bluuebunny/crossref_metadata_2025 huggingface dataset:
Rheumatoid arthritis with diffuse pulmonary rheumatoid nodules
Authors: Kitamura Atsuko , Matsuno Tadakatsu , Narita Michihiko , Shimokata Kaoru , Yamashita Yoriko , Mori Naoyoshi
Published: October 2004

Rheumatoid nodules in dermal or subcutaneous tissues, while indicative of rheumatoid arthritis, are very rare. It is even less common to identify these rheumatoid nodules by biopsy as well as in autopsy materials from lung tissue. These nodules may be single or multiple, which seldom cause respiratory symptoms. Here, a patient with diffuse pulmonary rheumatoid nodules and interstitial fibrosis throughout both lungs, is described. The patient, with articular symptoms and seropositivity, exhibited a rapid clinical course and died of respiratory failure 3  months after the appearance of dyspnea. Chest radiography indicated interstitial pneumonitis with bilateral diffuse peripheral shadows. At autopsy, numerous rheumatoid nodules and interstitial fibrosis had destroyed both lungs, such that no residual normal pulmonary tissue remained. It is believed that this was an extremely rare case exhibiting large numbers of rheumatoid nodules throughout the lungs. Findings with this patient indicate that, in patients with rheumatoid arthritis, clinical interstitial pneumonitis confirmed radiologically does not exclude the existence of rheumatoid lung nodules.
Esophageal carcinosarcoma with basaloid squamous carcinoma and rhabdomyosarcoma components with TP53 mutation
Authors: Amatya Vishwa Jeet , Takeshima Yukio , Kaneko Mayumi , Inai Kouki
Published: October 2004

Carcinosarcoma of the esophagus is a rare tumor with a distinct pathological entity having squamous cell carcinoma as the most described carcinomatous component. This paper reports the first case of carcinosarcoma of the esophagus that showed predominant basaloid squamous carcinoma component in addition to squamous cell carcinoma and poorly differentiated carcinoma and sarcoma component. A 64‐year‐old male patient consulted for dysphasia and chest pain was examined and found to have gastrointestinal fiber‐endoscope and a polypoid growth in the lower third of the esophagus. Partial esophagectomy was performed and the excised tumor showed histological features of carcinosarcoma with heterogeneous carcinomatous components with dominance of basaloid squamous carcinoma and minority of squamous cell carcinoma, poorly differentiated carcinoma, and sarcomatous component, immunohistochemically proven to be rhabdomyosarcoma. Immunohistochemical study and TP53 mutation analysis was carried out to explain the histogenesis of this rare tumor. The distinct immunohistochemical profiles of the carcinomatous and sarcomatous components suggested the possibility of transition from a carcinomatous to a sarcomatous component. The similar TP53 mutation in the carcinomatous and sarcomatous component suggested each of these components had the same origin, that is, the tumor was monoclonal in origin.
Productivity gradients cause positive diversity–invasibility relationships in microbial communities
Authors: Jiang Lin , Morin Peter J.
Published: October 2004

Models predict that community invasibility generally declines with species diversity, a prediction confirmed by small‐scale experiments. Large‐scale observations and experiments, however, find that diverse communities tend to be more heavily invaded than simple communities. One hypothesis states that large‐scale environmental heterogeneity, which similarly influences native and invasive species, can cause a positive correlation between diversity and invasibility, overriding the local negative effects of diversity on invasibility. We tested this hypothesis using aquatic microbial communities consisting of protists and rotifers consuming bacteria and nanoflagellates. We constructed a productivity gradient to simulate large‐scale environmental heterogeneity, started communities with the same number of species along this gradient, and subjected equilibrial communities to invasion by non‐resident consumer species. Both invaders and most resident species increased their abundances with resource enrichment, resulting in a positive correlation between diversity and invasibility. Intraspecific interference competition within resident species and the positive effect of enrichment on the number of available resources probably accounted for the higher invasibility with enrichment. Our results provide direct experimental evidence that environmental heterogeneity in productivity can cause a positive diversity–invasibility relationship.
The area requirements of an ecosystem service: crop pollination by native bee communities in California
Authors: Kremen Claire , Williams Neal M. , Bugg Robert L. , Fay John P. , Thorp Robin W.
Published: October 2004

Managing ecosystem services is critical to human survival, yet we do not know how large natural areas must be to support these services. We investigated how crop pollination services provided by native, unmanaged, bee communities varied on organic and conventional farms situated along a gradient of isolation from natural habitat. Pollination services from native bees were significantly, positively related to the proportion of upland natural habitat in the vicinity of farm sites, but not to any other factor studied, including farm type, insecticide usage, field size and honeybee abundance. The scale of this relationship matched bee foraging ranges. Stability and predictability of pollination services also increased with increasing natural habitat area. This strong relationship between natural habitat area and pollination services was robust over space and time, allowing prediction of the area needed to produce a given level of pollination services by wild bees within this landscape.
Protocols for listing threatened species can forecast extinction
Authors: Keith David A. , McCarthy Michael A. , Regan Helen , Regan Tracey , Bowles Christy , Drill Claire , Craig Corey , Pellow Belinda , Burgman Mark A. , Master Larry L. , Ruckelshaus Mary , Mackenzie Berin , Andelman Sandy J. , Wade Paul R.
Published: October 2004

Risk‐ranking protocols are used widely to classify the conservation status of the world's species. Here we report on the first empirical assessment of their reliability by using a retrospective study of 18 pairs of bird and mammal species (one species extinct and the other extant) with eight different assessors. The performance of individual assessors varied substantially, but performance was improved by incorporating uncertainty in parameter estimates and consensus among the assessors. When this was done, the ranks from the protocols were consistent with the extinction outcome in 70–80% of pairs and there were mismatches in only 10–20% of cases. This performance was similar to the subjective judgements of the assessors after they had estimated the range and population parameters required by the protocols, and better than any single parameter. When used to inform subjective judgement, the protocols therefore offer a means of reducing unpredictable biases that may be associated with expert input and have the advantage of making the logic behind assessments explicit. We conclude that the protocols are useful for forecasting extinctions, although they are prone to some errors that have implications for conservation. Some level of error is to be expected, however, given the influence of chance on extinction. The performance of risk assessment protocols may be improved by providing training in the application of the protocols, incorporating uncertainty in parameter estimates and using consensus among multiple assessors, including some who are experts in the application of the protocols. Continued testing and refinement of the protocols may help to provide better absolute estimates of risk, particularly by re‐evaluating how the protocols accommodate missing data.
No tree an island: the plant–caterpillar food web of a secondary rain forest in New Guinea
Authors: Novotny Vojtech , Miller Scott E. , Leps Jan , Basset Yves , Bito Darren , Janda Milan , Hulcr Jiri , Damas Kipiro , Weiblen George D.
Published: October 2004

We characterized a plant–caterpillar food web from secondary vegetation in a New Guinean rain forest that included 63 plant species (87.5% of the total basal area), 546 Lepidoptera species and 1679 trophic links between them. The strongest 14 associations involved 50% of all individual caterpillars while some links were extremely rare. A caterpillar randomly picked from the vegetation will, with ≥ 50% probability, (1) feed on one to three host plants (of the 63 studied), (2) feed on < 20% of local plant biomass and (3) have ≥ 90% of population concentrated on a single host plant species. Generalist species were quantitatively unimportant. Caterpillar assemblages on locally monotypic plant genera were distinct, while sympatric congeneric hosts shared many caterpillar species. The partitioning of the plant–caterpillar food web thus depends on the composition of the vegetation. In secondary forest the predominant plant genera were locally monotypic and supported locally isolated caterpillar assemblages.
Aggregated seed dispersal by spider monkeys limits recruitment to clumped patterns in Virola calophylla
Authors: Russo Sabrina E. , Augspurger Carol K.
Published: October 2004

The initial spatial pattern of seed deposition influences plant population and community structure, particularly when that pattern persists through recruitment. In a vertebrate‐dispersed rain forest tree, Virola calophylla, we found that spatially aggregated seed deposition strongly influenced the spatial structure of later stages. Seed dispersion was clumped, and seed densities were highest underneath V. calophylla females and the sleeping sites of spider monkeys (Ateles paniscus), the key dispersal agent. Although these site types had the lowest per capita seed‐to‐seedling survival, they had the highest seedling/sapling densities. Conversely, seed and seedling/sapling densities were lowest, and seed survival was highest, at sites of diurnal seed dispersal by spider monkeys. Negative density‐dependent and positive distance‐dependent seed survival thinned seed clumps. Nonetheless, the clumped dispersion at sleeping and parental sites persisted to the seedling/sapling stage because differences in seed deposition were large enough to offset differences in seed survival among these site types.
Parallel influence of climate on the behaviour of Pacific killer whales and Atlantic bottlenose dolphins
Authors: Lusseau David , Williams Rob , Wilson Ben , Grellier Kate , Barton Tim R. , Hammond Philip S. , Thompson Paul M.
Published: October 2004

The grouping behaviour of animals is governed by intrinsic and extrinsic factors which play an important role in shaping their social organization. We investigated the influence of ocean climate variation on the grouping behaviour of two widely separated populations of cetaceans, inhabiting north Atlantic and north Pacific coastal waters. The group size of both bottlenose dolphins in the Moray Firth, UK, and killer whales in Johnstone Strait, Canada, varied from year to year in relation to large‐scale ocean climate variation. Local indices of prey abundance were also related both to climate indices and predator group sizes. The cetaceans tended to live in smaller groups when there was less salmon available in both areas which seem to occur 2 years after a lower phase of the North Atlantic and Pacific Decadal Oscillations. These findings suggest that, even in highly social mammals, climate variation may influence social organization through changes in prey availability.
Maladaptive Peer Relationships and the Development of Relational and Physical Aggression During Middle Childhood
Authors: Werner Nicole E. , Crick Nicki R.
Published: October 2004

This study examined the unique roles of peer rejection and affiliation with aggressive peers in the development of relational and physical aggression in a sample of 979 2nd through 4th grade children. Information about target children and their best friends’ aggression and peer rejection was gathered via peer‐nominations when the majority of children were in the 3rd grade, and again approximately one year later. Friendships were identified by having target children nominate their three best friends in their classroom. Path analyses conducted with children who had at least one reciprocated friendship revealed that peer rejection and friends’ aggression predicted changes in target children's aggression; however, the patterns of relations varied by gender and form of aggression. Higher initial levels of rejection and friends’ relational aggression predicted increases in relational aggression among girls only, whereas rejection and friends’ physical aggression predicted increases in physical aggression among boys and girls. The significance of these results for the application of peer influence theories to relational aggression, and to females, is discussed.
Low and Middle Income Mothers’ Regulation of Negative Emotion: Effects of Children's Temperament and Situational Emotional Responses
Authors: Martini Tanya S. , Root Carol A. , Jenkins Jennifer M.
Published: October 2004

The present study investigated the effects of situational (child situational emotions) and dispositional (child temperament) child variables on mothers’ regulation of their own hostile (anger) and nonhostile (sadness and anxiety) emotions. Participants included 94 low and middle income mothers and their children (41 girls; 53 boys) aged 3 to 6 years. Children's situational emotions (anger, sadness, or fear) and parent emotion type (hostile or nonhostile) were important predictors of mothers’ regulation, but their effects were influenced by SES: Middle income mothers were more likely to control hostile than nonhostile emotions in response to child anger and sadness, and more likely than low income mothers to control hostile emotions in response to child sadness and fear. Low income mothers were more likely than middle income mothers to control nonhostile emotions in response to child anger. However, results also suggest that differences in emotion regulation between low and middle income mothers may stem from the link between SES and authoritarian parenting beliefs. Maternal regulation of negative emotion was not predicted by child temperament.
Stability in Center Day Care: Relations with Children's Well‐being and Problem Behavior in Day Care1
Authors: Schipper J. Clasien de , IJzendoorn Marinus H. Van , Tavecchio Louis W. C.
Published: October 2004

Mothers and primary professional caregivers of 186 children, aged 6–30 months, participated in this study in which a new measure for daily stability in center day care was developed, describing staffing, grouping, and program features. Relative contributions of infants’ daily experiences of care stability, quality of care, and mother's daily stress to the child's adjustment to day care were analyzed with hierarchical regressions. The child's adjustment was assessed with the Child Behavior Checklist (Achenbach, 1997) and with the Leiden Inventory for the Child's Well‐being in Day Care. Children enrolled in fewer care arrangements showed less internalizing behavior and more well‐being in the day care setting. Children had higher well‐being scores when trusted caregivers were more available. Mother's family management stress was related to more internalizing problem behavior. Interactions between mother's daily stress and stability in care were found to affect the child's adjustment to day care.
Children's Perceptions of Family Relationships as Assessed in a Doll Story Completion Task: Links to Parenting, Social Competence, and Externalizing Behavior
Authors: Laible Deborah , Carlo Gustavo , Torquati Julia , Ontai Lenna
Published: October 2004

This study was designed to examine the links between parenting, children's perceptions of family relationships, and children's social behavior. Seventy‐four children (M age=6.01 years; 39 boys; 35 girls) and their parents took part in the study. Children completed relationship‐oriented doll stories that were coded for coherence, prosocial themes, and aggressive themes. Parents completed a report of their child's social behavior, a parenting scale, and a number of demographic items. Teachers also completed measures of children's social competence and externalizing behavior. Warm parenting predicted both a child's representation of prosocial themes in the doll stories and social competence, whereas harsh parenting predicted both a child's use of aggressive themes in the doll stories and a child's externalizing behavior. These findings support the idea that children are constructing models of relationships out of the early interactions with caregivers, and that they use these representations to guide their social behavior.
Self‐perceptions of Social Competence and Self‐worth in Chinese Children: Relations with Social and School Performance
Authors: Chen Xinyin , He Yunfeng , Li Dan
Published: October 2004

The purpose of the study was to examine relations between self‐perceptions of social competence and general self‐worth and social and school performance in Chinese children. A sample of children, initially aged 12 years, in the People's Republic of China, participated in this longitudinal study. Data on self‐perceptions were collected from self‐reports. Data on social and school performance were obtained from multiple sources including peer assessments, teacher ratings and school records. The results indicated that relations between self‐perceptions and performance might vary across domains. Self‐perceptions of self‐worth and school competence mutually contributed to the prediction of each other. Whereas sociability and aggression predicted self‐perceptions of social competence and self‐worth, positive self‐perceptions might be a protective factor that buffered against the development of social‐behavioral problems. The results may help us understand developmental antecedents and outcomes of children's self‐perceptions of social competence and self‐worth in general, and the nature of the phenomena in the Chinese context.
EVIDENCE THEORY: A MATHEMATICAL FRAMEWORK FOR UNPREDICTABLE HYPOTHESES
Authors: Fioretti Guido
Published: October 2004

Shafer's evidence theory is a branch of the mathematics of uncertain reasoning that allows for novel possibilities to be conceived by a decision‐maker. Many of its findings exhibit striking similarities with an alternative decision theory put forward by Shackle in the 1950s, before expected utility maximization monopolized the scene. Evidence theory does not attempt to formalize the emergence of novelties, but it is a suitable framework for reconstructing the formation of beliefs when novelties appear. An application to decision‐making in the biotech and pharmaceutical industries illustrates the potentialities of evidence theory, as well as its shortcomings.
RETHINKING ENDOGENOUS MONEY: A CONSTRUCTIVE INTERPRETATION OF THE DEBATE BETWEEN HORIZONTALISTS AND STRUCTURALISTS
Authors: Fontana Giuseppe
Published: October 2004

Beyond a widespread agreement on the idea that ‘loans create deposits’ and ‘deposits make reserves’, there is much controversy in the endogenous money literature over the workings of the reserve market, the credit market and the financial markets. In this paper a constructive interpretation of the debate between horizontalists and structuralists is suggested and their arguments are taken forward by showing that these controversial issues can be explained rigorously once a single‐period–continuation framework is adopted.
ENDOGENOUS TECHNOLOGICAL INNOVATION, CAPITAL ACCUMULATION AND DISTRIBUTIONAL DYNAMICS
Authors: Lima Gilberto Tadeu
Published: October 2004

This paper develops a post‐Keynesian dynamic model of accumulation, growth and distribution in which endogenous technological innovation plays a significant role. Firms’ rate of labour‐saving technological innovation is made to depend non‐linearly on the distributive (wage and profit) shares, with the latter determining both the incentives to innovate and the availability of funding to carry it out. As it turns out, the direction and the intensity of the effect of a change in distribution on the rates of accumulation and growth depend on the prevailing distribution, with a similar dependence applying—alongside the relative bargaining power of capitalists and workers—to the dynamic stability properties of the system. Hence, the model does not rely on full capacity utilization being reached for a change in the accumulation and growth regime to take place.
DO RISING REAL WAGES INCREASE THE RATE OF LABOR‐SAVING TECHNICAL CHANGE? SOME ECONOMETRIC EVIDENCE
Authors: Marquetti Adalmir
Published: October 2004

The long‐run relationship between real wages and labor productivity is investigated using cointegration and Granger non‐causality tests for the US economy over the period 1869–1999. The series are cointegrated, indicating that there is a link between real wages and labor productivity in the long run. Granger non‐causality tests support unidirectional causation from real wages to labor productivity. This outcome corroborates the conception that increases in real wages drive profit‐seeking capitalists to raise labor productivity as their main weapon in defending their profitability. This result is consistent with a long tradition among economists that perceives technical change as being biased toward labor‐saving.
DECONSTRUCTING THE LABOUR SUPPLY CURVE
Authors: Spencer David A.
Published: October 2004

The nature and determinants of the supply of labour are re‐examined. Standard theories of labour supply, it is argued, have neglected to consider the affects of the quality of work activities on the motivation and welfare of workers. Work has tended to be seen as a means to an end rather than an end in itself and most attention has been given to the manipulation of wage incentives in affecting labour supply, to the neglect of changes in the work environment. The original contributions of W. Stanley Jevons and Alfred Marshall, in contrast, are shown to offer a fuller account of the work decision.
Multi‐Agency Collaboration: The Challenges for CAMHS
Authors: Salmon Gill
Published: October 2004

The importance of multi‐agency collaboration has been emphasised in virtually every piece of recently published guidance relating to the development of children's services including CAMHS. The Government Green Paper, Every child matters (DfES, 2003), which proposes the development of Children's Trusts, will further impact on this agenda. Surprisingly, there has been much less written about factors contributing to the success of multi‐agency collaboration than there has about barriers to it. Research is beginning to emerge informing on key criteria required for the development of multi‐agency collaborations for children with mental health problems. Much work remains to be undertaken on the use of language and definitions between agencies before a common understanding about children's needs and the services they require can evolve.
Working with Young People with Complex Needs: Practitioners’ Views
Authors: Worrall‐Davies Anne , Kiernan Katherine , Anderton Nicola , Cottrell David
Published: October 2004

Background:  We report the findings of a descriptive study exploring the views of practitioners working with young people with especially challenging and complex problems, currently cared for by children's services across Yorkshire. We present data on a sample of 79 young people with complex needs, aged 7 to 16 years, in contact with one or more of the children's services.

Method:  We identified the practitioner working most closely with each of these young people. The practitioners were interviewed using a semi‐structured interview schedule designed to encourage professionals to reflect on working practices. Interviews were recorded and transcribed and themes categorized using a coding framework.

Results and conclusions:  We describe and discuss the key themes in the context of current strategic developments of children's services.
Measuring Educational Standards
Authors: Goldstein Harvey
Published: October 2004

Every summer, when English public examination results appear, there is a debate within the media about whether “educational standards” are changing. Harvey Goldstein argues that much of what passes for informed debate in the English media is both irrelevant and ill informed, and that there is no purely objective, statistical, means for measuring changes in “standards”.
Business and Industrial Statistics: The Early Years
Authors: Barnard George
Published: October 2004

Before his death in July 2002, George Barnard had started writing a sketch of the history of business and industrial statistics in the first 50 years of the twentieth century. The piece was never finished, but it is nonetheless a valuable memoir of the early development of the discipline, from someone who knew those involved.
Exploring the Relationship Between Gold and the Dollar
Authors: Mills Terence
Published: October 2004

It has often been argued that one of the reasons for holding gold is as a hedge against currency movements. An exploratory data analysis to examine the validity of this theory can be carried out quickly and simply, using some of the wide and varied range of nonparametric techniques now incorporated into statistical software—but, as Terence Mills shows, such a superficial investigation can lead to interpretations that deeper data analysis shows to be flawed.
A Fairground Game
Authors: Atkinson Richard , Haigh John
Published: October 2004

People who play fairground games that offer monetary prizes do not expect to win money. Some bias in favour of the house is essential for a game to be viable, but how large a bias is reasonable? Richard Atkinson and John Haigh ask: Are some games too unfair?
The Pensions Crisis
Authors: Pomery Michael
Published: October 2004

Michael Pomery, the newly appointed President of the Institute of Actuaries, will be leading the actuarial profession in interesting times. Not only does the profession face a government review after criticism of its role in the Equitable Life drama, but, as Pomery tells Helen Joyce, it is at the centre of the unfolding pensions crisis.
Dicing with the Unknown
Authors: O'Hagan Tony
Published: October 2004

There are many things that I am uncertain about, says Tony O'Hagan. Some are merely unknown to me, while others are unknowable. This article is about different kinds of uncertainty, and how the distinction between them impinges on the foundations of Probability and Statistics.
Bastardy in the UK
Authors: Spiegelhalter David
Published: October 2004

Joseph Fletcher's monumental articles “Moral and educational statistics of England and Wales” were introduced as “a few facts illustrative of the moral and intellectual condition of the English people”, but went on to 237 pages of analysis and discussion of data on, for example, education, crime, “improvident marriages”, bastardy, pauperism and savings. The data are reported for individual counties and are notable for their illustration with early examples of shaded maps of relative rates.
A Model Company
Authors: Lauritzen Steffen
Published: October 2004

HUGIN Expert is a small company writing software that can be used to create expert systems, using probability in the guise of graphical models. Steffen Lauritzen describes his part in the genesis and development of the company.
A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression
Authors: Mandal Maumita , Lee Mark , Barrick Jeffrey E. , Weinberg Zasha , Emilsson Gail Mitchell , Ruzzo Walter L. , Breaker Ronald R.
Published: October 2004

We identified a previously unknown riboswitch class in bacteria that is selectively triggered by glycine. A representative of these glycine-sensing RNAs from
Bacillus subtilis
operates as a rare genetic on switch for the
gcvT
operon, which codes for proteins that form the glycine cleavage system. Most glycine riboswitches integrate two ligand-binding domains that function cooperatively to more closely approximate a two-state genetic switch. This advanced form of riboswitch may have evolved to ensure that excess glycine is efficiently used to provide carbon flux through the citric acid cycle and maintain adequate amounts of the amino acid for protein synthesis. Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors.
Rescue of Cardiac Defects in
Id
Knockout Embryos by Injection of Embryonic Stem Cells
Authors: Fraidenraich Diego , Stillwell Elizabeth , Romero Elizabeth , Wilkes David , Manova Katia , Basson Craig T. , Benezra Robert
Published: October 2004

We report that Id knockout mouse embryos display multiple cardiac defects, but mid-gestation lethality is rescued by the injection of 15 wild-type embryonic stem (ES) cells into mutant blastocysts. Myocardial markers altered in Id mutant cells are restored to normal throughout the chimeric myocardium. Intraperitoneal injection of ES cells into female mice before conception also partially rescues the cardiac phenotype with no incorporation of ES cells. Insulin-like growth factor 1, a long-range secreted factor, in combination with WNT5a, a locally secreted factor, likely account for complete reversion of the cardiac phenotype. Thus, ES cells have the potential to reverse congenital defects through Id-dependent local and long-range effects in a mammalian embryo.
Carbonyl Sulfide-Mediated Prebiotic Formation of Peptides
Authors: Leman Luke , Orgel Leslie , Ghadiri M. Reza
Published: October 2004

Almost all discussions of prebiotic chemistry assume that amino acids, nucleotides, and possibly other monomers were first formed on the Earth or brought to it in comets and meteorites, and then condensed nonenzymatically to form oligomeric products. However, attempts to demonstrate plausibly prebiotic polymerization reactions have met with limited success. We show that carbonyl sulfide (COS), a simple volcanic gas, brings about the formation of peptides from amino acids under mild conditions in aqueous solution. Depending on the reaction conditions and additives used, exposure of α-amino acids to COS generates peptides in yields of up to 80% in minutes to hours at room temperature.
Genome Sequence of a Polydnavirus: Insights into Symbiotic Virus Evolution
Authors: Espagne Eric , Dupuy Catherine , Huguet Elisabeth , Cattolico Laurence , Provost Bertille , Martins Nathalie , Poirié Marylène , Periquet Georges , Drezen Jean Michel
Published: October 2004

Little is known of the fate of viruses involved in long-term obligatory associations with eukaryotes. For example, many species of parasitoid wasps have symbiotic viruses to manipulate host defenses and to allow development of parasitoid larvae. The complete nucleotide sequence of the DNA enclosed in the virus particles injected by a parasitoid wasp revealed a complex organization, resembling a eukaryote genomic region more than a viral genome. Although endocellular symbiont genomes have undergone a dramatic loss of genes, the evolution of symbiotic viruses appears to be characterized by extensive duplication of virulence genes coding for truncated versions of cellular proteins.
Microscopic Observation Drug Susceptibility Assay, a Rapid, Reliable Diagnostic Test for Multidrug-Resistant Tuberculosis Suitable for Use in Resource-Poor Settings
Authors: Moore David A. J. , Mendoza Daniel , Gilman Robert H , Evans Carlton A. W. , Hollm Delgado María-Graciela , Guerra Jose , Caviedes Luz , Vargas Daniel , Ticona Eduardo , Ortiz Jaime , Soto Giselle , Serpa Jose
Published: October 2004

There is an urgent need for new tools to improve our ability to diagnose tuberculosis (TB) and multidrug-resistant TB (MDR-TB) in resource-poor settings. In a retrospective analysis undertaken in a region with a high incidence of TB, we evaluated the performance of the microscopic observation drug susceptibility assay (MODS), a novel assay developed in Perú which uses an inverted light microscope and culture in Middlebrook 7H9 broth to detect mycobacterial growth. MODS detected 94.0% of 1,908 positive sputum cultures, whereas Löwenstein-Jensen (LJ) culture detected only 86.9% (
P
< 0.001). The median time to culture positivity was 8 days (compared to 16 days for the same 208 samples by LJ culture;
P
< 0.001, Wilcoxon signed rank test). The results obtained by direct susceptibility testing using MODS demonstrated excellent concordance for isoniazid and rifampin and the detection of multidrug resistance with those obtained by indirect colorimetric methods: the microplate Alamar Blue assay (MABA) and the tetrazolium microplate assay (TEMA) (agreement, 95, 98, and 94%; kappa values, 0.8, 0.7, and 0.7, respectively). The concordance of the susceptibility testing results for ethambutol and streptomycin was poor. MODS is a novel assay which can detect the organisms responsible for TB and MDR-TB directly from sputum inexpensively, rapidly, and effectively. A comprehensive prospective evaluation of MODS is under way in Perú, and independent validation in nonresearch laboratories should be undertaken at the earliest opportunity.
Direct Detection of Rifampin-ResistantMycobacterium tuberculosisin Respiratory Specimens by PCR-DNA Sequencing
Authors: Yam W. C. , Tam C. M. , Leung C. C. , Tong H. L. , Chan K. H. , Leung E. T. Y. , Wong K. C. , Yew W. W. , Seto W. H. , Yuen K. Y. , Ho P. L.
Published: October 2004

This study evaluated the feasibility of a molecular strategy based on identification ofMycobacterium tuberculosisby IS6110PCR or Cobas Amplicor PCR, andrpoBPCR-DNA sequencing of the 81-bp rifampin resistance determining region (RRDR) for direct detection of rifampin resistance in respiratory specimens. A collection of 2,138 respiratory specimens and 352 nonduplicateM. tuberculosisisolates (including 233 isolates from the evaluated respiratory specimens and an additional collection of 119 stored isolates) from Southern China was investigated. Using culture as the reference test, the overall diagnostic sensitivities of an acid-fast bacillus (AFB) smear, Cobas Amplicor PCR, IS6110PCR were 54.5% (156 of 286), 86.7% (248 of 286), and 89.2% (255 of 286), respectively. The sensitivities of therpoBPCR for the specimens with positive AFB smears and with positive PCR results in the IS6110PCR and/or Cobas Amplicor PCR were 100% (156 of 156) and 92.3% (239 of 259), respectively. Of the 352 nonduplicateM. tuberculosisisolates, the agar proportion method for rifampin reported 39 resistant strains. Full agreement (352 of 352) was found with the agar proportion method and the genotype inferred from therpoBDNA sequencing data for rifampin. Thirty-nine mutations of nine distinct kinds, eight point mutations, and one deletion within the RRDR were found in the 39 resistant strains. For the direct DNA sequencing performed onrpoBPCR-positive respiratory specimens, the concordance with the agar proportion method and the subsequent PCR-sequencing for the culture isolate was 100%. This strategy has potential application for direct and rapid diagnosis of rifampin-resistantM. tuberculosisin IS6110PCR or Cobas Amplicor PCR-positive respiratory specimens.
Instability of the Restriction Fragment Length Polymorphism Pattern of Open Reading Frame 5 of Porcine Reproductive and Respiratory Syndrome Virus during Sequential Pig-to-Pig Passages
Authors: Cha Sang-Ho , Chang Chih-Cheng , Yoon Kyoung-Jin
Published: October 2004

Restriction fragment length polymorphism (RFLP) analysis is one of the tools commonly used to study the molecular epidemiology of porcine reproductive and respiratory syndrome viruses (PRRSVs). As PRRSVs are genetically variable, the stability of the RFLP pattern of a PRRSV during in vivo replication was evaluated by carrying out 13 sequential pig-to-pig passages (P1 to P13) of PRRSV ATCC VR-2332 in three independent pig lines for a total of 727 days. During P1 the pigs were inoculated with a homogeneous inoculum (CC-01) prepared through a series of plaque purifications, and during P2 to P13 the pigs were inoculated with a tissue filtrate from the corresponding pig in the previous passage. Fifteen viral plaque clones were directly isolated from CC-01 and the day 7 serum of each pig of each passage, open reading frame 5 of the clones was sequenced, and the clones were compared to CC-01 to assess the mutation rates and RFLP patterns (obtained by digestion with MluI, HincII, and SacII) over time. Among the 495 viral clones recovered during the passages, 398 clones, including CC-01, had pattern 2-5-2 (MluI-HincII-SacII); however, the remaining 97 viral clones showed different patterns (2-6-2 [P2], 1-5-2 [P3], 2-5-4 [P7], and 2-1-2 [P10]). Importantly, the MluI site that was reported to be present in only one of the PRRS modified live virus vaccine strains (Ingelvac) and its parental strain (ATCC VR-2332) can disappear during in vivo replication. Furthermore, sequence homology between CC-01 and clones with pattern 2-5-2 or clones with other patterns differed by 0.05 to 1.58% and 0.5 to 1.45%, respectively, suggesting that RFLP analysis cannot accurately predict genetic relatedness between PRRSVs. Collectively, precaution should be taken when the molecular epidemiology of PRRSVs is evaluated by RFLP analysis.
Development of a Multiplex PCR for the Detection of
asa1
,
gelE
,
cylA
,
esp
, and
hyl
Genes in Enterococci and Survey for Virulence Determinants among European Hospital Isolates of
Enterococcus faecium
Authors: Vankerckhoven Vanessa , Van Autgaerden Tim , Vael Carl , Lammens Christine , Chapelle Sabine , Rossi Rosaria , Jabes Daniela , Goossens Herman
Published: October 2004

A multiplex PCR for the simultaneous detection of five virulence genes (
asa1
,
gelE
,
cylA
,
esp
, and
hyl
) in enterococci was developed. The presence of these genes was investigated in 153 clinical and 118 fecal
Enterococcus faecium
isolates from inpatients at an increased risk of developing infections (such as patients in intensive care units and hematology wards) from 13 hospitals in eight European countries. Of the 271
E. faecium
isolates, 135 were vancomycin resistant
E. faecium
(VREF) isolates and 136 were vancomycin susceptible
E. faecium
(VSEF) isolates. Susceptibilities to ampicillin, gentamicin, streptomycin, vancomycin, teicoplanin, ramoplanin, quinupristin-dalfopristin, and linezolid were tested by the microdilution method. Overall, the prevalence of
esp
was significantly higher (
P
= 0.03) in clinical VREF isolates (92%) than in fecal VREF isolates (73%). In Italy, the prevalence of
esp
was significantly higher (
P
= 0.02) in VREF isolates (91%) than in VSEF isolates (68%), whereas in the United Kingdom,
hyl
was significantly more prevalent (
P
= 0.01) in VREF isolates (71%) than in VSEF isolates (29%). No significant differences were found for the other countries. Pulsed-field gel electrophoresis was used to check the clonality among the strains tested and showed the spread of two center-specific (
esp
-positive) VREF clones in Italy and one center-specific (
hyl
-positive) clone in the United Kingdom. These clones were resistant to ampicillin, gentamicin, and streptomycin. The multiplex PCR reported in this study is a convenient and rapid method for the simultaneous detection of the virulence genes
asa1
,
gelE
,
cylA
,
esp
, and
hyl
in enterococci. Molecular analysis showed the intrahospital spread of
esp
-positive VREF clones (in Italy) and
hyl
-positive VREF clones (in the United Kingdom); the role of
hyl
remains to be elucidated.
Detection of
Paracoccidioides brasiliensis
gp70 Circulating Antigen and Follow-Up of Patients Undergoing Antimycotic Therapy
Authors: Marques da Silva Silvia Helena , de Mattos Grosso Daniela , Lopes José Daniel , Colombo Arnaldo Lopes , Blotta Maria Heloisa Souza Lima , Queiroz-Telles Flávio , Pires de Camargo Zoilo
Published: October 2004

Paracoccidioidomycosis (PCM), one of the most important systemic mycoses in Central and South America, is caused by the dimorphic fungus
Paracoccidioides brasiliensis
and has a high prevalence in Brazil. Glycoproteins of 43 and 70 kDa are the main antigenic compounds of
P. brasiliensis
and are recognized by Western blotting by 100 and 96% of PCM patient sera, respectively. In the present study, an inhibition enzyme-linked immunosorbent assay (ELISA) was used to detect gp70 in different biological samples from patients with PCM. gp70 was detected in 98.76% of 81 serum samples, with an average concentration of 8.19 μg/ml. The test was positive for 100% of the patients with the acute and chronic unifocal forms of PCM and 98.43% of the patients with the multifocal chronic form, with average concentrations of 11.86, 4.83, and 7.87 μg/ml, respectively. Bronchoalveolar lavage fluid from 23 patients with pulmonary unifocal PCM and 14 samples of cerebrospinal fluid from patients with neurological PCM were also tested for gp70 detection, with the test showing 100% sensitivity and 100% specificity, with mean gp70 concentrations of 7.5 and 6.78 μg/ml, respectively. To investigate the potential of gp70 detection by inhibition ELISA for the follow-up of PCM patients during antimycotic therapy with itraconazole (ITZ), the sera of 23 patients presenting with the chronic multifocal form of PCM were monitored at regular intervals of 1 month for 12 months. The results showed a decrease in circulating gp70 levels during treatment which paralleled the reduction in anti-
P. brasiliensis
antibody levels. The detection of
P. brasiliensis
gp70 from the biological fluids of patients suspected of having PCM proved to be a promising method for diagnosing infection and evaluating the efficacy of ITZ treatment.
Multiple-Locus Variable-Number Tandem Repeat Analysis, a Novel Typing Scheme To Study the Genetic Relatedness and Epidemiology of
Enterococcus faecium
Isolates
Authors: Top Janetta , Schouls Leo M. , Bonten Marc J. M. , Willems Rob J. L.
Published: October 2004

Multiresistant
Enterococcus faecium
is a major cause of hospital acquired infections and outbreaks. Here, we describe the development of multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) as a novel typing method to assess the genetic relatedness of
E. faecium
isolates. Six VNTR loci were used to genotype 392 isolates recovered from different animals and human community, hospital survey, and clinical isolates. From 3 to 13 alleles were found per locus, resulting in 127 different MLVA profiles. Clustering of MLVA profiles confirmed the host-specific genogroups found by multilocus sequence typing (MLST) and showed the grouping of clinical and epidemic isolates that belonged to the MLST-C1 cluster in a distinct MLVA-C1 cluster (sensitivity of 97% and specificity of 90%). Furthermore, the discriminatory power of MLVA is comparable to MLST. MLVA profiles appeared to be relatively stable, since isolates from a single outbreak shared the same MLVA profile, which is a prerequisite when MLVA is used to study hospital outbreaks. Our data show that MLVA is a highly reproducible and portable typing method; in contrast to MLST, it is fast, relatively cheap, and easy to perform. Furthermore, it has the abilities of MLST to recognize genetically related and potential epidemic isolates. Submission of MLVA profiles is possible via a Web-based database for international comparison.
Development and Evaluation of a Chromogenic Agar Medium for Methicillin-Resistant
Staphylococcus aureus
Authors: Perry John D. , Davies Amie , Butterworth Lynne A. , Hopley Andrew L. J. , Nicholson Audrey , Gould F. Kate
Published: October 2004

We describe here the development and evaluation of MRSA ID, a new chromogenic agar medium for the specific isolation and identification of methicillin-resistant
Staphylococcus aureus
(MRSA). We used S. aureus ID (bioMérieux, La Balme Les Grottes, France) and supplemented it with various antimicrobials, including cefoxitin, ciprofloxacin, oxacillin, and methicillin. Cefoxitin proved to be superior to the other antimicrobials for the selection of MRSA from other strains of
S. aureus
. MRSA ID (consisting of S. aureus ID supplemented with 4 mg of cefoxitin/liter) was evaluated by the use of 747 swabs from various clinical sites. All specimens were also cultured on CHROMagar MRSA and oxacillin resistance screening agar base (ORSAB) and in selective mannitol broth (SMB). A total of 85 MRSA strains were isolated by a combination of all methods. After 22 to 24 h of incubation, 80% of the MRSA strains were isolated as green colonies on MRSA ID, compared with 59 and 62% of the strains that were isolated as colored colonies on CHROMagar MRSA and ORSAB, respectively. After 48 h of incubation, 89, 72, and 78% of the MRSA strains were isolated on MRSA ID, CHROMagar MRSA, and ORSAB, respectively. Sixty-five percent of the strains were isolated by growth in SMB. The specificities of MRSA ID, CHROMagar MRSA, ORSAB, and SMB were 99.5, 99.3, 97.9, and 92.8%, respectively, after 22 to 24 h of incubation. We conclude that MRSA ID is a sensitive and specific medium for the isolation and identification of MRSA.
Longitudinal Study of Viruses Associated with Canine Infectious Respiratory Disease
Authors: Erles Kerstin , Dubovi Edward J. , Brooks Harriet W. , Brownlie Joe
Published: October 2004

In this investigation a population of dogs at a rehoming center was monitored over a period of 2 years. Despite regular vaccination of incoming dogs against distemper, canine adenovirus type 2 (CAV-2), and canine parainfluenza virus (CPIV), respiratory disease was endemic. Tissue samples from the respiratory tract as well as paired serum samples were collected for analysis. The development of PCR assays for the detection of CPIV, canine adenovirus types 1 and 2, and canine herpesvirus (CHV) is described. Surprisingly, canine adenovirus was not detected in samples from this population, whereas 19.4% of tracheal and 10.4% of lung samples were positive for CPIV and 12.8% of tracheal and 9.6% of lung samples were positive for CHV. As reported previously, a novel canine respiratory coronavirus (CRCoV) was detected in this population (K. Erles, C. Toomey, H. W. Brooks, and J. Brownlie, Virology310:216-223, 2003). Infections with CRCoV occurred mostly during the first week of a dog's stay at the kennel, whereas CPIV and CHV were detected at later time points. Furthermore, the evaluation of an enzyme-linked immunosorbent assay for detection of antibodies to CPIV and an immunofluorescence assay for detection of antibodies to CHV is described. This study shows that CPIV is present at kennels despite vaccination. In addition, other agents such as CHV and CRCoV may play a role in the pathogenesis of canine respiratory disease, whereas CAV-2 and canine distemper virus were not present in this population, indicating that their prevalence in the United Kingdom is low due to widespread vaccination of dogs.
Nocardia mexicana
sp. nov., a New Pathogen Isolated from Human Mycetomas
Authors: Rodríguez-Nava Verónica , Couble Andrée , Molinard Claudie , Sandoval Horacio , Boiron Patrick , Laurent Frédéric
Published: October 2004

Three isolates collected from human mycetomas and showing an unusual brownish purple pigmentation on Bennett agar plates were analyzed by a polyphasic taxonomic approach, including morphological, biochemical, physiological, and chemotaxonomic properties coupled with genomic and phylogenetic analysis. It clearly appeared that these microorganisms were distinct from their closest phenotypic and genetic match, the most related species according to 16S rRNA gene sequence analysis being
Nocardia pseudobrasiliensis.
The data obtained indicated that the three clinical strains should be recognized as a new species for which the name
Nocardia mexicana
sp. nov. is proposed.