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PubMed2003

High occurrence of a basicranial feature in Homo erectus: anatomical description of the preglenoid tubercle.

The degree of differentiation between Western and Eastern Early Middle Pleistocene hominids (Homo erectus) is still under debate. On the one hand, the two populations are believed by some to belong to two separate taxonomic categories possessing their own exclusive features. On the other hand, they are considered by others to belong to a single but ubiquitous global population with regional specificities that are mainly due to variations in the frequency of certain features. In this context, an additional trait, the preglenoid tubercle (tuberculum anterius fossae mandibularis), may well shed light on the matter. The tubercle is often present on the anterior part of the fossa mandibularis at the anterior extent of the joint capsule and articular tubercle (tuber articulare) of fossils usually assigned to Homo erectus. This study describes the anatomy of the preglenoid tubercle, to indicate its occurrence and to try to improve its use in taxonomy and phylogeny, although its origin and functional significance have not yet been clarified.

Animals↗
PubMed2002

Altersetin, a new antibiotic from cultures of endophytic Alternaria spp. Taxonomy, fermentation, isolation, structure elucidation and biological activities.

A novel antibacterial antibiotic, for which the name altersetin is proposed, was isolated from the culture broth of two endophytic Alternaria species. The relative and absolute configuration were assigned by NOESY or CD data, respectively. Altersetin is chemically related to equisetin and showed potent MIC against several pathogenic gram-positive bacteria, whereas gram-negative bacteria and pathogenic yeast were not or much less susceptible. Moderate in vivo efficiacy was observed for altersetin in a murine sepsis model.

Alternaria↗
PubMed2001

Characterisation of Eubacterium-like strains isolated from oral infections.

The genus Eubacterium currently includes a heterogeneous group of gram-positive, non-spore-forming anaerobic bacilli, many of which are slow growing, fastidious and generally unreactive in biochemical tests. As a consequence, cultivation and identification of isolates are difficult and the taxonomy of the group remains indifferent. In this study, 105 isolates from odontogenic infections, infections associated with dental implants or saliva from healthy subjects and provisionally assigned to the genus Eubacterium were subjected to phenotypic and genotypic analysis. Ninety-one of the isolates were identified as belonging to one of 14 previously described species: Atopobium parvulum (5 isolates), A. rimae (29), Bulleidia extructa (2), Cryptobacterium curtum (1), Dialister pneumosintes (1), Eubacterium saburreum (2), E. sulci (8), E. yurii subsp. yurii (1), Filifactor alocis (3), Lactobacillus uli (1), Mogibacterium timidum (13), M. vescum (6), Pseudoramibacter alactolyticus (6) and Slackia exigua (13). The remaining 14 isolates did not correspond to existing species. This study confirms the diversity of organisms provisionally assigned to the genus Eubacterium by conventional identification methods. This group of organisms is frequently isolated from oral infections but their role in the aetiology of these conditions has yet to be determined.

Actinomycetales Infections↗
PubMed2000

The outcomes of outcomes and effectiveness research: impacts and lessons from the first decade.

OBJECTIVE: To assess the outcomes of the Agency for Healthcare Research and Quality's (AHRQ; formerly the Agency for Health Care Policy and Research, AHCPR) first decade of focus on outcomes and effectiveness research (OER) and to identify needs and opportunities for the study of OER in the coming years. DATA SOURCE: Study findings were collected in response to an inquiry by the Center for Outcomes and Effectiveness Research at AHRQ in July 1997 to all principal investigators (PIs) funded between 1989 and 1997. The request was for investigators to identify their "most salient findings" and supply material for up to three slides. STUDY DESIGN: A taxonomy of 11 non-mutually exclusive categories was used to group the investigators' salient findings by characteristics of methodology or purpose. Two health services researchers assigned findings to up to three categories for each discrete study. PRINCIPAL FINDINGS: Responses were received from 61 (64 percent) of the 91 PIs, reporting on 115 studies. Of the 246 category assignments made, descriptive epidemiology was the most common (24 percent), followed by comparative effectiveness (17 percent) and economic assessments (12 percent). Most studies were retrospective analyses of administrative data. Viewed within a conceptual framework for assessing the impact of research, OER has built a solid foundation for future quality improvement efforts by identifying problems, generating hypotheses, and developing new methodologies and has had limited impact on health care policies, practices and outcomes. CONCLUSIONS: OER has had moderate but significant success meeting initial expectations for the field. Challenges for the next generation of OER include advancing from hypothesis generation to definitive studies of effectiveness, and acceleration of the process by which findings effect policy, practice, and outcomes.

Attitude of Health Personnel↗
PubMed1991

Characteristics of lactobacilli isolated from the chicken intestine.

Nine strains of lactobacilli isolated from different parts of the intestinal tract of chicken were studied to determine their taxonomy and cultural characteristics. The experimental scheme included physiological and biochemical tests, morphological observations and determination of fermentation products from glucose. All isolates were heterofermentative organisms assigned to the Lactobacillus fermentum species. The relevance of intestinal lactobacilli to the nutrition of chickens was discussed.

Animals↗
PubMed1999

Recommended minimal standards for description of new staphylococcal species. Subcommittee on the taxonomy of staphylococci and streptococci of the International Committee on Systematic Bacteriology.

In accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria, minimal standards are proposed for the genus Staphylococcus and the description of newly recognized species in this genus. Assignment of a strain to the genus Staphylococcus requires that it is a Gram-positive coccus that forms clusters, produces catalase, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and G + C content of DNA in a range of 30-40 mol%. The recommended minimal standards for describing a new Staphylococcus species are based on the results of phenotypic and genomic studies of at least five independently isolated strains. They include colony morphology and the results of the following conventional tests: pigment production, growth requirements, fermentative and oxidative activity on carbohydrates, novobiocin susceptibility, enzymic activities (nitrate reductase, alkaline phosphatase, arginine dihydrolase, ornithine decarboxylase, urease, cytochrome oxidase, staphylocoagulase in rabbit plasma, heat-stable nuclease, amidases, oxidases, clumping factor, and haemolytic activity on sheep or bovine blood agar). DNA-DNA hybridization experiments may distinguish species when the difference between the binding in the homologous reaction and the binding in the heterologous reaction expressed as a percentage is less than 70%. In addition, rRNA signature sequence criteria, ribotyping characterization of the nomenclature type strain and other strains of the species, and reference strains of other species is recommended to describe the strains of the new species with sets of genetic attributes and reveal possible grouping errors. This proposal has been endorsed by the members of the Subcommittee on the taxonomy of staphylococci and streptococci of the international Committee on Systematic Bacteriology.

Animals↗
PubMed1993

New discoveries of Australopithecus at Maka in Ethiopia.

The taxonomy of Australopithecus afarensis, the oldest known hominid species, has been a matter of debate since its description in 1978 (ref. 1). Some authorities regard all specimens assigned to A. afarensis as belonging to a single taxon whereas others regard the Tanzanian and Ethiopian specimens as each representing a different species. Further controversy surrounds the issues of sexual dimorphism and locomotion among these hominids. Resolution of these problems would shed light on hominid phylogeny in general and on the ancestry of later Australopithecus and Homo. Fossils discovered in the Afar of Ethiopia in 1990 constitute the first major addition to the 3-4 million year (Myr) hominid record since the 1970s. We report here the discovery of new fossils from Maka, dated to 3.4 Myr ago, which provide powerful support for the interpretation of A. afarensis as a single, ecologically diverse, sexually dimorphic, bipedal Pliocene primate species whose known range encompassed Ethiopia and Tanzania.

Animals↗
PubMed1989

The epidemiology of delays in a teaching hospital. The development and use of a tool that detects unnecessary hospital days.

This study's purpose was to develop a tool that detects, quantifies, and assigns causes for medically unnecessary hospital delays and use it to describe the epidemiology of delays at a teaching tertiary care hospital. Based on observational data, a taxonomy of delays was constructed that included nine major categories and 166 subcategories. This formed the basis for an instrument for detecting inefficiency in hospital care: the Delay Tool. Initially designed for real-time concurrent assessment, in retrospective use it was also reliable, requiring about 6 minutes per medical record. In using the Delay Tool over a 6-month period on general internal medical and gastrointestinal services, it was discovered that 30% of 960 patients experienced delays, the average length of which was 2.9 days. This represented 17% of all hospital days. The most frequent causes of delays were scheduling of tests (31%), unavailability of post-discharge facilities (18%), physician decision-making (13%), discharge planning (12%), and scheduling of surgery (12%). Because of the longer lengths of the delays involved with awaiting postdischarge facilities (primarily nursing home beds), this was the most important cause of delays and represented 41% of all delay days. The general medicine and gastrointestinal services had significantly different distributions of delay types related to their different kinds of patients and care. The Delay Tool should be helpful in addressing hospital, and hospital-related, inefficiencies in health care delivery.

Appointments and Schedules↗
PubMed1996

Semantide- and chemotaxonomy-based analyses of some problematic phenotypic clusters of slowly growing mycobacteria, a cooperative study of the International Working Group on Mycobacterial Taxonomy.

During previous cooperative numerical taxonomic studies of slowly growing mycobacteria, the International Working Group on Mycobacterial Taxonomy described a number of strains whose taxonomic status was ambiguous. A new study of DNA, RNA, and proteins from 66 of these organisms was performed to correlate their properties with phenotypic clustering behavior; the results of this study permitted 51 of the strains studied to be assigned to known species. The methods used to characterize the semantides included nucleotide sequencing and assessment of levels of semantide relatedness by affinity binding techniques, including whole DNA-DNA hybridization, probe hybridization, and antibody binding. There was good overall agreement between the phenotypic and chemotaxonomic clusters and the groups of organisms identified by semantide analyses. Our results supported the conclusion that we should continue to rely on polyphasic taxonomy to provide satisfactory systematic resolution of members of the genus Mycobacterium. We identified no single 16S rRNA interstrain nucleotide sequence difference value that unequivocally defined species boundaries. DNA-DNA hybridization remains the gold standard, but common resources are needed to permit DNA-DNA hybridization analyses to be made available to laboratories that are not prepared to use this technology. One of the large novel clusters which we studied corresponds to the recently described species Mycobacterium interjectum, a pathogen that resembles the nonpathogen Mycobacterium gordonae phenotypically. We also identified strains that appear to represent ribovars of Mycobacterium intracellulare which do not react with the commercial diagnostic probes that are currently used for identification of this species. Other branches or clusters consisted of too few strains to permit a decision about their taxonomic status to be made.

Bacterial Proteins↗
PubMed2025

raxtax: a k-mer-based non-Bayesian taxonomic classifier.

MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases. RESULTS: We validate raxtax on three widely-used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100 000 and 1 000 000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge. AVAILABILITY AND IMPLEMENTATION: raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data, and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.

Software↗
PubMed1976

The taxonomy of haemophili isolated from conjunctivae.

The paper provides a description of 112 Haemophilus strains isolated from cases of conjunctivitis in Egypt, Tunisia, Denmark, and the U.S.A., and aims at a clarification of the taxonomy of haemophili implicated in conjunctivitis. Although the study confirms the diversity of haemophili which can be isolated from inflamed conjunctivae, the vast majority of strains could be assigned to either biotype II or III of H. influenzae. Thirteen strains possessed all the characteristics of the Koch-Weeks bacillus. However, judged by the findings the recognition of the Koch-Weeks bacillus as a separate species does not seem tenable. It is suggested that this organism is considered a haemagglutinating variety of H. influenzae biotype III. The study indicates that the haemagglutinating ability per se, which can be found in strains of several taxa of Haemophilus, is associated with a special pathogenic potential.

Child, Preschool↗
PubMed2006

Moving pieces in a taxonomic puzzle: venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones).

The Buthidae is the most clinically important scorpion family, with over 500 species distributed worldwide. Taxonomical positions and phylogenetic relationships concerning the representative genera and species of this family have been mostly inferred based upon comparisons between morphological characters. Yet, some authors have performed such inferences by comparing some structural properties of a few selected molecules found in the venoms from these scorpions. Here, we propose a novel methodology pipeline designed to address these issues. We have analyzed the whole venoms from some species that exemplify peculiar cases in the Buthidae family (Tityus stigmurus, Tityus serrulatus, Tityus bahiensis, Leiurus quinquestriatus quinquestriatus and Leiurus quinquestriatus hebraeus), by means of a proteomic approach using a 2D-LC/MS technique. The molecules found in these venoms were clustered according to their physicochemical properties (molecular mass and hydrophobicity), by using the machine learning-based Weka software. The clusters assessment, along with the number of molecules found in a given cluster for each scorpion, which assigns for the venom and structural family complexities, respectively, was used to generate a phenetic correlation tree for positioning these species. Our results were in accordance with the classical taxonomy viewpoint, which places T. serrulatus and T. stigmurus as very close species, T. bahiensis as a less related species in the Tityus genus and L. q. quinquestriatus and L. q. hebraeus with small differences within the same species (L. quinquestriatus). Therefore, we believe that this is a well-suited method to determine venom complexities that reflect the scorpions' evolutionary history, which can be crucial to reconstruct their phylogeny through the molecular evolution of their venoms.

Animals↗
PubMed1998

Reliability and validity of the adolescent health profile-types.

OBJECTIVES: The purpose of this study was to demonstrate the preliminary reliability and validity of a set 13 profiles of adolescent health that describe distinct patterns of health and health service requirements on four domains of health. METHODS: Reliability and validity were tested in four ethnically diverse population samples of urban and rural youths aged 11 to 17-years-old in public schools (N = 4,066). The reliability of the classification procedure and construct validity were examined in terms of the predicted and actual distributions of age, gender, race, socioeconomic status, and family type. School achievement, medical conditions, and the proportion of youths with a psychiatric disorder also were examined as tests of construct validity. RESULTS: The classification method was shown to produce consistent results across the four populations in terms of proportions of youths assigned with specific sociodemographic characteristics. Variations in health described by specific profiles showed expected relations to sociodemographic characteristics, family structure, school achievement, medical disorders, and psychiatric disorders. CONCLUSIONS: This taxonomy of health profile-types appears to effectively describe a set of patterns that characterize adolescent health. The profile-types provide a unique and practical method for identifying subgroups having distinct needs for health services, with potential utility for health policy and planning. Such integrative reporting methods are critical for more effective utilization of health status instruments in health resource planning and policy development.

Adolescent↗
PubMed2005

Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae.

A taxonomic study was carried out to clarify the taxonomy of representatives of a group of marine actinomycetes previously designated MAR 1 and considered to belong to the family Micromonosporaceae. The organisms had phenotypic properties consistent with their assignment to this taxon. The strains formed a distinct taxon in the 16S rRNA Micromonosporaceae gene tree and shared a range of phenotypic properties that distinguished them from members of all of the genera with validly published names classified in this family. The name proposed for this novel taxon is Salinispora gen. nov. The genus contains two species recognized using a range of genotypic and phenotypic criteria, including comparative 16S-23S rRNA gene spacer region and DNA-DNA relatedness data. The names proposed for these taxa are Salinispora arenicola sp. nov., the type species, and Salinispora tropica sp. nov.; the type strains of these novel species have been deposited in service culture collections as strain CNH-643(T) (=ATCC BAA-917(T)=DSM 44819(T)) and strain CNB-440(T) (=ATCC BAA-916(T)=DSM 44818(T)), respectively.

DNA, Bacterial↗
PubMed1999

Novel application of PhastSystem polyacrylamide gel electrophoresis using restriction fragment length polymorphism--internal transcribed spacer patterns of individuals for molecular identification of entomopathogenic nematodes.

différences! [editorial] [editorial]onomic way of identifying and assigning nematodes to taxons, which had already been determined either by comparative sequence analysis of nuclear rDNA internal transcribed spacer (ITS) region or by other methods of molecular or conventional taxonomy, is provided. Molecular identification of entomopathogenic nematodes (EPN) can be upgraded by basing it on PhastSystem polyacrylamide gel electrophoresis (PAGE) analysis of restriction fragment length polymorphism (RFLP) patterns of polymerase chain reaction (PCR)-amplified DNA derived from single nematodes of Steinernema or Heterorhabditis spp. Although analysis from single worms has previously been made on agarose gel, the resolution on PhastSystem PAGE gel is much higher. The DNA sequences selected for analysis were those constituting the internal transcribed spacer region between the 18S and 26S rDNA genes within the rRNA operon. RFLP analysis was carried out by gel electrophoresis on the PhastSystem (Pharmacia) as detailed elsewhere (Triga et al., Electrophoresis 1999, 20, 1272-1277. The downscaling from conventional agarose to PhastSystem gels resulted in pattern of DNA fragments differing from those obtained with agarose gel electrophoresis under conventional conditions by increasing the number of detected fragments. The approach supported previous species identifications and was able to identify several unclassified isolates, such as those from Hungary and Ireland, and provides a method for identification of previously unclassified strains. We confirmed that Heterorhabditis "Irish Type", represented by two strains of different geographical origin, comprise a species different from H. megidis. We also confirmed that strain IS5 belongs to the species H. indicus rather than to H. bacteriophora, as had been suggested previously.

Animals↗
PubMed1999

Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika.

The current phylogenetic hypothesis for the endemic Lake Tanganyika cichlid fishes of the tribe Eretmodini is based solely on morphology and suggests that more complex trophic morphologies derived only once from a less specialized ancestral condition. A molecular phylogeny of eretmodine cichlids based on partial mitochondrial DNA cytochrome b and control-region sequences was used to reconstruct the evolutionary sequence of trophic adaptations and to test alternative models of morphological divergence. The six mitochondrial lineages found disagree with the current taxonomy and the morphology-based phylogeny. Mitochondrial lineages with similar trophic morphologies are not grouped monophyletically but are typically more closely related to lineages with different trophic phenotypes currently assigned to other genera. Our results indicate multiple independent origins of similar trophic specializations in these cichlids. A pattern of repeated divergent morphological evolution becomes apparent when the phylogeography of the mitochondrial haplotypes is analyzed in the context of the geological and paleoclimatological history of Lake Tanganyika. In more than one instance within Lake Tanganyika, similar morphological divergence of dentitional traits occurred in sympatric species pairs. Possibly, resource-based divergent selective regimes led to resource partitioning and brought about similar trophic morphologies independently and repeatedly.

Animals↗
PubMed2004

Speciation, phylogeography and evolution of life history and morphology in plethodontid salamanders of the Eurycea multiplicata complex.

Understanding the complex interactions among environment, genotype and ontogeny in determining organismal phenotypes is cental to many biological disciplines. The Eurycea multiplicata complex, endemic to the Interior Highlands (Ozark Plateau and Ouachita Mountains) of eastern North America, comprises a diverse radiation of paedomorphic surface-dwelling (E. tynerensis), metamorphic surface-dwelling (E. multiplicata multiplicata and E. m. griseogaster) and metamorphic subterranean (Typhlotriton spelaeus) hemidactyliine plethodontid salamanders. Portions of two mitochondrial genes, cytochrome-b and NADH dehydrogenase-4, totalling 1818 base pairs (bp) were sequenced for 70 ingroup individuals plus numerous outgroup taxa, to examine the biogeography and relationships among these morphologically disparate species. Results show the E. multiplicata complex to be monophyletic, with its two most divergent clades corresponding to geography, not morphology or life history. Transforming surface-dwelling populations from the Ouachitas (E. m. multiplicata) are sister to the Ozark taxa, including paedomorphic surface-dwelling (E. tynerensis), subterranean (T. spelaeus) and transforming surface-dwelling salamanders assigned to the 'subspecies'E. m. griseogaster. Among Ozark taxa T. spelaeus (deeply nested within Eurycea) is sister to a clade that includes E. m. griseogaster and E. tynerensis. Current taxonomy suggests that paedomorphic populations (E. tynerensis) from the western Ozarks are distinct from nearby transforming populations (E. m. griseogaster). However, paedomorphic and transforming salamanders do not form reciprocally monophyletic groups and many populations share almost identical haplotypes. Ancestral state reconstruction of life history traits shows that paedomorphosis arose independently from three to nine times. Most populations are either completely paedomorphic or completely transforming. This suggests that local habitat parameters strongly influence life history mode in this complex, either facultatively or by selection for particular genotypes.

Animals↗