bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serrated polyps of the large intestine: a molecular study comparing sessile serrated adenomas and hyperplastic polyps
Authors: Sandmeier Dominique , Benhattar Jean , Martin Patricia , Bouzourene Hanifa 
Published: July 2009

Aims: To compare the molecular profile of a series of sessile serrated adenomas (SSAs) and hyperplastic polyps (HPs), in order to distinguish these lesions, SSAs having a potential role in the genesis of serrated adenocarcinomas through a serrated pathway in which methylation plays a key role.Methods and results: Twelve HPs and sixteen SSAs of the right and left colon were investigated for microsatellite instability, DNA mismatch repair genes, p53, p16, and β‐catenin expression, MLH1 and p16 (CDKN2A) gene methylation, and KRAS and BRAF mutations. Both SSAs and HPs were microsatellite stable. MLH1 and MSH2 protein silencing, aberrant cytoplasmic expression and methylation of p16 were found to be exclusive to right‐sided SSAs. The MLH1 promoter gene was frequently methylated in right‐sided SSAs in contrast with HPs. Abnormal p53 and β‐catenin expression was present in both SSAs and HPs. BRAF and KRAS mutation were mutually exclusive, but KRAS mutation was present only in left‐sided SSAs and HPs.Conclusions: HPs and SSAs may be related lesions. However, at least right‐sided SSAs differ from left‐sided SSAs and HPs in the occurrence of MLH1 and p16 methylation, supporting the hypothesis that SSAs could be precursors of serrated adenocarcinomas.
The routine use of histochemical stains in gastrointestinal pathology: a UK‐wide survey
Authors: Koenig Michael , Schofield John B , Warren Bryan F , Shepherd Neil A 
Published: July 2009

Aims:  A survey was conducted into the routine use of special stains on gastrointestinal (GI) biopsy specimens in histopathology departments within the National Health Service. The aim was to compare the sole use of haematoxylin and eosin (H&E) staining with the use of H&E and special stains, according to the biopsy site.Methods and results:  One hundred and sixty‐seven histopathology departments in the UK were contacted using an e‐mail questionnaire. Valid return rate was 55%. Sixty‐eight percent of departments employ H&E only for oesophageal biopsy specimens. Gastric specimens are stained using only H&E in 47% of departments and 53% use H&E combined with special stains. Duodenal, small and large bowel biopsy specimens are mostly stained with H&E.Conclusions:  The results show that the routine use of special stains in GI pathology in the UK is highly variable, especially for oesophageal and gastric biopsy specimens. The literature indicates that special stains in GI specimens can enhance sensitivity and specificity for the detection of pathological abnormalities, especially metaplasia and infections. The diversity of staining practice highlights the need to provide robust and evidence‐based guidelines for the routine use of special stains to ensure universal best practice.
Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size
Authors: MEDUGORAC IVICA , MEDUGORAC ANA , RUSS INGOLF , VEIT‐KENSCH CLAUDIA E. , TABERLET PIERRE , LUNTZ BERNHARD , MIX HENRY M. , FÖRSTER MARTIN 
Published: July 2009

AbstractIn times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North‐West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Buša breeds in the Anatolian and Balkan areas, when compared with the alpine and north‐western European breeds. Our results reflect long‐term evolutionary and short‐term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long‐term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.
Long‐term natal site‐fidelity by immature lemon sharks (Negaprion brevirostris) at a subtropical island
Authors: CHAPMAN DEMIAN D. , BABCOCK ELIZABETH A. , GRUBER SAMUEL H. , DIBATTISTA JOSEPH D. , FRANKS BRYAN R. , KESSEL STEVEN A. , GUTTRIDGE TRISTAN , PIKITCH ELLEN K. , FELDHEIM KEVIN A. 
Published: July 2009

AbstractAlthough many sharks begin their life confined in nursery habitats, it is unknown how rapidly they disperse away from their natal area once they leave the nursery. We examine this issue in immature lemon sharks (Negaprion brevirostris) from the time they leave the nursery (∼ age 3) at a subtropical island (Bimini, Bahamas), through to the onset of sexual maturity (∼ age 12). From 1995 to 2007 we tagged and genotyped a large fraction of the nursery‐bound sharks at this location (0–3 years of age, N = 1776 individuals). From 2003 to 2007 we sampled immature sharks aged from 3 to 11 years (N = 150) living around the island and used physical/genetic tag recaptures coupled with kinship analysis to determine whether or not each of these ‘large immature sharks’ was locally born. We show that many island‐born lemon sharks remain close to their natal area for long periods (years) after leaving the nursery; more than half of the sampled sharks up to 135 cm total length (∼6 years old) were locally born. The fraction of locally born sharks gradually declined with increasing shark size, indicating that dispersal is relatively slow and does not primarily occur after sharks reach a threshold size. Local conservation measures (e.g. localized fishery closures, marine protected areas) can therefore help protect island‐born lemon sharks even after they leave the nursery habitat.
Mating system variability in a mouthbrooding cichlid fish from a tropical lake
Authors: SEFC K. M. , HERMANN C. M. , KOBLMÜLLER S. 
Published: July 2009

AbstractIntraspecific variability in mating behaviour and disparities between social and reproductive behaviour add complexity to the description of animal mating systems. A previously published field study on a population of the maternally mouthbrooding cichlid fish Ctenochromis horei in the north of Lake Tanganyika suggested mate monopolization by the most dominant male. In the present study, genetic reconstructions of paternity in a population in the south of the lake provided no evidence for male mate monopolization, as none of the inferred sires had offspring in more than one brood. The ability to reconstruct sire genotypes from offspring alleles was confirmed by computer simulations. Multiple paternity occurred in several broods and was significantly more frequent in the sample taken in the rainy season than in the dry season sample (100% of broods vs. 14%, respectively; P = 0.005). The data suggest geographical and temporal variation in the mating behaviour of C. horei despite its continuous year‐round reproduction, invariable brood care behaviour and habitat‐specific distribution in the relatively constant and confined environment of a tropical lake. Moreover, our data show that inferences on the distribution of male reproductive success, if based on each geographical or temporal data set alone, would fail to describe the potential for sexual selection in this species.
Factors influencing time to smear conversion in patients with smear‐positive pulmonary tuberculosis
Authors: WANG Jann‐Yuan , LEE Li‐Na , YU Chong‐Jen , CHIEN Yin‐Ju , YANG Pan‐Chyr ,   The Tami Group
Published: July 2009

ABSTRACTBackground and objective:  Persistent smear‐positivity in patients with pulmonary tuberculosis has been shown to predict an unfavourable outcome. This study was conducted to identify the factors influencing time to sputum smear conversion.Methods:  From July 2003 to June 2007, all patients with smear‐positive and culture‐confirmed pulmonary tuberculosis, who had attended a medical centre and a local teaching hospital, were identified. Factors that might have influenced time to smear conversion were investigated using time‐to‐event analysis.Results:  Altogether 305 patients (mean age: 58.6 years) were studied. Diabetes mellitus was the most common underlying comorbidity. Eight patients (2.6%) had AIDS. After 2 months of treatment, 34 (11.1%) patients remained smear‐ and culture‐positive. Cox proportional hazard regression analysis indicated that the presence of a cavity on CXR, smear grading and the first 2‐month treatment regimen were independent factors influencing the time to sputum smear conversion. Among patients who had received isoniazid in the first 2 months of treatment, the time to sputum smear conversion in the 24 patients whose isolate showed isoniazid resistance was not different from that in the 236 patients whose isolate was isoniazid‐susceptible (hazard ratio 1.061; 95% CI: 0.697–1.616).Conclusions:  This analysis revealed that 11.1% of tuberculosis patients remained smear‐positive after 2 months of treatment. Patients with cavitation, higher smear grading and those who had not used isoniazid, rifampicin, ethambutol and pyrazinamide continuously in the initial treatment phase had a longer time to sputum smear conversion.
Urinary collecting system invasion in renal cell carcinoma: Incidence and long‐term prognosis
Authors: Schrader Andres Jan , Rustemeier Julia , Varga Zoltan , Hegele Axel , Olbert Peter Jochen , Frohme Carsten , Hofmann Rainer 
Published: July 2009

Objectives:  Current data on the prognostic impact of urinary collecting system (UCS) invasion by renal cell carcinoma (RCC) are highly conflicting. The aim of the present study was to assess incidence and long‐term prognosis of RCC patients with and without UCS involvement.Methods:  We evaluated 780 patients who had undergone renal surgery between 1990 and 2005. The mean follow‐up was 5.44 years.Results:  Sixty‐seven patients (8.6%) demonstrated UCS invasion. These patients had a significant increase in the likelihood of cancer‐related death (hazard ratio [HR] 1.9, 95% confidence interval: 1.4–2.7; P = 0.001). Their median 5‐year tumor‐specific survival rate was 61%, as opposed to 79% for patients without UCS invasion (P = 0.001). UCS invasion was significantly associated with tumor stage, grade, clinical symptoms, lymph node and visceral metastasis at diagnosis, but not with age, gender, histologic subtype or body mass index. However, by means of multivariate analysis, UCS invasion was disqualified as an individual prognostic marker for RCC.Conclusion:  We do not advocate the inclusion of UCS invasion into upcoming Tumor‐Nodes‐Metastasis staging systems. In contrast, future research should focus on the prognostic role of novel molecular tumor markers and/or specific immunological characteristics of RCC patients.
Peri‐operative management of anti‐platelet agents
Authors: Hermiz Samer , Larsen Peter , Galletly Duncan C. , Harding Scott A. 
Published: July 2009

AbstractBackground:  Increasing numbers of patients treated with anti‐platelet agents are presenting for non‐cardiac surgery. We examined the peri‐operative management of anti‐platelet therapy in patients undergoing elective non‐cardiac surgery and the process by which patients received instructions.Methods:  We interviewed and collected outcome data on 213 consecutive patients aged ≥45 years presenting for elective non‐cardiac surgery at our institution over a 6‐week period regarding the peri‐operative management of anti‐platelet and warfarin therapy.Results:  Anti‐platelet therapy was prescribed in 22.5% and warfarin in 5.2% of the study subjects. Aspirin was stopped peri‐operatively in 55.3%, while clopidogrel was stopped in the sole patient treated with this. The frequency of anti‐platelet agent discontinuation was similar for major and minor surgery. Warfarin was discontinued prior to surgery in all cases. Only 54.2% of those treated with anti‐platelet therapy recalled being given instruction regarding pre‐operative management of their anti‐platelet therapy compared with 90.9% of patients treated with warfarin (P= 0.04). In the absence of instructions, a number of patients made their own decision to stop their aspirin pre‐operatively. Post‐operatively, only 37% recalled receiving instructions regarding restarting anti‐platelet therapy. As a result, three patients failed to do so. In contrast, all those treated with warfarin received clear post‐operative instructions.Conclusion:  Peri‐operative anti‐platelet management and communication with patients appears to be sub‐optimal. There is a need for standardized processes whereby informed decisions regarding peri‐operative anti‐platelet therapy are made and communicated clearly to the patients.
Quality of clinical notes for vascular surgery admissions: A CRABEL score review
Authors: Suh Jun , Roake Justin A. , Lewis David R. 
Published: July 2009

AbstractAim:  To compare the quality of patient notes between acute and elective admissions in vascular surgery.Method:  Patient notes from the 50 most recent acute and elective admissions on a vascular surgical unit were reviewed using the CRABEL score. Points for quality of record keeping were awarded in four categories: Initial Clerking, Subsequent Entries, Consent and Discharge Summary. Total scores were calculated as a percentage. One hundred per cent represents the minimum quality standard expected. Overall CRABEL scores were compared for differences in the quality of note keeping between acute and elective admissions. Further analysis identified areas that need improvement.Results:  The mean CRABEL score for acute admissions was 79.2% (77.0–81.3, 95% C.I.) compared to 81.3% (78.8–83.8, 95% C.I.) for elective admissions (t‐test P= n.s.). When the individual categories were analysed no statistically significant difference was observed between the two groups for ‘Subsequent Entries’ and ‘Consent’ sections (t‐test p= n.s.). ‘Initial Clerking’ category scored significantly better for elective 16.3 out of 20 (15.7–16.9, 95% C.I.) admissions compared to acute admissions 14.6 out of 20 (13.9–15.3, 95% C.I.), (t‐test P= 0.00063). ‘Discharge Summary’ section also scored significantly better for elective admissions 9.9 out of 10 (9.9–10.0, 95% C.I.) compared to acute admissions 9.6 out of 10 (9.3–9.9, 95% C.I.), (t‐test P= 0.040).Conclusion:  There was no statistically significant difference in the overall quality of written patient notes between acute and elective admissions, however ‘Initial Clerking’ and ‘Discharge Summary’ were better documented for elective admissions. Both acute and elective admissions were observed to have substandard quality of record keeping.
Whole‐genome microarray analyses of Synechococcus–Vibrio interactions
Authors: Tai Vera , Paulsen Ian T. , Phillippy Katherine , Johnson D. Aaron , Palenik Brian 
Published: July 2009

SummaryMicrobes live in diverse communities yet their physiologies are typically studied in axenic culture. To begin to address this dichotomy, whole‐genome microarray analyses were used and revealed that several major metabolic pathways were affected in Synechococcus sp. WH8102, a model phototroph, when grown with Vibrio parahaemolyticus, a model heterotroph. In co‐cultures with V. parahaemolyticus, although phosphate was not depleted, Synechococcus sp. WH8102 may have experienced phosphate stress since the expression of phosphate acquisition genes increased and alkaline phosphatase activity was higher than in monocultures. Expression of cell wall synthesis genes and the components of a zinc transporter were also upregulated. In contrast, a ferric uptake regulation (Fur) family gene was downregulated as were genes that encode proteins rich in iron or involved in detoxifying oxygen radicals. Nitrogen use may also have been affected in co‐cultures as the gene expression changes share similarities with ammonia‐grown Synechococcus. This study demonstrates the multiple impacts that interspecific microbial interactions can have on the physiology of a major primary producer and the importance of investigating microbial physiology from a community perspective.
Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands
Authors: Hartmann Martin , Lee Sangwon , Hallam Steven J. , Mohn William W. 
Published: July 2009

SummaryDisturbances caused by timber harvesting have critical long‐term effects on the forest soil microbiota and alter fundamental ecosystem services provided by these communities. This study assessed the effects of organic matter removal and soil compaction on microbial community structures in different soil horizons 13 years after timber harvesting at the long‐term soil productivity site at Skulow Lake, British Columbia. A harvested stand was compared with an unmanaged forest stand. Ribosomal intergenic spacer profiles of bacteria, archaea and eukarya indicated significantly different community structures in the upper three soil horizons of the two stands, with differences decreasing with depth. Large‐scale sequencing of the ribosomal intergenic spacers coupled to small‐subunit ribosomal RNA genes allowed taxonomic identification of major microbial phylotypes affected by harvesting or varying among soil horizons. Actinobacteria and Gemmatimonadetes were the predominant phylotypes in the bacterial profiles, with the relative abundance of these groups highest in the unmanaged stand, particularly in the deeper soil horizons. Predominant eukaryal phylotypes were mainly assigned to known mycorrhizal and saprotrophic species of Basidiomycetes and Ascomycetes. Harvesting affected Basidiomycetes to a minor degree but had stronger effects on some Ascomycetes. Archaeal profiles had low diversity with only a few predominant crenarchaeal phylotypes whose abundance appeared to increase with depth. Detection of these effects 13 years after harvesting may indicate a long‐term change in processes mediated by the microbial community with important consequences for forest productivity. These effects warrant more comprehensive investigation of the effects of harvesting on the structure of forest soil microbial communities and the functional consequences.
Molecular taxonomy and phylogeny of the Geodiidae (Porifera, Demospongiae, Astrophorida) – combining phylogenetic and Linnaean classification
Authors: Cárdenas Paco , Rapp Hans Tore , Schander Christoffer , Tendal Ole S. 
Published: July 2009

Cárdenas, P., Rapp, H. T., Schander, C. & Tendal, O. S. (2009). Molecular taxonomy and phylogeny of the Geodiidae (Porifera, Demospongiae, Astrophorida) – combining phylogenetic and Linnaean classification.—Zoologica Scripta, 39, 89–106.According to the fossil records, the Geodiidae represents one of the oldest families of demosponges (Phylum Porifera). There are approximately 220 described extant species, geographically and bathymetrically widely distributed around the world. Species of this family all share a two‐layered cortex with ball‐shaped spicules called ‘sterrasters’ in the endocortex. However, molecular studies have questioned the monophyly of the group. Moreover, the evolutionary history and the intrafamily relationships of the Geodiidae are not fully resolved. Using a partial sequence of the cytochrome c oxidase subunit 1 (COI) gene and a partial sequence of the 28S rDNA gene (D1–D2 domains), we present the first molecular phylogeny focusing on this group. The congruent results from the two gene fragments suggest that (i) the Geodiidae is monophyletic, (ii) the Erylinae/Geodinae subdivision sensuSollas, 1888 is valid and that (iii) Isops and Sidonops are junior synonyms of Geodia. The synonymization of Isops and Sidonops implies that the oscule/pore morphology as a diagnostic character should be abandoned. Geodia hentscheli nom. nov. has been given for Geodia mesotriaena (Hentschel, 1929). This study served as the basis for a revised phylogenetic classification of the Geodiidae. Well‐supported clades led to the establishment of clade names following the PhyloCode. The Geodinae clade is strongly supported and notably composed of Depressiogeodia, Cydonium and Geodia. A morphological synapomorphy of Geodinae is the presence of euasters in the ectocortex. The Erylinae (Erylus, Penares, Caminus and Pachymatisma) form a strongly supported monophyletic group with three morphological synapomorphies: (i) loss of anatriaenes and protriaenes, (ii) microrhabds (or spherules) in the ectocortex and (iii) short‐shafted triaenes. The Erylus monophyly is ambiguous. Erylus species are distributed in three well‐supported clades. Finally, spicule homology in the cortex of the Geodiidae is discussed.
p53 expression in patients with advanced urothelial cancer of the urinary bladder
Authors: Shariat Shahrokh F. , Bolenz Christian , Karakiewicz Pierre I. , Fradet Yves , Ashfaq Raheela , Bastian Patrick J. , Nielsen Matthew E. , Capitanio Umberto , Jeldres Claudio , Rigaud Jérôme , Müller Stefan C. , Lerner Seth P. , Montorsi Francesco , Sagalowsky Arthur I. , Cote Richard J. , Lotan Yair 
Published: July 2009

Study Type – Prognosis (inception cohort)  Level of Evidence 1bOBJECTIVETo test whether assessing p53 expression could improve the ability to predict disease recurrence and disease‐specific survival in a multi‐institutional cohort of patients with advanced urothelial carcinoma of the urinary bladder (UCB).PATIENTS AND METHODSThe study comprised 692 patients with pT3–4 N0 or pTany N+ UCB treated with radical cystectomy and lymphadenectomy. The predictive accuracy (PA) was quantified using the 200 bootstrap‐corrected concordance index. The base model comprised age, gender, stage, grade, lymphovascular invasion, number of lymph nodes removed, number of lymph nodes positive, concomitant carcinoma in situ, and adjuvant chemotherapy.RESULTSp53 expression was altered in 341 (49.3%) patients. In multivariable analyses, p53 expression was independently associated with disease recurrence (hazard ratio, 1.66; P < 0.001) and cancer‐specific mortality (hazard ratio 1.65, P < 0.001). Overall, adding p53 did not significantly improve the PA of the base model (recurrence +0.7%, P = 0.085, and cancer‐specific mortality +1.2%, P = 0.050). In the subgroups of pT3N0 (280) and pT4N0 (83) patients, p53 slightly improved the PA of the base model by a statistically significant degree (recurrence +1.7% and +3.6%, respectively; cancer‐specific mortality +1.9% and +3.5%, respectively; all P < 0.001). In 329 patients with pTany N+ disease p53 status did not improve the PA of the base model.CONCLUSIONWhile assessing p53 expression has limited utility in patients with lymph node‐positive UCB, it marginally improves prognostication in patients with advanced non‐metastatic UCB. Integration of p53 into a panel of biomarkers might be necessary to capture a more accurate picture of the biological potential of advanced UCB.