bluuebunny/crossref_metadata_2025 huggingface dataset:
Effectiveness of tibolone on the reduction of menopausal problems—a Bayesian semi‐parametric interpretation
Authors: Das Kalyan , Naskar Malay
Published: August 2006

Two major physiological problems women experience at the time of menopause are hot flush and vaginal dryness. Exploratory investigations reveal that these two binary outcomes are very much dependent as both of them have predominant oestrogenic effects. A primary interest is to investigate how the bivariate association and the marginal univariate risks are affected by repeated measurements on each woman over several months. To achieve this we propose a very general class of bivariate binary models. Parametric inference is drawn on the basis of full non‐parametric Bayesian approach under Dirichlet process mixture. Study addresses some more interesting phenomena on the effectiveness of tibolone treatment in reducing menopausal problems. A simulation study further strengthens the proposed methodology. Copyright © 2006 John Wiley & Sons, Ltd.
Stochastically curtailed phase II clinical trials
Authors: Ayanlowo A. O. , Redden D. T.
Published: August 2006

Phase II trials often test the null hypothesis H0: p ⩽ p0 versus H1: p ⩾p1, where p is the true unknown proportion responding to the new treatment, p0 is the greatest response proportion which is deemed clinically ineffective, and p1 is the smallest response proportion which is deemed clinically effective. In order to expose the fewest number of patients to an ineffective therapy, phase II clinical trials should terminate early when the trial fails to produce sufficient evidence of therapeutic activity (i.e. if p ⩽p0). Simultaneously, if a treatment is highly effective (i.e. if p⩾p1), the trial should declare the drug effective in the fewest patients possible to allow for advancement to a phase III comparative trial. Several statistical designs, including Simon's minimax and optimal designs, have been developed that meet these requirements. In this paper, we propose three alternative designs that rely upon stochastic curtailment based on conditional power. We compare and contrast the properties of the three approaches: (1) stochastically curtailed (SC) binomial tests, (2) stochastically curtailed (SC) Simon's optimal design, and (3) SC Simon's minimax design to those of Simon's minimax and Simon's optimal designs. For each of these designs we compare and contrast the number of opportunities for study termination, the expected sample size of the trial under the null hypothesis (p ⩽p0), and the effective type I and type II errors. We also present graphical tools for monitoring phase II clinical trials with stochastic curtailment using conditional power. Copyright © 2006 John Wiley & Sons, Ltd.
Analysing and interpreting competing risk data
Authors: Pintilie Melania
Published: August 2006

When competing risks are present, two types of analysis can be performed: modelling the cause specific hazard and modelling the hazard of the subdistribution. This paper contrasts these two methods and presents the benefits of each. The interpretation is specific to the analysis performed. When modelling the cause specific hazard, one performs the analysis under the assumption that the competing risks do not exist. This could be beneficial when, for example, the main interest is whether the treatment works in general. In modelling the hazard of the subdistribution, one incorporates the competing risks in the analysis. This analysis compares the observed incidence of the event of interest between groups. The latter analysis is specific to the structure of the observed data and it can be generalized only to another population with similar competing risks. Copyright © 2006 John Wiley & Sons, Ltd.
A nonlinear latent class model for joint analysis of multivariate longitudinal data and a binary outcome
Authors: Proust‐Lima Cécile , Letenneur Luc , Jacqmin‐Gadda Hélène
Published: August 2006

We consider a joint model for exploring association between several correlated longitudinal markers and a clinical event. A nonlinear growth mixture model exhibits the different latent classes of evolution of the latent quantity underlying the correlated longitudinal markers and a logistic regression models the probability of occurence of the clinical event according to the latent classes. By introducing a flexible nonlinear transformation including parameters to be estimated between each marker and the latent process, the model also deals with non‐Gaussian continuous markers. Through an application on cognitive ageing, the two advantages of the model are underlined: (1) the latent profiles of evolution associated with the clinical event are described including covariate effects in the longitudinal model but also in the probability of class membership and in the probability of occurence of the event, and (2) a diagnostic and a prognostic tools are derived from the model for early detection of the clinical event using any available information about the longitudinal markers. Copyright © 2006 John Wiley & Sons, Ltd.
Comparing the small sample performance of several variance estimators under competing risks
Authors: Braun Thomas M. , Yuan Zheng
Published: August 2006

We examine several variance estimators for cumulative incidence estimators that have been proposed over time, some of which are derived from asymptotic martingale or counting process theory, and some of which are developed from the moments of the multinomial distribution. There is little published work comparing these variance estimators, largely because the variance estimators are algebraically complex and difficult to interpret and all but one have yet to be programmed for a standard statistical package. Through simulation and application to real data, we compare the performance of six variance estimators in relation to each other and the bootstrap in order to confirm earlier reports of their performance and to provide future direction toward their application. We find that the multinomial‐moment‐based estimators have performance close to that of the bootstrap, and are quite accurate for estimating the variance, even in samples of 20 subjects. All but one of the martingale theory‐based estimators tend to perform poorly in small samples, tending to either overestimate or underestimate the empirical variance in samples of fewer than 100 subjects. Copyright © 2006 John Wiley & Sons, Ltd.
On estimating treatment effects under non‐compliance in randomized clinical trials: are intent‐to‐treat or instrumental variables analyses perfect solutions?
Authors: Bang Heejung , Davis Clarence E.
Published: August 2006

In this report, we compared four estimators (intent‐to‐treat, as treated, per protocol, and instrumental variables estimators) that are conventionally considered for treatment effect estimation by simulation under different non‐compliance scenarios in typical clinical trial settings. We found that intent‐to‐treat and instrumental variables estimators are not perfect and can be problematic in some situations although these two estimators carry desirable properties as we assume. Copyright © 2006 John Wiley & Sons, Ltd.
Improving fault prediction using Bayesian networks for the development of embedded software applications
Authors: Pérez‐Miñana Elena , Gras Jean‐Jacques
Published: August 2006

Bayesian network (BN) models can be used to predict the level of fault injection in the different phases of the software development process. This paper describes the techniques used by Motorola to develop BN fault prediction models using product, usage and process information. It also includes a procedure created to validate and calibrate the BN models. Statistical techniques are applied that provide a measurement of the quality of the predictions made by the models, and directions on how the models could be improved. The validation method described in this paper considers two alternative ways to produce an improved network. The first is based mainly on modifying the ranges of the existing nodes, adding interdependencies between them, and varying the weight values associated with each of the nodes that are used as inputs to the intermediate nodes of the BN model. The second possibility uses linear regression and principal component analysis to build the intermediate and output nodes of the network. The paper closes with some encouraging results, and outlines a number of unresolved questions. Copyright © 2006 John Wiley & Sons, Ltd.
The specification logic νZ
Authors: Henson Martin C. , Deutsch Moshe , Kajtazi Besnik
Published: August 2006

This paper introduces a wide-spectrum specification logic νZ. The minimal core logic is extended to a more expressive specification logic which includes a schema calculus similar (but not equivalent) to Z, new additional schema operators, and extensions to programming and program development logics.
Day Care Laparoscopic Cholecystectomy: A Feasibility Study in a Public Health Service Hospital in a Developing Country
Authors: Chauhan A. , Mehrotra M. , Bhatia P.K. , Baj B. , Gupta A.K.
Published: August 2006

Background

Day care laparoscopic cholecystectomy (DCLC) has been shown to be safe in centers with adequate infrastructure for day care surgery in economically advanced countries. However, the feasibility of applying this concept in public health service hospitals in less developed and developing nation needs to studied. Unique protocols need to be developed and tested, taking into account local conditions and infrastructural constraints.

Patients and methods

Patients less than 60 years old, graded I and II on the American Society of Anesthesiologists (ASA) physical status score, living within one hour traveling time and willing to make their own arrangements for a return to hospital in case of problems, were selected for DCLC.

Results

291 cases (78%) out of 373 laparoscopic cholecystectomies done in one calendar year were found suitable for DCLC. The most common cause for omitting from DCLC was that the patient lived out of the defined area (57%). Four of 291 (1.3%) cases were cancelled due to medical condition; 270/287 (96.1%) were discharged the same evening as surgery; 6 patients were converted to open surgery; and 11 did not meet the necessary discharge criteria. Eight of 270 (2.9%) required readmission out of which 3 (1.1%) required intervention. Overall, incidence of complication rate was 3.4%. Analysis of data showed that results were comparable to previously published studies, hence extrapolating that inclusion and discharge criteria used in the study are valid. However, there are certain social constraints which hinder truly universal application of DCLC.

Conclusions

DCLC is a safe and technically feasible concept, even in public health service centers without dedicated ambulatory surgery units. It has potential for much economical and social benefit in these countries.
Relationship between quality management practices and knowledge transfer
Authors: Molina Luis M. , Lloréns‐Montes Javier , Ruiz‐Moreno Antonia
Published: August 2006

This paper analyzes the relationship between quality management (QM) and knowledge transfers. The study of QM was tackled by analyzing the degree of implementation of the different practices that compose it. Hypotheses are developed on the relationship between some QM practices and knowledge transfers. Both the proposed model and the hypotheses were tested on a sample of 197 Spanish firms. The results confirm the importance of the different QM practices on internal and external knowledge transfers.
Ground ice and slope sediments archiving late Quaternary paleoenvironment and paleoclimate signals at the margins of El'gygytgyn Impact Crater, NE Siberia
Authors: Schwamborn Georg , Meyer Hanno , Fedorov Grigory , Schirrmeister Lutz , Hubberten Hans-W.
Published: August 2006

An accumulation terrace close to the El'gygytgyn Impact Crater in northeastern Siberia contains stratigraphic and periglacial evidence of the paleoenvironmental and paleoclimatic history and permafrost dynamics during late Quaternary time. A succession of paleo active-layer deposits that mirror environmental changes records periods favorable for the establishment and growth of ice-wedge polygonal networks and sediment variations. These two elements of the periglacial landscape serve as complementary paleoenvironmental archives that can be traced back to ∼ 14,000 cal yr BP. The slope sediments and the ground ice contained therein have prominent relative maxima and minima in properties (grain size, total organic content, oxygen isotopes). They document a regional early Holocene thermal maximum at about 9000 cal yr BP, followed by a transition to slightly cooler conditions, and a subsequent transition to slightly warmer conditions after about 4000 cal yr BP. Results from sedimentary analysis resemble morphological and geochemical (oxygen and hydrogen isotopes) results from ice wedge studies, in which successive generations of ice-wedge polygonal networks record warmer winters in late Holocene time. Moreover, peaks of light soluble cation contents and quartz-grain surface textures reveal distinct traces of cryogenic weathering. We propose a conclusive sedimentation model illustrating terrace formation in a permafrost terrain.
Epidemiological tracing ofSalmonella entericaserotype Abortusovis from Spanish ovine flocks by PFGE fingerprinting
Authors: VALDEZATE S. , ASTORGA R. , HERRERA-LEÓN S. , PEREA A. , USERA M. A. , HUERTA B. , ECHEITA A.
Published: August 2006

Salmonella entericaserotype Abortusovis, an ovine host-specific serotype, rare in most countries, is responsible for epidemic abortion episodes in Spain. With the aim of surveillance and detection of the spread of specific clones, 55 Abortusovis isolates collected during 1996–2001 from flocks in 11 provinces, were studied usingXbaI–PFGE. Despite the fact that the strains were geographically and spatially related, PFGE demonstrated an epidemiologically acceptable discriminating power, identifying 20 clones (similarity, 52–96%). Clones Sabv6, 1, 5 were disseminated in seven, five and two areas respectively, while another 17 clones appeared in single places. Clones from nearby geographic regions showed a high relatedness (one band of difference in the PFGE profile) Sabv1-2-3, Sabv5-6, Sabv7-8, and Sabv13-14, suggesting a common ancestor. Co-isolation in the same flock (Sabv5-6, Sabv1-3, Sabv1-6) was detected. PFGE surveillance detected the predominance and widespread distribution of clone Sabv6 in 21 out of the 55 Abortusovis serotype episodes studied in Spain.
Static analysis for path correctness of XML queries
Authors: COLAZZO DARIO , GHELLI GIORGIO , MANGHI PAOLO , SARTIANI CARLO
Published: August 2006

A part of a query that will never contribute data to the query answer should be regarded as an error. This principle has been recently accepted into mainstream XML query languages, but was still waiting for a complete treatment. We provide here a precise definition for this class of errors, and define a type system that is sound and complete, in its search for such errors, for a core language, under mild restrictions on the use of recursion in type definitions. In the process, we describe a dichotomy among existential and universal type systems, which is essential to understand some specific features of our type system.
Making a fast curry: push/enter vs. eval/apply for higher-order languages
Authors: MARLOW SIMON , JONES SIMON PEYTON
Published: August 2006

Higher-order languages that encourage currying are typically implemented using one of two basic evaluation models: push/enter or eval/apply. Implementors use their intuition and qualitative judgements to choose one model or the other. Our goal in this paper is to provide, for the first time, a more substantial basis for this choice, based on our qualitative and quantitative experience of implementing both models in a state-of-the-art compiler for Haskell. Our conclusion is simple, and contradicts our initial intuition: compiled implementations should use eval/apply.
Slideshow: functional presentations
Authors: FINDLER ROBERT BRUCE , FLATT MATTHEW
Published: August 2006

Among systems for creating slide presentations, the dominant ones offer essentially no abstraction capability. Slideshow represents our effort over the last several years to build an abstraction-friendly slide system with PLT Scheme. We show how functional programming is well suited to the task of slide creation, we report on the programming contructs that we have developed for slides, and we describe our solutions to practical problems in rendering slides. We also describe experimental extensions to DrScheme that support a mixture of programmatic and WYSIWYG slide creation.
VISION, LIGHT AND COLOR IN AL-KINDĪ, PTOLEMY AND THE ANCIENT COMMENTATORS
Authors: ADAMSON PETER
Published: August 2006

Al-Kindī was influenced by two Greek traditions in his attempts to explain vision, light and color. Most obviously, his works on optics are indebted to Euclid and, perhaps indirectly, to Ptolemy. But he also knew some works from the Aristotelian tradition that touch on the nature of color and vision. Al-Kindī explicitly rejects the Aristotelian account of vision in his De Aspectibus, and adopts a theory according to which we see by means of a visual ray emitted from the eye. But in the same work, al-Kindī draws on Philoponus’ commentary on Aristotle's De Anima. His borrowing from this commentary, via an Arabic paraphrase of the De Anima, was crucial in the development of al-Kindī's new ‘ ‘ punctiform analysis of light.” Conversely, two broadly Aristotelian works by al-Kindī, which explain the reason things are colored, engage with problems about color dealt with in the Aristotelian tradition ( e.g. by Alexander of Aphrodisias ). But here the Aristotelian theory, and in particular the Aristotelian notion of the transparent, is abandoned in order to accommodate the visual ray theory expounded in De Aspectibus.
LA RELATION CHEZ AVICENNE
Authors: ZGHAL HATEM
Published: August 2006

This study consists in a commentary on some passages from Avicenna, which deal with the category of the relative. The commentary points out the promotion of the relative to the role of an exclusive determining factor. An attempt is made here to show how Avicenna tries to detach the relative accident from its subject, in order to transform it into the exclusive determining factor of a pure thingness. The relative determination of this thingness must be able to receive specifications, which may extend as far as the infimae species. These specifications are obtained by the consideration of the other attributes of the subject of the relative attribution, which are henceforth no more than the “modes of advent” of the relation.
Revisiting the idea of degeneration in urban Britain, 1830–1900
Authors: LUCKIN BILL
Published: August 2006

This article traces the evolution of the idea of degeneration in urban Britain between the early nineteenth and early twentieth centuries. Rejecting approaches that reduce this richly eclectic, though savagely negative, world-view to a random bundle of prejudices underpinning the emergence of the ‘science’ of eugenics, the article focuses on distinctive environmental, medical and anti-urban determinants. Strong emphasis is also placed on shifting interactions between moral and medico-environmental values and prescriptions which served as legitimation for the racially inflected view that residual elements of the inner city working class might soon be doomed to physiological and hereditary extinction.
A Big Ben with Chinese characteristics: the Customs House as urban icon in Old and New Shanghai
Authors: WASSERSTROM JEFFREY N.
Published: August 2006

A huge clock, made at Whitechurch by Messrs. J. B. Joyce and Co … has been sent to Shanghai, for the new Chinese Maritime Customs House. The clock, weighing nearly 30 tons, will probably be the Big Ben of the Far East.
The American contribution to the urban sociology of race relations in Britain from the 1940s to the early 1970s
Authors: CLAPSON MARK
Published: August 2006

From the influence of the Chicago School of sociology upon studies of black and white relations in England and Wales during and since the early 1940s, to the role of the Ford Foundation in funding research into inter-ethnic problems in Britain's cities during the 1950s and 1960s, the framework for British studies of urban race relations was primarily based upon American points of reference. This American contribution was benign, as was further evidenced in the relationship of urban research to race relations policy in Britain after 1965.
Crime stories in the historical urban landscape: narrating the theft of the Mona Lisa
Authors: FREUNDSCHUH AARON
Published: August 2006

Taking the 1911 theft of the Mona Lisa from the Louvre Museum as a case study, this article examines the historical relation between crime storytelling and the myriad local struggles for spatial control that animate urban life. Modern Europe's most staggering art heist left city officials and police wholly clueless, and inspired a two-year outpouring of explanatory narratives from Parisians of virtually all social strata. This article shows how, in ostensibly making sense of the ‘impossible’ theft, the city's inhabitants imaginatively wove it into the social fabric of everyday life, thereby bringing the event to bear on a broad range of spatial tensions and rivalries. As they re-fashioned mass press versions of the theft to fit local concerns – both public and intimate – contemporaries understood crime stories as a tool with which to shape the city as they knew it.
Investigations of Reaction Kinetics for Immobilized Enzymes—Identification of Parameters in the Presence of Diffusion Limitation
Authors: Berendsen Wouter R. , Lapin Alexei , Reuss Matthias
Published: August 2006

A method is proposed for identification of kinetic parameters when diffusion of substrates is limiting in reactions catalyzed by immobilized enzymes. This method overcomes conventional sequential procedures, which assume immobilization does not affect the conformation of the enzyme and, thus, consider intrinsic and inherent kinetics to be the same. The coupled equations describing intraparticle mass transport are solved simultaneously using numerical methods and are used for direct estimation of kinetic parameters by fitting modeling results to time‐course measurements in a stirred tank reactor. While most traditional procedures were based on Michaelis‐Menten kinetics, the method presented here is applicable to more complex kinetic mechanisms involving multiple state variables, such as ping‐pong bi‐bi. The method is applied to the kinetic resolution of (R/S)‐1‐methoxy‐2‐propanol with vinyl acetate catalyzed by Candida antarctica lipase B. A mathematical model is developed consisting of irreversible ping‐pong bi‐bi kinetics, including competitive inhibition of both enantiomers. The kinetic model, which fits to experimental data over a wide range of both substrates (5–95%) and temperatures (5–56 °C), is used for simulations to study typical behavior of immobilized enzyme systems.
Representations of integral quadratic forms over dyadic local fields
Authors: Beli Constantin
Published: August 2006

In this paper we give necessary and sufficient conditions for the representations of quadratic lattices over arbitrary dyadic fields. Our result is given in terms of Bases of Norm Generators (BONGs, for short). However, they can be translated in terms of the more traditional Jordan decompositions.
AgSwe1p Regulates Mitosis in Response to Morphogenesis and Nutrients in MultinucleatedAshbya gossypiiCells
Authors: Helfer Hanspeter , Gladfelter Amy S.
Published: August 2006

Nuclei in the filamentous, multinucleated fungus Ashbya gossypii divide asynchronously. We have investigated what internal and external signals spatially direct mitosis within these hyphal cells. Mitoses are most common near cortical septin rings found at growing tips and branchpoints. In septin mutants, mitoses are no longer concentrated at branchpoints, suggesting that the septin rings function to locally promote mitosis near new branches. Similarly, cells lacking AgSwe1p kinase (a Wee1 homologue), AgHsl1p (a Nim1-related kinase), and AgMih1p phosphatase (the Cdc25 homologue that likely counteracts AgSwe1p activity) also have mitoses distributed randomly in the hyphae as opposed to at branchpoints. Surprisingly, however, no phosphorylation of the CDK tyrosine 18 residue, the conserved substrate of Swe1p kinases, was detected in normally growing cells. In contrast, abundant CDK tyrosine phosphorylation was apparent in starving cells, resulting in diminished nuclear density. This starvation-induced CDK phosphorylation is AgSwe1p dependent, and overexpressed AgSwe1p is sufficient to delay nuclei even in rich nutrient conditions. In starving cells lacking septins or AgSwe1p negative regulators, the nuclear density is further diminished compared with wild type. We have generated a model in which AgSwe1p may regulate mitosis in response to cell intrinsic morphogenesis cues and external nutrient availability in multinucleated cells.
Essential Role of Phosphorylation of MCM2 by Cdc7/Dbf4 in the Initiation of DNA Replication in Mammalian Cells
Authors: Tsuji Toshiya , Ficarro Scott B. , Jiang Wei
Published: August 2006

We report the identification of Cdc7/Dbf4 phosphorylation sites in human MCM2 and the determination of the role of Cdc7/Dbf4 phosphorylation of MCM2 in the initiation of DNA replication. Using immunoblotting, immunofluorescence, and high-speed automated cell-imaging analyses with antibodies specific against MCM2 and Cdc7/Dbf4 phosphorylated MCM2, we show that the chromatin recruitment and phosphorylation of MCM2 are regulated during the cell cycle in HeLa cells. Chromatin-bound MCM2 is phosphorylated by Cdc7/Dbf4 during G1/S, which coincides with the initiation of DNA replication. Moreover, we show that baculovirus-expressed purified MCM2-7 complex and its phosphomimetic MCM2E-7 complex display higher ATPase activity when compared with the nonphosphorylatable MCM2A-7 complex in vitro. Furthermore, suppression of MCM2 expression in HeLa cells by siRNA results in the inhibition of DNA replication. The inhibition can be rescued by the coexpression of wild type MCM2 or MCM2E but not MCM2A. Taken together, these results indicate that Cdc7/Dbf4 phosphorylation of MCM2 is essential for the initiation of DNA replication in mammalian cells.
Solvated docking: introducing water into the modelling of biomolecular complexes
Authors: van Dijk Aalt D. J. , Bonvin Alexandre M. J. J.
Published: August 2006

Motivation: Interfacial water, which plays an important role in mediating biomolecular interactions, has been neglected in the modelling of biomolecular complexes.

Methods: We present a solvated docking approach that explicitly accounts for the presence of water in protein–protein complexes. Our solvated docking protocol is based on the concept of the first encounter complex in which a water layer is present in-between the molecules. It mimics the pathway from this initial complex towards the final assembly in which most waters have been expelled from the interface. Docking is performed from solvated biomolecules and waters are removed in a biased Monte Carlo procedure based on water-mediated contact propensities obtained from an analysis of high-resolution crystal structures.

Results: We demonstrate the feasibility of this approach for protein–protein complexes representing both ‘wet’ and ‘dry’ interfaces. Solvated docking leads to improvements both in quality and scoring. Water molecules are recovered that closely match the ones in the crystal structures.

Availabilty: Solvated docking will be made available in the future release of HADDOCK version 2.0 ().

Contact:  a.m.j.j.bonvin@chem.uu.nl

Supplementary information:  Supplementary Data are available at Bioinformatics Online.
Meganema perideroedes gen. nov., sp. nov., a filamentous alphaproteobacterium from activated sludge
Authors: Thomsen Trine R. , Blackall Linda L. , de Muro Marilena Aquino , Nielsen Jeppe L. , Nielsen Per H.
Published: August 2006

An industrial wastewater treatment plant at Grindsted, Denmark, has suffered from bulking problems for several years caused by filamentous bacteria. Five strains were isolated from the sludge by micromanipulation. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains formed a monophyletic cluster in the Alphaproteobacteria, and they were phenotypically different from their closest relatives and from all hitherto known filamentous bacteria described (closest relative Brevundimonas vesicularis ATCC 11426T, 89.8 % sequence similarity). In pure culture, the cells (1.5–2.0 μm) in filaments are Gram-negative and contain polyphosphate and polyhydroxyalkanoates. The optimum temperature for growth is 30 °C and the strains grow in 2 % NaCl and are oxidase- and catalase-positive. Ubiquinone 10 is the major quinone. The major fatty acid (C18 : 1
ω7c) and smaller amounts of unsaturated fatty acids, 3-hydroxy fatty acids with a chain length of 16 and 18 carbon atoms and small amounts of 10-methyl-branched fatty acids with 18 carbon atoms (C19 : 0 10-methyl) affiliated the strains with the Methylobacterium/Xanthobacter group in the Alphaproteobacteria. The G+C content of the DNA is 42.9 mol% (for strain Gr1T). The two most dissimilar isolates by 16S rRNA gene comparison (Gr1T and Gr10; 97.7 % identical) showed 71.5 % DNA–DNA relatedness. Oligonucleotide probes specific for the pure cultures were designed for fluorescence in situ hybridization and demonstrated that two filamentous morphotypes were present in the Grindsted wastewater treatment plant. It is proposed that the isolates represent a new genus and species, Meganema perideroedes gen. nov., sp. nov. The type strain of Meganema perideroedes is strain Gr1T (=DSM 15528T=ATCC BAA-740T).
Catenulispora acidiphila gen. nov., sp. nov., a novel, mycelium-forming actinomycete, and proposal of Catenulisporaceae fam. nov.
Authors: Busti Elena , Cavaletti Linda , Monciardini Paolo , Schumann Peter , Rohde Manfred , Sosio Margherita , Donadio Stefano
Published: August 2006

A novel, Gram-positive bacterial strain was isolated from forest soil. Among species with validly published names, the 16S rRNA gene sequence is related most closely (approx. 93 % similarity) to that of Sporichthya polymorpha DSM 43042T. However, differently from this species, it forms both vegetative and aerial mycelia. The aerial hyphae are straight to slightly flexuous, starting to septate to form chains of more than 20 cylindrical spores with a rugose surface. The strain is acidophilic, with a pH range for robust growth between 4.3 and 6.8 and an optimum around 6.0. The peptidoglycan type is A3γ
ll-Dpm–Gly. The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. Predominant menaquinones are MK-9(H6) and -9(H4), and iso- and anteiso-branched C16 : 0 and C17 : 0 are the main cellular fatty acids. The DNA G+C content is 71.9 mol%. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics justify the proposal of Catenulispora gen. nov., with the type species Catenulispora acidiphila sp. nov. (type strain, ID139908T =DSM 44928T=NRRL B-24433T). Catenulisporaceae fam. nov. is also proposed.
Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter
Authors: Hwang Chung Yeon , Choi Dong Han , Cho Byung Cheol
Published: August 2006

A Gram-negative, pink-coloured, rod-shaped, non-flagellated bacterium, designated CL-GP80T, was isolated from a hypertrophic pond located within the campus of Seoul National University, Korea. Analysis of its 16S rRNA gene sequence revealed that strain CL-GP80T belongs to the family Sphingobacteriaceae and is closely related to Pedobacter heparinus ATCC 13125T (95.8 % sequence similarity) and to other members of the genus Pedobacter (90.8–95.3 % similarity). Temperature and pH ranges for growth were 5–33 °C and pH 6–8, respectively. The DNA G+C content was 41.3 mol%. The major fatty acids were iso-C15 : 0 (37.0 %), iso-C15 : 0 2-OH and/or C16 : 1
ω7c (24.5 %), and iso-C17 : 0 3-OH (11.3 %). Phenotypic, chemotaxonomic and phylogenetic analyses indicated that strain CL-GP80T could be assigned to the genus Pedobacter, but distinguished from recognized species of the genus. Strain CL-GP80T (=KCCM 42272T=JCM 13399T) is therefore proposed as the type strain of a novel species, for which the name Pedobacter roseus sp. nov. is proposed.
Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan
Authors: Kageyama Akiko , Iida Soji , Yazawa Katsukiyo , Kudo Takuji , Suzuki Shin-ichi , Koga Takeharu , Saito Hiromi , Inagawa Hiroko , Wada Akihito , Kroppenstedt Reiner M. , Mikami Yuzuru
Published: August 2006

Two bacterial strains, IFM 10211Tand IFM 10200T, were isolated from the sputum of two Japanese patients, and were subjected to a polyphasic taxonomic study. The two strains were found to have morphological, physiological and chemotaxonomic properties that were consistent with their assignment to the genusGordonia, except for a few chemotaxonomic characteristics. Almost complete 16S rRNA gene sequences of the two strains were determined; the data showed that they are related distantly toGordonia amarae,Gordonia hirsuta,Gordonia hydrophobicaandGordonia sihwensis, showing 16S rRNA gene sequence similarities to the type strains of these species of 96.2–97.9 %. DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel, separate species. The names proposed to accommodate these two strains areGordonia araiisp. nov. (type strain IFM 10211T=DSM 44811T=NBRC 100433T=JCM 12131T) andGordonia effusasp. nov. (type strain IFM 10200T=DSM 44810T=NBRC 100432T=JCM 12130T).
Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium
Authors: Yoon Jung-Hoon , Lee Jung-Kee , Jung Seo-Youn , Kim Jung-Ae , Kim Ha-Kun , Oh Tae-Kwang
Published: August 2006

A Gram-positive, rod- or coccoid-shaped andN-hexanoyl-l-homoserine lactone-degrading bacterial strain, A2-4T, was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4Tgrew optimally at pH 7.0–8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4Tis most closely related to members of the genusNocardioides. Strain A2-4Tpossessed chemotaxonomic properties indicative of members of the genusNocardioides; the cell-wall peptidoglycan type was based onll-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0was the predominant fatty acid. The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence of strain A2-4Twas 98.3–99.1 % similar to those of the type strains ofNocardioides simplex,Nocardioides aromaticivoransandNocardioides nitrophenolicusand 93.8–96.3 % similar to those of the type strains of otherNocardioidesspecies. Strain A2-4Tcould be distinguished from the three phylogenetic relatives,N. nitrophenolicus,N. aromaticivoransandN. simplex, by DNA–DNA relatedness (25–42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genusNocardioides, for which the nameNocardioides kongjuensissp. nov. is proposed. The type strain is A2-4T(=KCTC 19054T=JCM 12609T).
Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea
Authors: Kim Byung-Yong , Weon Hang-Yeon , Yoo Seung-Hee , Chen Wen-Ming , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: August 2006

Strain R2A43-10T was isolated from a greenhouse soil in Korea. Cells were Gram-negative rods, motile by means of a single flagellum. Growth occurred at 10–40 °C and at pH 5–8. Ubiquinone-8 (Q-8) was the only respiratory lipoquinone. Major fatty acids were summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. 16S rRNA gene sequence analysis revealed that strain R2A43-10T was closely related to Chitinimonas taiwanensis cfT (sequence similarity of 94.8 %), but it exhibited low sequence similarities (<92 %) to other members of the Betaproteobacteria. The G+C content of the genomic DNA of strain R2A43-10T was 65.0 mol%. The novel isolate could be differentiated from C. taiwanensis cfT by several physiological properties. On the basis of genomic and phenotypic data, it is concluded that R2A43-10T (=KACC 11467T=DSM 17726T) is the type strain of a novel species of the genus Chitinimonas, for which the name Chitinimonas koreensis sp. nov. is proposed.
Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum
Authors: Vanparys Bram , Heylen Kim , Lebbe Liesbeth , De Vos Paul
Published: August 2006

Sixteen Gram-negative, rod-shaped, non-spore-forming isolates were obtained from a nitrifying inoculum. Analysis of repetitive sequence-based PCR and SDS-PAGE banding patterns, 16S rRNA gene sequence analysis and DNA–DNA hybridizations showed that the isolates belonged to various groups within the genusPseudomonas. One group of isolates could be assigned toPseudomonas migulaeand a second toPseudomonas veronii. Two groups could be differentiated genotypically from each other and from all other currently knownPseudomonasspecies. Analysis of the fatty acid composition and physiological and biochemical tests allowed differentiation of these groups from their closest phylogenetic neighbours and they therefore represent two novel species within the genusPseudomonas, for which the namesPseudomonas pelisp. nov. andPseudomonas borborisp. nov. are proposed, with strains LMG 23201T(=DSM 17833T=R-20805T) and LMG 23199T(=DSM 17834T=R-20821T), respectively, as the type strains.
Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm
Authors: Choi Dong H. , Cho Byung C.
Published: August 2006

A rod-shaped marine bacterium, CL-TA03T, isolated from a biofilm in a coastal fish farm in Tongyeong, Korea, was characterized for physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the family Rhodobacteraceae. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of CL-TA03T were Thalassobius gelatinovorus and Thalassobius mediterraneus (95.6 % similarity). The sequence similarities between CL-TA03T and other type species of the Roseobacter lineage ranged from 92.4 to 95.4 %. Strain CL-TA03T is motile and grows on marine agar as colourless or beige colonies. The strain is able to grow optimally in the range of 3–5 % sea salts. It grows within a temperature range of 15–35 °C and at pH 6–10. The fatty acids are dominated by 18 : 1ω7c (64.1 %) and 11-methyl 18 : 1ω7c (10.6 %). The DNA G+C content is 57.2 mol%. According to physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, CL-TA03T is considered to represent a new genus in the family Rhodobacteraceae and the name Shimia marina gen. nov., sp. nov. is proposed. The type strain of Shimia marina is CL-TA03T (=KCCM 42117T=JCM 13038T).
Hoeflea alexandrii sp. nov., isolated from the toxic dinoflagellate Alexandrium minutum AL1V
Authors: Palacios Lucía , Arahal David R. , Reguera Beatriz , Marín Irma
Published: August 2006

A Gram-negative, aerobic, non-symbiotic bacterium (AM1V30T) was isolated from the toxic dinoflagellate Alexandrium minutum AL1V. On the basis of 16S rRNA gene sequence similarity, strain AM1V30T was most closely related (97.4 % similarity) to the type strain of Hoeflea marina, which belongs to the family Phyllobacteriaceae within the order Rhizobiales of the class Alphaproteobacteria. A polyphasic approach was used to clarify the taxonomic position of strain AM1V30T. During the course of this study, a second species was described by others as belonging to the genus Hoeflea, namely Hoeflea phototrophica; it showed a somewhat higher level of 16S rRNA gene sequence similarity with respect to strain AM1V30T (98.2 %) and was also taken into account. The fatty acid profiles, physiological and biochemical data and DNA G+C content (59.7 mol%) support the classification of strain AM1V30T as a member of the genus Hoeflea. The characteristics of the novel strain were sufficiently distinct to indicate that it represents a separate species. To confirm this conclusion, DNA–DNA hybridizations were performed: low values (between 15.8 and 29.8 %) were obtained in all cases. Thus, AM1V30T represents a novel species within the genus Hoeflea, for which the name Hoeflea alexandrii sp. nov. is proposed. Strain AM1V30T (=CECT 5682T=DSM 16655T) is the type strain.
Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas
Authors: Takai Ken , Suzuki Masae , Nakagawa Satoshi , Miyazaki Masayuki , Suzuki Yohey , Inagaki Fumio , Horikoshi Koki
Published: August 2006

A novel mesophilic bacterium, strain GO25T, was isolated from a nest of hydrothermal vent polychaetes,Paralvinellasp., at the Iheya North field in the Mid-Okinawa Trough. Cells were motile short rods with a single polar flagellum. Growth was observed between 4 and 35 °C (optimum 30 °C; 13–16 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.1). The isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or thiosulfate as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source and elemental sulfur, thiosulfate or yeast extract as the sole sulfur source. Strain GO25Trepresents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation. Nitrate or molecular oxygen (up to 10 % partial pressure) could serve as the sole electron acceptor to support growth. Metabolic products of nitrate reduction shifted in response to the electron donor provided. The G+C content of genomic DNA was 37.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genusSulfurimonasand was most closely related toSulfurimonas autotrophicaOK10T(96.3 % sequence similarity). DNA–DNA hybridization demonstrated that the novel isolate could be differentiated genotypically fromSulfurimonas autotrophicaOK10T. On the basis of the physiological and molecular properties of the novel isolate, the nameSulfurimonas paralvinellaesp. nov. is proposed, with strain GO25T(=JCM 13212T=DSM 17229T) as the type strain.Thiomicrospira denitrificansDSM 1251T(=ATCC 33889T) is phylogenetically associated withSulfurimonas autotrophicaOK10TandSulfurimonas paralvinellaeGO25T. Based on the phylogenetic relationship betweenThiomicrospira denitrificansDSM 1251T,Sulfurimonas autotrophicaOK10TandSulfurimonas paralvinellaeGO25T, we propose the reclassification ofThiomicrospira denitrificansasSulfurimonas denitrificanscomb. nov. (type strain DSM 1251T=ATCC 33889T). In addition, an emended description of the genusSulfurimonasis proposed.
Description of Pseudochrobactrum gen. nov., with the two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov.
Authors: Kämpfer Peter , Rosselló-Mora Ramon , Scholz Holger C. , Welinder-Olsson Christina , Falsen Enevold , Busse Hans-Jürgen
Published: August 2006

Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (CCUG 46016T and CCUG 33852T), isolated from a knee aspirate of a 66-year-old man and an industrial glue, respectively, were studied for their taxonomic position. On the basis of chemotaxonomic data [i.e. major ubiquinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine) and major fatty acids (C18 : 1
ω7c and C19 : 0 cyclo ω8c)] and 16S rRNA gene sequence similarity, both strains belong to the Alphaproteobacteria. The presence of spermidine and putrescine as the predominant polyamines in CCUG 46016T were in agreement with its phylogenetic affiliation in the vicinity of the genus Ochrobactrum. 16S rRNA gene sequence similarities between both strains and established species within the genera Bartonella, Ochrobactrum and Brucella were less than 95 %. Although both organisms showed highest 16S rRNA gene sequence similarity to members of Brucella, phenotypic features (including chemotaxonomic features) were more like those of members of the genus Ochrobactrum. Sequence comparison of the recA genes confirmed the separate phylogenetic position of the two strains. On the basis of DNA–DNA pairing results and physiological and biochemical data, the two strains can be clearly differentiated from each other and from all known Ochrobactrum species. It is evident that these organisms represent two novel species in a new genus, Pseudochrobactrum gen. nov., for which the names Pseudochrobactrum asaccharolyticum sp. nov. (the type species, type strain CCUG 46016T=CIP 108977T) and Pseudochrobactrum saccharolyticum sp. nov. (type strain CCUG 33852T=CIP 108976T) are proposed.
Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan
Authors: Tai Chun-Ju , Kuo Hsiao-Ping , Lee Fwu-Ling , Chen Han-Ken , Yokota Akira , Lo Chi-Chu
Published: August 2006

Among a large collection of Taiwanese soil isolates, a novel Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterial strain, Soil-3-27T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, fatty acid analysis and comparative phenotypic characterization. The 16S rRNA gene sequence analysis indicated that the organism belongs to the genus Chryseobacterium. The organism contains menaquinone MK-6 as the predominant isoprenoid quinone and 15 : 0 iso (43 %), 17 : 1 isoω9c (17.5 %) and 17 : 0 iso 3-OH (16.6 %) as the major fatty acids. Phylogenetically, the closest relatives of strain Soil-3-27T are Chryseobacterium daecheongense, Chryseobacterium defluvii and Chryseobacterium taichungense with 96.7–97.2 % sequence similarity. DNA–DNA hybridization showed relatedness values of 8.5–24.2 % with these species. The DNA G+C content is 36.8 mol%. Strain Soil-3-27T is clearly distinguishable from other Chryseobacterium species and represents a novel species, for which the name Chryseobacterium taiwanense sp. nov. is proposed. The type strain is strain Soil-3-27T (=BCRC 17412T=IAM 15317T=LMG 23355T).
Molecular-genetic diversity of the ascomycetous yeast genus Arthroascus: Arthroascus babjevae sp. nov., Arthroascus fermentans var. arxii var. nov. and geographical populations of Arthroascus schoenii
Authors: Naumov Gennadi I. , Naumova Elena S. , Smith Maudy Th. , de Hoog G. Sybren
Published: August 2006

Using molecular and genetic analyses, 28Arthroascusstrains were analysed, isolated from widely different geographical localities in Europe, North America, Far-East Asia and Hawaii. Most of the strains have been assigned to the speciesArthroascus schoenii. PCR-RAPD revealed two JapaneseArthroascusstrains (UCD 67-278 and IFO 10138) to have peculiar patterns. Comparative rDNA (D1/D2 26S, ITS1 and ITS2) sequence analysis showed that the two strains respectively represent a novel species and a novel variety. Based on the results of sequence analysis, genetic hybridization and DNA–DNA reassociation, two new members of the genusArthroascusare formally described,Arthroascus babjevaesp. nov. (type strain UCD 67-278T=CBS 9167T) andArthroascus fermentansvar.arxiivar. nov. (type strain IFO 10138T=CBS 9168T). These results show thatA. schoeniihas a worldwide distribution, while the speciesArthroascus javanensisis represented only by the type culture CBS 2555T, isolated in Indonesia. Cluster analysis revealed a correlation between PCR-RAPD fingerprints and geographical origin of theA. schoeniistrains. Despite this molecular differentiation,A. schoeniistrains collected in different regions of the world formed predominantly fertile hybrids, with normal recombination of control markers.