bluuebunny/crossref_metadata_2025_split huggingface dataset:
IFN-γ Regulates the Requirement for IL-17 in Proteoglycan-Induced Arthritis
Authors: Doodes Paul D. , Cao Yanxia , Hamel Keith M. , Wang Yumei , Rodeghero Rachel L. , Mikecz Katalin , Glant Tibor T. , Iwakura Yoichiro , Finnegan Alison 
Published: December 2009

Abstract
The contribution of the proinflammatory cytokines IFN-γ and IL-17 to the pathogenesis of experimental arthritis is controversial. In proteoglycan (PG)-induced arthritis (PGIA), severe arthritis is dependent on the production of IFN-γ, whereas IL-17 is dispensable. In collagen-induced arthritis and Ag-induced arthritis, although high levels of IFN-γ are secreted, disease is exacerbated in IFN-γ or IFN-γ receptor-deficient mice due to the ability of IFN-γ to suppress IL-17 expression. In the current study, we investigated the effect of IFN-γ on the IL-17 response and its consequences in PGIA. In PG-immunized IFN-γ−/− mice, despite reduction in arthritis, the PG-specific CD4+ T cell IL-17 response was significantly increased. Elevated IL-17 contributed to development of arthritis, as disease in IFN-γ/IL-17−/− was significantly reduced in comparison with either IFN-γ−/− or IL-17−/− mice. A contribution of IFN-γ and IL-17 to the development of arthritis was also identified in T-bet−/− mice. PG-specific CD4+ T cells from T-bet−/− mice produced reduced IFN-γ and elevated concentrations of IL-17. Both IFN-γ and IL-17 contribute to arthritis, as T-bet−/− mice lacking IL-17 (T-bet/IL-17−/−) were resistant, whereas wild-type, T-bet−/−, and IL-17−/− mice were susceptible to PGIA. T cell proliferation and autoantibody production did not correlate with development of disease; however, expression of cytokines and chemokines in joint tissues demonstrate that IFN-γ and IL-17 cooperatively contribute to inflammation. These results demonstrate that both IFN-γ and IL-17 have the potential to induce PGIA, but it is the strength of the IFN-γ response that regulates the contribution of each of these Th effector cytokines to disease.
Occupational factors and risk of Parkinson's disease: A population‐based case–control study
Authors: Firestone Jordan A. , Lundin Jessica I. , Powers Karen M. , Smith‐Weller Terri , Franklin Gary M. , Swanson Phillip D. , Longstreth W.T. , Checkoway Harvey 
Published: December 2009

AbstractBackgroundParkinson's disease (PD) has been associated with various workplace factors, but the evidence is inconsistent.ObjectiveTo estimate the risk of PD associated with various jobs and workplace exposures.MethodsWe conducted a population‐based, case–control study of 404 incident PD cases and 526 age and sex‐matched controls, collecting self‐reported work histories including job titles and exposures to various industrial toxicants. Relative risks of PD from these exposures were estimated with odds ratios (OR) and 95% confidence intervals (CI) using logistic regression.ResultsRisk was not significantly affected by farming work, by metal work, or by exposure to pesticides, metals, or solvents.ConclusionsThese findings do not provide support for the hypothesis that workplace factors affect the risk of PD. Am. J. Ind. Med. 53:217–223, 2010. © 2009 Wiley‐Liss, Inc.
Dietary folate and vitamin B6 are not associated with p53 mutations in esophageal adenocarcinoma
Authors: Balbuena Lloyd , Casson Alan G. 
Published: December 2009

AbstractRecent studies have suggested an association between dietary folate, and related B‐vitamins, and risk for cancer, potentially mediated by the p53 tumor suppressor gene. The aim of this study was to explore the effect of dietary folate and vitamin B6 intake on p53 in the molecular pathogenesis of esophageal adenocarcinoma (EADC). For each participant, a structured questionnaire was used to obtain detailed sociodemographic and lifestyle risk factors, including diet, from which folate and vitamin B6 intake were calculated. Risks for p53 mutations, p53 mutations at CpG sites, and p53 protein overexpression among EADC cases (n = 54) were calculated using logistic regression with dietary folate and vitamin B6 intake as predictive variables, adjusting for age, gender, smoking, and alcohol consumption. No significant differences were found for patients with EADC who had p53 mutations (n = 21) compared with patients with wild‐type p53 (n = 33) with respect to selected clinicopathologic variables (age, gender, tumor grade, stage, alcohol, or tobacco consumption) and dietary intake of folate or vitamin B6. No statistically significant associations were seen between dietary folate and vitamin B6 intake (highest vs. lowest quartiles) and p53 mutations, p53 mutations at CpG sites (n = 12), and p53 protein overexpression (n = 17). We conclude that dietary intake of folate and vitamin B6 do not appear to have an effect on p53, suggesting alternative molecular mechanisms underlying esophageal adenocarcinogenesis. © 2009 Wiley‐Liss, Inc.
A radiologic classification of talocalcaneal coalitions based on 3D reconstruction
Authors: Rozansky Alison , Varley Eric , Moor Molly , Wenger Dennis R. , Mubarak Scott J. 
Published: December 2009

Purpose Talocalcaneal coalitions can be difficult to detect on plain radiographs, despite obvious clinical findings. The purpose of this study is two-fold: (1) to delineate the benefits of thin-cut computed tomography (CT) and 3D reconstructions and (2) to develop a classification scheme for talocalcaneal coalitions that will provide valuable information for surgical planning. Methods From 2005 to 2009, 54 feet (35 patients) with a talocalcaneal coalition were evaluated with thin-cut (1 mm) CT, using multi-planar 2D and 3D reconstructions. The talocalcaneal coalitions were classified into five types based on the cartilaginous or bony nature, location, and facet joint orientation. Results Bilateral coalitions were found in 22/35 patients. Types I and II were fibrocartilaginous coalitions, which was the most common type, comprising 40.7 and 16.7% of the coalitions, respectively. Of the patients, 14.8% had a shingled Type III coalition, while 11.1% of the feet examined had a complete bony coalition (Type IV). Small peripheral posterior bony coalitions (Type V), which are heretofore not described, were found in 16.7% of feet. Conclusions CT scans can provide valuable information regarding the bony or cartilaginous nature of coalitions, as well as the facet orientation, which is helpful in diagnosis and treatment. In this study, the 2D and 3D reconstructions revealed previously unreported peripheral posterior bony coalitions (Type V), as well as coalitions that are in the same plane as the standard CT cuts or Harris view radiographs (Type I). The CT scan also improved the crucial pre-operative planning of the resection in the more complex vertical and combined horizontal and vertical fibrocartilaginous coalitions (Type I and II). Additionally, the complete bony coalitions (Type IV) can be sized accurately, which is helpful in decision-making on the resectability of the coalition.
Controlling the enzymatic activity of a restriction enzyme by light
Authors: Schierling Benno , Noël Ann-Josée , Wende Wolfgang , Hien Le Thi , Volkov Eugeny , Kubareva Elena , Oretskaya Tatiana , Kokkinidis Michael , Römpp Andreas , Spengler Bernhard , Pingoud Alfred 
Published: December 2009

For many applications it would be desirable to be able to control the activity of proteins by using an external signal. In the present study, we have explored the possibility of modulating the activity of a restriction enzyme with light. By cross-linking two suitably located cysteine residues with a bifunctional azobenzene derivative, which can adopt a
cis
- or
trans
-configuration when illuminated by UV or blue light, respectively, enzymatic activity can be controlled in a reversible manner. To determine which residues when cross-linked show the largest “photoswitch effect,” i.e., difference in activity when illuminated with UV vs. blue light, > 30 variants of a single-chain version of the restriction endonuclease PvuII were produced, modified with azobenzene, and tested for DNA cleavage activity. In general, introducing single cross-links in the enzyme leads to only small effects, whereas with multiple cross-links and additional mutations larger effects are observed. Some of the modified variants, which carry the cross-links close to the catalytic center, can be modulated in their DNA cleavage activity by a factor of up to 16 by illumination with UV (azobenzene in
cis
) and blue light (azobenzene in
trans
), respectively. The change in activity is achieved in seconds, is fully reversible, and, in the case analyzed, is due to a change in
V
max
rather than
K

m

.
Cytoskeleton-based forecasting of stem cell lineage fates
Authors: Treiser Matthew D. , Yang Eric H. , Gordonov Simon , Cohen Daniel M. , Androulakis Ioannis P. , Kohn Joachim , Chen Christopher S. , Moghe Prabhas V. 
Published: December 2009

Stem cells that adopt distinct lineages cannot be distinguished based on traditional cell shape. This study reports that higher-order variations in cell shape and cytoskeletal organization that occur within hours of stimulation forecast the lineage commitment fates of human mesenchymal stem cells (hMSCs). The unique approach captures numerous early (24 h), quantitative features of actin fluororeporter shapes, intensities, textures, and spatial distributions (collectively termed morphometric descriptors). The large number of descriptors are reduced into “combinations” through which distinct subpopulations of cells featuring unique combinations are identified. We demonstrate that hMSCs cultured on fibronectin-treated glass substrates under environments permissive to bone lineage induction could be readily discerned within the first 24 h from those cultured in basal- or fat-inductive conditions by such cytoskeletal feature groupings. We extend the utility of this approach to forecast osteogenic stem cell lineage fates across a series of synthetic polymeric materials of diverse physicochemical properties. Within the first 24 h following stem cell seeding, we could successfully “profile” the substrate responsiveness prospectively in terms of the degree of bone versus nonbone predisposition. The morphometric methodology also provided insights into how substrates may modulate the pace of osteogenic lineage specification. Cells on glass substrates deficient in fibronectin showed a similar divergence of lineage fates, but delayed beyond 48 h. In summary, this high-content imaging and single cell modeling approach offers a framework to elucidate and manipulate determinants of stem cell behaviors, as well as to screen stem cell lineage modulating materials and environments.
A structure-based mechanism for benzalacetone synthase from
Rheum palmatum
Authors: Morita Hiroyuki , Shimokawa Yoshihiko , Tanio Michikazu , Kato Ryohei , Noguchi Hiroshi , Sugio Shigetoshi , Kohno Toshiyuki , Abe Ikuro 
Published: December 2009

Benzalacetone synthase (BAS), a plant-specific type III polyketide synthase (PKS), catalyzes a one-step decarboxylative condensation of malonyl-CoA and 4-coumaroyl-CoA to produce the diketide benzalacetone. We solved the crystal structures of both the wild-type and chalcone-producing I207L/L208F mutant of
Rheum palmatum
BAS at 1.8 Å resolution. In addition, we solved the crystal structure of the wild-type enzyme, in which a monoketide coumarate intermediate is covalently bound to the catalytic cysteine residue, at 1.6 Å resolution. This is the first direct evidence that type III PKS utilizes the cysteine as the nucleophile and as the attachment site for the polyketide intermediate. The crystal structures revealed that BAS utilizes an alternative, novel active-site pocket for locking the aromatic moiety of the coumarate, instead of the chalcone synthase’s coumaroyl-binding pocket, which is lost in the active-site of the wild-type enzyme and restored in the I207L/L208F mutant. Furthermore, the crystal structures indicated the presence of a putative nucleophilic water molecule which forms hydrogen bond networks with the Cys-His-Asn catalytic triad. This suggested that BAS employs novel catalytic machinery for the thioester bond cleavage of the enzyme-bound diketide intermediate and the final decarboxylation reaction to produce benzalacetone. These findings provided a structural basis for the functional diversity of the type III PKS enzymes.
webMGR: an online tool for the multiple genome rearrangement problem
Authors: Lin Chi Ho , Zhao Hao , Lowcay Sean Harry , Shahab Atif , Bourque Guillaume 
Published: December 2009

Abstract
Summary: The algorithm MGR enables the reconstruction of rearrangement phylogenies based on gene or synteny block order in multiple genomes. Although MGR has been successfully applied to study the evolution of different sets of species, its utilization has been hampered by the prohibitive running time for some applications. In the current work, we have designed new heuristics that significantly speed up the tool without compromising its accuracy. Moreover, we have developed a web server (webMGR) that includes elaborate web output to facilitate navigation through the results.
Availability: webMGR can be accessed via http://www.gis.a-star.edu.sg/~bourque. The source code of the improved standalone version of MGR is also freely available from the web site.
Contact: bourque@gis.a-star.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
Copy number variant detection in inbred strains from short read sequence data
Authors: Simpson Jared T. , McIntyre Rebecca E. , Adams David J. , Durbin Richard 
Published: December 2009

Abstract
Summary: We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms, to determine genomic copy number. We tested our algorithm on short read sequence data generated from re-sequencing chromosome 17 of the mouse strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the performance of our algorithm through comparison to CNVs previously identified by array-comparative genomic hybridization (array CGH). We performed quantitative-PCR validation on a subset of the calls that differed from the array CGH data sets.
Availability: The software described in this manuscript, named cnD for copy number detector, is free and released under the GPL. The program is implemented in the D programming language using the Tango library. Source code and pre-compiled binaries are available at http://www.sanger.ac.uk/resources/software/cnd.html
Contact: rd@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters
Authors: Benedito Vagner A. , Li Haiquan , Dai Xinbin , Wandrey Maren , He Ji , Kaundal Rakesh , Torres-Jerez Ivone , Gomez S. Karen , Harrison Maria J. , Tang Yuhong , Zhao Patrick X. , Udvardi Michael K. 
Published: December 2009

Abstract
Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters.
The Involvement of Lipid Peroxide-Derived Aldehydes in Aluminum Toxicity of Tobacco Roots
Authors: Yin Lina , Mano Jun'ichi , Wang Shiwen , Tsuji Wataru , Tanaka Kiyoshi 
Published: December 2009

Abstract
Oxidative injury of the root elongation zone is a primary event in aluminum (Al) toxicity in plants, but the injuring species remain unidentified. We verified the hypothesis that lipid peroxide-derived aldehydes, especially highly electrophilic α,β-unsaturated aldehydes (2-alkenals), participate in Al toxicity. Transgenic tobacco (Nicotiana tabacum) overexpressing Arabidopsis (Arabidopsis thaliana) 2-alkenal reductase (AER-OE plants), wild-type SR1, and an empty vector-transformed control line (SR-Vec) were exposed to AlCl3 on their roots. Compared with the two controls, AER-OE plants suffered less retardation of root elongation under AlCl3 treatment and showed more rapid regrowth of roots upon Al removal. Under AlCl3 treatment, the roots of AER-OE plants accumulated Al and H2O2 to the same levels as did the sensitive controls, while they accumulated lower levels of aldehydes and suffered less cell death than SR1 and SR-Vec roots. In SR1 roots, AlCl3 treatment markedly increased the contents of the highly reactive 2-alkenals acrolein, 4-hydroxy-(E)-2-hexenal, and 4-hydroxy-(E)-2-nonenal and other aldehydes such as malondialdehyde and formaldehyde. In AER-OE roots, accumulation of these aldehydes was significantly less. Growth of the roots exposed to 4-hydroxy-(E)-2-nonenal and (E)-2-hexenal were retarded more in SR1 than in AER-OE plants. Thus, the lipid peroxide-derived aldehydes, formed downstream of reactive oxygen species, injured root cells directly. Their suppression by AER provides a new defense mechanism against Al toxicity.
Time pressure, task complexity, and audit effectiveness
Authors: Bowrin Anthony R. , King James 
Published: December 2009

PurposeThe purpose of this paper is to examine the relationships among time pressure (TP), task complexity (TC), and audit effectiveness (AE). It is motivated by the conflicting results reported in prior TP studies.Design/methodology/approachThe research hypotheses are developed using McGrath's interactional model of the Yerkes‐Dodson Law. Data are collected using a two‐treatment field experiment involving 63 public accountants.FindingsThe results show a negative, interactional relationship among TP, TC, and AE.Research limitations/implicationsThe first limitation concerns the non‐random procedure used to recruit public accounting firms and auditors. Second, there is the less than perfect operationalization of the TC construct.Practical implicationsFirst, the findings suggest that public accounting firms may need to resist the urge to reduce the time allowed for performing compliance tests, and provide training to improve the detection rate for all type of compliance deviations. Second, the fact that the rate of change in AE, in response to changes in TP, is different for the two audit tasks studied, suggests that it may not be appropriate for audit planners to assume a uniform TP effect across the various tasks involved in an audit. This insight has implication for the trade‐offs between the lower direct audit costs associated with tighter time budgets, and possible increases in audit risk associated with lower AE.Originality/valueTwo unique aspects of this paper are the operationalization of TP as a continuous random variable and the use of z‐scores to standardize the AE measure.
Risks in the labor market and social insurance preferences: Germany and the USA
Authors: Duman Anil 
Published: December 2009

PurposeThe purpose of this paper is to attempt to look at the link between labor market risks and social insurance demands by taking occupational unemployment rates, and specificity of skills into account.Design/methodology/approachOccupational unemployment rate is treated as an estimate of labor market risk in addition to human capital investment. Then, the variations in Germany and the USA – with diverse labor markets and a considerable difference in terms of social insurance support – are examined.FindingsThe results suggest that occupational unemployment rate is explanatory for the demands for social insurance along with income.Practical implicationsConclusions reached in the paper aim to contribute to the understanding of the political support for social insurance and hence provide tools for the design of such insurance mechanisms.Originality/valueContrary to the widespread association between the type of human capital and social insurance preferences in the literature, the paper argues that the cross‐country variations can be explained by occupational unemployment rates.
Synthesis and characterisation of low‐cost cardanol polyurethanes
Authors: Athawale Vilas , Shetty Narendra 
Published: December 2009

PurposeThe purpose of this paper is to develop a flexible, as well as a rigid, polyurethane (PU) product using polyols derived from renewable resource for suitable application.Design/methodology/approachCardanol is converted into corresponding glycidyl ether by reacting it with epichlorohydrin. The resulting glycidyl ether is hydrolysed to the corresponding diol in the presence of a heteropolyacid, which acted as a catalyst. The diol obtained is used for synthesising PU's by reacting it with various mole ratios of toluene diisocyanate (TDI) and isophorone diisocyanate (IPDI) and their physicomechanical, chemical and morphological properties are studied.FindingsThe polyol selected for the present paper has unique structural characteristics such as C15 chain length, which contributes to flexibility, and an aromatic ring, which imparts rigidity in the final application of resulting PU. By choosing optimum ratio of NCO/OH, it is possible to obtain a system, which can be used for the development of a flexible as well as a rigid polymer for suitable application.Research limitations/implicationsThe cardanol and dodecatungstosilic acid used are of a particular grade and of a particular manufacturer. Furthermore, it could be obtained from different sources and of different grades. The spectral studies done are purely qualitative. Gloss is tested for the samples at 600, whereas other angles can also be used.Practical implicationsThe method developed provided a simple and practical solution to improve performance characteristics of PU resins, which also proves to be cost effective.Originality/valueThe PU product developed due to its enhanced coating properties can be used in various surface‐coating applications.