bluuebunny/crossref_metadata_2025_split huggingface dataset:
Air temperature and inflammatory and coagulation responses in men with coronary or pulmonary disease during the winter season
Authors: Hampel Regina , Breitner Susanne , Rückerl Regina , Frampton Mark W , Koenig Wolfgang , Phipps Richard P , Wichmann H Erich , Peters Annette , Schneider Alexandra 
Published: November 2009

Background and ObjectiveAir temperature changes are associated with increased cardiovascular and respiratory risk, but the roles of inflammatory and coagulation markers are not well understood. We investigated the associations between temperature and several blood markers in patients with coronary heart disease (CHD) and pulmonary disease (PD).MethodsTwo studies were conducted in Erfurt, Germany, over two successive winters. 578 and 381 repeated blood measurements were collected from 57 CHD and 38 PD patients, respectively. Data on patient characteristics and disease history were gathered at baseline. Meteorological data were collected from existing networks. Associations were analysed using additive mixed models with random patient effects. Effect modification by diabetes status was investigated only in CHD patients, as only two PD patients had diabetes.ResultsMean daily air temperature varied between −13°C and 16°C in both study periods. A 10°C decrease in the 5-day temperature average before blood withdrawal led to an increase in platelet counts (% change from the mean: 3.0%, 95% CI 0.6% to 5.5%) and fibrinogen (5.5%, 1.3% to 9.7%), no change in C-reactive protein in PD patients, and a decrease in C-reactive protein in CHD patients. A 2-day delayed increase in factor VII associated with temperature decrease was seen in CHD patients (4.9%; 0.7% to 9.2%), while PD patients showed no effect. ‘Effects in CHD patients without diabetes’ into ‘Effects on factor VII in CHD patients without diabetes’.ConclusionsThis study suggests that temperature decrease is associated with change in several blood parameters. The complex interplay of blood markers at low temperature may contribute to the observed association between cold and cardiovascular mortality and morbidity.
ULTRASOUND AS A PROBE OF PLASTICITY? THE INTERACTION OF ELASTIC WAVES WITH DISLOCATIONS
Authors: MAUREL AGNES , PAGNEUX VINCENT , BARRA FELIPE , LUND FERNANDO 
Published: November 2009

An overview of recent work on the interaction of elastic waves with dislocations is given. The perspective is provided by the wish to develop nonintrusive tools to probe plastic behavior in materials. For simplicity, ideas and methods are first worked out in two dimensions, and the results in three dimensions are then described. These results explain a number of recent, hitherto unexplained, experimental findings. The latter include the frequency dependence of ultrasound attenuation in copper, the visualization of the scattering of surface elastic waves by isolated dislocations in LiNbO3, and the ratio of longitudinal to transverse wave attenuation in a number of materials.Specific results reviewed include the scattering amplitude for the scattering of an elastic wave by a screw, as well as an edge, dislocation in two dimensions, the scattering amplitudes for an elastic wave by a pinned dislocation segment in an infinite elastic medium, and the wave scattering by a sub-surface dislocation in a semi-infinite medium. Also, using a multiple scattering formalism, expressions are given for the attenuation coefficient and the effective speed for coherent wave propagation in the cases of anti-plane waves propagating in a medium filled with many, randomly placed screw dislocations; in-plane waves in a medium similarly filled with randomly placed edge dislocations with randomly oriented Burgers vectors; elastic waves in a three-dimensional medium filled with randomly placed and oriented dislocation line segments, also with randomly oriented Burgers vectors; and elastic waves in a model three-dimensional polycrystal, with only low angle grain boundaries modeled as arrays of dislocation line segments.
Environmental Displacement in European Asylum Law
Authors: Myrstad Finn , Kolmannskog Vikram 
Published: November 2009

AbstractEnvironmentally displaced persons can be included in several existing categories of protected persons under international law, but there may be a normative protection gap for many of those who cross an international border. This article looks at protection possibilities within the EU framework and national European legislations. Environmental displacement can arguably trigger temporary protection according to the EU Temporary Protection Directive. There may also be environmentally displaced persons who require longer-term or permanent protection. Drawing on the EU Qualification Directive and case-law from the European Court of Human Rights, one can argue that subsidiary protection should be granted in certain cases of extreme natural disaster or degradation. In less extreme cases, humanitarian asylum could be granted. Human rights principles such as non-refoulement could also be used to extend at least basic protection. In addition, legal labour migration could supply a work force, assist distressed countries and enhance protection of the individual. A strategy to meet the challenge of environmental displacement must also include climate change mitigation and external measures such as adaptation. Most of the displaced persons in the world today and in the near future do not arrive at the EU borders.
Identifying and Testing Engagement and Public Literacy Indicators for River Health
Authors: Metcalfe Jenni , Riedlinger Michelle 
Published: November 2009

Natural resource management (NRM) organisations in Australia are increasingly recognising the need for complement studies of biophysical condition of the environment with studies of social condition, such as values, understanding, and participation related to the environment. Relevant and reliable social indicators that can be scaled and measured on a regular basis are essential to meet this need. In this study, we identified four indicators to test the social condition of the public in the State of Victoria in Australia with regard to river health. These indicators were river use, river knowledge and literacy, values and aspirations, and river health behaviours. We tested the four indicators through telephone and web-based surveys with over 1000 people in three areas of Victoria. We analysed the survey data statistically and gathered baseline data on the social condition of river health in the three regions. We made recommendations for how this data could be interpreted and used in community engagement and science communication programmes about river health. We also examined the limitations of the methodology and recommended modifications to the survey design and application for an anticipated roll-out of the survey across the entire State of Victoria. The Victorian Department of Sustainability and Environment (DSE) will use this survey instrument to test social indicators on a regular basis.
RNAi mediated acute depletion of Retinoblastoma protein (pRb) promotes aneuploidy in human primary cells via micronuclei formation
Authors: Amato Angela , Lentini Laura , Schillaci Tiziana , Iovino Flora , Di Leonardo Aldo 
Published: November 2009

Abstract

Background
Changes in chromosome number or structure as well as supernumerary centrosomes and multipolar mitoses are commonly observed in human tumors. Thus, centrosome amplification and mitotic checkpoint dysfunctions are believed possible causes of chromosomal instability. The Retinoblastoma tumor suppressor (RB) participates in the regulation of synchrony between DNA synthesis and centrosome duplication and it is involved in transcription regulation of some mitotic genes. Primary human fibroblasts were transfected transiently with short interfering RNA (siRNA) specific for human pRb to investigate the effects of pRb acute loss on chromosomal stability.

Results
Acutely pRb-depleted fibroblasts showed altered expression of genes necessary for cell cycle progression, centrosome homeostasis, kinetochore and mitotic checkpoint proteins. Despite altered expression of genes involved in the Spindle Assembly Checkpoint (SAC) the checkpoint seemed to function properly in pRb-depleted fibroblasts. In particular AURORA-A and PLK1 overexpression suggested that these two genes might have a role in the observed genomic instability. However, when they were post-transcriptionally silenced in pRb-depleted fibroblasts we did not observe reduction in the number of aneuploid cells. This finding suggests that overexpression of these two genes did not contribute to genomic instability triggered by RB acute loss although it affected cell proliferation. Acutely pRb-depleted human fibroblasts showed the presence of micronuclei containing whole chromosomes besides the presence of supernumerary centrosomes and aneuploidy.

Conclusion
Here we show for the first time that RB acute loss triggers centrosome amplification and aneuploidy in human primary fibroblasts. Altogether, our results suggest that pRb-depleted primary human fibroblasts possess an intact spindle checkpoint and that micronuclei, likely caused by mis-attached kinetochores that in turn trigger chromosome segregation errors, are responsible for aneuploidy in primary human fibroblasts where pRb is acutely depleted.
Regulation of intestinal epithelial cells transcriptome by enteric glial cells: impact on intestinal epithelial barrier functions
Authors: Van Landeghem Laurianne , Mahé Maxime M , Teusan Raluca , Léger Jean , Guisle Isabelle , Houlgatte Rémi , Neunlist Michel 
Published: November 2009

AbstractBackgroundEmerging evidences suggest that enteric glial cells (EGC), a major constituent of the enteric nervous system (ENS), are key regulators of intestinal epithelial barrier (IEB) functions. Indeed EGC inhibit intestinal epithelial cells (IEC) proliferation and increase IEB paracellular permeability. However, the role of EGC on other important barrier functions and the signalling pathways involved in their effects are currently unknown. To achieve this goal, we aimed at identifying the impact of EGC upon IEC transcriptome by performing microarray studies.ResultsEGC induced significant changes in gene expression profiling of proliferating IEC after 24 hours of co-culture. 116 genes were identified as differentially expressed (70 up-regulated and 46 down-regulated) in IEC cultured with EGC compared to IEC cultured alone. By performing functional analysis of the 116 identified genes using Ingenuity Pathway Analysis, we showed that EGC induced a significant regulation of genes favoring both cell-to-cell and cell-to-matrix adhesion as well as cell differentiation. Consistently, functional studies showed that EGC induced a significant increase in cell adhesion. EGC also regulated genes involved in cell motility towards an enhancement of cell motility. In addition, EGC profoundly modulated expression of genes involved in cell proliferation and cell survival, although no clear functional trend could be identified. Finally, important genes involved in lipid and protein metabolism of epithelial cells were shown to be differentially regulated by EGC.ConclusionThis study reinforces the emerging concept that EGC have major protective effects upon the IEB. EGC have a profound impact upon IEC transcriptome and induce a shift in IEC phenotype towards increased cell adhesion and cell differentiation. This concept needs to be further validated under both physiological and pathophysiological conditions.
Continuous 5-fluorouracil infusion plus long acting octreotide in advanced well-differentiated neuroendocrine carcinomas. A phase II trial of the Piemonte Oncology Network
Authors: Brizzi Maria P , Berruti Alfredo , Ferrero Anna , Milanesi Enrica , Volante Marco , Castiglione Federico , Birocco Nadia , Bombaci Sebastiano , Perroni Davide , Ferretti Benedetta , Alabiso Oscar , Ciuffreda Libero , Bertetto Oscar , Papotti Mauro , Dogliotti Luigi 
Published: November 2009

Abstract

Background
Well-differentiated neuroendocrine carcinomas are highly vascularized and may be sensitive to drugs administered on a metronomic schedule that has shown antiangiogenic properties. A phase II study was designed to test the activity of protracted 5-fluorouracil (5FU) infusion plus long-acting release (LAR) octreotide in patients with neuroendocrine carcinoma.

Methods
Twenty-nine patients with metastatic or locally advanced well-differentiated neuroendocrine carcinoma were treated with protracted 5FU intravenous infusion (200 mg/m2 daily) plus LAR octreotide (20 mg monthly). Patients were followed for toxicity, objective response, symptomatic and biochemical response, time to progression and survival.

Results
Assessment by Response Evaluation Criteria in Solid Tumors (RECIST) criteria showed partial response in 7 (24.1%), stable disease in 20 (69.0%), and disease progression in 2 patients. Response did not significantly differ when patients were stratified by primary tumor site and proliferative activity. A biochemical (chromogranin A) response was observed in 12/25 assessable patients (48.0%); symptom relief was obtained in 9/15 symptomatic patients (60.0%). There was non significant decrease in circulating vascular epithelial growth factor (VEGF) over time. Median time to progression was 22.6 months (range, 2.7-68.5); median overall survival was not reached yet. Toxicity was mild and manageable.

Conclusion
Continuous/metronomic 5FU infusion plus LAR octreotide is well tolerated and shows activity in patients with well-differentiated neuroendocrine carcinoma. The potential synergism between metronomic chemotherapy and antiangiogenic drugs provides a rationale for exploring this association in the future.

Trial registration
NCT00953394
Predicting prognosis in hepatocellular carcinoma after curative surgery with common clinicopathologic parameters
Authors: Hao Ke , Luk John M , Lee Nikki PY , Mao Mao , Zhang Chunsheng , Ferguson Mark D , Lamb John , Dai Hongyue , Ng Irene O , Sham Pak C , Poon Ronnie TP 
Published: November 2009

Abstract

Background
Surgical resection is one important curative treatment for hepatocellular carcinoma (HCC), but the prognosis following surgery differs substantially and such large variation is mainly unexplained. A review of the literature yields a number of clinicopathologic parameters associated with HCC prognosis. However, the results are not consistent due to lack of systemic approach to establish a prediction model incorporating all these parameters.

Methods
We conducted a retrospective analysis on the common clinicopathologic parameters from a cohort of 572 ethnic Chinese HCC patients who received curative surgery. The cases were randomly divided into training (n = 272) and validation (n = 300) sets. Each parameter was individually tested and the significant parameters were entered into a linear classifier for model building, and the prediction accuracy was assessed in the validation set

Results
Our findings based on the training set data reveal 6 common clinicopathologic parameters (tumor size, number of tumor nodules, tumor stage, venous infiltration status, and serum α-fetoprotein and total albumin levels) that were significantly associated with the overall HCC survival and disease-free survival (time to recurrence). We next built a linear classifier model by multivariate Cox regression to predict prognostic outcomes of HCC patients after curative surgery This analysis detected a considerable fraction of variance in HCC prognosis and the area under the ROC curve was about 70%. We further evaluated the model using two other protocols; leave-one-out procedure (n = 264) and independent validation (n = 300). Both were found to have excellent prediction power. The predicted score could separate patients into distinct groups with respect to survival (p-value = 1.8e-12) and disease free survival (p-value = 3.2e-7).

Conclusion
This described model will provide valuable guidance on prognosis after curative surgery for HCC in clinical practice. The adaptive nature allows easy accommodation for future new biomarker inputs, and it may serve as the foundation for future modeling and prediction for HCC prognosis after surgical treatment.
BioDEAL: community generation of biological annotations
Authors: Breimyer Paul , Green Nathan , Kumar Vinay , Samatova Nagiza F 
Published: November 2009

Abstract

Background
Publication databases in biomedicine (e.g., PubMed, MEDLINE) are growing rapidly in size every year, as are public databases of experimental biological data and annotations derived from the data. Publications often contain evidence that confirm or disprove annotations, such as putative protein functions, however, it is increasingly difficult for biologists to identify and process published evidence due to the volume of papers and the lack of a systematic approach to associate published evidence with experimental data and annotations. Natural Language Processing (NLP) tools can help address the growing divide by providing automatic high-throughput detection of simple terms in publication text. However, NLP tools are not mature enough to identify complex terms, relationships, or events.

Results
In this paper we present and extend BioDEAL, a community evidence annotation system that introduces a feedback loop into the database-publication cycle to allow scientists to connect data-driven biological concepts to publications.

Conclusion
BioDEAL may change the way biologists relate published evidence with experimental data. Instead of biologists or research groups searching and managing evidence independently, the community can collectively build and share this knowledge.
Targeting EGFR with photodynamic therapy in combination with Erbitux enhances in vivo bladder tumor response
Authors: Bhuvaneswari Ramaswamy , Gan Yik Yuen , Soo Khee Chee , Olivo Malini 
Published: November 2009

Abstract

Background
Photodynamic therapy (PDT) is a promising cancer treatment modality that involves the interaction of the photosensitizer, molecular oxygen and light of specific wavelength to destroy tumor cells. Treatment induced hypoxia is one of the main side effects of PDT and efforts are underway to optimize PDT protocols for improved efficacy. The aim of this study was to investigate the anti-tumor effects of PDT plus Erbitux, an angiogenesis inhibitor that targets epidermal growth factor receptor (EGFR), on human bladder cancer model. Tumor-bearing nude mice were assigned to four groups that included control, PDT, Erbitux and PDT plus Erbitux and tumor volume was charted over 90-day period.

Results
Our results demonstrate that combination of Erbitux with PDT strongly inhibits tumor growth in the bladder tumor xenograft model when compared to the other groups. Downregulation of EGFR was detected using immunohistochemistry, immunofluorescence and western blotting. Increased apoptosis was associated with tumor inhibition in the combination therapy group. In addition, we identified the dephosphorylation of ErbB4 at tyrosine 1284 site to play a major role in tumor inhibition. Also, at the RNA level downregulation of EGFR target genes cyclin D1 and c-myc was observed in tumors treated with PDT plus Erbitux.

Conclusion
The combination therapy of PDT and Erbitux effectively inhibits tumor growth and is a promising therapeutic approach in the treatment of bladder tumors.
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities
Authors: Stoeck Thorsten , Behnke Anke , Christen Richard , Amaral-Zettler Linda , Rodriguez-Mora Maria J , Chistoserdov Andrei , Orsi William , Edgcomb Virginia P 
Published: November 2009

AbstractBackgroundRecent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.ResultsThe analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses.ConclusionOur data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.