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PubMed1997

Association of hemorrhoidal disease with diarrheal disorders: potential pathogenic relationship?

UNLABELLED: Despite frequent occurrence of hemorrhoidal disease, its etiology remains controversial. Recent evidence suggests that diarrhea may represent a pathogenic risk factor. The present study examined prevalence of diarrheal disorders in elderly patients with hemorrhoidal disease to provide further insight into its pathogenic mechanisms. METHODS: Using 8.8 million Medicare patients hospitalized in the United States during 1987, the frequency distribution of all three-digit International Classification of Diseases codes was compared in patients with and without hemorrhoidal disease. A more frequent occurrence of a specific disorder in patients with hemorrhoidal disease compared with the general Medicare population suggests that this disorder may be pathophysiologically related or share common etiologic risk factors with hemorrhoidal disease. RESULTS: Strong associations were observed between hemorrhoidal disease and a number of diarrheal disorders, including ulcerative colitis, noninfectious gastroenteritis, and functional diarrhea. Hemorrhoidal disease was likewise closely associated with benign and malignant anorectal neoplasms. CONCLUSIONS: Results of this study must be interpreted with caution because epidemiologic studies cannot establish cause and effect relationships. Nevertheless, these data would seem to further support the pathogenic influence of diarrhea in development of hemorrhoidal disease.

Aged↗
PubMed2002

Molecular epidemiology and immunology of hepatitis B virus infection - an update.

Hepatitis B virus (HBV) continues to be one of the most important viral pathogens in humans. This review provides an update on the molecular epidemiology and immunology of HBV infection. DNA sequencing has allowed replacement of the initial serotypic classification of HBV strains by a more systematic genotype system that currently consists of 7 members (genotypes A-G). More recently, sequence analysis of virus isolates from many individual patients has revealed the occurrence of certain mutational hot spots in the genome, some of which appear to correlate with the patient's immunological and/or disease status; however, cause and effect are not always easily discernible. This holds particularly for the issue of whether virus variants exist that have, per se, an increased pathogenic potential; due to the scarcity of appropriate experimental in vivo models, such hypotheses are difficult to prove. Similarly, because of the compact organization of the HBV genome, almost every single mutation may have pleiotropic phenotypic effects. Nonetheless, there is accumulating evidence that at least some frequently observed mutations are causally related to viral escape from selective pressures, such as the presence of antibodies against dominant B cell epitopes, or drugs that inhibit the viral reverse transcriptase; possibly, this is also true for the cellular immune response. Therefore, despite the availability of an effective prophylactic vaccine, further extensive efforts are required to monitor the emergence of vaccination- and therapy-resistant HBV variants and to prevent their spread in the general population.

Amino Acid Sequence↗
PubMed1980

[A new classification of so-called benign tumors of the bone based on their association with visceral pseudo-tumors].

The combination of benign pseudo-tumors of the bone and visceral lesions are relatively frequent for chondromas, osteomas, fibromas and angiomas, which suggests for this group a pathogenic relationship between the bone lesions and others (dyschromias, endocrinian tumors, leiomyomas, naevus and gliomas) and a common dysembryoplasic origin. In contrast to these " bone hamartomas " there are pseudo-tumoral reactions where associations are exceptional. Also, there are slow tumors, a typical one being the myeloplaxis tumor. This logical classification makes it possible to better understand the pathogeny, the development and the prognosis of the disparate lesion generally described as " benign tumors of the bone ".

Adolescent↗
PubMed1976

Recommendations for the description of species and biotypes of the genus Brucella.

The properties of the genus Brucella are summarized and recommendations made for the definition of species and biotypes within the genus. In the first instance it is recommended that the classification of an organism as a member of the genus should be based on the following criteria: gramnegative coccobacillary morphology, a G + C content for the DNA of 56-58 moles %, a minimum of 90% homology with the DNA of reference strains in hybridization tests, disk electrophoretograms of acid-phenol soluble proteins of identical pattern to reference strains, a cytochrome C absorption spectrum with absorption maxima between 522-530 nm and 552-560 nm, extensive serological cross-reactions of intra-cellular antigens with those of reference strains. Supporting evidence is obtained from cultural, biochemical and pathogenic properties, although variations in these occur within the genus. Subdivision into species is dependent upon principal natural host, oxidative metabolic pattern and phage sensitivity. Classification into biotypes is dependent upon CO2 requirement, H2S production, dye sensitivity and reaction with monospecific antisera to A and M antigens. It is recommended that any organism proposed as a new member of the genus should have characters which approximate the ranges quoted. In all cases comparisons should be made with the established reference/neotype strains.

Antigens, Bacterial↗
PubMed1990

Characterization of dihydrofolate reductase of Pneumocystis carinii and Toxoplasma gondii.

Pneumocystis carinii and Toxoplasma gondii are opportunistic pathogens of immunosuppressed patients that are susceptible to therapy with inhibitors of dihydrofolate reductase (DHFR). The DHFR of these two organisms was characterized to facilitate the identification of more selective inhibitors. Similar to all reported protozoa, T. gondii has a bifunctional enzyme, of 120,000 Da, that possesses both DHFR and thymidylate synthase (TS) activity. Unexpectedly, P. carinii DHFR activity was present on a small molecule, of 26,000 Da. T. gondii DHFR and TS activity coeluted during affinity chromatography using a methotrexate-Sepharose column, whereas P. carinii DHFR and TS activity could be separated by affinity chromatography using the same column. P. carinii DHFR could be easily distinguished from rat DHFR, which is similar in size, by the differences in Km for dihydrofolate (P. carinii, 17.6 +/- 3.9 microM; rat, 4.0 +/- 2.2 microM). Since all protozoa reported have a large molecular weight, bifunctional DHFR, these studies support the classification of P. carinii as a fungus. These studies also provide a basis for the development of more effective therapeutic agents for these pathogens.

Animals↗
PubMed2025

Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria.

PURPOSE: We previously developed an approach to calibrate computational tools for clinical variant classification, updating recommendations for the reliable use of variant impact predictors to provide evidence strength up to Strong. A new generation of tools using distinctive approaches has since been released, and these methods must be independently calibrated for clinical application. METHODS: Using our local posterior probability-based calibration and our established data set of ClinVar pathogenic and benign variants, we determined the strength of evidence provided by 3 new tools (AlphaMissense, ESM1b, and VARITY) and calibrated scores meeting each evidence strength. RESULTS: All 3 tools reached the Strong level of evidence for variant pathogenicity and Moderate for benignity, although sometimes for few variants. Compared with previously recommended tools, these yielded at best only modest improvements in the trade-offs between evidence strength and false-positive predictions. CONCLUSION: At calibrated thresholds, 3 new computational predictors provided evidence for variant pathogenicity at similar strength to the 4 previously recommended predictors (and comparable with functional assays for some variants). This calibration broadens the scope of computational tools for application in clinical variant classification. Their new approaches offer promise for future advancement of the field.

Humans↗
PubMed2002

Molecular phylogenetic study of Theileria sp. (Thung Song) based on the thymidylate synthetase gene.

Theileria type Thung Song is an indigenous hemoparasite of dairy cattle from the south of Thailand. It has previously been classified using the analysis of a comparative set of small subunit ribosomal RNA nucleotide sequences. However, the classification of this parasite is still questionable since the Theileria type Thung Song was located as the intermediate parasite between pathogenic and benign groups. We use the thymidylate synthetase gene (TS) as an alternative for the rapid molecular phylogenetic tree construction of benign Theileria type Thung Song, Theileria sergenti and Theileria buffeli with Babesia bovis as an out-group. The partial nucleotide sequences were determined using PCR, cloning and dideoxy sequencing. The TS nucleotide sequence data were aligned and analyzed by distance and maximum likelihood methods to construct the phylogenetic trees. Bootstrap analysis was used to test the strength of the different phylogenetic reconstructions. All tree-building methods gave similar results. This study shows that T. sergenti and T. buffeli are closely related whereas Theileria type Thung Song is more distantly related.

Animals↗
PubMed2006

GIS, geostatistics, metadata banking, and tree-based models for data analysis and mapping in environmental monitoring and epidemiology.

By the example of environmental monitoring, some applications of geographic information systems (GIS), geostatistics, metadata banking, and Classification and Regression Trees (CART) are presented. These tools are recommended for mapping statistically estimated hot spots of vectors and pathogens. GIS were introduced as tools for spatially modelling the real world. The modelling can be done by mapping objects according to the spatial information content of data. Additionally, this can be supported by geostatistical and multivariate statistical modelling. This is demonstrated by the example of modelling marine habitats of benthic communities and of terrestrial ecoregions. Such ecoregionalisations may be used to predict phenomena based on the statistical relation between measurements of an interesting phenomenon such as, e.g., the incidence of medically relevant species and correlated characteristics of the ecoregions. The combination of meteorological data and data on plant phenology can enhance the spatial resolution of the information on climate change. To this end, meteorological and phenological data have to be correlated. To enable this, both data sets which are from disparate monitoring networks have to be spatially connected by means of geostatistical estimation. This is demonstrated by the example of transformation of site-specific data on plant phenology into surface data. The analysis allows for spatial comparison of the phenology during the two periods 1961-1990 and 1991-2002 covering whole Germany. The changes in both plant phenology and air temperature were proved to be statistically significant. Thus, they can be combined by GIS overlay technique to enhance the spatial resolution of the information on the climate change and use them for the prediction of vector incidences at the regional scale. The localisation of such risk hot spots can be done by geometrically merging surface data on promoting factors. This is demonstrated by the example of the transfer of heavy metals through soils. The predicted hot spots of heavy metal transfer can be validated empirically by measurement data which can be inquired by a metadata base linked with a geographic information system. A corresponding strategy for the detection of vector hot spots in medical epidemiology is recommended. Data on incidences and habitats of the Anophelinae in the marsh regions of Lower Saxony (Germany) were used to calculate a habitat model by CART, which together with climate data and data on ecoregions can be further used for the prediction of habitats of medically relevant vector species. In the future, this approach should be supported by an internet-based information system consisting of three components: metadata questionnaire, metadata base, and GIS to link metadata, surface data, and measurement data on incidences and habitats of medically relevant species and related data on climate, phenology, and ecoregional characteristic conditions.

Databases, Factual↗
PubMed2003

Advantage of rare HLA supertype in HIV disease progression.

The highly polymorphic human leukocyte antigen (HLA) class I molecules help to determine the specificity and repertoire of the immune response. The great diversity of these antigen-binding molecules confers differential advantages in responding to pathogens, but presents a major obstacle to distinguishing HLA allele-specific effects. HLA class I supertypes provide a functional classification for the many different HLA alleles that overlap in their peptide-binding specificities. We analyzed the association of these discrete HLA supertypes with HIV disease progression rates in a population of HIV-infected men. We found that HLA supertypes alone and in combination conferred a strong differential advantage in responding to HIV infection, independent of the contribution of single HLA alleles that associate with progression of the disease. The correlation of the frequency of the HLA supertypes with viral load suggests that HIV adapts to the most frequent alleles in the population, providing a selective advantage for those individuals who express rare alleles.

Amino Acid Motifs↗
PubMed2002

Phylogenetic classification of Bartonella species by comparing groEL sequences.

Bartonella is a bacterial genus classified in the alpha-Proteobacteria on the basis of 165 rDNA sequence comparison. The highly conserved heat-shock chaperonin protein, GroEL, has proved to be a valuable resolving tool to classify ten Bartonella species. The groEL gene was amplified and sequenced from ten Bartonella isolates: Bartonella alsatica, Bartonella vinsonii subsp. arupensis, Bartonella taylorii, Bartonella tribocorum, Bartonella birtlesii, Bartonella henselae Marseille (URLLY8), B. henselae (90-615), B. henselae (Fizz), B. henselae (CAL-1) and B. henselae (SA-2). Then, phylogenetic relationships were inferred between our isolates and eight other species and subspecies from the comparison of both 16S rDNA and groEL sequences using parsimony, neighbour-joining and maximum-likelihood methods. By using groEL sequences, the first reliable classification of most known Bartonella species and subspecies was established. Four strongly supported subgroups were distinguished: firstly, the two human pathogens B. henselae and Bartonella quintana; secondly, a cluster including four rodent isolates, Bartonella elizabethae, B. tribocorum, Bartonella grahamii and B. taylorii; thirdly, a cluster including the B. vinsonii subspecies (B. vinsonii subsp. vinsonii, arupensis and berkhoffii); and lastly, B. birtlesii and 'Bartonella weissi'. 'Bartonella washoensis', B. alsatica, Bartonella doshiae, Bartonella bacilliformis and Bartonella clarridgeiae did not reliably cluster with any other Bartonella species. In addition, the groEL gene was shown to be useful in subtyping six B. henselae isolates into three variants: Houston, Marseille and Fizz.

Amino Acid Sequence↗
PubMed1975

Plaque production by arboviruses in Singh's Aedes albopictus cells.

We report plaquing tests of 124 virus strains, mostly arboviruses of 21 serological groups, in Singh's line of Aedes albopictus cells. Thirty of these plaqued: all were arboviruses of six groups and were known or presumed to be mosquito borne. Failing to plaque were 86 strains of arboviruses, mostly tick borne, two strains of insect pathogens, and six animal viruses not classified as arboviruses. Among mosquito-borne agents, plaquing ability appeared related to serological classification. California group and most A-group viruses failed to plaque, but nearly all members of B and Bunyamwera groups readily plaqued. Within serological group B, 14 of 16 mosquito-borne agents plaqued, but none of 13 tick-borne or vector-unassociated viruses did so. Some implications of these results for recognition and classification of arboviruses are discussed.

Aedes↗
PubMed1989

16S rRNA sequence indicates that plant-pathogenic mycoplasmalike organisms are evolutionarily distinct from animal mycoplasmas.

The plant-pathogenic mycoplasmalike organisms (MLOs) are so named because they lack cell walls. Many features that are essential to a definitive classification remain uncharacterized, because these organisms have resisted attempts at in vitro culturing. To establish the taxonomic position of the MLOs, the DNA region containing the 16S rRNA gene from a representative of the MLOs has been cloned and sequenced. Sequence comparisons indicate that the MLOs are related to Mycoplasma capricolum and that these two bacteria share their phylogenetic origin with Bacillus subtilis. The low G + C content of this gene and features of its deduced secondary structure further support this grouping. However, the presence of a single tRNAIle gene in the spacer between the 16S rRNA and 23S rRNA genes of the MLOs differentiates the MLOs from other representatives of the mycoplasmas, which indicates an early divergence in the evolution of the members of the class Mollicutes. The presence of certain characteristic oligonucleotides in the 16S rRNA sequence indicates that MLOs may be closely related to acholeplasmas.

Animals↗
PubMed2002

Acne vulgaris, I: pathogenesis and diagnosis.

Acne vulgaris is a chronic inflammatory disease of the pilosebaceous units. It is a pleomorphic disorder with multifactorial pathogenesis. The many expressions of acne rarely present a diagnostic challenge, but correct classification of acne is crucial in choosing the appropriate therapies. Although previous research has provided a better understanding of the pathogenic factors, there is still a great deal to be learned.

Acne Vulgaris↗
PubMed1996

Periodontal diseases in children and adolescents: classification, aetiology and management.

The human periodontal diseases are a complex group of disorders that span the entire length of the human life cycle. They are infective in nature, but are mediated by host parasite interactions that are influenced not only by the nature of the pathogens present but also by a variety of underlying immunological and connective tissue anomalies. Thus, on occasion they may reflect systemic disorders that have previously been undiagnosed. As such abnormalities frequently present in childhood or adolescence, knowledge of the potential implications of this broad group of diseases is important. This paper reviews the current classification of childhood periodontal disease and outlines the clinical presentation and management of the more common disorders.

Acute Disease↗
PubMed2003

Update on burning mouth syndrome: overview and patient management.

Burning Mouth Syndrome (BMS) is a chronic pain syndrome that mainly affects middle-aged/old women with hormonal changes or psychological disorders. This condition is probably of multifactorial origin, often idiopathic, and its etiopathogenesis remains largely enigmatic. The present paper discusses several aspects of BMS, updates current knowledge, and provides guidelines for patient management. There is no consensus on the diagnosis and classification of BMS. The etiopathogenesis seems to be complex and in a large number of patients probably involves interactions among local, systemic, and/or psychogenic factors. In the remaining cases, new interesting associations have recently emerged between BMS and either peripheral nerve damage or dopaminergic system disorders, emphasizing the neuropathic background in BMS. Based on these recent data, we have introduced the concepts of "primary" (idiopathic) and "secondary" (resulting from identified precipitating factors) BMS, since this allows for a more systematic approach to patient management. The latter starts with a differential diagnosis based on the exclusion of both other orofacial chronic pain conditions and painful oral diseases exhibiting muco-sal lesions. However, the occurrence of overlapping/overwhelming oral mucosal pathologies, such as infections, may cause difficulties in the diagnosis ("complicated BMS"). BMS treatment is still unsatisfactory, and there is no definitive cure. As a result, a multidisciplinary approach is required to bring the condition under better control. Importantly, BMS patients should be offered regular follow-up during the symptomatic periods and psychological support for alleviating the psychogenic component of the pain. More research is necessary to confirm the association between BMS and systemic disorders, as well as to investigate possible pathogenic mechanisms involving potential nerve damage. If this goal is to be achieved, a uniform definition of BMS and strict criteria for its classification are mandatory.

Age Factors↗
PubMed2006

Microbial exposure assessment of an urban recreational lake: a case study of the application of new risk-based guidelines.

New WHO and Australian guidelines promote a risk-management approach for minimising exposure to pathogens in recreational waters. Between 2003 and 2005, they were applied to Lake Parramatta (10 ha, 450 ML), a potential recreation site in Sydney, Australia. A three stage approach was developed involving (1) initial suitability assessment using historic data, (2) revised suitability assessment based on new data and (3) characterisation of hazardous (especially wet weather) events. Contrary to the stage 1 suitability classification, stage 2 baseline data indicated that during dry weather the lake had water quality sufficient for primary contact recreation (95th percentiles for enterococci = 19 MPN/100, n = 50) and the major pathogen source was wildfowl. Guideline principles provided a rationale for collecting microbiological and geographic data needed to understand local cycles of lake contamination/recovery. The concept of hazardous events was particularly useful. Studies of stormwater events led us to identify a transition point (> 10 mm rainfall in 24 h) where human-faecal pathogen risks increased and access needed to be controlled. Together baseline and event data yielded operational tools (i.e. event detection methods, action triggers, auditing criteria, remediation priorities) for minimising bather exposure.

Clostridium perfringens↗
PubMed2024

WilsonGenAI a deep learning approach to classify pathogenic variants in Wilson Disease.

BACKGROUND: Advances in Next Generation Sequencing have made rapid variant discovery and detection widely accessible. To facilitate a better understanding of the nature of these variants, American College of Medical Genetics and Genomics and the Association of Molecular Pathologists (ACMG-AMP) have issued a set of guidelines for variant classification. However, given the vast number of variants associated with any disorder, it is impossible to manually apply these guidelines to all known variants. Machine learning methodologies offer a rapid way to classify large numbers of variants, as well as variants of uncertain significance as either pathogenic or benign. Here we classify ATP7B genetic variants by employing ML and AI algorithms trained on our well-annotated WilsonGen dataset. METHODS: We have trained and validated two algorithms: TabNet and XGBoost on a high-confidence dataset of manually annotated, ACMG & AMP classified variants of the ATP7B gene associated with Wilson's Disease. RESULTS: Using an independent validation dataset of ACMG & AMP classified variants, as well as a patient set of functionally validated variants, we showed how both algorithms perform and can be used to classify large numbers of variants in clinical as well as research settings. CONCLUSION: We have created a ready to deploy tool, that can classify variants linked with Wilson's disease as pathogenic or benign, which can be utilized by both clinicians and researchers to better understand the disease through the nature of genetic variants associated with it.

Hepatolenticular Degeneration↗