PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “pathogenicity classification”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 163 records · Page 9Linked to original sources
PubMed1996

[Malformations of the nasal fossa and paramedian facial clefts. New perspectives].

Since choanal atresia may be associated with other cranio-facial malformations, including various degrees of nasal fossa malformation, and be a part of paramedian facial clefts, (as described by Tessier), they can be integrated into the larger group of neurocristopathies. We identified four such cases with combined clinical elements corresponding to Tessier's paramedian facial cleft, including eyelid coloboma, mild to severe choanal and nasal fossa anomalies, ethmoidal hypoplasia and anterior skull base malformation, sometimes with proboscis lateralis. These various malformations are due to abnormality of the olfactive placode and the adjacent mesenchyme. These discoveries incited us to elaborate a conception first of all on the pertinent embryology involved, second, to propose a new classification based on anatomical and pathogenic embryological considerations. And finally, since endonasal laser therapy is particularly dangerous in such cases, to propose the use of transpalatal approach to restore choanal permeability. Pediatric ENT surgeons should pay special attention to any small stigmatism of facial cleft when dealing with children affected by choanal atresia.

Abnormalities, Multiple↗
PubMedDate not supplied

[Tympanosclerosis. I: proposed anatomical-surgical classification].

Tyrnpanosclerosis continues to be a clinically and pathogenically controversial topic. The options for dealing with it range from a conservative approach using hearing aids to surgery. With a view to justifying our therapeutic criteria, 29 cases of tympanosclerosis, out of a total of 200 surgical operations for otorrhea, were reviewed. An anatormical-surgical classification was established for use in approaching specific therapy for each particular case.

Cerebrospinal Fluid Otorrhea↗
PubMed1991

Differentiation of pathogenic from nonpathogenic Entamoeba histolytica by restriction fragment analysis of a single gene amplified in vitro.

We previously reported the identification of homologous cDNA clones derived from a pathogenic isolate and a nonpathogenic isolate of Entamoeba histolytica, which had been designated cEh-P1 and cEh-NP1, respectively. Sequence analysis of both clones had revealed 10% nucleic acid substitutions, which were dispersed over the entire sequence. This genetic difference had been found to be conserved between all four pathogenic and all five nonpathogenic laboratory strains of E. histolytica tested. On the basis of nucleic acid substitutions, we have now developed a sensitive assay to distinguish pathogenic from nonpathogenic forms of E. histolytica by using fresh clinical isolates. Comparing the sequence of cEh-P1 and cEh-NP1, we identified a 482-bp segment that contained identical 5' and 3' ends but differed in internal cleavage sites for restriction endonucleases. By using oligonucleotide primers corresponding to the 5' and 3' ends of this segment, the corresponding gene was amplified by the polymerase chain reaction. Endonuclease digestion of the amplified DNA yielded restriction fragments that are characteristic for pathogenic and nonpathogenic forms. This assay allows the detection and classification of fewer than 10 amoebae within a few hours. The differentiation of 48 isolates into pathogenic and nonpathogenic strains by using this method corresponded to the clinical status of the infected individuals and to the classification obtained by isoenzyme determination. The results further support the concept that pathogenic and nonpathogenic strains of E. histolytica constitute distinct subspecies.

Animals↗
PubMed2002

A probabilistic neural network approach for modeling and classification of bacterial growth/no-growth data.

In this paper, we propose to use probabilistic neural networks (PNNs) for classification of bacterial growth/no-growth data and modeling the probability of growth. The PNN approach combines both Bayes theorem of conditional probability and Parzen's method for estimating the probability density functions of the random variables. Unlike other neural network training paradigms, PNNs are characterized by high training speed and their ability to produce confidence levels for their classification decision. As a practical application of the proposed approach, PNNs were investigated for their ability in classification of growth/no-growth state of a pathogenic Escherichia coli R31 in response to temperature and water activity. A comparison with the most frequently used traditional statistical method based on logistic regression and multilayer feedforward artificial neural network (MFANN) trained by error backpropagation was also carried out. The PNN-based models were found to outperform linear and nonlinear logistic regression and MFANN in both the classification accuracy and ease by which PNN-based models are developed.

Bacteria↗
PubMed1983

Interstrain mitochondrial DNA polymorphism detected in Acanthamoeba by restriction endonuclease analysis.

The genus Acanthamoeba includes pathogenic and nonpathogenic strains of amebas with unclear taxonomic and evolutionary relationships. To explore these relationships further, we have examined mitochondrial DNA fragment patterns obtained for 15 Acanthamoeba strains by use of five restriction endonucleases. The mitochondrial DNA molecules were circular, averaging 41.6 +/- 1.5 kilobase pairs. Fragments resulting from endonuclease digestion of the DNA were separated by agarose gel electrophoresis. Ten distinct families of electrophoretic patterns (digestion phenotypes) were observed. Seven phenotypes were found for seven strains considered nonpathogenic or of unknown pathogenicity. Three phenotypes were associated with pathogenic strains. One of these phenotypes included a single pathogenic strain, a second included one pathogen and one strain of unknown pathogenicity, and the third included five pathogenic strains. The latter five were of widespread geographic origin and previously were assigned to two different species. The results suggest that extensive nucleotide sequence diversity occurs among strains from a single species of Acanthamoeba, but that subgroups of strains with similar sequences also occur. Thus, restriction enzyme analysis can identify clusters of strains and may be a useful approach to classification in the genus. Improvements in classification should help clarify relationships among pathogenic and non-pathogenic strains.

Amoeba↗
PubMed2000

Discrimination of the notifiable pathogen Gyrodactylus salaris from G. thymalli (Monogenea) using statistical classifiers applied to morphometric data.

The identification and discrimination of 2 closely related and morphologically similar species of Gyrodactylus, G. salaris and G. thymalli, were assessed using the statistical classification methodologies Linear Discriminant Analysis (LDA) and k-Nearest Neighbours (KNN). These statistical methods were applied to morphometric measurements made on the gyrodactylid attachment hooks. The mean estimated classification percentages of correctly identifying each species were 98.1% (LDA) and 97.9% (KNN) for G. salaris and 99.9% (LDA) and 73.2% (KNN) for G. thymalli. The analysis was expanded to include another 2 closely related species and the new classification efficiencies were 94.6% (LDA) and 98.% (KNN) for G. salaris; 98.2% (LDA) and 72.6% (KNN) for G. thymalli; 86.7% (LDA) and 91.8% (KNN) for G. derjavini; and 76.5% (LDA) and 77.7% (KNN) for G. truttae. The higher correct classification scores of G. salaris and G. thymalli by the LDA classifier in the 2-species analysis over the 4-species analysis suggested the development of a 2-stage classifier. The mean estimated correct classification scores were 99.97% (LDA) and 99.99% (KNN) for the G. salaris-G. thymalli pairing and 99.4% (LDA) and 99.92% (KNN) for the G. derjavini-G. truttae pairing. Assessment of the 2-stage classifier using only marginal hook data was very good with classification efficiencies of 100% (LDA) and 99.6% (KNN) for the G. salaris G. thymalli pairing and 97.2% (LDA) and 99.2% (KNN) for the G. derjavini-G. truttae pairing. Paired species were then discriminated individually in the second stage of the classifier using data from the full set of hooks. These analyses demonstrate that using the methods of LDA and KNN statistical classification, the discrimination of closely related and pathogenic species of Gyrodactylus may be achieved using data derived from light microscope studies.

Animals↗
PubMed2026

TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

Software↗
PubMed1994

[Entamoeba histolytica (Schaudinn 1903) and Entamoeba dispar (E. Brumpt 1925) are 2 different species].

On the basis of epidemiologic and clinical data in humans, and of experimental studies in kittens, E. Brumpt in 1925 showed that Entamoeba histolytica producing quadrinucleate cysts was a complex of 2 species. He differentiated a pathogenic and invasive form, from a non pathogenic and non invasive one that he called Entamoeba dispar. His explanation gained little support until recently, when Sargeaunt reported a study of isoenzyme typing and allow then the classification of amoebae resembling E. histolytica in pathogenic and non pathogenic species. Monoclonal antibodies and PCR have recently been used and have shown to react specifically with the two forms of amoebae. Genetic evidence has also demonstrated that the pathogenic and non pathogenic amoebae represent different species.

Animals↗
PubMed2026

[Genetic and functional characterization of a novel KIT splicing variant in a Chinese three-generation pedigree with piebaldism].

OBJECTIVES: To investigate the genetic etiology of a three-generation pedigree affected with piebaldism. METHODS: Next-generation sequencing and Sanger sequencing were employed to detect and verify gene variants. Bioinformatics tools were used to predict the effects of candidate variants on splicing and protein function. RT-PCR and Sanger sequencing were further performed to validate the impact of the variant on RNA splicing, and homology modeling was applied to predict its effect on the three-dimensional structure of the KIT protein. The pathogenicity of the variant was then classified according to the guidelines of the American College of Medical Genetics and Genomics (ACMG) and the UK Association for Clinical Genomic Science (ACGS). RESULTS: A heterozygous insertion variant near the splice site, c.1990+8_1990+9insTGCACCATTGGAGGTAAA, was identified in the KIT gene in the proband and was found to co-segregate with the phenotype within the family. RT-PCR and cDNA sequencing revealed that this variant led to aberrant splicing during transcription, resulting in a 21 bp in-frame insertion in the mRNA, which encodes an extra 7 amino acids within the tyrosine kinase domain and may thus affect protein function. In silico predictions, together with the experimental findings, supported classification of this variant as likely pathogenic according to relevant variant interpretation guidelines. CONCLUSIONS: The heterozygous splice-site insertion variant KIT:c.1990+8_1990+9insTGCACCATTGGAGGTAAA is the genetic cause of piebaldism in this pedigree.

Genetics diagnosis↗
PubMed1997

The challenge of postoperative infections: does the surgeon make a difference?

Postoperative infections remain a challenge in many surgical procedures despite improved surgical technique and powerful antibiotics. The number of sepsis cases has tripled from 1979 to 1992 due to increased invasive procedures in older and immune-suppressed patients. Increasingly, in recent years, outbreaks of resistant pathogens have been published, provoking the question of how postoperative infections and resistant pathogens should be dealt with. Wound classification and risk stratification were developed to identify patients at risk for postoperative infection. However, other important intrinsic factors of the patient were not included, and further attempts have been made to increase sensitivity and specificity (eg, Study on the Efficacy of Nosocomial Infection Control project, National Nosocomial Infection Surveillance System score); the American Society of Anesthesiologists preoperative assessment score and the operation duration for specific procedures were introduced into the system as risk stratifiers. Advances in immunology have identified new ways in which the surgeon can moderate the immune response (eg, hemorrhage and blood transfusion-induced immune suppression). The increased rate of resistance in enterococci and staphylococci has refocused attention on infection control in surgery. However, there are recent reports from both sides of the Atlantic indicating that guidelines for infection control and antibiotic policy have not become reflected in standard procedures in many hospitals. New antibiotics may be developed, but resistance soon may follow. Sound techniques in surgery, with careful infection control and antibiotic policies, may be the only strategy to prevent further increases in resistance of pathogens in postoperative infections.

Antibiotic Prophylaxis↗
PubMed1981

Early diagnosis and prompt treatment by surgery in Jorge Lobo's disease (keloidal blastomycosis).

In 1931 the Brazilian doctor Jorge Lobo examined a patient from the Amazon Basin who had nodular confluent skin lesions over the lumbosacral region and encountered a new fungus pathogenic for man Paracoccidioides loboi. This classification was based on the morphological aspect of the parasite which was very similar to Paracoccidioides brasiliensis the causative agent of a systemic mycosis Paracoccidioidomycosis or South American Blastomycosis. Other authors use the name Loboa loboi. The final determination of the name must await cultivation of the fungus.

Adult↗
PubMed1988

Infections caused by antibiotic-resistant Corynebacterium group D2.

A coryneform bacteria known as Corynebacterium group D2 pending definitive taxonomic classification, has emerged as a human pathogen. Although first described 16 years ago, the organism has only recently been implicated in clinical infections. It differs from all previously recognized species of Corynebacterium, and in common with Corynebacterium jeikeium exhibits a broad spectrum of antimicrobial resistance, being sensitive to only vancomycin, teicoplanin and some quinolones. The microorganisms is mainly involved in urinary tract infections, and its strong urease activity seems to play an important role in its pathogenicity. Corynebacterium jeikeium and group D2 are very different from the clinical and microbiological point of view. Corynebacterium group D2, like other coryneform bacteria, may be isolated from healthy skin in hospitalized patients, mainly females, while Corynebacterium jeikeium is more prevalent in males. Microbiologists should be aware that such a slow-growing microorganism may be responsible for clinical infections and should not be overlooked in routine cultures of clinical specimens.

Anti-Bacterial Agents↗
PubMed1990

Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level.

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationship among different serovars of the Mycobacterium avium-M. intracellulare complex as well as to define signature nucleotides characteristic for different serovars. In general, the groups defined by rRNA sequencing reflect the classification obtained with sensitin tests and pathogenicity examinations in chickens. Unique 16S rRNA sequence patterns could be defined for (1) M. avium, (2) M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11, (3) M. intracellulare serovars 12, 13, 14, 15, 17, 19 and 20, (4) M. intracellulare serovar 7 and (5) M. intracellulare serovar 18. Phylogenetically, groups 1 and 2 on one hand and groups 3, 4 and 5 on the other hand each share a common ancestor. M. paratuberculosis was indistinguishable from M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11 by this kind of analysis.

Base Sequence↗
PubMed1975

Clinical aspects of bilateral renal dysplasia in children.

Despite recent attempts to improve classification and to provide data on pathogenic mechanisms, there is a paucity of information concerning the clinical aspects of bilateral renal dysplasia. Therefore, the clinical features and long-term prognosis of eight patients with bilateral renal dysplasia have been evaluated. Three important observations were made, namely (1) a large proportion of patients had an impairment of urinary concentration and acidification, (2) the clinical course was characterized by progressive renal deterioration in patients with bilateral involvement, and (3) four children with renal dysplasia had the clinical features of Laurence-Moon-Biedl syndrome.

Adolescent↗
PubMed1992

A cohort study of coagulase negative staphylococcal mastitis in selected dairy herds in Prince Edward Island.

The epidemiology and importance of coagulase negative staphylococcal (CNS) mastitis in Prince Edward Island had not been documented. To investigate this, a cohort of 84 cows at seven farms were quarter sampled eight times over a lactation, commencing with samples taken prior to drying off in the previous lactation. Thirteen species of CNS were isolated. The quarter prevalence of CNS mastitis varied from 4.8% to 6.4% in the first five months of lactation and increased to 14.2 to 16.6% in the last four months of lactation. The geometric mean somatic cell counts (SCC) for quarters infected with CNS and uninfected quarters were 90 x 10(3) and 64 x 10(3) respectively (difference significant at p > 0.005). The two month new infection risk of CNS was 9.0% while the two month elimination risk was 74.4%. Infection with CNS did not alter the risk of subsequent infection with Staphylococcus aureus. The results from this project support the classification of CNS as a minor pathogen in mastitis control programs.

Animals↗
PubMed1980

[Cephalic neural crests and disorders of craniofacial morphogenesis. Neurocristopathies (author's transl)].

To establish the pathogenicity, and attempt to define a classification of craniofacial malformations is a difficult task, both in animals and humans. Mention is often made of the classification developed by Paul Tessier, which according to this author "is neither based on a theory nor on an embryonic definition. It is the by-product of anatomical findings during clinical examination and operative dissections" (31). The authors propose an embryologic classification of facial malformations, based on disorders of embryonic development of cells derived from the neural crests (NC) of cephalic origin, and constituting the craniofacial ectomesenchyme. The importance of the cephalic NC derivatives in craniofacial morphogenesis is stressed, and the principal malformations of the cephalic shelf outlined, as a function of disorders occurring during the formation of the NC; migrations, proliferation, and differentiation of their derivatives. The main objective of this study was to formulate pathogenetic hypotheses, to propose a classification, and to stimulate interest in further studies in the realm of physiological and pathological craniofacial morphogenesis.

Bone Diseases, Developmental↗
PubMed2019

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.

Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.

Child↗