonads based on nine genes: support for metamonada and excavata.

Circumscribing major eukaryote groups and resolving higher order relationships between them are among the most challenging tasks facing molecular evolutionists. Recently, evidence suggesting a new supergroup (the Excavata) comprising a wide array of flagellates has been collected. This group consists of diplomonads, retortamonads, Carpediemonas, heteroloboseans, Trimastix, jakobids, and Malawimonas, all of which possess a particular type of ventral feeding groove that is proposed to be homologous. Euglenozoans, parabasalids, and oxymonads have also been associated with Excavata as their relationships to one or more core excavate taxa were demonstrated. However, the main barrier to the general acceptance of Excavata is that its existence is founded primarily on cytoskeletal similarities, without consistent support from molecular phylogenetics. In gene trees, Excavata are typically not recovered together. In this paper, we present an analysis of the phylogenetic position of oxymonads (genus Monocercomonoides) based on concatenation of eight protein sequences (alpha-tubulin, beta-tubulin, gamma-tubulin, EF-1alpha, EF-2, cytosolic (cyt) HSP70, HSP90, and ubiquitin) and 18S rRNA. We demonstrate that the genes are in conflict regarding the position of oxymonads. Concatenation of alpha- and beta-tubulin placed oxymonads in the plant-chromist part of the tree, while the concatenation of other genes recovered a well-supported group of Metamonada (oxymonads, diplomonads, and parabasalids) that branched weakly with euglenozoans--connecting all four excavates included in the analyses and thus providing conditional support for the existence of Excavata.

Animals↗

Salivary duct carcinoma- contemporary nuts and bolts from pathologist perspective.

INTRODUCTION: Salivary gland carcinomas are highly heterogeneous malignancies that present a complex variety of histological features and distinct clinical behaviors, with salivary duct carcinoma (SDCa) as the most clinically severe and aggressive subtype. The standard of care for these patients is a combined approach of surgery followed by radiotherapy. The aggressive clinical course of SDCa is primarily driven by frequent disease recurrences and systemic spread. AREAS COVERED: The publication of WHO 5th Classification of Head and Neck tumors has sparked a surge in research targeting SDCa. Owing to the highly aggressive behavior of the tumor, most literature heavily emphasizes the molecular pathology of SDCa.A systematic literature search was conducted using the PubMed with the following search terms: salivary duct carcinoma AND pathology OR updates OR molecular OR signaling pathway OR gene expression OR mutation OR oncogene OR tumor suppressor OR DNA methylation OR tumor microenvironment. Results were limited to primary research articles in English language. EXPERT OPINION: This article outlines key advancements in SDCa morphology, molecular pathology, and targeted therapies. Patient management in precision oncology will be fundamentally transformed by the classification of new morphologic subtypes, the discovery of molecular biomarkers, and an enhanced comprehension of tumor microenvironment.

HER 2↗

Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching.

A method is described for the rapid comparison of protein binding sites using geometric matching to detect similar three-dimensional structure. The geometric matching detects common atomic features through identification of the maximum common sub-graph or clique. These features are not necessarily evident from sequence or from global structural similarity giving additional insight into molecular recognition not evident from current sequence or structural classification schemes. Here we use the method to produce an all-against-all comparison of phosphate binding sites in a number of different nucleotide phosphate-binding proteins. The similarity search is combined with clustering of similar sites to allow a preliminary structural classification. Clustering by site similarity produces a classification of binding sites for the 476 representative local environments producing ten main clusters representing half of the representative environments. The similarities make sense in terms of both structural and functional classification schemes. The ten main clusters represent a very limited number of unique structural binding motifs for phosphate. These are the structural P-loop, di-nucleotide binding motif [FAD/NAD(P)-binding and Rossman-like fold] and FAD-binding motif. Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods.

Algorithms↗

A molecular signature of the Nottingham prognostic index in breast cancer.

The Nottingham prognostic index (NPI) is a widely used clinicopathological staging system for breast cancer prognostication. Using a step-wise classification approach where breast tumor expression profiles were first divided into general "molecular subtypes" [estrogen receptor (ER)+, ER-, ERBB2+], followed by an independent analysis of each subtype, we identified a 62-gene expression signature (NPI-ES) highly correlated to the NPI in ER+ tumors. The NPI-ES classified the majority of ER+ tumors into two distinct groups with high confidence and was significantly correlated to NPI status in two independent sets of ER+ tumors derived from different centers. The NPI-ES is comparable to the classical NPI in identifying patients likely to exhibit a poor clinical prognosis, as well as to a recently described "prognosis signature" for breast cancer. Our findings demonstrate how expression profiling can complement classical staging systems employing histopathological parameters scored over a continuous range of values.

Breast Neoplasms↗

Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes.

We present a most comprehensive phylogenetic analysis of the family Cichlidae. New data analyzed include mitochondrial 16S rRNA sequences and two nuclear loci (Tmo-M27 and Tmo-4C4) for a large taxonomic sampling with emphasis on South American species. We also incorporate a published morphological data set for a total evidence analysis. Character congruence among mitochondrial (74 taxa) and nuclear data (50 taxa) was high. However, partition-homogeneity tests suggest significant heterogeneity among molecular and morphological data. In agreement with results obtained from molecular data alone, total evidence analysis (1,460 characters for 34 taxa) supports a robust phylogenetic hypothesis for the family Cichlidae that is congruent with drift-vicariance events associated with the fragmentation of Gondwana. Our analyses confirm the placement of Malagasy/Indian cichlids as the most basal lineages, with a sister-group relationship to the monophyletic African and Neotropical clades. Total evidence suggests that the controversial African genus Heterochromis is at the base of the African radiation. Among more than 50 Neotropical genera analyzed, Retroculus is identified as the basal taxon, with successive branching of Cichla, Astronotus, geophagines (including crenicichlines) + chaetobranchines, and cichlasomines + heroines. Relative rate tests applied to mitochondrial DNA suggest significantly higher rates of genetic variation in Neotropical than in African taxa, and both mitochondrial and nuclear sequences show that rate heterogeneity among Neotropical lineages is confined to the geophagine cichlids.

Animals↗

How shall we apply the new biology to diagnostics in surgical pathology?

Molecular technology plays an ever-increasing role in academic pathology and frequent claims are made that these technical developments will revolutionize diagnostic histopathology. In reviewing the role and potential utility of molecular genetics in the clinical practice of tumour pathology, it is evident that claims have outweighed facts, at least to date, and while molecular data have helped to clarify specific small areas of tumour classification and have facilitated the diagnosis of certain relatively rare tumours (especially on limited tissue), the overall impact on cancer management has been small. In particular, molecular markers of prognosis or tumour response have yet to impact substantially on the role of conventional light microscopic examination. We believe that these shortcomings have more to do with the generally different goals of basic medical science and clinical practice. In order to optimize the benefit to patients of modern molecular pathology, these techniques need to be rigorously appraised in the clinical setting and properly analysed in terms of cost-benefit. This requires close collaboration between the basic research community and histopathologists. Suggestions that 'H&E' pathology will be superceded in the near future are both premature and unrealistic.

Biomarkers, Tumor↗

Bleeding following coronary surgery after preoperative low-molecular-weight heparin.

Low-molecular-weight heparin and acetyl salicylic acid have become an established treatment for unstable angina. A retrospective study on our database of one year was carried out to see what impact preoperative low-molecular-weight heparin versus none had on the postoperative course of 473 patients having coronary surgery exclusively. Apart from the fact that the low-molecular-weight heparin patients had a higher New York Heart Association classification and marginally more grafts, longer bypass and cross-clamp time, the preoperative characteristics and surgery of the two groups were similar. The low-molecular-weight heparin group had twice as many (9.7% versus 4.7%) re-operations for bleeding, 46% versus 26% had blood transfusion and 22.3% versus 12.6% plasma transfusion. The postoperative outcome was otherwise similar. Preoperative treatment of unstable angina with low-molecular-weight heparin carries a definite risk of postoperative bleeding. Although this study did not reveal any serious consequences, bleeding, transfusions and re-operations are associated with infections, wound healing problems and death. The indications and length of treatment with low-molecular-weight heparin in unstable angina patients have to be appropriate and the perioperative management of these patients has to address the bleeding tendency.

Age Distribution↗

Classification of kinase inhibitors using BCUT descriptors.

BCUTs are an interesting class of molecular descriptor which have been proposed for a number of design and QSAR type tasks. It is important to understand what kind of information any particular descriptor encodes and to be able to relate this to the biological properties of the molecules. In this paper we present studies with BCUTs for the classification of ATP site directed kinase inhibitors active against five different protein kinases: three from the serine/threonine family and two from the tyrosine kinase family. In combination with a chemometric method, PLS discriminant analysis, the BCUTs are able to correctly classify the ligands according to their target. A novel class of kinase inhibitors is correctly predicted as inhibitors of the EGFR tyrosine kinase. Comparison with other descriptor types such as two-dimensional fingerprints and three-dimensional pharmacophore-based descriptors allows us to gain an insight into the level of information contained within the BCUTs.

Enzyme Inhibitors↗

Flow cytometry in the diagnosis of acute leukemia.

Acute leukemias are a heterogeneous group of malignancies with varying clinical, morphologic, immunologic, and molecular characteristics. Many distinct types are known to carry predictable prognoses and warrant specific therapy. Distinction between lymphoid and myeloid leukemias, most often made by flow cytometry, is crucially important. Several advances in flow cytometry, including availability of new monoclonal antibodies, improved gating strategies, and multiparameter analytic techniques, have all dramatically improved the utility of flow cytometry in the diagnosis and classification of leukemia. Acute leukemias reflect the pattern of antigen acquisition seen in normal hematopoietic differentiation, yet invariably demonstrate distinct aberrant immunophenotypic features. Detailed understanding of these phenotypic patterns of differentiation, particularly in myeloid leukemia, allows for more precise classification of leukemia than does morphology alone. However, morphologic and differentiation-based classifications of leukemia are limited in their prognostic value; cytogenetics and molecular genetics appear to be most important for identifying entities with distinct prognoses and clinical behavior. Increasingly, many of these genetically distinct subgroups of leukemia have been found to be closely associated with distinct immunophenotypes. For example, translocations such as t(8;21), t(15;17), and inv(16) in acute myeloid leukemia (AML), and t(1;19) and t(12;21) in acute lymphoblastic leukemia (ALL) have distinctive immunophenotypic profiles. Thus, in addition to classification into differentiation-based subtypes, detailed flow cytometric studies can define complex antigenic profiles that are associated with specific molecular defects and well-defined biology. In summary, multiparameter flow cytometry is an invaluable tool in the diagnosis, classification, and monitoring of patients with acute leukemia. Semin Hematol 38:124-138.

Acute Disease↗

The complex clinical and genetic classification of inherited ataxias. I. Dominant ataxias.

The clinical classification of autosomal dominant cerebellar ataxias (ADCAs) is intricate due to the variable and unpredictable association of signs and symptoms of central nervous system (CNS) and peripheral nervous system (PNS) deterioration during the life of a patient. However, for many purposes, particularly patient management, clinical systematics is the most useful method for labelling patients; in some instances there is no basis for any more fundamental classification of phenotypes. On the other hand, recent molecular-genetic approaches to dominant ataxias have had a profound impact in nosology, diagnostic procedures and the management of patients, since they are based on the fact that all mendelian neurological diseases can be precisely classified according to the locus involved as well as the particular mutant allele at that locus. Therefore, a clinical and genetic classification of dominant ataxias is herewith proposed as the best nosographical choice. Clinical, neuropathological, genetic, and pathogenetic aspects of ADCAs are reviewed and discussed to help the clinical neurologist guide diagnostic procedures and manage ataxic patients.

Cerebellar Ataxia↗

Multivariate statistical classification of noisy images (randomly oriented biological macromolecules).

Multivariate Statistical Analysis (MSA) methods have recently been introduced for analyzing images of biological macromolecules [Van Heel and Frank, Ultramicroscopy 6 (1981) 187]. With these techniques, the significant characteristics of each molecular image can be expressed in merely 2 to 8 factorial coordinate values rather than in the typical 64 X 64 = 4096 pixel grey values that originally described the image. This very large reduction in total amount of data facilitates the understanding of the general behavior of a set of molecular images in terms of classes or of general trends in the data set. The (artificial) intelligence of the procedure, however, lies in the decision-making or classification phase. The theory and philosophy of multivariate statistical classification are reviewed using generalized metrics. Problem-dependent classification rationales are proposed. A set of computer-generated "randomly oriented molecular images" are used to test the classification schemes. This model experiment is a step towards 3D structure analysis of macromolecules based on large numbers of (noisy) electron microscopical images of randomly oriented biological macromolecules.

Animals↗

Molecular characterization of Iranian wheat stripe virus shows its taxonomic position as a distinct species in the genus Tenuivirus.

The full lengths of three genome segments of Iranian wheat stripe virus (IWSV) were amplified by reverse transcription (RT) followed by polymerase chain reaction (PCR) using a primer complementary to tenuivirus conserved terminal sequences. The segments were sequenced and found to comprise 3469, 2337, and 1831 nt, respectively. The gene organization of these segments is similar to that of other known tenuiviruses, each displaying an ambisense coding strategy. IWSV segments, however, are different from those of other viruses with respect to the number of nucleotides and deduced amino acid sequence for each ORF. Depending on the segment, the first 16-22 nt at the 5' end and the first 16 nt at the 3' end are highly conserved among IWSV and rice hoja blanca virus (RHBV), rice stripe virus (RSV) and maize stripe virus (MStV). In addition, the first 15-18 nt at the 5' end are complementary to the first 16-18 nt at the 3' end. Phylogenetic analyses showed close similarity and a common ancestor for IWSV, RHBV, and Echinochloa hoja blanca virus (EHBV). These findings confirm the position of IWSV as a distinct species in the genus Tenuivirus.

Classification↗

[The contribution of molecular genetics to the nosology and diagnosis of neurological disorders of childhood].

INTRODUCTION: The recent spectacular development of molecular genetics has considerably amplified the role of genetics in classification and diagnosis, especially in degenerative diseases but also in other conditions such as developmental brain disorders and predisposition to some acquired diseases (e.g. infections and immunological maladies). OBJECTIVE: The aim of this article is not to review the ever growing list of disorders due to gene abnormalities but to present a few reflections on their consequences and to try to assess their impact on some of the basic concepts in clinical medicine. DEVELOPMENT: The main advantages attributable to the use of molecular genetics are the identification of clinical conditions with different clinical phenomena and due to a single cause and vice versa the existence of clinical conditions in which many different genetic abnormalities can be found. Its main drawbacks derive from its application for establishing nosologic classifications only on the basis of its findings, mainly due to the lack of congruence between phenotype and genotype. CONCLUSION: The information from molecular biology should be integrated with that of other sources in a significant profile, which is the intellectual basis of clinical medicine.

Chromosome Aberrations↗

[Genetic tests for leukemia].

The diagnosis of leukemia is mainly based on chromosome analysis and genetic testing. The analysis of molecular genetics associated with chromosome abnormalities has contributed to new classifications of leukemia. The minimal residual disease(MRD) in its currently accepted application refers to low-level disease detected by quantitative PCR techniques in clinical situations. It is anticipated that efforts in characterization of molecular genetics in leukemia will ultimately translate into better clinical outcomes for patients.

Chromosome Aberrations↗

Myelodysplastic and myeloproliferative disorders in children.

PURPOSE OF REVIEW: Myelodysplastic and myeloproliferative disorders are clonal myeloid malignancies characterized by the triad of a growth advantage of clonal cells, disturbed differentiation and increased apoptosis. The rarity of these disorders in children and the lack of a widely accepted classification have contributed to the paucity of reports on these malignancies in the pediatric literature. A number of significant advances have been achieved in recent years. The present review will focus on diagnostics and therapy. RECENT FINDINGS: International consensus has been achieved on classifying these disorders into three main groups; myelodysplastic syndrome (MDS), myeloid leukemia of Down syndrome (ML-DS) and juvenile myelomonocytic leukemia (JMML). In the last few years we have witnessed important advances, especially regarding the therapy of these disorders, and we have gained insights into the molecular pathogenesis of ML-DS and JMML. SUMMARY: Classification of myelodysplastic and myeloproliferative disorders has been facilitated. Chemotherapy regimens for ML-DS have been reduced, resulting in fewer toxic deaths and improved survival. The results of stem-cell transplantation for MDS and JMML have improved. Insight into the molecular mechanisms involved may open new therapeutic avenues.

Child↗

High-resolution computed tomographic appearance of MALToma of the lung.

MALToma of the lung is rare and advances in molecular techniques have only recently allowed accurate diagnostic classification of the previously termed "pseudolymphomas" by demonstrating that many are monoclonal B-cell proliferations of MALT tissue and therefore true low-grade lymphomas. No significant previous contribution was found in the literature regarding the high-resolution CT appearance (HRCT) of these tumours. We describe the high-resolution CT appearances in five cases presenting to our institution from 1994 to 1997. The HRCT scans (1-mm sections at 10- to 15-mm intervals) were performed as the opacities seen radiographically were thought to be part of a diffuse lung process. In one patient a spiral sequence was performed through the main airway. Multifocal, ill-defined nodules containing air bronchograms were seen in four cases and focal lobar consolidation in one case. Interlobular septal thickening, centrilobular micronodules and bronchial wall thickening were seen in two cases. Mediastinal lymphadenopathy and pleural reaction do not appear to be characteristic features. The appearance of multifocal consolidation is similar to that seen in bronchoalveolar cell carcinoma and cryptogenic organising pneumonia.

Adenocarcinoma, Bronchiolo-Alveolar↗

State of the science in brain tumor classification.

OBJECTIVES: To review the incidence of metastatic and primary brain tumors and the most widely used brain tumor classification systems, and to discuss discoveries advancing the understanding, classification, and grading of selected brain tumor histologies. DATA SOURCES: Journal articles, text books, epidemiologic and statistical reports. CONCLUSION: Recent advances in understanding the molecular biology of brain tumors have shown that molecular and genetic signatures may predict brain tumor behavior and may soon guide tumor classification, diagnosis, and tumor-specific treatment strategies. IMPLICATIONS FOR NURSING PRACTICE: Understanding recent advances in the molecular biology of brain tumors is important because these advances may soon guide treatment decisions. New tumor-specific therapeutic opportunities may improve outcomes as well as the care of persons with brain tumors.

Astrocytoma↗