bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inter‐ and intra‐observer reliability of radiographic scores commonly used for the evaluation of haemophilic arthropathy
Authors: SILVA M. , LUCK J. V. , QUON D. , YOUNG C. R. , CHIN D. M. , EBRAMZADEH E. , FONG Y.‐J. 
Published: April 2008

Summary.  Although the severity of haemophilic arthropathy is commonly assessed using established radiographic scoring systems, there is limited available information about their inter‐ and intra‐observer reliability. The purpose of the present study was to establish the inter‐observer reliability (IEOR) and intra‐observer reliability (IAOR) of three different methods available for the classification of haemophilic arthropathy, including the Arnold and Hilgartner classification, a modification to the Arnold and Hilgartner system described by Luck et al., and the classification described by Pettersson et al. Antero‐posterior and lateral radiographs of 54 haemophilic joints were included for the analysis. To determine the IEOR for each one of the three radiographic systems, the radiographs were randomly evaluated by four observers, including two orthopaedic surgeons, one orthopaedic resident and one haematologist. For the determination of IAOR, all four reviewers repeated the assessment in a similar fashion, after a period of at least 2 weeks. IEOR and IAOR for the three classification systems was established using kappa (κ) statistics. A Spearman rank correlation was used to determine the similarities between each reviewer’s own interpretative scales. The IEOR was low for the Arnold and Hilgartner system (κ = 0.35, P ≤ 0.001) and the Luck system (κ = 0.38, P ≤ 0.001), but even lower for the Pettersson system (κ = 0.06, P = 0.1). For the Pettersson system, particularly low κ values were observed for the presence or absence of osteoporosis (κ = 0.11, P = 0.0027), enlarged epiphysis (κ = 0.10, P = 0.0039), erosion of joint margins (κ = 0.11, P = 0.0018), and joint deformity (κ = 0.16, P = 0.00001). However, a relatively high Spearman rank correlation for all three scales [rs = 0.75 (P < 0.001) for Arnold and Hilgartner system, rs = 0.74 (P < 0.001) for the Luck system and rs = 0.81 (P < 0.001) for Pettersson system] indicated an overall, general agreement among the reviewers with regard to the severity of the haemophilic arthropathy. There was a moderate IAOR value for both, the Arnold and Hilgartner system (κ = 0.57, P = 0.00001) and the Luck system (κ = 0.62, P = 0.00001) with a low IAOR value for the Pettersson system [κ = 0.22, P = 0.00001). Currently available radiographic scoring systems for haemophilic arthropathy have low inter‐ and intra‐observer reliability rates. Improvements, either through education or modification of the scoring systems, are critical in an era where correlations between clinical and radiographic scores have received significant attention.
Local and landscape effects of organic farming on butterfly species richness and abundance
Authors: Rundlöf Maj , Bengtsson Janne , Smith Henrik G. 
Published: April 2008

SummaryAgri‐environmental schemes (AES) are commonly adopted in Europe to reduce the loss of farmland biodiversity. These schemes have, however, been criticized as not fulfilling this goal, partly because their effectiveness is thought to differ depending on external factors such as landscape heterogeneity, the focal organism and scale of application.We used one AES, organic farming, as a landscape‐scale experiment to test whether its effect on butterflies depends on the spatial scale at which it is applied. Our study system consisted of organically and conventionally managed fields within eight pairs of matched landscapes, differing in the proportion of land under organic management at the landscape scale. Butterflies and their nectar and host‐plant resources were surveyed along the fields and adjacent field borders.Butterfly species richness and abundance were significantly increased by organic farming at the local scale. However, local butterfly species richness was also positively affected by a large proportion of organic farming in the surrounding landscape, independent of the local farming practice. Local and landscape farming practices interacted such that the farming practice within fields had a larger effect on butterfly abundance if surrounded by conventionally rather than organically managed fields. These results could only partly be explained by variation in local availability of nectar and host‐plant resources.The total observed species richness (γ‐diversity) was higher in organically managed landscapes, mainly because of higher within‐field diversity (α‐diversity), whereas the between‐field diversity (β‐diversity) tended to be similar in both landscape types.Synthesis and applications. Butterflies were positively affected by organic farming at a local scale, but the amount of organic farming in the surrounding landscape had either an additive (species richness) or interactive (abundance) effect. Therefore, the spatial distribution of AES must be taken into account to maximize their potential to increase farmland biodiversity. We have shown that organic farming affected butterfly species richness on nearby conventionally managed land. This suggests a landscape effect of organic farming that may indicate a wider benefit of AES for biodiversity conservation.
The interplay of pollinator diversity, pollination services and landscape change
Authors: Steffan‐Dewenter Ingolf , Westphal Catrin 
Published: April 2008

Summary

Pollinators are a functional group with high relevance for ensuring cross‐pollination in wild plant populations and yields in major crops. Both pollinator declines and losses of pollination services have been identified in the context of habitat destruction and land use intensification.
This editorial synthesizes and links the findings presented in seven papers in this Special Profile, focusing on pollinator diversity and plant–pollinator interactions in natural habitats and agricultural landscapes.
The results contribute to our understanding of local and landscape scale effects of land use intensification on pollinator densities and diversity, and pollination functions in wild plant communities and crops.
Synthesis and applications. We emphasize the exceptional coverage in pollination ecology ranging from basic ecological relationships to applied aspects of ecosystem services and ecosystem management, and conclude with identifying gaps in current knowledge and challenging research areas for the future.
Phylogenetic structure of local communities predicts the size of the regional species pool
Authors: Gerhold Pille , Pärtel Meelis , Liira Jaan , Zobel Kristjan , Prinzing Andreas 
Published: April 2008

Summary

The regional species pool is a set of species available in a region and ecologically suitable for growing in the particular environment occupied by a local community. As species pools are largely influenced by evolutionary processes such as the conservation of ecological niches within lineages we hypothesize that the size of the regional species pool increases with the variety of distinct phylogenetic lineages represented in a local community. We contrast this with hypotheses invoking diversification of individual lineages within environments or stochastic present‐day assembly of local communities.
We calculated phylogenetic distinctness for a local community as the number of nodes separating two species averaged over all pairwise comparisons across a phylogenetic topology of a regional flora. We calculated the size of the regional species pool for a local community as the number of species in the regional flora that share the ecological niche position of the species constituting the local community.
Analysing field‐layer communities across a wide range of environments, we indeed found that local communities composed of phylogenetically highly distinct species recruit from larger species pools than communities of low phylogenetic distinctness. Accounting for the presence of two particularly diversifying lineages (Poaceae and Cyperaceae) confirmed these results.
These results help us to understand how the species pool was assembled throughout evolution in different types of environments (immigration vs. in situ radiation of individual lineages).
The phylogenetic approach is of large practical value to infer the size of the regional species pool because phylogenies have become available for many groups of species worldwide, while knowledge of the species’ ecological requirements or habitat affiliation (needed for the classical definition of species pools) is often still lacking.
Synthesis. We show that the size of the regional species pool can be predicted by the average phylogenetic distinctness between the species present in a local community. This approach contributes to the understanding of the causes of species richness in regional species pools and local communities. The approach is also an important tool for determining the size of the regional species pool when parameters other than species phylogeny are not known.
The fragile X continuum: new advances and perspectives
Authors: Cornish K. , Turk J. , Hagerman R. 
Published: April 2008

AbstractFragile X syndrome is the world's most common hereditary cause of intellectual disability in men and to a lesser extent in women. The disorder is caused by the silencing of a single gene on the X chromosome, the Fragile X Mental Retardation Gene‐1. A substantial body of research across the disciplines of molecular genetics, child psychiatry and developmental neuroscience bears testament to a decade of exciting and innovative science that has advanced our knowledge about the fragile X ‘signature’ or influence across cognitive and social development. The core aims of this review are to first discuss fragile X syndrome and premutation involvement in the context of current advances that demonstrate the dynamic nature of the genotype on phenotypic outcomes. Second, to discuss the implications of these recent advances for the development of clinical and educational interventions and resource tools that target specific phenotypic ‘signatures’ within the fragile X continuum.
Multiple paternity in reptiles: patterns and processes
Authors: ULLER TOBIAS , OLSSON MATS 
Published: April 2008

AbstractThe evolution of female promiscuity poses an intriguing problem as benefits of mating with multiple males often have to arise via indirect, genetic, effects. Studies on birds have documented that multiple paternity is common in natural populations but strong evidence for selection via female benefits is lacking. In an attempt to evaluate the evidence more broadly, we review studies of multiple paternity in natural populations of all major groups of nonavian reptiles. Multiple paternity has been documented in all species investigated so far and commonly exists in over 50% of clutches, with particularly high levels in snakes and lizards. Marine turtles and lizards with prolonged pair‐bonding have relatively low levels of multiple paternity but levels are nevertheless higher than in many vertebrates with parental care. There is no evidence that high levels of polyandry are driven by direct benefits to females and the evidence that multiple paternity arises from indirect genetic benefits is weak. Instead, we argue that the most parsimonious explanation for patterns of multiple paternity is that it represents the combined effect of mate‐encounter frequency and conflict over mating rates between males and females driven by large male benefits and relatively small female costs, with only weak selection via indirect benefits. A crucial step for researchers is to move from correlative approaches to experimental tests of assumptions and predictions of theory under natural settings, using a combination of molecular techniques and behavioural observations.
Scavenger receptor gp340 aggregates group A streptococci by binding pili
Authors: Edwards Andrew M. , Manetti Andrea G. O. , Falugi Fabiana , Zingaretti Chiara , Capo Sabrina , Buccato Scilla , Bensi Giuliano , Telford John L. , Margarit Immaculada , Grandi Guido 
Published: April 2008

SummaryGroup A streptococci (GAS) are the most frequent cause of bacterial pharyngitis. The first obstacle to GAS colonization of the pharynx is saliva. As well as forming a physical barrier, saliva contains components of innate and acquired immunity. Previous work has shown that saliva induces bacterial aggregation, which may serve as a clearance mechanism. As the aggregation of some oral streptococci in saliva is mediated by long proteinaceous appendages, we hypothesized that pili of GAS might behave similarly. Wild‐type GAS M1 strain SF370 aggregated in saliva, while pilus‐defective mutants did not. Similarly, heterologous expression of diverse GAS pili on the surface of Lactococcus lactis induced aggregation in saliva, while control strains were unaffected. Further studies revealed that aggregating bacteria bound salivary component gp340. Purified gp340 aggregated wild‐type GAS and L. lactis expressing GAS pili, but not control strains. GAS pilus‐defective mutants were abrogated in gp340 binding and aggregation. Furthermore, gp340‐mediated aggregation reduced bacterial adhesion to human epithelial cells, suggesting a role in host defence.
Selective repression by Fis and H‐NS at the Escherichia coli dps promoter
Authors: Grainger David C. , Goldberg Martin D. , Lee David J. , Busby Stephen J. W. 
Published: April 2008

SummaryDps is a nucleoid‐associated protein that plays a major role in condensation of the Escherichia coli chromosome in stationary phase. Here we show that two other nucleoid‐associated proteins, Fis and H‐NS, can bind at the dps gene promoter and downregulate its activity. Both Fis and H‐NS selectively repress the dps promoter, preventing transcription initiation by RNA polymerase containing σ70, the housekeeping σ factor, but not by RNA polymerase containing σ38, the stationary‐phase σ factor. Fis represses by trapping RNA polymerase containing σ70 at the promoter. In contrast, H‐NS functions by displacing RNA polymerase containing σ70, but not RNA polymerase containing σ38. Dps levels are known to be very low in exponentially growing cells and rise sharply as cells enter stationary phase. Conversely, Fis levels are high in growing cells but fall to nearly zero in stationary‐phase cells. Our data suggest a simple model to explain how the Dps‐dependent super‐compaction of the folded chromosome is triggered as cell growth ceases.
Staphylococcus aureus primase has higher initiation specificity, interacts with single‐stranded DNA stronger, but is less stimulated by its helicase than Escherichia coli primase
Authors: Koepsell Scott A. , Larson Marilynn A. , Frey Christopher A. , Hinrichs Steven H. , Griep Mark A. 
Published: April 2008

SummaryThe study of primases from model organisms such as Escherichia coli, phage T7 and phage T4 has demonstrated the essential nature of primase function, which is to generate de novo RNA polymers to prime DNA polymerase. However, little is known about the function of primases from other eubacteria. Their overall low primary sequence homology may result in functional differences. To help understand which primase functions were conserved, primase and its replication partner helicase from the pathogenic Gram‐positive bacteria Staphylococcus aureus were compared in detail with that of E. coli primase and helicase. The conserved properties were to primer initiation and elongation and included slow kinetics, low fidelity and poor sugar specificity. The significant differences included S. aureus primase having sixfold higher kinetic affinity for its template than E. coli primase under equivalent conditions. This naturally higher activity was balanced by its fourfold lower stimulation by its replication fork helicase compared with E. coli primase. The most significant difference between the two primases was that S. aureus helicase stimulation did not broaden the S. aureus primase initiation specificity, which has important biological implications.
Large‐scale transposon mutagenesis ofMycoplasma pulmonis
Authors: French Christopher T. , Lao Ping , Loraine Ann E. , Matthews Brian T. , Yu Huilan , Dybvig Kevin 
Published: April 2008

SummaryTo obtain mutants for the study of the basic biology and pathogenic mechanisms of mycoplasmas, the insertion site of transposon Tn4001Twas determined for 1700 members of a library ofMycoplasma pulmonismutants. After evaluating several criteria for gene disruption, we concluded that 321 of the 782 protein coding regions were inactivated. The dispensable and essential genes ofM. pulmoniswere compared with those reported forMycoplasma genitaliumandBacillus subtilis. Perhaps the most surprising result of the current study was that unlike other bacteria, ribosomal proteins S18 and L28 were dispensable. Carbohydrate transport and the susceptibility of selected mutants to UV irradiation were examined to assess whether active transposition of Tn4001Twithin the genome would confound phenotypic analysis. In contrast to earlier reports suggesting that mycoplasmas were limited in their DNA repair machinery, mutations inrecA,uvrA,uvrBanduvrCresulted in a DNA‐repair deficient phenotype. A mutant with a defect in transport ofN‐acetylglucosamine was identified.
Regulation of bacterial gene expression by the NTP substrates of transcription initiation
Authors: Turnbough, Jr Charles L. 
Published: April 2008

SummaryMany mechanisms of gene regulation in bacteria do not employ repressor or activator proteins. One class of these mechanisms includes those in which the key regulatory element is the control of transcription initiation by the availability of NTP substrates. In this commentary, several distinct examples of initiating NTP‐mediated gene regulation are discussed, including a mechanism reported by Krásnýet al. in this issue of Molecular Microbiology. These researchers show that during the stringent response induced by amino acid starvation of Bacillus subtilis, increases in the intracellular level of ATP permit upregulation of promoters with +1A start sites, while concurrent decreases in the intracellular level of GTP cause downregulation of promoters with +1G start sites. This regulation is restricted to stringently controlled promoters.
Chilling Stress Accelerates Degradation of Seed Storage Protein and Photosynthetic Protein during Cotton Seed Germination
Authors: Gai Y. P. , Li X. Z. , Ji X. L. , Wu C. A. , Yang G. D. , Zheng C‐C. 
Published: April 2008

AbstractLow temperature is one of the major abiotic stresses limiting the productivity and geographical distribution of many important crops. To gain a better understanding of chilling stress responses in cotton (Gossypium hirsutum L.), we carried out a comparative proteomic analysis. Cotyledon proteins of 1‐week‐old cotton seedlings treated with or without chilling treatment at 4 °C were extracted, separated by a two‐dimensional gel electrophoresis and compared. Among 1500 protein spots reproducibly detected on each gel, 25 protein spots were down‐regulated and 29 were up‐regulated. Seven cotton proteins were identified by mass spectrometry analysis as beta‐globulin A precursor fragments. One was identified as a Rubisco large subunit fragment, providing evidence of both seed storage protein and photosynthetic protein destruction by chilling stress. The related physiological and biochemical analysis showed that there was a significant increase in endopeptidase activity and activated oxygen generation rate, and an obvious decrease in carboxylation efficiency and maximum net photosynthetic rate of cotton seedlings under chilling stress. Based on the above results, the degradation mechanisms of beta‐globulin and Rubisco under chilling stress were discussed. In conclusion, our study provides new insights into chilling‐stress responses in cotton and demonstrates the advantages of proteomic analysis.
TransgenicBt‐Cotton Affects Enzyme Activity and Nutrient Availability in a Sub‐Tropical Inceptisol
Authors: Sarkar B. , Patra A. K. , Purakayastha T. J. 
Published: April 2008

AbstractWe investigated the dynamics of N and P availability in the rhizosphere ofBtand non‐Btcotton crops during their growth. In a net‐house pot culture experiment at the Indian Agricultural Research Institute, New Delhi,Bt‐cotton (cv. MRC‐6301Bt) and its non‐transgenic near‐isoline (MRC‐6301) were grown on a sandy loam soil until maturity. A control (no‐crop) treatment was also included. Rhizosphere soil and root samples were collected at 60, 90, and 120 days after sowing (DAS). Soil samples were analysed for dehydrogenase activity, soil respiration, mineral‐N and Olsen‐P. Results have revealed a significant reduction in dehydrogenase activity (−17 %) and soil respiration (−3.5 %) in the rhizosphere ofBt‐cotton over non‐Btisoline. Total mineral‐N (NH4+‐N + ‐N) in soil was reduced by 14 %, whereas Olsen‐P was increased by 8 % because ofBt‐cotton. Root biomass yields were not different (P > 0.05), but root volume was significantly higher inBtthan non‐Btisoline. Time of sampling strongly (P < 0.05) affected the above parameters, showing their highest values at 60 or 90 DAS. A significant interactive effect of sampling time and treatments was also indicated. Our results suggest thatBt‐cotton may constrain the availability of N, but enhances P‐availability in these soils.
European Hornbeam Powdery Mildew Erysiphe arcuata in Slovakia
Authors: Pastirčáková K. , Takamatsu S. , Shiroya Y. , Pastirčák M. 
Published: April 2008

Abstract Erysiphe arcuata found on European hornbeam (Carpinus betulus) is reported from Slovakia for the first time. Taxonomic characters of the anamorphic and teleomorphic states of E. arcuata were described and illustrated. Additionally, disease symptoms caused by this pathogen were presented. The identification of the fungus is based on morphological data combined with the results of a sequence analysis.
Aspergilloma in a pulmonary hydatid cyst: a case report
Authors: Bal Amanjit , Bagai Maneesh , Mohan Harsh , Dalal Usha 
Published: April 2008

SummaryThe most common predisposing factor for aspergillomas is the presence of a pre‐existing lung cavity secondary to tuberculosis, bronchial cysts and bullae, neoplasms, and pulmonary infarction. However, Aspergilloma within a hydatid cyst is a rare occurrence. A 52‐year‐old female was presented with chest pain and shortness of breath. Computerized tomography‐guided fine needle aspiration (FNA) showed fragment of lamellated membrane of hydatid cyst in a background of amorphous debris. Surgical enucleation of the cyst revealed lamellated hyaline acellular ectocyst of hydatid cyst and collections of acute angle branching septate hyphae conforming to morphology of Aspergillus. Here we describe this rare entity of aspergilloma in a pulmonary hydatid cyst and discuss its management.