bluuebunny/crossref_metadata_2025_split huggingface dataset:
Head and neck squamous cell carcinoma is not associated with interleukin-18 promoter gene polymorphisms: a case–control study
Authors: Asefi V , Mojtahedi Z , Khademi B , Naeimi S , Ghaderi A 
Published: October 2008

AbstractObjective:To investigate the association of two functional single nucleotide polymorphisms in the promoter region of the interleukin-18 gene, at positions −607 and −137, with head and neck squamous cell carcinoma.Design:Genomic deoxyribonucleic acid was extracted, by the salting-out method, from peripheral blood leukocytes. Single nucleotide polymorphisms of the interleukin-18 gene at positions −607 (cytosine/adenine) and −137 (guanine/cytosine) were analysed by sequence-specific polymerase chain reaction.Subjects:One hundred and eleven patients (86 men and 25 women; mean age 56.7±13.7 years) and 212 regional controls (165 men and 47 women; mean age 53.3±12.2 years) were studied. Control subjects comprised healthy volunteers or cancer-free individuals presenting with otolaryngological disease. The diagnosis of squamous cell carcinoma was confirmed histopathologically. Various clinical parameters were collected at diagnosis, including tumour site, tumour size, lymph node involvement, distant metastasis and stage.Results:There was no significant association between the allele, genotype or haplotype frequencies of the two single nucleotide polymorphisms of the interleukin-18 promoter and the head and neck squamous cell carcinoma susceptibility or clinical parameters at diagnosis.Conclusion:Interleukin-18 polymorphisms at positions −607 and −137 did not confer susceptibility to head and neck squamous cell carcinoma in southern Iranian patients.
Quantitative analysis of tympanic membrane perforation: a simple and reliable method
Authors: Ibekwe T S , Adeosun A A , Nwaorgu O G 
Published: October 2008

AbstractBackground:Accurate assessment of the features of tympanic membrane perforation, especially size, site, duration and aetiology, is important, as it enables optimum management.Aim and objectives:To describe a simple, cheap and effective method of quantitatively analysing tympanic membrane perforations.Materials and methods:The system described comprises a video-otoscope (capable of generating still and video images of the tympanic membrane), adapted via a universal serial bus box to a computer screen, with images analysed using the Image J geometrical analysis software package. The reproducibility of results and their correlation with conventional otoscopic methods of estimation were tested statistically with the pairedt-test and correlational tests, using the Statistical Package for the Social Sciences version 11 software.Results:The following equation was generated: P/T × 100 per cent = percentage perforation, where P is the area (in pixels2) of the tympanic membrane perforation and T is the total area (in pixels2) for the entire tympanic membrane (including the perforation). Illustrations are shown. Comparison of blinded data on tympanic membrane perforation area obtained independently from assessments by two trained otologists, of comparative years of experience, using the video-otoscopy system described, showed similar findings, with strong correlations devoid of inter-observer error (p = 0.000,r = 1). Comparison with conventional otoscopic assessment also indicated significant correlation, comparing results for two trained otologists, but some inter-observer variation was present (p = 0.000,r = 0.896). Correlation between the two methods for each of the otologists was also highly significant (p = 0.000).Conclusion:A computer-adapted video-otoscope, with images analysed by Image J software, represents a cheap, reliable, technology-driven, clinical method of quantitative analysis of tympanic membrane perforations and injuries.
Mental capacity, diagnosis and insight in psychiatric in-patients: a cross-sectional study
Authors: Owen G. S. , David A. S. , Richardson G. , Szmukler G. , Hayward P. , Hotopf M. 
Published: October 2008

BackgroundMental capacity is now a core part of UK mental health law and clinicians will increasingly be expected to assess it. Because it is a legal concept there is a need to clarify associations with variables that clinicians are more familiar with, especially insight.MethodIn this cross-sectional study we recruited consecutive psychiatric admissions to the Maudsley Hospital, London. We carried out structured assessments of decision making using the MacArthur Competence Assessment Tool for Treatment (MacCAT-T), resulting in a clinical judgement about capacity status. We analysed associations with a range of sociodemographic and clinical variables, including insight score on the Expanded Schedule for the Assessment of Insight (SAI-E). The same variables were compared in an analysis stratified according to diagnostic group: psychotic disorders/bipolar affective disorder (BPAD)/non-psychotic disorders.ResultsPsychotic disorders and manic episodes of BPAD are most strongly associated with incapacity. In such patients, insight is the best discriminator of capacity status. In patients with non-psychotic disorders, insight is less strongly associated with capacity; in this group depressed mood discriminates capacity status whereas it does not in psychotic disorders. Cognitive performance does not discriminate capacity status in patients with psychotic disorders.ConclusionsMental capacity has complex relationships with psychopathological variables, and these relationships are different according to diagnostic group. Insight is the best discriminator of capacity status in psychotic disorders and BPAD but not in non-psychotic disorders.
Special issue on interactive question answering: Introduction
Authors: WEBB N. , WEBBER B. 
Published: October 2008

AbstractIn this introduction, we present our overview of interactive question answering (IQA). We contextualize IQA in the wider field of question answering, and establish connections to research in Information Retrieval and Dialogue Systems. We highlight the development of QA as a field, and identify challenges in the present research paradigm for which IQA is a potential solution. Finally, we present an overview of papers in this special issue, drawing connections between these and the challenges they address.
Long-term effects of the Dutch Schoolgruiten Project – promoting fruit and vegetable consumption among primary-school children
Authors: Tak Nannah I , te Velde Saskia J , Brug Johannes 
Published: October 2008

AbstractObjectivesTo evaluate the long-term effects of the Schoolgruiten Project, a Dutch primary school-based intervention providing free fruit and vegetables (F&V). In addition, we assessed whether children’s appreciation of the project mediated these intervention effects.Design and methodsParticipating schoolchildren (mean age 9·9 years at baseline) and their parents completed parallel questionnaires at baseline, at 1-year and at 2-year follow-up, including questions on usual F&V intake of the child, potential behavioural determinants, their appreciation of the project and general demographics. Primary outcomes were usual F&V intakes as assessed by parent and child self-reported food frequency measures. Secondary outcome measures were taste preference, knowledge of daily recommendations, availability and accessibility for fruit intake. Multilevel linear regression analyses were used to assess differences at second follow-up adjusted for baseline values between control and intervention groups.SubjectsReports were available for 346 intervention children (148 parents) and 425 control children (287 parents).ResultsBoth child and parent reports indicated that the intervention group had a significantly higher fruit intake at 2-year follow-up (difference, servings/d: 0·15; 95 % CI 0·004, 0·286 for child reports; 0·19; 95 % CI 0·030, 0·340 for parent reports). No significant effects on vegetable intake were observed. Significant positive intervention effects were also found for knowledge of fruit recommendations among boys. Some evidence was found for partial mediation analyses of the effects on fruit intake.ConclusionThe present study indicates that the Schoolgruiten scheme was effective in increasing children’s fruit intake and that appreciation of the project partially mediated this effect.
New Software Architecture for Integrated Water Modeling: CUAHSI/OpenMI Workshop for Integrating Water Models; Wallingford, United Kingdom, 7–10 April 2008
Authors: Goodall Jonathan , Tarboton David G. , Peckham Scott D. , Hooper Richard 
Published: October 2008

European researchers have created a software standard named the Open Modeling Interface (OpenMI; http://www.openmi.org) that facilitates the integration of numerical hydrologic models with each other. Nearly 10 million euros have been invested in the development and testing of OpenMI through projects cofunded by the European Commission.Seven hydrologists representing various modeling‐related initiatives in the United States traveled to Wallingford, United Kingdom, to learn about OpenMI and to discuss with European hydrologists the experiences and challenges inherent with developing integrated hydrologic models. The workshop was sponsored by the U.S. National Science Foundation (NSF) and the European Union (EU).
Biogenic Secondary Organic Aerosols: From Observations to Global Modeling: A Workshop Series for Early Career Scientists From the United States and Nordic Countries; Hyytiälä, Finland, 1–4 July 2007, and Tovetorp, Sweden, 11–15 August 2008
Authors: Heald Colette Lara 
Published: October 2008

Globally, secondary organic aerosols (SOAs) from biogenic precursors surpass those from anthropogenic sources. These organic particles have important impacts on air quality and climate, the latter through their direct interactions with radiation and by the modulation of cloud condensation nuclei. These processes exert a substantial influence back upon the Earth system through links to the terrestrial carbon and water cycles.The questions that currently confront researchers working in the fields of biogenic SOAs (BSOAs) and their impact on the Earth system are numerous and multidisciplinary. Such challenges motivated a 2‐year workshop series, with meetings held at Hyytiälä Research Station (Finland) in 2007 and Tovetorp Research Station (Sweden) in 2008, which was attended by 25 early career scientists from the United States and Nordic countries. Five internationally distinguished researchers gave keynote lectures and contributed to scientific and professional development discussions.
The internal limits to firms' nonmarket activities
Authors: Bonardi Jean‐Philippe 
Published: October 2008

AbstractIt is well documented that firms develop nonmarket strategies to try to shape public policy changes to their advantage. But are there no limits to this? This paper argues that there is in fact an important limitation, internal to the firm, which comes from the necessity for firms to integrate market and nonmarket activities. Because the two types of activities are not always complements but sometimes substitutes, firms end up giving up part of their nonmarket activities to avoid restricting the development of their market strategies. This argument is tested in the context of the European telecommunications industry. Results suggest that there is reasonable ground for optimism regarding the potentially negative influence that firms' nonmarket activities might play in a democracy.
Social issues in the study of management
Authors: Guthrie Doug , Durand Rodolphe 
Published: October 2008

AbstractThe last 30 years have seen an explosion of activity in the areas of corporate social responsibility (CSR) and social enterprise. With these emergent corporate practices has come a significant amount of attention among scholars and practitioners to how we should understand this phenomenon. What forces have driven managers and owners to re‐think their responsibilities as extending beyond profit maximization and increasing shareholder value? In this paper, we introduce some of the key issues that have guided research on the social issues of management over the last 30 years. We argue that, despite the growing strength of research in this area, there are four key ways in which we would like to see scholarship in this area develop further: (i) Scholarship in this area should incorporate a greater appreciation for the institutional history in which these practices have emerged. Research in this area tends to be ahistorical, and it is often the case that corporate social practices have emerged because of deep‐seated institutional struggles. (ii) Scholarship should rely more on comparative analysis to illuminate the importance of the contexts in which these practices emerge. (iii) Scholarship should engage more thoroughly with the legal and finance literatures on corporate governance. Many of the issues that fall under the ‘social issues of management’ rubric are fundamentally issues of corporate governance, and while some management scholars have embraced the corporate governance literature, research on the social issues of management rarely draws upon this important body of work. (iv) Methodological plurality is key to thinking through the mechanisms that drive organizational practices, and we would like to see more work in this area that employs multi‐method approaches to examine the organizational practices.
The Role of Theoretical Modeling in Microcirculation Research
Authors: SECOMB TIMOTHY W. , BEARD DANIEL A. , FRISBEE JEFFERSON C. , SMITH NICOLAS P. , PRIES AXEL R. 
Published: October 2008

ABSTRACTTheoretical modeling approaches have made important contributions to research in the biological sciences, including the microcirculation, and their value is increasingly recognized. However, misconceptions about the nature and role of theoretical models persist, and such work is often presented in a way that does not maximize its value, especially for scientists who are not themselves using such models. In this review, a categorization of models as phenomenological, qualitative conceptual, quantitative conceptual, or predictive is proposed, and the characteristics of each type are discussed. Recommendations are made for the presentation of models and for the future development of modeling approaches. The concepts discussed are generally applicable to the theoretical modeling of biological systems and are illustrated by using examples of modeling in microcirculation research.
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Authors: Busch Anke , Richter Andreas S. , Backofen Rolf 
Published: October 2008

Abstract
Motivation: During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.
Results: We introduce INTARNA, a new general and fast approach to the prediction of RNA–RNA interactions incorporating accessibility of target sites as well as the existence of a user-definable seed. We successfully applied INTARNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
Availability: http://www.bioinf.uni-freiburg.de/Software/
Contact: IntaRNA@informatik.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of kinase-specific phosphorylation sites using conditional random fields
Authors: Dang Thanh Hai , Van Leemput Koenraad , Verschoren Alain , Laukens Kris 
Published: October 2008

Abstract
Motivation: Phosphorylation is a crucial post-translational protein modification mechanism with important regulatory functions in biological systems. It is catalyzed by a group of enzymes called kinases, each of which recognizes certain target sites in its substrate proteins. Several authors have built computational models trained from sets of experimentally validated phosphorylation sites to predict these target sites for each given kinase. All of these models suffer from certain limitations, such as the fact that they do not take into account the dependencies between amino acid motifs within protein sequences in a global fashion.
Results: We propose a novel approach to predict phosphorylation sites from the protein sequence. The method uses a positive dataset to train a conditional random field (CRF) model. The negative training dataset is used to specify the decision threshold corresponding to a desired false positive rate. Application of the method on experimentally verified benchmark phosphorylation data (Phospho.ELM) shows that it performs well compared to existing methods for most kinases. This is to our knowledge that the first report of the use of CRFs to predict post-translational modification sites in protein sequences.
Availability: The source code of the implementation, called CRPhos, is available from http://www.ptools.ua.ac.be/CRPhos/
Contact: kris.laukens@ua.ac.be
Suplementary Information: Supplementary data are available at http://www.ptools.ua.ac.be/CRPhos/
Effective cluster-based seed design for cross-species sequence comparisons
Authors: Zhou Leming , Mihai Ingrid , Florea Liliana 
Published: October 2008

Abstract
Summary: To annotate newly sequenced organisms, cross-species sequence comparison algorithms can be applied to align gene sequences to the genome of a related species. To improve the accuracy of alignment, spaced seeds must be optimized for each comparison. As the number and diversity of genomes increase, an efficient alternative is to cluster pairwise comparisons into groups and identify seeds for groups instead of individual comparisons. Here we investigate a measure of comparison closeness and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed.
Availability: Source code is freely available at http://dna.cs.gwu.edu and from Bioinformatics online.
Contact: lmzhou@gwmail.gwu.edu, florea@gwu.edu
Supplementary information: Supplementary data are available at http://dna.cs.gwu.edu and Bioinformatics online.
Dynamics of closed areas in Norway lobster fisheries
Authors: Smith I. Philip , Jensen Antony C. 
Published: October 2008

AbstractSmith, I. P., and Jensen, A. C. 2008. Dynamics of closed areas in Norway lobster fisheries. – ICES Journal of Marine Science, 65: 1600–1609. A dynamic, age-structured population model was developed to investigate the potential effects of introducing a closed area to a fishery for a species with limited adult mobility and planktonic dispersal of larvae, using biological and fishery information from a Norway lobster fishery in eastern Scotland. Simulated closure of part of the fishing grounds led to a long-term increase in total biomass and recruitment to the fished zone, but the larval subsidy did not compensate for the loss of fishing ground, and fishery yield was reduced under all modelled combinations of closed-area size and prior fishing effort. Concentration of effort in the fished zone and increased recruitment there led to reduced average size, and therefore value, of animals in the catch, as well as increased destruction of biomass by discarding undersized lobsters. Implementation of a closed area also led to oscillations in stock biomass, recruitment, and yield over several years after the closure, particularly with large closed areas and high fishing effort.
A Geometric Description of them-cluster Categories of TypeDn
Authors: Baur Karin , Marsh Bethany Rose 
Published: October 2008

AbstractWe show that the m-cluster category of type Dn is equivalent to a certain geometrically-defined category of arcs in a punctured regular nm − m + 1-gon. This generalizes a result of Schiffler for m = 1. We use the notion of the mth power of a translation quiver to realize the m-cluster category in terms of the cluster category.
Phenotype/Genotype Correlations in a DFNB1 Cohort With Ethnical Diversity
Authors: Angeli Simon I. 
Published: October 2008

AbstractObjectives/Hypothesis: The aim of this study was to 1) determine the prevalence of DFNB1 in a cohort of children with prelingual nonsyndromic sensorineural hearing loss (HL), 2) study phenotype/genotype correlations, and 3) establish guidelines for genetic counseling of DFNB1.Study Design: Prospective cohort study.Methods: A total of 119 unrelated children (107 sporadic and 12 familial cases) with prelingual nonsyndromic HL underwent mutational screening for DFNB1 in the noncoding and coding exons of GJB2, in addition to the del(GJB6‐D13S1830) mutation of GJB6. Information regarding demographics, HL, developmental milestones, inner ear high resolution computed tomography, hearing habilitation, and associated phenotypic manifestations were collected in probands with biallelic pathogenic mutations.Results: The prevalence of DFNB1 in cases of prelingual nonsyndromic HL was 26% (25% in sporadic and 50% in familial cases). In regards to ethnicity, 19 probands were white and 12 probands of Hispanic ancestry had a mixed racial origin (black, Native‐American, white). Greater allelic heterogeneity was shown with Hispanics of mixed descent exhibiting 10 of 12 GJB2 allelic variants, whereas whites had 4 of 10 allelic variants (Fisher exact test, P = .033); both ethnic groups had theGJB6 deletion. The frequency of deaf carriers of the most commonly found mutation (c.35delG) was 8% and higher than that of expected for the general population (Fisher exact test, P = .015). The hearing phenotype was variable in terms of degree of impairment (from mild to profound),onset, symmetry and progression, and there was no correlation with any specific genotype class. DFNB1 probandshad normal gross motor development, and the frequency of computed tomography abnormalities of the inner ear was low at 8%. No other specific associated phenotypic manifestations were identified.Conclusions: DFNB1 is the most common identifiable etiology of nonsyndromic prelingual deafness both in sporadic and familial cases in this cohort with ethnic diversity. The greater allelic variability observed in Hispanics and the high frequency of deaf probands carrying a single allelic variant of DFNB1 support extending the screening to noncoding regions of GJB2 and to the remaining DFNB1 locus. Most probands have a congenital HL that is stable, symmetrical and without associated manifestations, but the audiometric profile should not be the only criteria for offering mutational screening of DFNB1 because of the observed variability. These data can be applied to direct the clinical evaluation and effectively counsel families of children with DFNB1.