bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soluble CD146 displays angiogenic properties and promotes neovascularization in experimental hind-limb ischemia
Authors: Harhouri Karim , Kebir Abdeldjalil , Guillet Benjamin , Foucault-Bertaud Alexandrine , Voytenko Serge , Piercecchi-Marti Marie-Dominique , Berenguer Caroline , Lamy Edouard , Vely Frédéric , Pisano Pascale , Ouafik L'Houcine , Sabatier Florence , Sampol José , Bardin Nathalie , Dignat-George Françoise , Blot-Chabaud Marcel 
Published: February 2010

Abstract
CD146, an endothelial molecule involved in permeability and monocyte transmigration, has recently been reported to promote vessel growth. As CD146 is also detectable as a soluble form (sCD146), we hypothesized that sCD146 could stimulate angiogenesis. Experiments of Matrigel plugs in vivo showed that sCD146 displayed chemotactic activity on endogenous endothelial cells, and exogenously injected late endothelial progenitor cells (EPCs). Recruited endothelial cells participated in formation of vascular-like structures. In vitro, sCD146 enhanced angiogenic properties of EPCs, with an increased cell migration, proliferation, and capacity to establish capillary-like structures. Effects were additive with those of vascular endothelial growth factor (VEGF), and sCD146 enhanced VEGFR2 expression and VEGF secretion. Consistent with a proangiogenic role, gene expression profiling of sCD146-stimulated EPCs revealed an up-regulation of endothelial nitric oxide synthase, urokinase plasminogen activator, matrix metalloproteinase 2, and VEGFR2. Silencing membrane-bound CD146 inhibited responses. The potential therapeutic interest of sCD146 was tested in a model of hind limb ischemia. Local injections of sCD146 significantly reduced auto-amputation, tissue necrosis, fibrosis, inflammation, and increased blood flow. Together, these findings establish that sCD146 displays chemotactic and angiogenic properties and promotes efficient neovascularization in vivo. Recombinant human sCD146 might thus support novel strategies for therapeutic angiogenesis in ischemic diseases.
Correlation of the autoantibody response to the ALK oncoantigen in pediatric anaplastic lymphoma kinase–positive anaplastic large cell lymphoma with tumor dissemination and relapse risk
Authors: Ait-Tahar Kamel , Damm-Welk Christine , Burkhardt Birgit , Zimmermann Martin , Klapper Wolfram , Reiter Alfred , Pulford Karen , Woessmann Wilhelm 
Published: February 2010

Abstract
Anaplastic lymphoma kinase (ALK)–positive anaplastic large cell lymphoma (ALCL) constitutes an ideal model disease to study tumor-specific immune responses. All the tumor cells express oncogenic ALK resulting from a chromosomal translocation involved in lymphomagenesis. Although antibodies and T-cell responses to ALK have previously been detected in ALK-positive ALCL patients, their prognostic significance is unknown. We investigated a large cohort of uniformly treated ALK-positive pediatric ALCL patients to ascertain whether the titers of preexisting ALK autoantibodies correlated with clinical and histologic characteristics, tumor dissemination, and patient outcome. ALK autoantibodies were analyzed in pretherapeutic serum samples from 95 patients enrolled into 2 therapy studies between 1996 and 2007. ALK autoantibodies were detected in 87/95 patients. The titers inversely correlated with stage and amount of circulating tumor cells. High antibody titers correlated with significantly lower cumulative incidence of relapses (CI-R): titers ≥ 1/60 750, n = 29, CI-R 11% ± 6%; titers 1/2025-< 1/60 750, n = 39, CI-R 31% ± 8%; and titers 0-≤ 1/750, n = 27, CI-R of 63% ± 10% (P < .001). Our results provide the first clinical evidence that a robust preexisting immune response to an oncoantigen resulting from an oncogenic chromosomal translocation inhibits lymphoma dissemination and decreases the risk of relapse.
A novel clinical role for angiopoietin-1 in malignant pleural mesothelioma
Authors: Tabata C. , Hirayama N. , Tabata R. , Yasumitsu A. , Yamada S. , Murakami A. , Iida S. , Tamura K. , Fukuoka K. , Kuribayashi K. , Terada T. , Nakano T. 
Published: February 2010

Malignant pleural mesothelioma (MPM) is an aggressive malignant tumour associated with asbestos exposure that has only a limited response to conventional therapy; therefore, diagnosing MPM early is very important. We have previously reported that angiopoietin (Ang)-1 was correlated with bleomycin-induced pulmonary fibrosis.Here, we investigated the association of Ang-1 with the development of MPM cells, which originate from mesenchymal cells similar to lung fibroblasts, and demonstrated that Ang-1 stimulated the growth and migration of MPM cellsin vitro. We also demonstrated that patients with MPM had significantly higher serum levels of Ang-1 in comparison to a population who had been exposed to asbestos but had not developed MPM. The patients with advanced-stage MPM showed higher levels of Ang-1 than the early-stage MPM patients and the Kaplan–Meier method revealed a significant correlation between serum Ang-1 levels and survival.We propose the possibility that Ang-1 plays an important role in MPM tumour growth and our data suggest that the serum concentration of Ang-1 could be useful as prognostic factor.
The impact of a delay in intensive care unit admission for community-acquired pneumonia
Authors: Phua J. , Ngerng W.J. , Lim T.K. 
Published: February 2010

The primary objective of the present study was to evaluate the effect on hospital mortality of a delay in intensive care unit (ICU) admission for severe community-acquired pneumonia (CAP). The secondary objectives were to assess if such delays were associated with treatment variations by the emergency department (ED) and deterioration in the general wards, and to evaluate the prognostic ability of the Infectious Disease Society of America (IDSA)/American Thoracic Society (ATS) minor criteria.We retrospectively compared patients who were admitted straight from the ED to the ICU (direct group, n = 54) and those who were first admitted from the ED to the general wards before ICU transfer (delayed group, n = 49), over 2.5 yrs.Even after excluding patients who required mechanical ventilation and/or vasopressors at the ED, delayed ICU admission was an independent predictor of hospital mortality (OR 9.61). The delayed group received fewer fluid boluses in the ED and rapidly deteriorated in the general wards. The presence of ≥3 IDSA/ATS minor criteria was associated with increased mortality in the delayed group.In conclusion, prompt recognition of severe CAP using the IDSA/ATS minor criteria, followed by aggressive management at the ED and direct ICU admission, are all crucial toward improving outcomes.
Procalcitonin guidance and reduction of antibiotic use in acute respiratory tract infection
Authors: Burkhardt O. , Ewig S. , Haagen U. , Giersdorf S. , Hartmann O. , Wegscheider K. , Hummers-Pradier E. , Welte T. 
Published: February 2010

Increasing worldwide development of antimicrobial resistance and the association of resistance development and antibiotic overuse make it necessary to seek strategies for safely reducing antibiotic use and selection pressure.In a first step, in a non-interventional study, the antibiotic prescription rates, initial procalcitonin (PCT) levels and outcome of 702 patients presenting with acute respiratory infection at 45 primary care physicians were observed. The second part was a randomised controlled non-inferiority trial comparing standard care with PCT-guided antimicrobial treatment in 550 patients in the same setting. Antibiotics were recommended at a PCT threshold of 0.25 ng·mL−1. Clinical overruling was permitted. The primary end-point for non-inferiority was number of days with significant health impairment after 14 days.Antibiotics were prescribed in 30.3% of enrolled patients in the non-interventional study. In the interventional study, 36.7% of patients in the control group received antibiotics as compared to 21.5% in the PCT-guided group (41.6% reduction). In the modified intention-to-treat analysis, the numbers of days with significant health impairment were similar (mean 9.04versus9.00 for PCT-guided and control group, respectively; difference 0.04; 95% confidence interval -0.73–0.81). This was also true after adjusting for the most important confounders. In the PCT group, advice was overruled in 36 cases. There was no significant difference in primary end-point when comparing the PCT group treated as advised, the overruled PCT group and the control group (9.008versus9.250versus9.000 days; p = 0.9605).A simple one-point PCT measurement for guiding decisions on antibiotic treatment is non-inferior to standard treatment in terms of safety, and effectively reduced the antibiotic treatment rate by 41.6%.
Characteristics of hospitalised patients with 2009 H1N1 influenza in Chile
Authors: Riquelme R. , Riquelme M. , Rioseco M.L. , Inzunza C. , Gomez Y. , Contreras C. , Riquelme J. , Peyrani P. , Wiemken T. , Ramirez J. 
Published: February 2010

As the pandemic of 2009 H1N1 influenza A virus progressed, more patients required hospitalisation. The objective of this study is to describe the characteristics and clinical course of hospitalised patients with 2009 H1N1 virus infection in Chile.This was a prospective, observational study of 100 consecutive hospitalised patients with RT-PCR-confirmed 2009 H1N1 influenza A, admitted to Puerto Montt General Hospital (Puerto Montt, Chile). Information was obtained regarding contact history, demographics, laboratory values and clinical course.The primary reason for hospitalisation was pneumonia, in 75% of patients. Rapid influenza A test was positive in 51% of patients. Prior exposure to 2009 H1N1 virus was documented in 21% of patients. Clinical failure, documented in 18% of cases, was characterised by respiratory failure and acute respiratory distress syndrome. Failure was more common in patients with obesity, tachypnoea, confusion and multilobar infiltrates.When evaluating a patient hospitalised with influenza-like illness, a negative rapid test for influenza A or negative contact with a suspected case should not alter physicians' considerations regarding the likelihood of 2009 H1N1 virus infection. Patients with 2009 H1N1 virus infection with obesity, tachypnoea, confusion and multilobar infiltrates should be closely monitored since they are at high risk for clinical failure.
SplicerAV: a tool for mining microarray expression data for changes in RNA processing
Authors: Robinson Timothy J , Dinan Michaela A , Dewhirst Mark , Garcia-Blanco Mariano A , Pearson James L 
Published: February 2010

Abstract

Background
Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but has not been previously mined en masse for changes in mRNA processing. We explored the possibility of using HG-U133 microarray data to identify changes in alternative mRNA processing in several available archival datasets.

Results
Data from these and other gene expression microarrays can now be mined for changes in transcript isoform abundance using a program described here, SplicerAV. Using in vivo and in vitro breast cancer microarray datasets, SplicerAV was able to perform both gene and isoform specific expression profiling within the same microarray dataset. Our reanalysis of Affymetrix U133 plus 2.0 data generated by in vitro over-expression of HRAS, E2F3, beta-catenin (CTNNB1), SRC, and MYC identified several hundred oncogene-induced mRNA isoform changes, one of which recognized a previously unknown mechanism of EGFR family activation. Using clinical data, SplicerAV predicted 241 isoform changes between low and high grade breast tumors; with changes enriched among genes coding for guanyl-nucleotide exchange factors, metalloprotease inhibitors, and mRNA processing factors. Isoform changes in 15 genes were associated with aggressive cancer across the three breast cancer datasets.

Conclusions
Using SplicerAV, we identified several hundred previously uncharacterized isoform changes induced by in vitro oncogene over-expression and revealed a previously unknown mechanism of EGFR activation in human mammary epithelial cells. We analyzed Affymetrix GeneChip data from over 400 human breast tumors in three independent studies, making this the largest clinical dataset analyzed for en masse changes in alternative mRNA processing. The capacity to detect RNA isoform changes in archival microarray data using SplicerAV allowed us to carry out the first analysis of isoform specific mRNA changes directly associated with cancer survival.
Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7
Authors: Bai Xufeng , Luo Lijun , Yan Wenhao , Kovi Mallikarjuna Rao , Zhan Wei , Xing Yongzhong 
Published: February 2010

Abstract

Background
The three-dimensional shape of grain, measured as grain length, width, and thickness (GL, GW, and GT), is one of the most important components of grain appearance in rice. Determining the genetic basis of variations in grain shape could facilitate efficient improvements in grain appearance. In this study, an F7:8 recombinant inbred line population (RIL) derived from a cross between indica and japonica cultivars (Nanyangzhan and Chuan7) contrasting in grain size was used for quantitative trait locus (QTL) mapping. A genetic linkage map was constructed with 164 simple sequence repeat (SSR) markers. The major aim of this study was to detect a QTL for grain shape and to fine map a minor QTL, qGL7.

Results
Four QTLs for GL were detected on chromosomes 3 and 7, and 10 QTLs for GW and 9 QTLs for GT were identified on chromosomes 2, 3, 5, 7, 9 and 10, respectively. A total of 28 QTLs were identified, of which several are reported for the first time; four major QTLs and six minor QTLs for grain shape were also commonly detected in both years. The minor QTL, qGL7, exhibited pleiotropic effects on GL, GW, GT, 1000-grain weight (TGW), and spikelets per panicle (SPP) and was further validated in a near isogenic F2 population (NIL-F2). Finally, qGL7 was narrowed down to an interval between InDel marker RID711 and SSR marker RM6389, covering a 258-kb region in the Nipponbare genome, and cosegregated with InDel markers RID710 and RID76.

Conclusion
Materials with very different phenotypes were used to develop mapping populations to detect QTLs because of their complex genetic background. Progeny tests proved that the minor QTL, qGL7, could display a single mendelian characteristic. Therefore, we suggested that minor QTLs for traits with high heritability could be isolated using a map-based cloning strategy in a large NIL-F2 population. In addition, combinations of different QTLs produced diverse grain shapes, which provide the ability to breed more varieties of rice to satisfy consumer preferences.
Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus
Authors: Koyama Takashi , Asakawa Shuichi , Katagiri Takayuki , Shimizu Atsushi , Fagutao Fernand F , Mavichak Rapeepat , Santos Mudjekeewis D , Fuji Kanako , Sakamoto Takashi , Kitakado Toshihide , Kondo Hidehiro , Shimizu Nobuyoshi , Aoki Takashi , Hirono Ikuo 
Published: February 2010

Abstract

Background
Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome.

Results
Mj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences.

Conclusions
Our results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.
JAM-A is a novel surface marker for NG2-Glia in the adult mouse brain
Authors: Stelzer Sandra , Ebnet Klaus , Schwamborn Jens C 
Published: February 2010

Abstract

Background
Junctional adhesion molecule-A (JAM-A) is an adhesive protein expressed in various cell types. JAM-A localizes to the tight junctions between contacting endothelial and epithelial cells, where it contributes to cell-cell adhesion and to the control of paracellular permeability.

Results
So far, the expression pattern of JAM-A has not been described in detail for the different cell types of the adult brain. Here we show that a subset of proliferating cells in the adult mouse brain express JAM-A. We further clarify that these cells belong to the lineage of NG2-glia cells. Although these mitotic NG2-glia cells express JAM-A, the protein never shows a polarized subcellular distribution. Also non-mitotic NG2-glia cells express JAM-A in a non-polarized pattern on their surface.

Conclusions
Our data show that JAM-A is a novel surface marker for NG2-glia cells of the adult brain.
Calcium imaging in the ant Camponotus fellah reveals a conserved odour-similarity space in insects and mammals
Authors: Dupuy Fabienne , Josens Roxana , Giurfa Martin , Sandoz Jean-Christophe 
Published: February 2010

Abstract

Background
Olfactory systems create representations of the chemical world in the animal brain. Recordings of odour-evoked activity in the primary olfactory centres of vertebrates and insects have suggested similar rules for odour processing, in particular through spatial organization of chemical information in their functional units, the glomeruli. Similarity between odour representations can be extracted from across-glomerulus patterns in a wide range of species, from insects to vertebrates, but comparison of odour similarity in such diverse taxa has not been addressed. In the present study, we asked how 11 aliphatic odorants previously tested in honeybees and rats are represented in the antennal lobe of the ant Camponotus fellah, a social insect that relies on olfaction for food search and social communication.

Results
Using calcium imaging of specifically-stained second-order neurons, we show that these odours induce specific activity patterns in the ant antennal lobe. Using multidimensional analysis, we show that clustering of odours is similar in ants, bees and rats. Moreover, odour similarity is highly correlated in all three species.

Conclusion
This suggests the existence of similar coding rules in the neural olfactory spaces of species among which evolutionary divergence happened hundreds of million years ago.
Mammographic density and markers of socioeconomic status: a cross-sectional study
Authors: Aitken Zoe , Walker Kate , Stegeman Bernardine H , Wark Petra A , Moss Sue M , McCormack Valerie A , dos Santos Silva Isabel 
Published: February 2010

Abstract

Background
Socioeconomic status (SES) is known to be positively associated with breast cancer risk but its relationship with mammographic density, a marker of susceptibility to breast cancer, is unclear. This study aims to investigate whether mammographic density varies by SES and to identify the underlying anthropometric, lifestyle and reproductive factors leading to such variation.

Methods
In a cross-sectional study of mammographic density in 487 pre-menopausal women, SES was assessed from questionnaire data using highest achieved level of formal education, quintiles of Census-derived Townsend scores and urban/rural classification of place of residence. Mammographic density was measured on digitised films using a computer-assisted method. Linear regression models were fitted to assess the association between SES variables and mammographic density, adjusting for correlated variables.

Results
In unadjusted models, percent density was positively associated with SES, with an absolute difference in percent density of 6.3% (95% CI 1.6%, 10.5%) between highest and lowest educational categories, and of 6.6% (95% CI -0.7%, 12.9%) between highest and lowest Townsend quintiles. These associations were mainly driven by strong negative associations between these SES variables and lucent area and were attenuated upon adjustment for body mass index (BMI). There was little evidence that reproductive factors explained this association. SES was not associated with the amount of dense tissue in the breast before or after BMI adjustment. The effect of education on percent density persisted after adjustment for Townsend score. Mammographic measures did not vary according to urban/rural place of residence.

Conclusions
The observed SES gradients in percent density paralleled known SES gradients in breast cancer risk. Although consistent with the hypothesis that percent density may be a mediator of the SES differentials in breast cancer risk, the SES gradients in percent density were mainly driven by the negative association between SES and BMI. Nevertheless, as density affects the sensitivity of screen-film mammography, the higher percent density found among high SES women would imply that these women have a higher risk of developing cancer but a lower likelihood of having it detected earlier.