Effect of reclassification of chloracne cases.
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Acne Vulgaris↗
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Reclassification of lupus glomerulonephritis: back to the future.
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Forecasting↗
Risk-informed radioactive waste classification and reclassification.
Radioactive waste classification systems have been developed to allow wastes having similar hazards to be grouped for purposes of storage, treatment, packaging, transportation, and/or disposal. As recommended in the National Council on Radiation Protection and Measurements' Report No. 139, Risk-Based Classification of Radioactive and Hazardous Chemical Wastes, a preferred classification system would be based primarily on the health risks to the public that arise from waste disposal and secondarily on other attributes such as the near-term practicalities of managing a waste, i.e., the waste classification system would be risk informed. The current U.S. radioactive waste classification system is not risk informed because key definitions--especially that of high-level waste--are based on the source of the waste instead of its inherent characteristics related to risk. A second important reason for concluding the existing U.S. radioactive waste classification system is not risk informed is there are no general principles or provisions for exempting materials from being classified as radioactive waste which would then allow management without regard to its radioactivity. This paper elaborates the current system for classifying and reclassifying radioactive wastes in the United States, analyzes the extent to which the system is risk informed and the ramifications of its not being so, and provides observations on potential future direction of efforts to address shortcomings in the U.S. radioactive waste classification system as of 2004.
Decision Making↗
Characterization and reclassification of titanium dioxide-related pulmonary lesions.
OBJECTIVE: Using current diagnostic criteria, this work summarizes the microscopic review of 16 proliferative squamous lesions, previously diagnosed as cystic keratinizing squamous cell carcinoma, in the lungs of rats from a 2-year inhalation study with pigment-grade titanium dioxide particles. METHODS: In the aftermath of two international pathology workshops designed, in part, to establish histological criteria for classifying pulmonary keratin lesions, these lesions were evaluated by four pathologists using current diagnostic criteria. RESULTS: Unanimous agreement was reached as to the diagnosis of each of the lesions. Two of the lesions were diagnosed as squamous metaplasia and one as a poorly keratinizing squamous cell carcinoma. The remaining 13 lesions were diagnosed as non-neoplastic pulmonary keratin cysts. CONCLUSIONS: These keratin cysts are a species-specific lesion that is unique to the rat lung under conditions of particle overload exposure.
Animals↗
Histological reclassification of lupus nephritis.
PURPOSE OF REVIEW: This review examines the progress in clinico-pathologic studies following the publication of the International Society of Nephrology (ISN)/Renal Pathology Society (RPS) 2003 classification of lupus nephritis. Major features in this classification system include non-ambiguous diagnostic criteria based on quantitative assessment of histological abnormalities and further classification of Class IV lesions with regard to the predominance of segmental or global lesions. RECENT FINDINGS: The new classification has been applied in two recent retrospective studies. Key findings included improved diagnostic concordance compared with the World Health Organization classification for lupus nephritis, but no observable difference in renal outcome between Classes IV-S and IV-G during short-term follow up. The data also suggested that fibrinoid necrosis and interstitial inflammation may be more prominent in the IV-S group. While the new classification stipulates the description of individual lesions indicating activity or chronicity, it has not devised new composite histological scores. In this regard, recent studies on novel histological indices of lupus renal biopsies based on digital imaging and computerized data analysis have demonstrated a better correlation with clinical parameters. SUMMARY: The ISN/RPS 2003 classification facilitates accurate communication between pathologists and clinicians. It also provides a clear framework for standardization, upon which the clinical and pathogenetic significance of individual lesions and histological subtypes require further elucidation.
Humans↗
Prognosis after hepatic resection for stage IVA hepatocellular carcinoma: a need for reclassification.
OBJECTIVE: To evaluate whether the prognosis of the four categories of patients with hepatocellular carcinoma (HCC) classified as stage IVA in the tumor-node-metastasis (TNM) classification of the International Union Against Cancer (UICC) is homogeneous. SUMMARY BACKGROUND DATA: Hepatic resection has been proposed as the treatment of choice for patients with TNM stage IVA HCC, which consists of four different categories. It is unknown whether the prognosis of the four categories of patients is homogeneous. METHODS: Clinicopathologic and follow-up data of 106 patients with resection of stage IVA HCC from 1989 to 2000 were prospectively collected. Survival results of the four categories of stage IVA patients were compared. RESULTS: Among stage IVA patients, survival was significantly worse in those with tumors involving a major branch of the portal or hepatic veins than in those with tumors invading adjacent organs, bilobar multiple tumors, or perforated visceral peritoneum. There were no significant differences in survival among the latter three groups. By Cox regression analysis, invasion of the portal or hepatic veins and presence of cirrhosis were independent adverse prognostic factors of overall survival among stage IVA patients, and invasion of the portal or hepatic veins was the only significant adverse prognostic factor of disease-free survival. CONCLUSIONS: The prognosis of the four categories of patients with stage IVA HCC under the current UICC TNM staging was not homogeneous. A refined classification of stage IV HCC is needed to take into consideration the worse prognosis associated with tumor invasion of a major branch of the portal or hepatic veins.
Analysis of Variance↗
The reclassification of asthma based on subphenotypes.
PURPOSE OF REVIEW: Despite asthma being widely regarded as a heterogeneous disease, a consensus for an accurate system of classification has not been agreed. Recent studies have suggested that the recognition of subphenotypes of asthma based on the pattern of airway inflammation may be particularly useful in increasing our understanding of the disease. The present review discusses the important literature in this field, placing current work in its historical context. RECENT FINDINGS: The use of noninvasive markers of airway inflammation has suggested the presence of four distinct phenotypes: eosinophilic, neutrophilic, mixed inflammatory and paucigranulocytic asthma. Recent studies suggest that these subgroups may differ in their aetiology, immunopathology and response to treatment. Several studies have focused on refractory asthma as a distinct phenotype with evidence of a more distal pattern of airway inflammation and of upregulation of the tumour necrosis factor-alpha axis. Finally, novel treatment approaches targeted at specific patterns of airway inflammation are emerging, making an appreciation of subphenotypes particularly relevant. SUMMARY: The present review will discuss limitations to current classification systems, identify key current studies based on identifying inflammatory subphenotypes and provide suggestions for a novel approach that may further improve our understanding in this area.
Animals↗
Reclassification of Treponema hyodysenteriae and Treponema innocens in a new genus, Serpula gen. nov., as Serpula hyodysenteriae comb. nov. and Serpula innocens comb. nov.
The intestinal anaerobic spirochetes Treponema hyodysenteriae B78T (T = type strain), B204, B169, and A-1, Treponema innocens B256T and 4/71, Treponema succinifaciens 6091T, and Treponema bryantii RUS-1T were compared by performing DNA-DNA reassociation experiments, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of cell proteins, restriction endonuclease analysis of DNA, and 16S rRNA sequence analysis. DNA-DNA relative reassociation experiments in which the S1 nuclease method was used showed that T. hyodysenteriae B78T and B204 had 93% sequence homology with each other and approximately 40% sequence homology with T. innocens B256T and 4/71. Both T. hyodysenteriae B78T and T. innocens B256T exhibited negligible levels of DNA homology (less than or equal to 5%) with T. succinifaciens 6091T. The results of comparisons of protein electrophoretic profiles corroborated the DNA-DNA reassociation results. We found high levels of similarity (greater than or equal to 96%) in electrophoretic profiles among T. hyodysenteriae strains, moderate levels of similarity (43 to 49%) between T. hyodysenteriae and T. innocens, and no detectable similarity between the profiles of either T. hyodysenteriae or T. innocens and those of T. succinifaciens, T. bryantii, and Escherichia coli. Restriction endonuclease analysis of DNA was not useful in assessing genetic relationships since there was heterogeneity even between strains of T. hyodysenteriae. Partial 16S rRNA sequences of the intestinal spirochetes were determined by using a modified Sanger method and were compared in order to evaluate the phylogenetic relationships among these and other spirochetes.(ABSTRACT TRUNCATED AT 250 WORDS)
Bacterial Proteins↗
Reclassification of two strains of Arthrobacter oxydans and proposal of Arthrobacter nicotinovorans sp. nov.
Arthrobacter oxydans DSM 419 and DSM 420 have chemical and microbiological properties that are consistent with assignment to the genus Arthrobacter. Both organisms have the lysine-alanine-threonine-alanine peptidoglycan type. DNA-DNA pairing studies indicated that A. oxydans DSM 419 should be reclassified as Arthrobacter ureafaciens and that A. oxydans DSM 420T forms the nucleus of a distinct genomic species. We propose that A. oxydans DSM 420 should be reclassified as Arthrobacter nicotinovorans sp. nov. The type strain is strain DSM 420.
Amino Acid Sequence↗
Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov.
A new Rhizobium species that nodulates Phaseolus vulgaris L. is proposed on the basis of a sequence analysis of 16S ribosomal DNA. This taxon, Rhizobium etli sp. nov., was previously named Rhizobium leguminosarum biovar phaseoli (type I strains) and is characterized by the capacity to establish an effective symbiosis with bean plants, the reiteration of the nitrogenase structural genes, the organization of the common nodulation genes into two separate transcriptional units bearing nodA and nodBC, the presence of the polysaccharide inhibition gene, psi, and the 16S ribosomal DNA sequence. An analysis of the sequence of a fragment of the 16S rRNA gene shows that this gene is quite different from the gene of R. leguminosarum. In addition, all R. etli strains have identical sequences. We describe these analyses and discuss additional evidence supporting our proposal.
Base Sequence↗
Chemotaxonomic analyses of Bacteroides gracilis and Bacteroides ureolyticus and reclassification of B. gracilis as Campylobacter gracilis comb. nov.
The cellular fatty acids, respiratory quinones, and proteins of the generically misnamed taxa Bacteroides gracilis and Bacteroides ureolyticus were analyzed and compared with the corresponding chemotaxonomic features of their closest relatives, the campylobacters. Our results and previously published data for genotypic and phenotypic characteristics were used in a polyphasic approach to reconsider the classification of these organisms. We transfer B. gracilis to the genus Campylobacter as Campylobacter gracilis comb. nov. B. ureolyticus can be considered a campylobacter on genotypic grounds; in contrast, the proteolytic metabolism and fatty acid components of this taxon exclude it from the genus Campylobacter. We prefer to consider this taxon a species incertae sedis pending the isolation and characterization of additional B. ureolyticus-like bacteria.
Bacterial Proteins↗
Phylogenetic analysis of Ruminococcus flavefaciens, the type species of the genus Ruminococcus, does not support the reclassification of Streptococcus hansenii and Peptostreptococcus productus as ruminococci.
The 16S rRNA gene sequence of the type strain of Ruminococcus flavefaciens, the type species of the genus Ruminococcus, was determined by PCR direct sequencing. A comparative sequence analysis showed that R. flavefaciens is phylogenetically related to a small cluster (cluster IV of Collins et al. [M. D. Collins, P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994]) of organisms which includes several Clostridium and Eubacterium species. R. flavefaciens was found to be phylogenetically only remotely related to Ruminococcus gnavus, Ruminococcus torques, Peptostreptococcus productus, and Streptococcus hansenii. These findings demonstrate that the genus Ruminococcus is not a monophyletic group, and the proposed transfer of P. productus and S. hansenii to this genus (T. Ezaki, N. Li, Y. Hashimoto, H. Miura, and H. Yamamoto, Int. J. Syst. Bacteriol. 44:130-136, 1994) is not supported.
Base Sequence↗
Reclassification of Oribaculum catoniae (Moore and Moore 1994) as Porphyromonas catoniae comb. nov. and emendation of the genus Porphyromonas.
A partial 16S rRNA gene sequence of the type strain of Oribaculum catoniae was determined by using PCR direct sequencing. A comparative sequence analysis demonstrated that this species, although saccharolytic, is phylogenetically a member of the genus Porphyromonas. On the basis of the phylogenetic and phenotypic distinctiveness of O. catoniae, we formally propose that this species should be reclassified in the genus Porphyromonas catoniae comb. nov. An emended description of the genus Porphyromonas is presented.
Bacteroidaceae↗
Phylogenetic inferences and taxonomic consequences of 16S ribosomal DNA sequence comparison of Chromohalobacter marismortui, Volcaniella eurihalina, and Deleya salina and reclassification of V. eurihalina as Halomonas eurihalina comb. nov.
The phylogenetic positions of the moderately halophilic bacteria Chromohalobacter marismortui, Volcaniella eurihalina, and Deleya salina were determined by PCR amplification of rRNA genes and direct sequencing. The resulting data were compared with data for other bacteria obtained from 16S rRNA sequence databases. C. marismortui, V. eurihalina, and D. salina clustered phylogenetically within the gamma subclass of the Proteobacteria and are closely related to other species on the Halomonas-Deleya branch. C. marismortui belongs in the family Halomonadaceae and has the characteristic 16S rRNA signatures defined for this family, including the distinctive cytosine residue at position 486 found in all members of the Halomonadaceae. V. eurihalina is closely related to the type species of the genus Halomonas, Halomonas elongata, and we formally propose that V. eurihalina should be transferred to the genus Halomonas as Halomonas eurihalina comb. nov. The type strain of this species is strain F9-6 (= ATCC 49336). D. salina is not as closely related to other species belonging to the Halomonas-Deleya complex, but is more closely related to Halomonas elongata than to Deleya aquamarina, the type species of the genus Deleya. A polyphasic approach will be necessary to determine the natural taxonomic positions of the species belonging to the genera Halomonas and Deleya, as well as C. marismortui, V. eurihalina, Halovibrio variabilis, and Paracoccus halodenitrificans.
Base Sequence↗
Reclassification of Micrococcus agilis (Ali-Cohen 1889) to the genus Arthrobacter as Arthrobacter agilis comb. nov. and emendation of the genus Arthrobacter.
Phylogenetic evidence derived from a 16S ribosomal DNA analysis indicated that the type strain of Micrococcus agilis, DSM 20550 (= ATCC 966 = CCM 2390), is less closely related to the type species of the genus Micrococcus, Micrococcus luteus, than to the type species of the genus Arthrobacter, Arthrobacter globiformis, and related Arthrobacter species. The phylogenetic position of M. agilis is supported by the presence of peptidoglycan variation A3 alpha and by the presence of MK-9(H2) as the major isoprenolog, a characteristic also found in strains of A. globiformis, Arthrobacter crystallopoietes, Arthrobacter atrocyaneus, Arthrobacter citreus, Arthrobacter aurescens, Arthrobacter ilicis, Arthrobacter ureafaciens, Arthrobacter oxydans, Arthrobacter histidinolovorans, and Arthrobacter nicotinovorans. The last six species and M. agilis are characterized by the presence of threonine in the interpeptide bridge of the peptidoglycan. Threonine has not been found in the peptidoglycans of other Arthrobacter species or in members of the genus Micrococcus. Despite the fact that a morphological life cycle is not known, these data support the proposal that M. agilis should be transferred to the genus Arthrobacter as Arthrobacter agilis comb. nov.
Arthrobacter↗
Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the neotype of L. casei subsp. casei, and rejection of the name Lactobacillus paracasei.
The type strain of Lactobacillus casei subsp. casei (ATCC 393) exhibits low levels of DNA homology with other strains of L. casei subsp. casei (8 to 46%) and strains of Lactobacillus paracasei (30 to 50%), but exhibits a level of DNA similarity of 80% with Lactobacillus rhamnosus ATCC 15820, the original type strain of "Lactobacterium zeae" Kuznetsov 1959. Strains ATCC 393T (T = type strain) and ATCC 15820T are members of one protein profile cluster that is separate from the other Lactobacillus spp. The randomly amplified polymorphic DNA PCR profile of strain ATCC 393T is also different from the profiles obtained for the other species. L. casei ATCC 334T is genetically closely related to L. casei subsp. casei strains (71 to 97%) and L. paracasei strains (71 to 91%), is a member of the same protein profile cluster as these organisms, and shares several DNA amplicons with L. paracasei strains. On the basis of these results, we propose that L. casei subsp. casei ATCC 393T and L. rhamnosus ATCC 15820 should be reclassified as members of Lactobacillus zeae nom. rev. (type strain, ATCC 15820), that strain ATCC 334 should be designated the neotype strain of L. casei subsp. casei, and that the name L. paracasei should be rejected.
Base Sequence↗
Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain B1, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing.
A bacterium isolated from a polluted stream, capable of metabolizing biphenyl, naphthalene, phenanthrene, and higher-molecular-weight polycyclic aromatic hydrocarbons (D. Gibson, V. Mahadevan, D. Jerina, H. Yagi, and H. Yeh, Science 189:295-297, 1975), was previously identified as Beijerinckia sp. strain B1. In this investigation, 16S rRNA gene sequencing, biochemical tests, fatty acid methyl ester analysis, polyacrylamide gel electrophoresis of protein, and DNA-DNA hybridization were used to determine the taxonomic relationship of Beijerinckia sp. strain B1. The sequence of the 16S rRNA gene of B1 was identical to that of Sphingomonas yanoikuyae ATCC 51230T. The biochemical tests, fatty acid analysis, and sodium dodecyl sulfate-polacrylamide gel electrophoresis profile of soluble proteins of strain B1 showed results similar to those of S. yanoikuyae. DNA-DNA hybridization indicated that B1 and S. yanoikuyae ATCC 51230T are 75% homologous at the DNA level. We propose that Beijerinckia sp. strain B1 be reclassified as S. yanoikuyae.
Bacterial Proteins↗
Phylogenetic relationships of the genera Acetobacterium and Eubacterium sensu stricto and reclassification of Eubacterium alactolyticum as Pseudoramibacter alactolyticus gen. nov., comb. nov.
16S rRNA gene sequences of the type strains of the seven previously described Acetobacterium species were determined. The Acetobacterium species were found to form a tight phylogenetic cluster within the Clostridium subphylum of the gram-positive bacteria. Within this subphylum these organisms belong to cluster XV as defined by Collins et al. (M.D. Collins, P.A. Lawson, A. Willems, J.J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994) together with Eubacterium alactolyticum barkeri, Eubacterium callanderi, and Eubacterium limosum. Our data indicate that Clostridium cluster XV consists of at least the following three genera: the genus Acetobacterium, the genus Eubacterium sensu stricto (comprising E. limosum, E. barkeri, and E. callanderi), and the genus Pseudoramibacter gen. nov., which is created for E. alactolyticum, which we reclassify as Pseudoramibacter alactolyticus comb. nov.
Base Sequence↗