Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “pathogenicity 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 199 records · Page 11Linked to original sources
PubMed1996

[Proposal of a new topographic classification of mandibular fractures].

There has been a certain amount of confusion in publications concerning fractures of the mandible due to the lack of consensus on classification. Starting with the embryological, anatomic, biomechanical, pathogenic and epidemiological features of these fractures, we propose a new terminology and a new distribution of the units and subunits of the mandible in traumatology. The main point is to incorporate the angle subunit into the ramus unit.

Adult↗
PubMed1991

Protein pI alteration related to strain variation of infectious bronchitis virus, an avian Coronavirus.

Viral proteins of two strains of infectious bronchitis virus (IBV), which have different tissue trophism and serology, were separated on the basis of their isoelectric points (pI). The viruses have four structural proteins; the protein of greatest serological importance is found at the peplomer tip. The viral structural proteins separated by isoelectric focusing were identified by comparison to SDS-PAGE separations. Three protein bands were identical in pI and one protein band showed a difference in pI between strains. When the renatured viral proteins were Western blotted and reacted with strain-specific antiserum, antigen-antibody complexing was seen only at points corresponding to the strain-specific variant bands. For IBV strain Mass-41, antigen-antibody complexing occurred at a pI of 6.8, and, for IBV strain Ark-99, at 7.2. No cross reaction of antisera was observed for either strain. Since tissue affinities are a function of the viral peplomer-mediated attachment of virus to cells and are often directly related to pathogenicity, it appears that altered pathogenicity of strains of IBV may be detected by alteration of pI of the proteins. Classification by pI of proteins of at least the smaller viruses allows untypeable, highly pathogenic or persistent strains of these viruses to be characterized on the basis of variant proteins.

Antibodies, Viral↗
PubMed2025

Distinct rates of VUS reclassification are observed when subclassifying VUS by evidence level.

PURPOSE: Genetic testing commonly yields a plethora of variants of uncertain significance (VUS) that can lead to ongoing uncertainty for patients and their caregivers. Although all VUS hold uncertainty, some VUS have more evidence in support of pathogenicity, whereas others have more evidence of a benign role. Sharing these nuances can help guide the investment in follow-up clinical and research investigations and may, at times, influence medical decision making despite appreciated uncertainty. METHODS: Four clinical laboratories have been subclassifying VUS to help prioritize investigation and guide reporting decisions. Each laboratory developed a distinct approach for how these subclasses are used in their laboratories and, in some cases, displayed on reports. We examined the composition of each laboratory's VUS subclasses and the likelihood variants from each subclass were reclassified toward pathogenic or benign. RESULTS: We found that variants in the lowest subclass of VUS were never reclassified as likely pathogenic or pathogenic, whereas those in the highest subclass were much more likely to be reclassified as pathogenic or likely pathogenic. CONCLUSION: Given that forthcoming professional guidance in variant classification will advise the use of VUS subclasses, the experience of our laboratories in using VUS subclasses can inform future practices.

Humans↗
PubMedDate not supplied

Subgenus systematics of Acanthamoeba: four nuclear 18S rDNA sequence types.

Classification of Acanthamoeba at the subgenus level has been problematic, but increasing reports of Acanthamoeba as an opportunistic human pathogen have generated an interest in finding a more consistent basis for classification. Thus, we are developing a classification scheme based on RNA gene sequences. This first report is based on analysis of complete sequences of nuclear small ribosomal subunit RNA genes (Rns) from 18 strains. Sequence variation was localized in 12 highly variable regions. Four distinct sequence types were identified based on parsimony and distance analyses. Three were obtained from single strains: Type T1 from Acanthamoeba castellanii V006, T2 from Acanthamoeba palestinensis Reich, and T3 from Acanthamoeba griffini S-7. T4, the fourth sequence type, included 15 isolates classified as A. castellanii, Acanthamoeba polyphaga, Acanthamoeba rhysodes or Acanthamoeba sp., and included all 10 Acanthamoeba keratitis isolates. Interstrain sequence differences within T4 were 0%-4.3%, whereas differences among sequence types were 6%-12%. Branching orders obtained by parsimony and distance analyses were inconsistent with the current classification of T4 strains and provided further evidence of a need to reevaluate criteria for classification in this genus. Based on this report and others in preparation, we propose that Rns sequence types provide the consistent quantititive basis for classification that is needed.

Acanthamoeba↗
PubMed1985

Classification and pathogenesis of vulvovaginal candidiasis.

Although candidiasis of the female genital tract is one of the most common of the vaginitides, it is a poorly understood disease entity. Vulvovaginal candidiasis is a monoetiologic disease, but the pathways by which pathogenic expression is attained are sufficiently divergent to constitute a classification schema that influences therapy. For selection of appropriate therapy, the following three broad categories are proposed: (1) primary candidiasis, (2) antibiotic-induced candidiasis, and (3) systemically induced candidiasis.

Anti-Bacterial Agents↗
PubMed1980

Persistent hog cholera infection detected during virulence typing of 135 field isolates.

During the hog cholera (HC) eradication program in the United States, 135 field isolates were characterized by inoculation into specific-pathogen-free pigs. This gave origin to the classification of 61 (45%) as high virulent, 37 (27%) as low virulent, 29 (22%) as avirulent or immunizing, and 8 (6%) as capable of causing persistent infection. The persistent infections caused by the eight isolates were of long durtion, lasting in one instance to 152 days. The persistently infected pigs remained relatively free of clinical signs of HC but had high concentrations of HC virus (HCV) in their blood. When 6 of these pigs were given a second inoculation (with the virulent Ames strain of HCV), 2 died while the health status of 4 remained unchanged.

Animals↗
PubMed2025

NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.

MOTIVATION: Oncoviruses, pathogens known to cause or increase the risk of cancer, include both common viruses such as human papillomaviruses and rarer pathogens such as human T-lymphotropic viruses. Computational methods for detecting viral DNA from data acquired by modern DNA sequencing technologies have enabled studies of the association between oncoviruses and cancers. Those studies are rendered particularly challenging when multiple species of oncovirus are present in a tumor sample. In such scenarios, merely detecting the presence of a sequencing read of viral origin is insufficiently informative-instead, a more precise characterization of the viral content in the sample is required. RESULTS: We address this need with NextVir, to our knowledge the first multi-class viral classification framework that adapts genomic foundation models to detecting and classifying sequencing reads of oncoviral origin. Specifically, NextVir explores several foundation models-DNABERT-S, Nucelotide Transformer, and HyenaDNA-and efficiently fine-tunes them to enable accurate identification of the sequencing reads' origin. The results demonstrate superior performance of the proposed framework over existing deep learning methods and suggest downstream potential for foundational models in genomics.

Humans↗
PubMed1994

DNA probe-based classification of Simulium damnosum s. l.-borne and human-derived filarial parasites in the onchocerciasis control program area.

The development of polymerase chain reaction-based methods using strain- and species-specific DNA probes for Onchocerca volvulus has permitted classification of individual parasites from every stage of the parasite's life cycle. This technology has been applied on a large scale basis by Onchocerciasis Control Program (OCP) in West Africa. The primary objective of the OCP in using the DNA probes was to obtain accurate estimates of the annual transmission potential of the blinding strain of O. volvulus. The DNA probe classification of larvae collected throughout the OCP area demonstrated that larvae of less pathogenic strains of O. volvulus and other filarial parasites carried by Simulium damnosum s.l. have resulted in a significant overestimation of the annual transmission potential for blinding onchocerciasis. This effect is particularly pronounced along the southern border of the OCP, where the blinding and less pathogenic strains of O. volvulus coexist, and in the north of the control area, where animal parasites, particularly O. ochengi, may even predominate. A second objective of the OCP in applying the DNA probe technology was to determine the distribution of blinding and less pathogenic O. volvulus in infected individuals along the southern border of the control area. Results obtained from these studies have generally confirmed the distribution pattern established by previous epidemiologic studies. In addition, DNA probe classifications have demonstrated that in areas where the blinding and less pathogenic strains of O. volvulus coexist, a single individual may simultaneously be infected with both strains of the parasite.

Africa, Western↗
PubMed1994

From shaman to human clinical trials: the role of industry in ethnobotany, conservation and community reciprocity.

Shaman Pharmaceuticals is a development-stage company engaged in developing traditional pharmaceuticals identified through a discovery process focused on isolating active compounds from tropical plants with a history of medicinal use. This process has resulted in two products in clinical trials: Provir, an oral product for the treatment of respiratory viral infections, and Virend, a topical antiviral product for the treatment of herpes. Shaman's drug-discovery process targets specific plants that have been used for medicinal purposes by native peoples. By integrating the sciences of ethnobotany, medicine and plant natural product chemistry, Shaman has been able to achieve time and cost savings for the identification of active compounds and preclinical development of its initial products. Numerous drugs have entered the international pharmacopoeia via the study of ethnobotany and traditional medicine. Two important elements of this approach to drug discovery are the percentage of plants that show activity against specific viral pathogens and the correlation between the folk therapeutic classification of plants used and the percentage of those plants that have shown activity in our antiviral screens. Conservation and direct reciprocity to indigenous communities are important features of Shaman Pharmaceuticals' drug-discovery process.

Clinical Trials as Topic↗
PubMed1992

Potyviruses, chaos or order?

At first potyviruses were easily distinguished by biological and serological properties because only a few were known and information on their host ranges was limited. The first evidence of serological cross reaction between two of these viruses was reported in 1951 and was further corroborated for three obviously distinct members of the group in 1960. In 1968 attention was drawn to the fact that some legume and non-legume potyviruses have much wider host ranges than previously known and that within the potyvirus group there is as much biological variation within viruses and overlap between viruses as there is in serology. The concept of continuity within the group was soon supported by others and became known as the "continuum hypothesis." Results with highly sensitive serological methods using polyclonal antisera were conflicting, and nucleic acid hybridization techniques did not unambiguously discriminate between potyviruses. Recent results, obtained with antibodies directed toward epitopes located in the N-termini of the coat proteins of potyviruses, suggest that there are ways to more definitely group strains of one potyvirus and distinguish them from other potyviruses. However, there are exceptions to this rule, as in the case of bean yellow mosaic virus and clover yellow vein virus which are clearly distinct in host range, inclusion bodies, and migration velocity of coat protein, but which still react with antibodies to the N-terminal epitopes of one virus. So the question remains of whether coat-protein properties, especially the serological reactivity of N-termini, which do not alter overall virus integrity when lost, sufficiently represent the genome of a pathogenic virus entity as a single criterion for classification.

Capsid↗
PubMed1987

Early evaluation of coagulase negative staphylococcus in blood samples of intensive care unit patients. A clinically uncertain judgement.

Of 2160 intensive care unit patients, 36 patients with positive blood cultures had coagulase-negative staphylococcus in one blood bottle, whereas the organism was present in two or more bottles in 38 cases. The groups were not significantly different in 27 clinical variables, obtained at the time of their first positive blood culture. There was also no significant difference in the antimicrobial sensitivities. No initial clinical data supported the classification of coagulase-negative staphylococcus as either pathogen or contaminant. When the 74 patients with blood culture positive coagulase-negative staphylococcus were compared with three "control groups" ("absent septicemia," "probable septicemia" and "proven septicemia") they were not different from those with "probable septicemia." A discriminant analysis was performed comparing patients with "absent septicemia" and with "proven septicemia" in an attempt to classify patients with isolates of coagulase-negative staphylococcus in one of these groups at an early stage. Patients with two or more positive blood cultures were not statistically classified more frequently as septicemic than patients with one blood bottle positive for this organism. However, patients categorized as septicemic had a significantly higher mortality (59%) than those classified as non-septicemic (35%) (p less than 0.05).

Coagulase↗
PubMed2001

[Therapy of prostatitis syndrome].

The chronic prostatitis syndrome is a multifactorial disease of mainly unknown etiology. Quite different therapeutic options are therefore recommended. According to the new NIH classification only in acute and chronic bacterial prostatitis pathogens can be cultured. A long-term antimicrobial therapy, mainly with fluoroquinolones, is therefore recommended. Most of the patients, however, suffer from a chronic pelvic pain syndrome (CPPS) which can be subdivided into an inflammatory and a non-inflammatory CPPS. Whether the inflammatory CPPS is an infectious disease, remains uncertain. An antibiotic therapy therefore is not the first choice. Several patients, however, have been improved by such a therapy, especially in combination with alpha-receptor blockers. In case of proven or suspected functional obstruction of the bladder neck long-term treatment with relatively high dosages of alpha-receptor blockers is recommended. In case of failure other treatment modalities, including psychosomatics, may be applied, of which usually only results of sporadic reports but not of controlled studies are available. It is important, however, to keep the patient fully informed about the diagnostic and therapeutic problems not to interfere with a trustful therapist-patient relationship.

Adrenergic alpha-Antagonists↗
PubMed1997

Maternal diabetes and fetal malformations: a case associating cardiovascular, facial and skeletal malformations.

Maternal diabetes is known to be a condition associated with a high frequency of fetal malformations. However, pathogenic factors for these malformations and their possible classification into different entities are not yet well established. We present the case of an infant born to a diabetic mother and affected by several malformations. This report consolidates different hypotheses put forward in recent years.

Abnormalities, Multiple↗
PubMed1993

Pathogenetic differences between coxsackie A and B virus infections in newborn mice.

Coxsackieviruses are divided into A and B subgroups on the basis of their pathogenicity in newborn mice. Although used in the classification of these viruses, our understanding of the details of the infection is incomplete due to the lack of sensitive and specific techniques to localize the viruses in affected tissue. We have used in situ hybridization to detect coxsackievirus genomes in tissues of newborn mice after infection by five serotypes (A2, A9, A21, B3 and B4) through different administration routes. Our results indicate that coxsackie A viruses are able to affect both skeletal and heart muscle while the coxsackievirus B subgroup infects a wide range of tissues. In addition to striated muscle these include central nervous system, liver, exocrine pancreas and brown fat. This model will make it possible to analyze molecular factors determining tissue tropism.

Animals↗
PubMed2002

Postoperative mediastinitis in cardiac surgery - microbiology and pathogenesis.

OBJECTIVE: During 1992-2000, postoperative mediastinitis developed after 126 (1.32%) of 9557 consecutive cardiac surgery procedures. The study was done to describe the variation in clinical characteristics and microbiological etiology in mediastinitis. METHODS: The records of 126 cases of postoperative mediastinitis were reviewed. RESULTS: The median time from operation to the development of mediastinitis was 7 days. Sternal dehiscence was seen in 86 patients (68%). Coagulase negative staphylococci (CNS) were isolated in 46% of the cases with a verified microbiological etiology, Staphylococcus aureus in 26% and gram-negative bacteria in 18%. CNS were more frequently isolated in patients with sternal dehiscence (44/80, 55%) than in patients with stable sternum (10/38, 26%) (P=0.003). However, S. aureus was more frequent in patients with stable sternum (18/38, 47%) than in patients with sternal dehiscence (13/80, 16%) (P<0.001). High body mass index was associated with coagulase negative staphylococci (P<0.001) and with sternal dehiscence (P=0.008). Chronic obstructive pulmonary disease was also associated with sternal dehiscence (P<0.001) and with coagulase negative staphylococci (P=0.04). Patients who had been reoperated before onset of mediastinitis tended to have an increased risk for a gram-negative etiology (32 vs. 15% in patients not reoperated, P=0.06). The overall 90-day all cause mortality in patients with mediastinitis was 19%. High age, need for reoperation before mediastinitis, and a long primary operation time was associated with increased mortality (P=0.02, P=0.007 and P=0.001, respectively). No specific bacterial etiology was associated with increased mortality nor was the presence of bacteriemia. CONCLUSIONS: Three different types of postoperative mediastinitis can be distinguished: (1) mediastinitis associated with obesity, chronic obstructive pulmonary disease, and sternal dehiscence, typically caused by coagulase negative staphylococci; (2) mediastinitis following peroperative contamination of the mediastinal space, often caused by S. aureus, and (3) mediastinitis mainly caused by spread from concomitant infections in other sites during the postoperative period, often caused by gram negative rods. The proposed classification of mediastinitis into three groups with different pathogenic mechanisms may be useful in understanding which prophylactic counter measures have the potentials to be effective in a given situation.

Adult↗
PubMed2001

Eccrine syringofibroadenoma: case report and review of the literature.

Eccrine syringofibroadenoma (ESFA) is a rare disorder that shows differentiation toward eccrine sweat apparatus. There is a controversy concerning the pathogenesis and differentiation of this tumour. We report a case of ESFA in a 63-year-old Japanese man. We review the literature presenting a classification, including a newly reported subtype. Clinically and pathogenically, ESFA is probably a group of heterogeneous disorders.

Adenoma, Sweat Gland↗
PubMed1984

[Noninvasive tomographic measurement of regional cerebral blood flow].

The measurement of the regional cerebral bloodflow by means of the dynamic single-photon-emission-computed tomography is a method of examination which is completely free of risk for the patient, causes no inconvenience and can be repeated whenever it seems necessary. This method gives a quantitative explanation for the distribution of the effective cerebral perfusion and can only be substituted by the very complicated positron-emission-computed tomography. As well as the exact assessment of the hemodynamic relevance of cerebral vascular disease, this method enables us to prove whether or not in various types of psychiatric disorders an interference in the regional perfusion exists. This method can also contribute to the clarification of pathogenic mechanisms, as well as to the nosological classification of specific psychopathological conditions.

Adult↗
PubMed1998

Arthritis due to mycobacterium fortuitum.

Mycobacterium fortuitum is classified as a rapidly growing mycobacterium (RGM) according to the Runyon classification. RGM are increasingly being recognized as human pathogens. Joint infection due to M. fortuitum is a rare, but serious disease. This report describes a patient with acquired immunodeficiency syndrome (AIDS) and septic arthritis of the knee due to M. fortuitum in a previously normal joint with no history of surgery or intra-articular injections.

Acquired Immunodeficiency Syndrome↗