bluuebunny/crossref_metadata_2025_split huggingface dataset:
Satellite‐based vessel Automatic Identification System: A feasibility and performance analysis
Authors: Cervera Miguel A. , Ginesi Alberto , Eckstein Knut 
Published: March 2010

AbstractThe Automatic Identification System (AIS) is a VHF communication system that provides identification/location information to vessels and shore stations by exchanging data such as position, identification, course, speed, etc. Recently, the interest in detecting and tracking ships at distances from coastlines larger than what can be accomplished by normal terrestrial VHF communications has grown, driven by requirements of long‐range applications such as better handling of hazardous cargo, improved security and countering illegal operations. This paper presents an extension of AIS to a long‐range positioning reporting through a constellation of LEO satellites. It outlines technical challenges like the high rate of message collisions from ships in the field of view of a satellite. Technical solutions are proposed at system and sub‐system level to address these challenges. A computer‐based system simulator is used to assess the system performance and carry out a high‐level system sizing. Results show that a relatively small constellation of LEO satellites can guarantee good ship position detection probability as well as a reporting time interval of a few hours. System performance aspects to be addressed in future work are the possible impact of terrestrial mobile communications interference as well as variations of the estimated traffic data. Copyright © 2009 John Wiley & Sons, Ltd.
Nuclear Transfer-Derived Epiblast Stem Cells Are Transcriptionally and Epigenetically Distinguishable from Their Fertilized-Derived Counterparts
Authors: Maruotti Julien , Dai Xiang Peng , Brochard Vincent , Jouneau Luc , Liu Jun , Bonnet-Garnier Amélie , Jammes Hélène , Vallier Ludovic , Brons I. Gabrielle M. , Pedersen Roger , Renard Jean-Paul , Zhou Qi , Jouneau Alice 
Published: March 2010

AbstractMouse embryonic pluripotent stem cells can be obtained from the inner cell mass at the blastocyst stage (embryonic stem cells, ESCs) or from the late epiblast of postimplantation embryos (epiblast stem cells, EpiSCs). During normal development, the transition between these two stages is marked by major epigenetic and transcriptional changes including DNA de novo methylation. These modifications represent an epigenetic mark conserved in ESCs and EpiSCs. Pluripotent ESCs derived from blastocysts generated by nuclear transfer (NT) have been shown to be correctly reprogrammed. However, NT embryos frequently undergo abnormal development. In the present study, we have examined whether pluripotent cells could be derived from the epiblast of postimplantation NT embryos and whether the reprogramming process would affect the epigenetic changes occurring at this stage, which could explain abnormal development of NT embryos. We showed that EpiSCs could be derived with the same efficiency from NT embryos and from their fertilized counterparts. However, gene expression profile analyses showed divergence between fertilized- and nuclear transfer-EpiSCs with a surprising bias in the distribution of the differentially expressed genes, 30% of them being localized on chromosome 11. A majority of these genes were downregulated in NT-EpiSCs and imprinted genes represented a significant fraction of them. Notably, analysis of the epigenetic status of a downregulated imprinted gene in NT-EpiSCs revealed complete methylation of the two alleles. Therefore, EpiSCs derived from NT embryos appear to be incorrectly reprogrammed, indicating that abnormal epigenetic marks are imposed on cells in NT embryos during the transition from early to late epiblast.
Epidermal Growth Factor and Perlecan Fragments Produced by Apoptotic Endothelial Cells Co-Ordinately Activate ERK1/2-Dependent Antiapoptotic Pathways in Mesenchymal Stem Cells
Authors: Soulez Mathilde , Sirois Isabelle , Brassard Nathalie , Raymond Marc-André , Nicodème Frédéric , Noiseux Nicolas , Durocher Yves , Pshezhetsky Alexei V. , Hébert Marie-Josée 
Published: March 2010

Abstract
Mounting evidence indicates that mesenchymal stem cells (MSC) are pivotal to vascular repair and neointima formation in various forms of vascular disease. Yet, the mechanisms that allow MSC to resist apoptosis at sites where other cell types, such as endothelial cells (EC), are dying are not well defined. In the present work, we demonstrate that apoptotic EC actively release paracrine mediators which, in turn, inhibit apoptosis of MSC. Serum-free medium conditioned by apoptotic EC increases extracellular signal-regulated kinases 1 and 2 (ERK1/2) activation and inhibits apoptosis (evaluated by Bcl-xL protein levels and poly (ADP-ribose) polymerase cleavage) of human MSC. A C-terminal fragment of perlecan (LG3) released by apoptotic EC is one of the mediators activating this antiapoptotic response in MSC. LG3 interacts with β1-integrins, which triggers downstream ERK1/2 activation in MSC, albeit to a lesser degree than medium conditioned by apoptotic EC. Hence, other mediators released by apoptotic EC are probably required for induction of the full antiapoptotic phenotype in MSC. Adopting a comparative proteomic strategy, we identified epidermal growth factor (EGF) as a novel mediator of the paracrine component of the endothelial apoptotic program. LG3 and EGF cooperate in triggering β1-integrin and EGF receptor-dependent antiapoptotic signals in MSC centering on ERK1/2 activation. The present work, providing novel insights into the mechanisms facilitating the survival of MSC in a hostile environment, identifies EGF and LG3 released by apoptotic EC as central antiapoptotic mediators involved in this paracrine response.
Pain‐related fear predicts disability, but not pain severity: A path analytic approach of the fear‐avoidance model
Authors: Gheldof Els L.M. , Crombez Geert , van den Bussche Eva , Vinck Jan , Van Nieuwenhuyse An , Moens Guido , Mairiaux Philippe , Vlaeyen Johan W.S. 
Published: February 2010

AbstractTwo studies are reported that tested the fear‐avoidance (FA) model using path analytic techniques. In study 1, 429 employees with back pain at baseline and back pain at 18 months follow‐up completed questionnaires assessing sociodemographic information, pain severity, negative affect, pain‐related fear, and disability. Results indicated that pain severity at baseline predicted pain‐related fear and disability at follow‐up, and that pain‐related fear is rather a consequence than an antecedent of pain severity. Results further revealed that the disposition to experience negative affect has a low impact upon pain severity and disability, and is best viewed as a precursor of pain‐related fear. Study 2 included 238 employees without back pain at baseline, but who developed back pain at 1 year follow‐up. A similar model as in study 1 was tested. Overall, results are in line with those of study 1. Results are discussed in terms of theoretical relevance and clinical implications.
Is chronic pain associated with subsequent cancer? A cohort record linkage study
Authors: Elliott Alison M. , Torrance Nicola , Smith Blair H. , Lee Amanda J. 
Published: February 2010

AbstractA previous study has reported that chronic pain is associated with a higher incidence of overall and site‐specific cancer in subsequent years. The aim of this study was to confirm or refute these findings. In 1996, a cohort of 6940 individuals was recruited, and information on chronic pain, general health and socio‐demographic details collected. Ten years later, a record linkage study was conducted between these data and the routinely collected national dataset for cancer registration. Hazard ratios for the incidence of all cancers and eight cancer‐specific sites by chronic pain status were calculated. Eighty‐four percent of individuals from the original cohort were linked. After excluding those with a known previous cancer diagnosis, all non‐melanoma skin cancers and cancers which were not first occurrences, a total of 646 cancers had occurred in 607 people since the baseline study. The overall cancer incidence in the cohort was 10.4% over the 10 years. There were no significant associations between chronic pain and all cancer, or any of the eight cancer‐specific sites, after adjustment for age and sex. There was a significant increased risk of developing lymphoma/leukaemia amongst those with all chronic pain and various causes of chronic pain on univariate analysis. After adjustment, these trends remained, although most of the associations were no longer significant. There were no significant differences between those with severe chronic pain compared to those with mild chronic pain. The findings suggest that those with chronic pain are not at a significantly increased risk of developing cancer.
Deliberative assessment of surrogate consent in dementia research
Authors: Kim Scott Y.H. , Uhlmann Rebecca A. , Appelbaum Paul S. , Knopman David S. , Kim H. Myra , Damschroder Laura , Beattie Elizabeth , Struble Laura , De Vries Raymond 
Published: February 2010

BackgroundResearch involving incapacitated persons with dementia entails complex scientific, legal, and ethical issues, making traditional surveys of layperson views on the ethics of such research challenging. We therefore assessed the impact of democratic deliberation (DD), involving balanced, detailed education and peer deliberation, on the views of those responsible for persons with dementia.MethodsOne hundred and seventy‐eight community‐recruited caregivers or primary decision‐makers for persons with dementia were randomly assigned to either an all‐day DD session group or a control group. Educational materials used for the DD session were vetted for balance and accuracy by an interdisciplinary advisory panel. We assessed the acceptability of family‐surrogate consent for dementia research (“surrogate‐based research”) from a societal policy perspective as well as from the more personal perspectives of deciding for a loved one or for oneself (surrogate and self‐perspectives), assessed at baseline, immediately post‐DD session, and 1 month after DD date, for four research scenarios of varying risk‐benefit profiles.ResultsAt baseline, a majority in both the DD and control groups supported a policy of family consent for dementia research in all research scenarios. The support for a policy of family consent for surrogate‐based research increased in the DD group, but not in the control group. The change in the DD group was maintained 1 month later. In the DD group, there were transient changes in attitudes from surrogate or self‐perspectives. In the control group, there were no changes from baseline in attitude toward surrogate consent from any perspective.ConclusionsIntensive, balanced, and accurate education, along with peer deliberation provided by democratic deliberation, led to a sustained increase in support for a societal policy of family consent in dementia research among those responsible for dementia patients.
Oral sensitivity to fatty acids, food consumption and BMI in human subjects
Authors: Stewart Jessica E. , Feinle-Bisset Christine , Golding Matthew , Delahunty Conor , Clifton Peter M. , Keast Russell S. J. 
Published: March 2010

Fatty acids are the chemical moieties that are thought to stimulate oral nutrient sensors, which detect the fat content of foods. In animals, oral hypersensitivity to fatty acids is associated with decreased fat intake and body weight. The aims of the present study were to investigate oral fatty acid sensitivity, food selection and BMI in human subjects. The study included two parts; study 1 established in thirty-one subjects (29 (sem 1·4) years, 22·8 (sem 0·5) kg/m2) taste thresholds using 3-AFC (3-Alternate Forced Choice Methodology) for oleic, linoleic and lauric acids, and quantified oral lipase activity. During study 2, fifty-four subjects (20 (sem 0·3) years, 21·5 (sem 0·4) kg/m2) were screened for oral fatty acid sensitivity using oleic acid (1·4 mm), and they were defined as hypo- or hypersensitive via triplicate triangle tests. Habitual energy and macronutrient intakes were quantified from 2 d diet records, and BMI was calculated from height and weight. Subjects also completed a fat ranking task using custard containing varying amounts (0, 2, 6 and 10 %) of fat. Study 1 reported median lipase activity as 2 μmol fatty acids/min per l, and detection thresholds for oleic, linoleic and lauric acids were 2·2 (sem 0·1), 1·5 (sem 0·1) and 2·6 (sem 0·3) mm. Study 2 identified twelve hypersensitive subjects, and hypersensitivity was associated with lower energy and fat intakes, lower BMI (P < 0·05) and an increased ability to rank custards based on fat content (P < 0·05). Sensitivity to oleic acid was correlated to performance in the fat ranking task (r 0·4, P < 0·05). These data suggest that oral fatty acid hypersensitivity is associated with lower energy and fat intakes and BMI, and it may serve as a factor that influences fat consumption in human subjects.
Genetic architecture of rainbow trout survival from egg to adult
Authors: VEHVILÄINEN HARRI , KAUSE ANTTI , KOSKINEN HEIKKI , PAANANEN TUIJA 
Published: March 2010

SummarySurvival from birth to a reproductive adult is a challenge that only robust individuals resistant to a variety of mortality factors will overcome. To assess whether survival traits share genetic architecture throughout the life cycle, we estimated genetic correlations for survival within fingerling stage, and across egg, fingerling and grow-out stages in farmed rainbow trout. Genetic parameters of survival at three life cycle stages were estimated for 249 166 individuals originating from ten year classes of a pedigreed population. Despite being an important fitness component, survival traits harboured significant but modest amount of genetic variation (h2=0·07–0·27). Weak associations between survival during egg-fry and fingerling periods, between early and late fingerling periods (rG=0·30) and generally low genetic correlations between fingerling and grow-out survival (meanrG=0·06) suggested that life-stage specific survival traits are best regarded as separate traits. However, in the sub-set of data with detailed time of death records, positive genetic correlations between early and late fingerling survival (rG=0·89) showed that during certain years the best genotypes in the early period were also among the best in the late period. That survival across fingerling period can be genetically the same, trait was indicated also by only slightly higher heritability (h2=0·15) estimated with the survival analysis of time to death during fingerling period compared to the analysis treating fingerling survival as a binary character (h2=0·11). The results imply that (1) inherited resistance against unknown mortality factors exists, but (2) ranking of genotypes changes across life stages.
Review of recent research (2000–2008) on applied linguistics and language teaching with specific reference to L2 Italian
Authors: Macaro Ernesto 
Published: March 2010

L'apprendimento della lingua italiana come lingua straniera (L2), probabilmente per motivazioni storico-culturali, è di carattere specialistico. Di conseguenza, l'impronta globale della lingua italiana, rispetto ad altre lingue straniere come l'inglese, lo spagnolo ed il francese, risulta essere abbastanza limitata. Sorprende quindi il fatto che in diversi progetti di ricerca, nel campo della linguistica applicata e dell'apprendimento delle L2, l'italiano sia la lingua studiata dai partecipanti oggetto di studio. Questa rassegna di studi verte ad identificare gli approfondimenti della ricerca nel campo dell'apprendimento della lingua italiana come seconda lingua piuttosto che il contributo dell'italiano alla teoria della SLA in genere. Inoltre, ha l'obbiettivo di valutare lo stato attuale della lingua italiana nell'ambito dell'istruzione formale. L'autore suggerisce la presenza di un rapporto tra la comprensione del processo di apprendimento della lingua italiana e la richiesta dell'italiano come L2. Questa rassegna riassume e categorizza quasi settanta studi condotti in una varietà di contesti educativi e offre proposte e stimoli per futuri progetti di ricerca.Italian has for many years been considered somewhat of a specialist language when studied as a second language (L2) and this is perhaps due to historical and cultural factors. Its footprint worldwide compared to such languages as English, Spanish and French is therefore somewhat limited. Surprisingly, however, there is a considerable body of research in applied linguistics and second language acquisition (SLA) in which Italian features as the language being studied. This review sought to identify the extent to which the research provided specific insights into how Italian as a second or foreign language (L2 Italian) is learnt as opposed to the ways in which it has contributed to SLA theory-building more generally. In addition, it sought to assess how well Italian is holding up as a language being learnt in formal instructed contexts. The author suggests that insights into the learning of Italian and uptake by Italian students may be inter-related. The present review summarises and categorises nearly seventy empirical studies conducted in a variety of educational contexts and offers suggestions for future avenues of research.
BAAL/CUP seminars 2009
Authors: Cutting Joan , Murphy Bróna 
Published: March 2010

The Moray House School of Education, The University of Edinburgh, UK; 7–8 May 2009The seminar, organised by Joan Cutting and Bróna Murphy, aimed
•to bring together researchers involved in both emergent and established academic corpora (written and spoken) as well as linguists, lecturers and teachers researching in education, be it language teaching, language-teacher training or continuing professional development in language awareness, all of whom may be new to corpora and its applications;•to explore the possibilities of working together with researchers in speech recognition and synthesis, and other specialists in technological innovation;•to provide an opportunity to disseminate the latest developments in academic language corpora.
The seminar strengthened links between institutions and created networks for researchers to explore ways that corpora can help to study general classroom practice and be used as part of language classroom teaching. It attracted 30 participants from universities in the Czech Republic, the Republic of Ireland, Italy, Japan, Switzerland and the UK; there were two plenary papers and 14 individual papers.
Prevalence and characteristics of asymptomatic norovirus infection in the community in England
Authors: PHILLIPS G. , TAM C. C. , RODRIGUES L. C. , LOPMAN B. 
Published: March 2010

SUMMARYNorovirus is a major cause of infectious intestinal disease, and a substantial prevalence of asymptomatic infection has been reported. We describe the prevalence, seasonality and characteristics of asymptomatic norovirus infection in England. Healthy individuals were recruited at random from the general population during the Study of Infectious Intestinal Disease (1993–1996). Norovirus was identified using real-time RT–PCR. The age-adjusted prevalence of asymptomatic norovirus infection was 12%; prevalence was highest in children aged <5 years and showed wintertime seasonality. More work is needed to understand whether asymptomatic infections are important for norovirus transmission leading to sporadic illness and outbreaks.
CPFP: a central proteomics facilities pipeline
Authors: Trudgian David C. , Thomas Benjamin , McGowan Simon J. , Kessler Benedikt M. , Salek Mogjiborahman , Acuto Oreste 
Published: February 2010

Abstract
Summary: The central proteomics facilities pipeline (CPFP) provides identification, validation, and quantitation of peptides and proteins from LC-MS/MS datasets through an easy to use web interface. It is the first analysis pipeline targeted specifically at the needs of proteomics core facilities, reducing the data analysis load on staff, and allowing facility clients to easily access and work with their data. Identification of peptides is performed using multiple search engines, their output combined and validated using state-of-the-art techniques for improved results. Cluster execution of jobs allows analysis capacity to be increased easily as demand grows.
Availability: Released under the Common Development and Distribution License at http://cpfp.sourceforge.net/. Demonstration available at https://cpfp-master.molbiol.ox.ac.uk/cpfp_demo
Contact: dctrud@ccmp.ox.ac.uk
A min-cut algorithm for the consistency problem in multiple sequence alignment
Authors: Corel Eduardo , Pitschi Florian , Morgenstern Burkhard 
Published: February 2010

Abstract
Motivation: Multiple sequence alignments can be constructed on the basis of pairwise local sequence similarities. This approach is rather flexible and can combine the advantages of global and local alignment methods. The restriction to pairwise alignments as building blocks, however, can lead to misalignments since weak homologies may be missed if only pairs of sequences are compared.
Results: Herein, we propose a graph-theoretical approach to find local multiple sequence similarities. Starting with pairwise alignments produced by DIALIGN, we use a min-cut algorithm to find potential (partial) alignment columns that we use to construct a final multiple alignment. On real and simulated benchmark data, our approach consistently outperforms the standard version of DIALIGN where local pairwise alignments are greedily incorporated into a multiple alignment.
Availability: The prototype is freely available under GNU Public Licence from E.C.
Contact: ecorel@gwdg.de
Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules
Authors: Chou Wei-Yao , Chou Wei-I , Pai Tun-Wen , Lin Shu-Chuan , Jiang Ting-Ying , Tang Chuan-Yi , Chang Margaret Dah-Tsyr 
Published: February 2010

Abstract
Motivation: Carbohydrate-binding modules (CBMs) share similar secondary and tertiary topology, but their primary sequence identity is low. Computational identification of ligand-binding residues allows biologists to better understand the protein–carbohydrate binding mechanism. In general, functional characterization can be alternatively solved by alignment-based manners. As alignment accuracy based on conventional methods is often sensitive to sequence identity, low sequence identity among query sequences makes it difficult to precisely locate small portions of relevant features. Therefore, we propose a feature-incorporated alignment (FIA) to flexibly align conserved signatures in CBMs. Then, an FIA-based target-template prediction model was further implemented to identify functional ligand-binding residues.
Results: Arabidopsis thaliana CBM45 and CBM53 were used to validate the FIA-based prediction model. The predicted ligand-binding residues residing on the surface in the hypothetical structures were verified to be ligand-binding residues. In the absence of 3D structural information, FIA demonstrated significant improvement in the estimation of sequence similarity and identity for a total of 808 sequences from 11 different CBM families as compared with six leading tools by Friedman rank test.
Contact: dtchang@life.nthu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.