bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic review: the global incidence and prevalence of peptic ulcer disease
Authors: SUNG J. J. Y. , KUIPERS E. J. , EL‐SERAG H. B. 
Published: February 2009

SummaryBackground  Peptic ulcer disease (PUD) is most commonly associated with Helicobacter pylori infection and the use of acetylsalicylic acid (ASA) and nonsteroidal anti‐inflammatory drugs (NSAIDs). The management of H. pylori infection has improved radically in recent years; however, the prescription of ASA and NSAIDs has increased over the same period.Aim  To evaluate the current global incidence and prevalence of PUD by systematic review of the literature published over the last decade.Methods  Systematic searches of PubMed, EMBASE and the Cochrane library.Results  The annual incidence rates of PUD were 0.10–0.19% for physician‐diagnosed PUD and 0.03–0.17% when based on hospitalization data. The 1‐year prevalence based on physician diagnosis was 0.12–1.50% and that based on hospitalization data was 0.10–0.19%. The majority of studies reported a decrease in the incidence or prevalence of PUD over time.Conclusions  Peptic ulcer disease remains a common condition, although reported incidence and prevalence are decreasing. This decrease may be due to a decrease in H. pylori‐associated PUD.
Genome‐wide scan for bovine twinning rate QTL using linkage disequilibrium
Authors: Kim E.‐S. , Berger P. J. , Kirkpatrick B. W. 
Published: February 2009

SummaryTwinning is a complex trait with negative impacts on health and reproduction, which cause economic loss in dairy production. Several twinning rate quantitative trait loci (QTL) have been detected in previous studies, but confidence intervals for QTL location are broad and many QTL are unreplicated. To identify genomic regions or genes associated with twinning rate, QTL analysis based on linkage combined with linkage disequilibrium (LLD) and individual marker associations was conducted across the genome using high‐throughput single nucleotide polymorphism (SNP) genotypes. A total of 9919 SNP markers were genotyped with 200 sires and sons in 19 half‐sib North American Holstein dairy cattle families. After SNPs were genotyped, informative markers were selected for genome‐wide association tests and QTL searches. Evidence for twinning rate QTL was found throughout the genome. Thirteen markers significantly associated with twinning rate were detected on chromosomes 2, 5 and 14 (P < 2.3 × 10−5). Twenty‐six regions on fourteen chromosomes were identified by LLD analysis at P < 0.0007. Seven previously reported ovulation or twinning rate QTL were supported by results of single marker association or LLD analyses. Single marker association analysis and LLD mapping were complementary tools for the identification of putative QTL in this genome scan.
Availability of and access to critical habitats in regulated rivers: effects of low‐head barriers on threatened lampreys
Authors: LUCAS MARTYN C. , BUBB DAMIAN H. , JANG MIN‐HO , HA KYONG , MASTERS JEROME E. G. 
Published: February 2009

Summary1. Conservation of freshwater animal populations requires their access to, as well as sufficient availability of, critical habitats, such as those for reproduction. Abundant small‐scale barriers may cause extensive fragmentation of freshwater habitat but, by comparison to larger structures their effects are rarely considered by catchment managers. The relationship between the distribution of, and access to, spawning habitat in a regulated river, characterized by abundant small barriers, was examined for river lampreyLampetra fluviatilis, a threatened migratory fish.2. Telemetry of adult lamprey in the River Derwent, North East England was used to quantify upriver migration and access to spawning habitat, together with surveys of spawning habitat availability and spawning activity between 2002 and 2007.3. Access in to the Derwent appeared severely restricted by a tidal barrage, beyond which lamprey migrated rapidly in unobstructed reaches. Of all lamprey tagged in the lower 4 km of river, or ascending the barrage, 64% and 17% passed the first and second weirs respectively, with high flows crucial for this. Although over 98% of lamprey spawning habitat occurred more than 51 km upstream, on average just 1.8% of river lamprey spawners were recorded there.4. In order to protect or rehabilitate species or species assemblages, greater attention needs to be paid to the relative spatial distribution of low‐head barriers and the resultant availability of key habitats within individual catchments. This is particularly important given the renewed emphasis internationally on low‐head hydropower solutions as a source of renewable energy, and the rapid growth in numbers of low‐head barriers in many catchments.
Influence of lateral gradients of hydrologic connectivity on trophic positions of fishes in the Upper Mississippi River
Authors: ROACH KATHERINE A. , THORP JAMES H. , DELONG MICHAEL D. 
Published: February 2009

Summary1. Riverscapes consist of the main channel and lateral slackwater habitats along a gradient of hydrological connectivity from maximum connection in main channel habitats to minimum connection in backwaters. Spatiotemporal differences in water currents along this gradient produce dynamic habitat conditions that influence species diversity, population densities and trophic interactions of fishes.2. We examined the importance of lateral connectivity gradients for food web dynamics in the Upper Mississippi River during spring (high flow, moderately low temperatures) and summer (low flow, higher temperatures). We used literature information and gut contents analyses to determine feeding guilds and stable isotope analysis to estimate mean trophic position of local fish assemblages. During June and August 2006, we collected over 1000 tissue samples from four habitats (main channel, secondary channels, tertiary channels and backwaters) distributed within four hydrologic connectivity gradients.3. Mean trophic position differed among feeding guilds and seasons, with highest values in spring. Mean trophic position of fish assemblages, variability in trophic position and food chain length (maximum trophic position) of the two dominant piscivore species (Micropterus salmoides and M. dolomieu) in both seasons were significantly associated with habitat along the lateral connectivity gradient. Food chain length peaked in tertiary channels in both seasons, probably due to higher species diversity of prey at these habitats. We infer that food chain length and trophic position of fish assemblages were lower in backwater habitats in the summer mainly because of the use of alternative food sources in these habitats.4. A greater number of conspecifics exhibited significant among‐habitat variation in trophic position during the summer, indicating that low river stages can constrain fish movements in the Upper Mississippi River.5. Results of this study should provide a better understanding of the fundamental structure of large river ecosystems and an improved basis for river rehabilitation and management through knowledge of the importance of lateral complexity in rivers.
Distinct biphasic histomorphological pattern in gastrointestinal stromal tumours (GISTs) with common primary mutations but divergent molecular cytogenetic progression
Authors: Agaimy Abbas , Haller Florian , Gunawan Bastian , Wünsch Peter H , Füzesi László 
Published: February 2009

Aims:  The morphological diversity of gastrointestinal stromal tumours (GISTs) is well appreciated. The aim of this study was to shed light on the molecular pathogenesis of GISTs displaying a distinct biphasic histomorphological pattern, which is poorly understood.Methods and results:  Six biphasic gastric GISTs (four high, one intermediate and one low risk for aggressive behaviour) were studied by histological, immunohistochemical, molecular and comparative genomic hybridization methods. The different tumour components were designated as primary and secondary compartments, based on cellularity and mitotic index. In addition, metastases from two patients were analysed separately. According to the classification of Miettinen et al., four biphasic histomorphological patterns were seen: (i) sclerosing spindle cell/dyscohesive or paraganglioma‐like epithelioid (n = 2); (ii) sarcomatous spindle cell/pleomorphic sarcomatous spindle cell (n = 1); (iii) sarcomatous spindle cell/sarcomatous epithelioid (n = 2); and (iv) sclerosing epithelioid/hypercellular epithelioid/sarcomatous epithelioid (n = 1) morphology. In each case, both tumour compartments revealed the same KIT (n = 5) or platelet‐derived growth factor receptor‐alpha (n = 1) mutation, as well as common chromosomal imbalances reflecting their common clonal origin. Additional chromosomal imbalances were detected in the secondary tumour compartments and their respective metastases.Conclusions:  Our results indicate that the intratumoral phenotypic diversity in GIST reflects histomorphological progression, which is associated with higher chromosomal instability, irrespective of the primary mutation.
Haeme oxygenase‐1 promoter polymorphism is an independent prognostic marker of gastrointestinal stromal tumour
Authors: Vashist Yogesh K , Uzunoglu Guentac , Cataldegirmen Guelle , Kalinin Viacheslar , Schurr Paulus , Koenig Alexandra M , Thieltges Sabrina , Zehler Oliver , Schneider Claus , Izbicki Jacob R , Yekebas Emre F 
Published: February 2009

Aims:  Gastrointestinal stromal tumours (GISTs) display genetic alterations on chromosome 22. GTn repeat (GTn) length polymorphism in the promoter of haeme oxygenase‐1 gene (HMOX‐1) is located on chromosome 22 and associated with malignant growth. The aim was to investigate the role of HMOX‐1 promoter polymorphism in GIST patients.Methods and results:  Tumour and corresponding healthy tissue DNA of 44 patients who underwent surgical resection of GIST were analysed by polymerase chain reaction, capillary electrophoresis and DNA sequencing. GTn polymorphism was classified into short (S) and long (L) allele. There was no difference detected in GTn genotype between tumour and healthy tissue DNA. Short GTn allele (SGTn) was significantly associated with metastatic disease, higher tumour recurrence rates and high risk GIST (consensus criteria 2001). Furthermore, SGTn allele carriers had significantly shorter disease‐free and overall survival (log rank test, P < 0.0001). On multivariate Cox regression analysis, GTn polymorphism was identified as an independent prognostic factor for survival (P = 0.001).Conclusions:  HMOX‐1 promoter GTn polymorphism is a potential prognostic marker and may help to allocate patients to different risk groups, customized therapy and follow‐up. Haeme oxygenase‐1 could represent an important candidate gene in the pathogenesis and growth of GIST.
Down‐regulated expression of the TSAP6 protein in liver is associated with a transition from cirrhosis to hepatocellular carcinoma
Authors: Caillot Frédérique , Daveau Romain , Daveau Maryvonne , Lubrano Jean , Saint‐Auret Gaëlle , Hiron Martine , Goria Odile , Scotte Michel , Francois Arnaud , Salier Jean‐Philippe 
Published: February 2009

Aims:  Hepatocellular carcinoma (HCC) results from cirrhosis and, in Western Europe, hepatitis C virus and alcoholism are the predominant causes of this disease. We recently documented a global transcript repression in hepatocarcinoma nodules. The tumour suppressor activated pathway‐6 (TSAP6) transcript codes for a transmembrane molecule that is an inducer of a caspase‐3‐dependent apoptotic pathway. The down‐regulation of TSAP6 transcripts in HCC and perinodular cirrhosis, which contrasts with a sustained transcript level in HCC‐free cirrhosis, has suggested that this hepatic protein level may provide a prognostic marker for HCC occurrence.Methods and results:  This protein was quantified by semiquantitative assessment of immunohistochemistry on samples from 42 cases HCC‐free cirrhosis, 49 cases cirrhosis with HCC, 43 HCC associated with healthy liver and 31 controls. TSAP6 expression was linked to the liver state, healthy or cirrhotic without or with an HCC and to tumour grade.Conclusions:  With biopsies periodically performed for surveillance purposes, the decreased expression of TSAP6 in cirrhotic tissue could reflect a decrease in the apoptotic process and could be interpreted as a warning sign. This evaluation of the TSAP6 level in cirrhotic liver conveys predictive information for the development of HCC.
Prognostic value of PRL‐3 overexpression in early stages of colonic cancer
Authors: Xing Xiaofang , Peng Lirong , Qu Like , Ren Tingting , Dong Bin , Su Xiangqian , Shou Chengchao 
Published: February 2009

Aims:  High expression of phosphatase of regenerating liver (PRL‐3) has been implicated in cancer invasion and metastasis, indicating a close link between PRL‐3 and cancer development. The aim was to investigate the significance of PRL‐3 expression in the prognosis of colonic cancer.Methods and results:  Expression of PRL‐3 protein in tissue slides obtained from surgical resection of primary colonic cancer was measured by immunohistochemistry using a specific anti‐PRL‐3 monoclonal antibody. Archived tissue specimens from 273 colonic cancers and 236 matched specimens of adjacent normal colonic mucosa with a median follow‐up of 57 months were examined. Multivariate analysis showed that PRL‐3 was an independent prognostic marker for disease‐free survival [DFS; hazard ratio (HR) 1.538, P = 0.035]. More importantly, the expression of PRL‐3 showed significant negative correlation with DFS (P = 0.018) in patients in the early stages (stage I and II). Patients with high levels of PRL‐3 expression in the adjacent normal mucosa also had a significant worse survival rate (DFS 0.0% versus 74.4%, P = 0.001), and PRL‐3 expression remained an independent prognostic marker for DFS (HR 3.0, 95% confidence interval 1.7, 5.3, P < 0.001).Conclusions:  PRL‐3 may predict poor survival and act as a promising biomarker for individualized therapy for patients with colonic cancer, especially for those diagnosed at an early stage.
Differentiation markers in pancreatic head adenocarcinomas: MUC1 and MUC4 expression indicates poor prognosis in pancreatobiliary differentiated tumours
Authors: Westgaard Arne , Schjølberg Aasa R , Cvancarova Milada , Eide Tor J , Clausen Ole Petter F , Gladhaug Ivar P 
Published: February 2009

Aims:  To examine how accurately immunohistochemical markers discriminate between pancreatobiliary and intestinal‐type adenocarcinomas in the pancreatic head and to explore the prognostic importance of these markers among each of these histological types.Methods and results:  Histopathological features of 114 consecutively resected adenocarcinomas of pancreatobiliary (n = 67) and intestinal (n = 47) type of differentiation were recorded according to a standardized protocol. Immunohistochemistry for cytokeratin (CK) 7, CK20, MUC1, MUC2, MUC4 and CDX2 was performed on tissue microarrays. Classification of the adenocarcinomas based on immunohistochemistry was compared with the morphological evaluation of histological type. Presence of CK7 and MUC4, and absence of CDX2, were independent predictors of pancreatobiliary versus intestinal type. Using these markers to optimize immunohistochemical classification, agreement between immunohistochemical and morphological classification was only moderate (κ = 0.53). In pancreatobiliary differentiated tumours, MUC1 and/or MUC4 expression was an independent prognostic factor (hazard ratio 2.02, 95% confidence interval 1.02, 3.98) when adjusting for nodal involvement, vessel involvement and tumour size. In intestinally differentiated tumours, none of the markers was significantly associated with prognosis.Conclusions:  Agreement between immunohistochemical and morphological classification of pancreatic head adenocarcinomas is moderate. In pancreatobiliary adenocarcinomas, MUC1 and/or MUC4 expression indicates a particularly poor prognosis.
Patterns of seed dispersal and pollen flow inQuercus garryana(Fagaceae) following post‐glacial climatic changes
Authors: Marsico Travis D. , Hellmann Jessica J. , Romero‐Severson Jeanne 
Published: February 2009

AbstractAim We examined the genetic structure ofQuercus garryanato infer post‐glacial patterns of seed dispersal and pollen flow to test the hypotheses that (1) peripheral populations are genetically distinct from core populations and from one another; (2) genetic diversity declines towards the poleward edge of the species’ range; and (3) genetic diversity in the chloroplast genome, a direct measure of seed dispersal patterns, declines more sharply with increasing latitude than diversity in the nuclear genome. We address our findings in the context of known historical oak distribution from pollen core data derived from previously published research.Location Oak–savanna ecosystems from southern Oregon, USA (core populations/non‐glaciated range) northward to Vancouver Island, British Columbia, Canada (peripheral populations/glaciated range).Methods We genotyped 378 trees from 22 sites with five chloroplast and seven nuclear microsatellite loci. For both sets of markers, we estimated genetic diversity and differentiation using an analysis of molecular variance and generated Mantel correlograms to detect genetic and geographical distance correlations. For the nuclear markers, we also used a Bayesian approach to infer population substructure.Results There was a large degree of population differentiation revealed by six chloroplast haplotypes, with little (≤ 3) or no haplotype diversity within sites. Peripheral island locations shared the same, maternally inherited chloroplast haplotype, whereas locations in mainland Washington had greater haplotype diversity. In contrast, genetic diversity of the nuclear markers was high at all locations sampled. Populations clustered into two groups and were significantly positively correlated over large spatial scales (≤ 200 km), although allele richness decreased significantly with latitude. Population substructure was observed between core and peripheral populations because rare alleles were absent in peripheral localities and common allele frequencies differed.Main conclusions The observed pattern of chloroplast haplotype loss at the northern periphery suggests restricted seed dispersal events from mainland sites to peripheral islands. This pattern was unexpected, however, as refugial oak populations remained near the current post‐glacial range even during the Last Glacial Maximum. Using nuclear markers, we found high within‐population diversity and population differentiation only over large spatial scales, suggesting that pollen flow is relatively high among populations.
Closing the ring: historical biogeography of the salamander ring species Ensatina eschscholtzii
Authors: Kuchta Shawn R. , Parks Duncan S. , Mueller Rachel Lockridge , Wake David B. 
Published: February 2009

AbstractAim  The salamander Ensatina eschscholtzii Gray is a classic example of a ring species, or a species that has expanded around a central barrier to form a secondary contact characterized by species‐level divergence. In the original formulation of the ring species scenario, an explicit biogeographical model was proposed to account for the occurrence of intraspecific sympatry between two subspecies in southern California (the ‘southern closure’ model). Here we develop an alternative ring species model that is informed by the geomorphological development of the California Coast Ranges, and which situates the point of ring closure in the Monterey Bay region of central coastal California (the ‘Monterey closure’ model). Our study has two aims. The first is to use phylogenetic methods to evaluate the two competing biogeographical models. The second is to describe patterns of phylogeographical diversity throughout the range of the Ensatina complex, and to compare these patterns with previously published molecular systematic data.Location  Western North America, with a focus on the state of California, USA.Methods  We obtained mitochondrial DNA sequence data from 385 individuals from 224 populations. A phylogeny was inferred using Bayesian techniques, and the geographical distributions of haplotypes and clades were mapped. The two biogeographical ring species models were tested against our Bayesian topology, including the associated Bayesian 95% credible set of trees.Results  High levels of phylogeographical diversity were revealed, especially in central coastal and northern California. Our Bayesian topology contradicts the Monterey closure model; however, 0.08% of the trees in our Bayesian 95% credible set are consistent with this model. In contrast, the classic ring species biogeographical model (the southern closure model) is consistent with our Bayesian topology, as were 99.92% of the trees in our 95% credible set.Main conclusions  Our Bayesian phylogenetic analysis most strongly supports the classic ring species model, modified to accommodate an improved understanding of the complex geomorphological evolution of the California Coast Ranges. In addition, high levels of phylogeographical diversity in central and northern California were identified, which is consistent with the striking levels of allozymic differentiation reported previously from those regions.
A phylogeographical analysis across three biogeographical provinces of the south‐eastern Pacific: the case of the marine gastropod Concholepas concholepas
Authors: Cárdenas Leyla , Castilla Juan Carlos , Viard Frédérique 
Published: February 2009

AbstractAim  The present‐day population structure of a species reflects the influence of population history as well as contemporary processes. Little is known about the mechanisms that have shaped the geographical distribution of genetic diversity in marine species present on the south‐eastern Pacific (SEP) coast. Here we provide the first comprehensive phylogeographical study of a species distributed along the SEP coast by analysing the endemic and emblematic muricid gastropod Concholepas concholepas.Location  The study localities were distributed along the SEP coast ranging from Matarani (11° S) to Puerto Eden (49° S), crossing three major biogeographical provinces: Peruvian Province, Intermediate Area and Magellanic Province.Methods  A total of 337 specimens of C. concholepas were collected from 14 localities in the three biogeographical provinces/areas. Mitochondrial cytochrome oxidase I (COI) gene partial sequences (658 bp) were obtained and analysed using coalescence‐based methods to infer molecular diversity and phylogeographical patterns.Results  Across the 337 individuals, we found a large diversity, with a total of 179 haplotypes at the COI gene fragment. Although a slight decrease in gene diversity was observed from north to south, an analysis of molecular variance did not reveal any significant spatial population differentiation from Peru to the tip of Chile, not even across the recognized biogeographical boundaries at 30° S and 42° S. In addition, a star‐like haplotype network suggested the past occurrence of a rapid demographic and geographical expansion over the total range examined. Calculations of the onset of this expansion suggest that it might be due to climatic conditions during the period of the marine isotope stage 11 (MIS 11, 400,000 years ago), the longer and warmer interglacial episode during the Pleistocene epoch.Main conclusions  Our phylogeographical analyses indicate that in the recent past C. concholepas mitochondrial DNA lineages underwent a sudden population expansion event. In addition, our data do not support the hypothesis of concordance between biogeographical barriers and phylogeographical breaks along the SEP coast. These two results are in accordance with the paradigm of high larval dispersal ability in marine species with an extended pelagic larval phase.