bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interobserver variation in the classification of thymic tumours – a multicentre study using the WHO classification system
Authors: Verghese E T , Den Bakker M A , Campbell A , Hussein A , Nicholson A G , Rice A , Corrin B , Rassl D , Langman G , Monaghan H , Gosney J , Seet J , Kerr K , Suvarna S K , Burke M , Bishop P , Pomplun S , Willemsen S , Addis B 
Published: July 2008

Aims:  To test the reproducibility of the current World Health Organization (WHO) classification of thymic epithelial tumours and to determine the level of interobserver variation within a group of pathologists, all with experience and expertise in thoracic pathology.Methods and results:  Ninety‐five thymic tumours were circulated to a group of 17 pathologists in the UK and The Netherlands over a 1‐year period. Participants were asked to classify them according to WHO criteria. The diagnoses were subjected to statistical analysis and κ values calculated. The overall level of agreement was moderate (κ 0.45). When the categories were reduced in number by creating two groups, (A + AB + B1 + B2 and B3 + C), the level of agreement increased to 0.62. An alternative grouping (A + AB + B1 and B2 + B3 + C) increased it slightly further. The best agreement was in tumour types A and AB. Difficulties arose in distinguishing B1 tumours from B2 tumours and B2 tumours from B3 tumours.Conclusions:  Although the WHO system describes a number of well‐defined tumour types with clear diagnostic criteria, the overall level of agreement was moderate and improved if some groups were amalgamated.
Handling and reporting of radical prostatectomy specimens in Europe: a web‐based survey by the European Network of Uropathology (ENUP)
Authors: Egevad L , Algaba F , Berney D M , Boccon‐Gibod L , Griffiths D F , Lopez‐Beltran A , Mikuz G , Varma M , Montironi R 
Published: July 2008

Aims:  To survey current European practices in handling and reporting of radical prostatectomy (RP) specimens.Methods and results:  A European Network of Uropathology (ENUP) was organized for the dissemination of information, survey studies and research collaborations. Contact data of uropathologists were collected from 321 pathology laboratories in 15 West European countries. In the first ENUP survey, 67.6% (217/321) of the members replied to a web‐based questionnaire. Some practices were adopted by a large majority, e.g. inking of the specimen (96.6%), Gleason grading (99.5%), stratifying extraprostatic extension (EPE) according to extent (88.2%), reporting TNM stage (88.6%) and reporting location of positive margins (98%). As many as 71.6% of respondents always embedded the entire prostate and only 10.8% always practised partial embedding. Whole mounts were routinely used by 37.5% and standard blocks by 55.5%. Among areas with variable routines were methods to define focal versus extensive EPE and methods to quantify margin positivity, probably reflecting that the optimal method has yet to be determined.Conclusions:  Some practices are almost universally adopted in Europe, whereas others still need to be standardized. The results of the study may be helpful when judging what recommendations are reasonable to issue.
Phosphate‐rich deposits associated with the Mio‐Pliocene unconformity in south‐east Australia
Authors: DICKINSON JULIE A. , WALLACE MALCOLM W. 
Published: July 2008

AbstractPhosphates are present on the surface of the Mio‐Pliocene unconformity in the Otway, Port Phillip and Gippsland basins of south‐east Australia. The phosphates occur as lenticular lag deposits and include reworked phosphatic intraclasts, vertebrate bone and teeth. In situ phosphatized burrows are also found in sediments of Late Miocene and Early Pliocene age. The phosphatic intraclasts on the unconformity are interpreted as reworked phosphatized burrows derived from latest Miocene sediments (6 to 5 Ma). The phosphatization of these intraclasts is temporally related to the unconformity. The timing of phosphogenesis coincides with a period of transgression across the south‐east Australian margin following Late Miocene uplift. This transgression is responsible for initial marine erosion of the underlying Miocene sequence, creation of a period of very slow sedimentation that was favourable to phosphate formation and subsequent deposition of the latest Miocene through to Pliocene sediments. The continental weathering of the uplifted highlands adjacent to the sedimentary basins, global phosphorus enrichment in the Late Miocene oceans and localized upwelling may all have contributed to phosphatization in south‐eastern Australia.
RING1 E3 ligase localizes to plasma membrane lipid rafts to trigger FB1‐induced programmed cell death in Arabidopsis
Authors: Lin Shih‐Shun , Martin Raquel , Mongrand Sebastien , Vandenabeele Steven , Chen Kuan‐Chun , Jang In‐Cheol , Chua Nam‐Hai 
Published: July 2008

SummaryUbiquitination plays important roles in plant development, including programmed cell death. Here, we characterize a novel membrane‐bound RING motif protein, encoded by RING1, that is expressed at a low level in all Arabidopsis tissues but can be upregulated by fumonisin B1 (FB1) treatment and pathogen infection. RING1 displays E3 ubiquitin ligase activity in vitro, which is dependent on the integrity of the RING motif. GFP fusion protein localization and cell fractionation experiments show that this E3 ligase is associated with the lipid rafts of plasma membranes. Knock‐down of RING1 transcripts using artificial microRNA (amiR‐R1159) leads to FB1 hyposensitivity, but overexpression of RING1 confers hypersensitivity. Additionally, expression of the pathogenesis‐related 1 (PR‐1) gene is lower and delayed in amiR‐R1159 plants compared with wild‐type and RING1‐overexpressing plants. The FB1 hyposensitivity of amiR‐R1159 plants can be rescued by expression of cleavage‐resistant RING1mut transcripts. Our results suggest that RING1 acts as a signal from the plasma membrane lipid rafts to trigger the FB1‐induced plant programmed cell death pathway.
High‐resolution chromosome mapping of BACs using multi‐colour FISH and pooled‐BAC FISH as a backbone for sequencing tomato chromosome 6
Authors: Szinay Dóra , Chang Song‐Bin , Khrustaleva Ludmila , Peters Sander , Schijlen Elio , Bai Yuling , Stiekema Willem J. , Van Ham Roeland C.H.J. , De Jong Hans , Klein Lankhorst René M. 
Published: July 2008

SummaryWithin the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a ‘BAC‐by‐BAC’ approach that aims to deliver high‐quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five‐colour high‐resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross‐over recombination in that region. In a so called pooled‐BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot‐100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.
Mechanism of plant eIF4E‐mediated resistance against a Carmovirus (Tombusviridae): cap‐independent translation of a viral RNA controlled in cis by an (a)virulence determinant
Authors: Truniger Verónica , Nieto Cristina , González‐Ibeas Daniel , Aranda Miguel 
Published: July 2008

SummaryTranslation initiation factors are universal determinants of plant susceptibility to RNA viruses, but the underlying mechanisms are poorly understood. Here, we show that a sequence in the 3′ untranslated region (3′‐UTR) of a viral genome that is responsible for overcoming plant eIF4E‐mediated resistance (virulence determinant) functions as a 3′ cap‐independent translational enhancer (3′‐CITE). The virus/plant pair studied here is Melon necrotic spot virus (MNSV) and melon, for which a recessive resistance controlled by melon eIF4E was previously described. Chimeric viruses between virulent and avirulent isolates enabled us to map the virulence and avirulence determinants to 49 and 26 nucleotides, respectively. The translational efficiency of a luc reporter gene flanked by 5′‐ and 3′‐UTRs from virulent, avirulent and chimeric viruses was analysed in vitro, in wheatgerm extract, and in vivo, in melon protoplasts, showing that: (i) the virulence determinant mediates the efficient cap‐independent translation in vitro and in vivo; (ii) the avirulence determinant was able to promote efficient cap‐independent translation in vitro, but only when eIF4E from susceptible melon was added in trans, and, coherently, only in protoplasts of susceptible melon, but not in the protoplasts of resistant melon; (iii) these activities required the 5′‐UTR of MNSV in cis. Thus, the virulence and avirulence determinants function as 3′‐CITEs. The activity of these 3′‐CITEs was host specific, suggesting that an inefficient interaction between the viral 3′‐CITE of the avirulent isolate and eIF4E of resistant melon impedes the correct formation of the translation initiation complex at the viral RNA ends, thereby leading to resistance.
The characterization and impact of microparticles on haemostasis within fresh‐frozen plasma
Authors: Lawrie A. S. , Harrison P. , Cardigan R. A. , Mackie I. J. 
Published: July 2008

Background  We have previously demonstrated that clot formation in fresh‐frozen plasma (FFP) is influenced by the presence of microparticles (MP). In this study, the cellular source(s), properties and influence of MPs on clot formation within FFP were further characterized.Methods  Fresh‐frozen plasma was prepared after an overnight hold of whole blood at 4°C. We examined the effect of a 0·2 µm filtration device designed to remove cellular MPs on thrombin generation test (TGT) and Thrombelastography (TEG®) as well as clotting factors and physiological inhibitors: prothrombin time (PT); activated partial thromboplastin time (APTT), fibrinogen (Fg), factor VIII (FVIII), von Willebrand factor antigen (VWF:Ag), antithrombin III (AT‐III) and protein C (PC). MPs were measured using a functional assay and also by flow cytometry.Results  Microparticle levels by functional assay were reduced by filtration (pre‐ 5·11 vs. post‐ 4·43 nmol/l phosphatidylserine equivalent, P < 0·0001). Flow cytometry showed that the most numerous MPs were derived from red blood cells, with ~87% binding annexin V, most of which (94%) were removed by filtration. MP removal had minimal effect on the PT, APTT, Fg, VWF:Ag, AT‐III or PC or FVIII, but a major effect on TGT (endogenous thrombin potential: pre‐ 1722 vs. post‐ 990 nM thrombin, P < 0·0001; peak thrombin: pre‐ 91 vs. post‐ 44 nM thrombin, P < 0·0001), which in turn reflected the changes seen in TEG®, where post‐filtration clots started forming more slowly and the rate of clot formation was reduced.Conclusion  These data suggest that MPs contribute towards clot formation in FFP.
Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny
Authors: Shalchian‐Tabrizi Kamran , Bråte Jon , Logares Ramiro , Klaveness Dag , Berney Cédric , Jakobsen Kjetill S. 
Published: July 2008

SummaryThe cryptomonads is a well‐defined lineage of unicellular eukaryotes, composed of several marine and freshwater groups. However, the evolutionary relationships among these groups are unclear due to conflicting inferences between morphological and molecular phylogenies. Here, we have inferred the evolutionary relationships among marine and freshwater species in order to better understand the importance of the marine–freshwater boundary on the historical diversification patterns of cryptomonads. We have constructed improved molecular phylogenies by taking into account rate variation both across sites and across sequences (covarion substitutions), and by analysing the vast majority of publicly available cryptomonad 18S rRNA sequences and related environmental phylotypes. The resulting phylogenies included 55 sequences, and revealed two novel freshwater cryptomonad clades (CRY1 and CRY2) and a large hidden diversity of cryptomonads. CRY1 was placed deeply within the cryptomonad phylogeny together with all the major freshwater lineages (i.e.GoniomonasandCryptomonas), while CRY2 was placed within a lineage of marine species identified asPlagioselmis‐like with the aid of a new sequence generated from a cultured species. The inferred phylogenies suggest only few successful marine–freshwater transitions over the history of cryptomonads. Most of the transitions seem to have occurred from marine to fresh waters, but re‐colonizations of marine habitats have also taken place. This implies that the differences in the biogeophysical conditions between marine and fresh waters constitute a substantial barrier for the cross‐colonization of these environments by cryptomonads.
Burkholderia cenocepacia strains isolated from cystic fibrosis patients are apparently more invasive and more virulent than rhizosphere strains
Authors: Pirone Luisa , Bragonzi Alessandra , Farcomeni Alessio , Paroni Moira , Auriche Cristina , Conese Massimo , Chiarini Luigi , Dalmastri Claudia , Bevivino Annamaria , Ascenzioni Fiorentina 
Published: July 2008

SummaryGiven the widespread presence of Burkholderia cenocepacia in the rhizosphere it is important to determine whether rhizosphere strains are pathogenic for cystic fibrosis patients or not. Eighteen B. cenocepacia strains of rhizosphere and clinical origin were typed by multi‐locus sequence typing (MLST) analysis and compared for their ability to invade pulmonary epithelial cells and their virulence in a mouse model of airway infection. Although there was great variability, clinical strains were the most invasive in vitro. Almost all the rhizosphere and two clinical strains were defined as non‐invasive, six clinical strains as invasive, and two strains of both clinical and environmental origin as indeterminate. Exposure of murine airways to clinical strains caused higher acute mortality than that seen after challenge with rhizosphere strains. Furthermore, both clinical and environmental strains were able to persist in the lungs of infected mice, with no significant differences in bacterial loads and localization 14 days after challenge. DNA dot blot analyses of AHL synthase, porin and amidase genes, which play a role in B. cenocepacia virulence, showed that they were present in B. cenocepacia strains irrespective of their origin. Overall, our results suggest that rhizosphere strains do not differ from clinical strains in some pathogenic traits.
The Mth60 fimbriae of Methanothermobacter thermoautotrophicus are functional adhesins
Authors: Thoma Christine , Frank Monika , Rachel Reinhard , Schmid Silvia , Näther Daniela , Wanner Gerhard , Wirth Reinhard 
Published: July 2008

SummaryThe ability to adhere onto surfaces is of very high importance for microorganisms, enabling them to stay in a favourable habitat for life. In the case of Bacteria cell surface organelles called fimbriae/pili have been shown to be used for adhesion; corresponding cell surface appendages of Archaea have not yet been defined. The first detailed characterization of archaeal fimbriae, namely those of Methanothermobacter thermoautotrophicus, allowed us to identify mth60 as the main structural fimbrin gene. Recombinant expression of mth60 in Escherichia coli was used to generate sufficient amounts of Mth60 to induce antibodies in rabbits. The antiserum reacted specifically with the 16 kDa fimbrial glycoprotein and could specifically detach adhering M. thermoautotrophicus cells from various surfaces. In addition we proved that cells adhering to solid surfaces – organic and inorganic ones – express many more fimbriae than cells growing in liquid cultures. The Mth60 fimbriae therefore are used by M. thermoautotrophicus as adhesins.
The Interplay between Conscious and Automatic Self‐Regulation and Adolescents’ Physical Activity: The Role of Planning, Intentions, and Lack of Awareness
Authors: Dombrowski Stephan , Luszczynska Aleksandra 
Published: July 2008

This study investigated the interplay between conscious and automatic self‐regulatory variables and adolescents’ physical activity. It was hypothesised that intention, planning, and lack of awareness would predict adolescents’ behaviour. One hundred and fifty‐five individuals (aged 13 to 17 years) completed questionnaires in two waves (with a time gap of 10 days). The results of cross‐lagged panel analysis suggested that both past behaviour and planning predicted physical activity at follow‐up, whereas physical activity predicted intention. Although lack of awareness, a facet of automatic processes, was negatively related to physical activity, the nested model comparison analysis indicated that the relation between lack of awareness and physical activity might be negligible. Among the self‐regulatory processes, planning was found to be the most important predictor of adolescents’ physical activity, although past behaviour remained the strongest predictor of future behaviour.Cette recherche porte sur l’interaction entre les variables autorégulatrices conscientes et automatiques et l’activité physique des adolescents. On a fait l’hypothèse que l’intention, la planification et l’absence de prise de conscience allaient prédire le comportement des adolescents. 155 individus âgés de 13 à 17 ans ont rempli des questionnaires en deux temps avec un intervalle de dix jours. Les résultats d’une analyse en panel retardé croisé montrent que la conduite antérieure et la planification prédisent l’activité physique qui s’ensuit alors que l’activité physique prédit l’intention. Bien que le manque de prise de conscience, une facette des processus automatiques, soit négativement corréléà l’activité physique, l’analyse de variance indique que la relation entre l’absence de prise de conscience et l’activité physique pourrait être négligeable. Des différents processus d’autorégulation, c’est la planification qui est apparue comme étant le prédicteur majeur de l’activité physique des adolescents, bien que la conduite passée reste le prédicteur le plus fiable du comportement à venir.
Diagnostic compatibility of structural and haemodynamic parameters in open‐angle glaucoma patients
Authors: Janulevičienė Ingrida , Sliesoraitytė Ieva , Siesky Brent , Harris Alon 
Published: July 2008

Abstract.Purpose:  Current evidence indicates that alteration in ocular blood flow may be relevant in open‐angle glaucoma (OAG) patients independent of intraocular pressure (IOP). Presently, the lack of an adequate methodology capable of assessing all vascular beds limits the clinical role of blood flow parameters in glaucoma management. We aimed to compare differences in retinal nerve fibre layer (RNFL) thickness and retrobulbar haemodynamics between OAG patients and healthy age‐matched control subjects.Methods:  Sixty eyes of 30 OAG patients and 30 healthy age‐matched controls were enrolled into the prospective, randomized study. Retinal nerve fibre layer thickness was analysed by scanning laser polarimetry (SLP). Standard SLP parameters were determined, including: average temporal, superior, nasal, inferior thickness (TSNIT); superior and inferior averages; TSNIT standard deviation (TSNIT‐SD), and nerve fibre indicator (NFI). Retrobulbar haemodynamics were assessed using colour Doppler imaging (CDI). Peak systolic velocity (PSV), end‐diastolic velocity (EDV), pulsatility index (PI) and resistivity index (RI) in the ophthalmic artery (OA), central retinal artery (CRA) and short posterior ciliary artery (SPCA) were evaluated.Results:  The RNFL in OAG patients was statistically significantly thinner compared with that in age‐matched controls: the NFI was 24.9 ± 10.24 in OAG patients and 16.13 ± 7.95  in healthy controls (p < 0.05). Statistically significant differences were observed: CRA PSV was 20.54 ± 7.84 cm/second in OAG subjects and 16.5 ± 6.19 cm/second in healthy controls (p = 0.0038); OA EDV was 8.99 ± 4.71 cm/second in OAG subjects and 5.93 ± 3.23 cm/second in healthy controls (p = 0.0048). Correlation analysis of NFI was in positive association with CRA EDV (r = 0.395; p < 0.05) and CRA PI (r = 0.403; p < 0.05) in OAG subjects, but no statistically significant association was seen in healthy controls.Conclusions:  Statistically significant thinning of the RNFL in association with reduced retrobulbar blood flow velocities was observed in OAG patients. Combining ocular structural alterations with ocular circulation assessment may increase our ability to elucidate potential IOP‐independent glaucomatous risk factors.
Single vs. Multiple Discount Rates: How to Limit “Influence Costs” in the Capital Allocation Process*
Authors: Martin John , Titman Sheridan 
Published: July 2008

Most finance textbooks suggest that companies evaluate investment projects using discount rates that reflect both the debt capacity and the unique risks of the project. In practice, however, companies often use their company‐wide WACC to evaluate such investments because of the difficulty of (and subjectivity involved in) estimating the risk of individual projects, and the potential for managerial bias and influence to distort the estimates.This article proposes a practicable method for calculating the cost of capital that produces different discount rates for investment projects with different risks while minimizing the “influence costs” that arise when managers have discretion in the choice of discount rates. The proposed approach makes use of market information (in the form of the firm‐wide costs of debt and equity), thereby limiting managerial discretion, while typically still providing a good approximation of theoretically correct, project‐specific discount rates. The key to the method's effectiveness is its use of a project's debt capacity to define the capital structure weights, where debt capacity is defined by the amount of debt financing the project will support without lowering the firm's credit rating.