bluuebunny/crossref_metadata_2025_split huggingface dataset:
A possible mechanism for endogenous activation of the type I interferon system in myositis patients with anti–Jo‐1 or anti–Ro 52/anti–Ro 60 autoantibodies
Authors: Eloranta Maija‐Leena , Barbasso Helmers Sevim , Ulfgren Ann‐Kristin , Rönnblom Lars , Alm Gunnar V. , Lundberg Ingrid E. 
Published: August 2007

AbstractObjectiveTo investigate type I interferon (IFN) system activation and its correlation with autoantibodies and organ manifestations in polymyositis (PM), dermatomyositis (DM), and inclusion body myositis.MethodsSera from 30 patients and 16 healthy controls, or purified IgG, were combined with material released from necrotized cells to stimulate IFNα production by peripheral blood mononuclear cells (PBMCs) from healthy blood donors. Muscle biopsy specimens from 25 patients and 7 healthy controls were investigated for blood dendritic cell antigen 2 (BDCA‐2)–positive plasmacytoid dendritic cells (PDCs) and IFNα/β‐inducible myxovirus resistance 1 (MX‐1) protein.ResultsSera from 13 patients who were positive for anti–Jo‐1 or anti–Ro 52/anti–Ro 60 autoantibodies induced IFNα production in PBMCs when combined with necrotic cell material. In addition, IgG prepared from anti–Jo‐1–positive PM sera induced IFNα with necrotic material, but not when the latter was treated with RNase. BDCA‐2 expression in PDCs in muscle tissue was increased in PM patients with anti–Jo‐1 autoantibodies, while MX‐1 staining in capillaries was increased in DM patients, compared with healthy individuals. IFNα‐inducing capacity correlated with interstitial lung disease, while MX‐1 expression in the capillaries correlated with DM.ConclusionImmune complexes containing anti–Jo‐1 or anti–Ro 52/anti–Ro 60 autoantibodies and RNA may act as endogenous IFNα inducers that activate IFNα production in PDCs. These PDCs could be of importance for inducing myositis, whereas in DM patients without autoantibodies the presence of MX‐1 protein in capillaries suggests another cellular IFNα source and induction mechanism. Consequently, the type I IFN system may be of importance in both PM and DM, but via different pathways.
Anti–Jo‐1 antibody levels correlate with disease activity in idiopathic inflammatory myopathy
Authors: Stone Kerry B. , Oddis Chester V. , Fertig Noreen , Katsumata Yasuhiro , Lucas Mary , Vogt Molly , Domsic Robyn , Ascherman Dana P. 
Published: August 2007

AbstractObjectivePrevious case series have examined the relationship between anti–Jo‐1 antibody levels and myositis disease activity, demonstrating equivocal results. Using enzyme‐linked immunosorbent assays (ELISAs) and novel measures of myositis disease activity, the current study was undertaken to systematically reexamine the association between anti–Jo‐1 antibody levels and various disease manifestations of myositis.MethodsSerum anti–Jo‐1 antibody levels were quantified using 2 independent ELISA methods, while disease activity was retrospectively graded using the Myositis Disease Activity Assessment Tool, which measures disease activity in 7 different organ systems via the Myositis Disease Activity Assessment Visual Analog Scale (VAS) and the Myositis Intention‐to‐Treat Index (MITAX) components. Spearman's rank correlation coefficients and mixed linear regression analysis were used to identify associations between anti–Jo‐1 antibody levels and organ‐specific disease activity in cross‐sectional and longitudinal analyses, respectively.ResultsCross‐sectional assessment of 81 patients with anti–Jo‐1 antibody revealed a modest correlation between the anti–Jo‐1 antibody level and the serum creatine kinase (CK) level, as well as muscle and joint disease activity. Correlation coefficients were similar for CK levels (rs = 0.38, P = 0.002), myositis VAS (rs = 0.36, P = 0.002), and arthritis VAS (rs = 0.40, P = 0.001). In multiple regression analyses of 11 patients with serial samples, anti–Jo‐1 antibody levels correlated significantly with CK levels (R2 = 0.65, P = 0.0002), myositis VAS (R2 = 0.53, P = 0.0008), arthritis VAS (R2 = 0.53, P = 0.006), pulmonary VAS (R2 = 0.69, P = 0.005), global VAS (R2 = 0.63, P = 0.002), and global MITAX (R2 = 0.64, P = 0.0003).ConclusionIn this large series of patients with idiopathic inflammatory myopathy, anti–Jo‐1 antibody levels correlated modestly with muscle and joint disease, an association confirmed by a custom ELISA using recombinant human Jo‐1. More striking associations emerged in a smaller longitudinal subset of patients that link anti–Jo‐1 antibody levels to muscle, joint, lung, and global disease activity.
Distinct regulation of interleukin‐17 in human T helper lymphocytes
Authors: Chen Zhi , Tato Cristina M. , Muul Linda , Laurence Arian , O'Shea John J. 
Published: August 2007

AbstractObjectiveInterleukin‐17 (IL‐17)–producing T helper cells have been proposed to represent a separate lineage of CD4+ cells, designated Th17 cells, which are regulated by the transcription factor retinoic acid–related orphan receptor γt (RORγt). However, despite advances in understanding murine Th17 differentiation, a systematic assessment of factors that promote the differentiation of naive human T cells to Th17 cells has not been reported. The present study was undertaken to assess the effects on naive human CD4+ T cells of cytokines known to promote murine Th17 cells.MethodsHuman naive and memory CD4+ T cells isolated from peripheral blood were activated and cultured with various cytokines. Cytokine production was measured by enzyme‐linked immunosorbent assay and flow cytometry. Messenger RNA was measured by quantitative polymerase chain reaction.ResultsIn response to anti‐CD3/anti‐CD28 stimulation alone, human memory T cells rapidly produced IL‐17, whereas naive T cells expressed low levels. Transforming growth factor β1 and IL‐6 up‐regulated RORγt expression but did not induce Th17 differentiation of naive CD4+ T cells. However, IL‐23 up‐regulated its own receptor and was an important inducer of IL‐17 and IL‐22.ConclusionThe present data demonstrate the differential regulation of IL‐17 and RORγt expression in human CD4+ T cells compared with murine cells. Optimal conditions for the development of IL‐17–producing T cells from murine naive precursors are ineffective in human T cells. Conversely, IL‐23 promoted the generation of human Th17 cells but was also a very potent inducer of other proinflammatory cytokines. These findings may have important implications in the pathogenesis of human autoimmunity as compared with mouse models.
The performance of anti–cyclic citrullinated peptide antibodies in predicting the severity of radiologic damage in inflammatory polyarthritis: Results from the Norfolk Arthritis Register
Authors: Bukhari M. , Thomson W. , Naseem H. , Bunn D. , Silman A. , Symmons D. , Barton A. 
Published: August 2007

AbstractObjectiveAnti–cyclic citrullinated peptide (anti‐CCP) antibodies are a stronger predictor of the severity of rheumatoid arthritis than is rheumatoid factor (RF). Their role in predicting outcome in unselected patients with new‐onset inflammatory polyarthritis (IP) has not been examined. The aims of this study were to examine the role of baseline RF and anti‐CCP antibodies in determining the likelihood of patients having erosions at presentation or in predicting future radiologic damage, and to determine whether anti‐CCP antibodies or RF is sufficiently robust to be clinically useful in guiding treatment decisions in early IP.MethodsPatients were recruited from the Norfolk Arthritis Register. Logistic regression models were fitted to test the ability of anti‐CCP antibodies and RF to predict erosions. Further models were investigated to examine the role of anti‐CCP antibodies in patients stratified by RF status.ResultsThe presence of anti‐CCP antibodies at baseline was strongly associated with both prevalent erosions (odds ratio [OR] 2.53 [95% confidence interval (95% CI) 1.48–4.30]) and developing erosions at 5 years (OR 10.2 [95% CI 6.2–16.9]). These ORs were higher than those for RF (OR 1.63 [95% CI 0.94–2.82] and OR 3.4 [95% CI 2.2–5.2], respectively). The likelihood ratio (LR) for the prediction of prevalent erosions and erosions at 5 years was highest in the RF−subgroup (LR 2.2 and 5.8, respectively). However, 27% of anti‐CCP−patients had developed erosions by 5 years.ConclusionDespite their strong association with the presence, development, and extent of erosions, anti‐CCP antibodies alone are not a sufficiently accurate measure upon which to base clinical treatment decisions. Knowledge of anti‐CCP antibody status is most informative in RF−negative patients.
Association of a CD24 gene polymorphism with susceptibility to systemic lupus erythematosus
Authors: Sánchez Elena , Abelson Anna‐Karin , Sabio Jose M. , González‐Gay Miguel A. , Ortego‐Centeno Norberto , Jiménez‐Alonso Juan , de Ramón Enrique , Sánchez‐Román Julio , López‐Nevot Miguel A. , Gunnarsson Iva , Svenungsson Elisabet , Sturfelt Gunnar , Truedsson Lennart , Jönsen Andreas , González‐Escribano Maria Francisca , Witte Torsten , Alarcón‐Riquelme Marta E. , Martín Javier 
Published: August 2007

AbstractObjectiveTo determine the potential role of the CD24 A57V gene polymorphism in systemic lupus erythematosus (SLE).MethodsWe studied 3 cohorts of Caucasian patients and controls. The Spanish cohort included 696 SLE patients and 539 controls, the German cohort included 257 SLE patients and 317 controls, and the Swedish cohort included 310 SLE patients and 247 controls. The CD24 A57V polymorphism was genotyped by polymerase chain reaction, using a predeveloped TaqMan allele discrimination assay. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated.ResultsIn the Spanish cohort there was a statistically significant difference in the distribution of the CD24 V allele between SLE patients and controls (OR 3.6 [95% CI 2.13–6.16], P < 0.0001). In addition, frequency of the CD24 V/V genotype was increased in SLE patients compared with controls (OR 3.7 [95% CI 2.16–6.34], P < 0.00001). We sought to replicate this association with SLE in a German population and a Swedish population. A similar trend was found in the German group. The CD24 V/V genotype and the CD24 V allele were more frequent in SLE patients than in controls, although this difference was not statistically significant. No differences were observed in the Swedish group. A meta‐analysis of the Spanish and German cohorts demonstrated that the CD24 V allele has a risk effect in SLE patients (pooled OR 1.25 [95% CI 1.08–1.46], P = 0.003). In addition, homozygosity for the CD24 V risk allele significantly increased the effect (pooled OR 2.19 [95% CI 1.50–3.22], P = 0.00007).ConclusionThese findings suggest that the CD24 A57V polymorphism plays a role in susceptibility to SLE in a Spanish population.
The effect of “open access” on citation impact: An analysis of ArXiv's condensed matter section
Authors: Moed Henk F. 
Published: August 2007

AbstractThis article statistically analyzes how the citation impact of articles deposited in the Condensed Matter section of the preprint server ArXiv (hosted by Cornell University), and subsequently published in a scientific journal, compares to that of articles in the same journal that were not deposited in the archive. Its principal aim is to further illustrate and roughly estimate the effect of two factors, “early view” and “quality bias,” on differences in citation impact between these two sets of papers, using citation data from Thomson Scientific's Web of Science. It presents estimates for a number of journals in the field of condensed matter physics. To discriminate between an “open access” effect and an early view effect, longitudinal citation data were analyzed covering a time period as long as 7 years. Quality bias was measured by calculating ArXiv citation impact differentials at the level of individual authors publishing in a journal, taking into account coauthorship. The analysis provided evidence of a strong quality bias and early view effect. Correcting for these effects, there is in a sample of six condensed matter physics journals studied in detail no sign of a general “open access advantage” of papers deposited in ArXiv. The study does provide evidence that ArXiv accelerates citation due to the fact that ArXiv makes papers available earlier rather than makes them freely available.
The role of Web‐based information in the scholarly communication of chemists: Citation and content analyses of American Chemical Society Journals
Authors: Brown Cecelia 
Published: August 2007

AbstractCitation and content analyses of eight American Chemical Society (ACS) journals in a range of fields of chemistry were used to describe the use of Web‐based information resources by the authors and readers of the scholarly literature of chemistry. The analyses indicate that even though the number of Web‐based information resources has grown steadily over the past decade, chemists are not taking full advantage of freely available Web‐based resources. They are, however, making use of the ACS Electronic Supporting Information archive. The content of the Web‐based resources that are used is primarily text based, and the URLs are provided in the articles' reference lists and experimental sections. The presence of a reference to a Web‐based resource in a chemistry article does not influence its rate of citation, even though the viability of the URLs was found to erode with time. Comparison of citation and online access data reveals that at the highest levels of citation, articles also garner high levels of online access. This was especially true for articles describing a technique or methodology. Even though chemists do not incorporate large numbers of freely available Web‐based resources into their publications, an increasingly important component of a chemist's information behavior for the direct support of his or her research is unfettered bench‐top access via the Web.
A classification of mental models of undergraduates seeking information for a course essay in history and psychology: Preliminary investigations into aligning their mental models with online thesauri
Authors: Cole Charles , Lin Yang , Leide John , Large Andrew , Beheshti Jamshid 
Published: August 2007

AbstractThe article reports a field study which examined the mental models of 80 undergraduates seeking information for either a history or psychology course essay when they were in an early, exploration stage of researching their essay. This group is presently at a disadvantage when using thesaurus‐type schemes in indexes and online search engines because there is a disconnect between how domain novice users of IR systems represent a topic space and how this space is represented in the standard IR system thesaurus. The study attempted to (a) ascertain the coding language used by the 80 undergraduates in the study to mentally represent their topic and then (b) align the mental models with the hierarchical structure found in many thesauri. The intervention focused the undergraduates' thinking about their topic from a topic statement to a thesis statement. The undergraduates were asked to produce three mental model diagrams for their real‐life course essay at the beginning, middle, and end of the interview, for a total of 240 mental model diagrams, from which we created a 12‐category mental model classification scheme. Findings indicate that at the end of the intervention, (a) the percentage of vertical mental models increased from 24 to 35% of all mental models; but that (b) 3rd‐year students had fewer vertical mental models than did 1st‐year undergraduates in the study, which is counterintuitive. The results indicate that there is justification for pursuing our research based on the hypothesis that rotating a domain novice's mental model into a vertical position would make it easier for him or her to cognitively connect with the thesaurus's hierarchical representation of the topic area.
Impact of data sources on citation counts and rankings of LIS faculty: Web of science versus scopus and google scholar
Authors: Meho Lokman I. , Yang Kiduk 
Published: August 2007

AbstractThe Institute for Scientific Information's (ISI, now Thomson Scientific, Philadelphia, PA) citation databases have been used for decades as a starting point and often as the only tools for locating citations and/or conducting citation analyses. The ISI databases (or Web of Science [WoS]), however, may no longer be sufficient because new databases and tools that allow citation searching are now available. Using citations to the work of 25 library and information science (LIS) faculty members as a case study, the authors examine the effects of using Scopus and Google Scholar (GS) on the citation counts and rankings of scholars as measured by WoS. Overall, more than 10,000 citing and purportedly citing documents were examined. Results show that Scopus significantly alters the relative ranking of those scholars that appear in the middle of the rankings and that GS stands out in its coverage of conference proceedings as well as international, non‐English language journals. The use of Scopus and GS, in addition to WoS, helps reveal a more accurate and comprehensive picture of the scholarly impact of authors. The WoS data took about 100 hours of collecting and processing time, Scopus consumed 200 hours, and GS a grueling 3,000 hours.
Does domain knowledge matter: Mapping users' expertise to their information interactions
Authors: Ju Boryung 
Published: August 2007

AbstractThe purpose of this study is to investigate the role that domain knowledge plays in users' interactions with information systems. Two groups of users with two different areas of expertise were recruited for 34 experimental sessions to answer two research questions: (a) Does one group's domain knowledge (Geography majors) affect their performance on an information system more than another group's domain knowledge (Computer Science majors)? (b) Are there any differences and/or similarities in the performance of the two groups in terms of the information problem‐solving processes? Task completion time, task completeness, and mouse movements were collected while users performed six tasks during the experimental sessions. Data were analyzed through repeated measures. An ANOVA was used for task completion time and task completeness. GOMS (Goals, Operators, Methods, and Selection rules) was also used for mouse movements to identify some of the similarities and differences between the two groups' information problem‐solving processes. The GOMS analysis found the two groups' processing activities to be remarkably similar. The ANOVA results indicate that expertise type was not a major factor influencing user performance, but task and task combined with the type of expertise played a significant role in the users' interactions with the interface. External operators, goal decompositions, and methods related to the problem solving process through GOMS are also presented.
Comparison of full‐text searching to metadata searching for genes in two biomedical literature cohorts
Authors: Hemminger Bradley M. , Saelim Billy , Sullivan Patrick F. , Vision Todd J. 
Published: August 2007

AbstractResearchers have traditionally used bibliographic databases to search out information. Today, the full‐text of resources is increasingly available for searching, and more researchers are performing full‐text searches. This study compares differences in the number of articles discovered between metadata and full‐text searches of the same literature cohort when searching for gene names in two biomedical literature domains. Three reviewers additionally ranked 100 articles in each domain. Significantly more articles were discovered via full‐text searching; however, the precision of full‐text searching also is significantly lower than that of metadata searching. Certain features of articles correlated with higher relevance ratings. A significant feature measured was the number of matches of the search term in the full‐text of the article, with a larger number of matches having a statistically significant higher usefulness (i.e., relevance) rating. By using the number of hits of the search term in the full‐text to rank the importance of the article, performance of full‐text searching was improved so that both recall and precision were as good as or better than that for metadata searching. This suggests that full‐text searching alone may be sufficient, and that metadata searching as a surrogate is not necessary.
Estimation and Confidence Regions for Multi‐Dimensional Effective Dose
Authors: Li Jialiang , Nordheim Erik V. , Zhang Chunming , Lehner Charles E. 
Published: August 2007

AbstractThe problem of finding confidence regions for multiple predictor variables corresponding to given expected values of a response variable has not been adequately resolved. Motivated by an example from a study on hyperbaric exposure using a logistic regression model, we develop a conceptual framework for the estimation of the multi‐dimensional effective dose for binary outcomes. Thek‐dimensional effective dose can be determined by conditioning onk– 1 components and solving for the last component as a conditional univariate effective dose. We consider various approaches for calculating confidence regions for the multi‐dimensional effective dose and compare them via a simulation study for a range of possible designs. We analyze data related to decompression sickness to illustrate our procedure. Our results provide a practical approach to finding confidence regions for predictor variables for a given response value. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Molecular characterization of reconstructed skin model by Raman microspectroscopy: Comparison with excised human skin
Authors: Tfayli Ali , Piot Olivier , Draux Florence , Pitre Franck , Manfait Michel 
Published: August 2007

AbstractHuman skin is directly exposed to different exogenous agents. Many research works have studied the diffusion, interactions, absorption mechanisms, and/or toxicity of these agents toward different cutaneous structures. With the use of living animals for such tests being more and more rejected; and the number of human volunteers being limited; different types of skin models are used. In the last few years, reconstructed epidermis from cell cultures has been frequently employed, and recent changes in the European chemical policy have approved and encouraged the use of these reconstructed models for skin‐related research works and assessments. Among the techniques used actually to study the skin, Raman microspectroscopy is a rising and powerful nondestructive technique that detects characteristic molecular vibrations. In this study, we created a spectral database to index the vibration peaks and bands of a well‐known reconstructed epidermis model, the Episkin®. The comparison with a native epidermis signal enabled us to put in evidence several spectral differences associated with molecular and structural differences between the skin and the reconstructed model, both maintained in living conditions. In addition to that, we have showed the feasibility of tracking the penetration of a pharmaceutical molecule through the Episkin model. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 261–274, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com