bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isomerization of Vaccenic Acid to cis and trans C18:1 Isomers During Biohydrogenation by Rumen Microbes
Authors: Laverroux S. , Glasser F. , Gillet M. , Joly C. , Doreau M. 
Published: June 2011

AbstractIn ruminants, cis and trans C18:1 isomers are intermediates of fatty acid transformations in the rumen and their relative amounts shape the nutritional quality of ruminant products. However, their exact synthetic pathways are unclear and their proportions change with the forage:concentrate ratio in ruminant diets. This study traced the metabolism of vaccenic acid, the main trans C18:1 isomer found in the rumen, through the incubation of labeled vaccenic acid with mixed ruminal microbes adapted to different diets. [1‐13C]trans‐11 C18:1 was added to in vitro cultures with ruminal fluids of sheep fed either a forage or a concentrate diet. 13C enrichment in fatty acids was analyzed by gas‐chromatography‐mass spectrometry after 0, 5 and 24 h of incubation. 13C enrichment was found in stearic acid and in all cis and trans C18:1 isomers. Amounts of 13C found in fatty acids showed that 95% of vaccenic acid was saturated to stearic acid after 5 h of incubation with the concentrate diet, against 78% with the forage diet. We conclude that most vaccenic acid is saturated to stearic acid, but some is isomerized to all cis and trans C18:1 isomers, with probably more isomerization in sheep fed a forage diet.
Are emotion regulation skills related to adjustment among people with chronic pain, independent of pain coping?
Authors: Agar‐Wilson M. , Jackson T. 
Published: June 2011

AbstractAlthough emotion regulation capacities have been linked to adjustment among people with chronic pain, researchers have yet to determine whether these capacities are related to functioning independent of established facets of pain coping. The present study was designed to address this gap. A sample 128 Australian adults with chronic pain (44 men, 84 women) completed self‐report measures of adjustment (quality of life, negative affect, and pain‐related disability), pain coping, and features of emotion regulation (emotion appraisal, perceived efficacy in emotion regulation, emotion utilization). Hierarchical multiple regression analyses indicated that efficacy in emotion regulation was related to quality of life and reduced negative affect even after statistically controlling for effects of other measures of adjustment, pain coping efficacy, and pain coping. Conversely, features of emotion regulation did not improve the prediction model for pain‐related disability. Findings suggest emotion regulation capacities may have a unique role in the prediction of specific facets of adjustment among people with chronic pain.
A protective genetic variant for adverse environments? The role of childhood traumas and serotonin transporter gene on resilience and depressive severity in a high-risk population
Authors: Carli V. , Mandelli L. , Zaninotto L. , Roy A. , Recchia L. , Stoppia L. , Gatta V. , Sarchiapone M. , Serretti A. 
Published: June 2011

AbstractGenetic aspects may influence the effect of early adverse events on psychological well being in adulthood. In particular, a common polymorphism within the serotonin transporter gene (5-HTTLPRshort/long) has been associated to the risk for stress-induced psychopathology. In the present study we investigated the role of childhood traumas and 5-HTTLPR on measures of psychological resilience and depression in a sample of individuals at a high risk for psychological distress (763 male prisoners). The 5-HTTLPR genotype did not influence resilience and depressive severity. However, a significant interaction was observed between 5-HTTLPR and childhood traumas on both resilience and depressive severity. In particular, among subjects exposed to severe childhood trauma only, the long-allele was associated to lower resilience scores and increased current depressive severity as compared to short/short homozygous. Sex specific effects, difference in type and duration of stressors and the specific composition of the sample may explain discrepancy with many studies reporting the short-allele as a vulnerability factor for reactivity to stress. We here speculated that in males the long-allele may confer lower resilience and therefore higher vulnerability for depressive symptoms in subjects exposed to early stress and currently living in stressful environments.
Bacterial vaginosis as a risk factor for high‐grade cervical lesions and cancer in HIV‐seropositive women
Authors: Denslow Sheri A. , Westreich Daniel J. , Firnhaber Cynthia , Michelow Pam , Williams Sophie , Smith Jennifer S. 
Published: June 2011

AbstractObjectiveTo assess the effect of bacterial vaginosis (BV) on the risk of high‐grade squamous intraepithelial lesions (HSIL) among HIV‐seropositive women.MethodsA hospital‐based prospective cohort study of HIV‐seropositive women was conducted in Johannesburg, South Africa from January 2005 to September 2009. Multivariate log‐binomial and Poisson regressions were used to estimate prevalence and rate ratios, respectively.ResultsAmong 1954 HIV‐seropositive women, the baseline prevalence of HSIL was 17%. BV prevalence was high (54%) and showed no association with prevalence of HSIL (adjusted prevalence ratio, 1.12; 95% confidence intervals (CI), 0.92–1.35) nor with cervical lesion progression at follow‐up visit (n = 503) (adjusted rate ratio: 1.00; 95% CI, 0.65–1.53).ConclusionAmong HIV‐seropositive women, BV was not associated with an increased risk of HSIL or cervical lesion progression.
Anabolic/Catabolic Balance in Pathogenesis of Osteoarthritis: Identifying Molecular Targets
Authors: Mueller Michael B. , Tuan Rocky S. 
Published: June 2011

AbstractOsteoarthritis is the most common degenerative musculoskeletal disease. In healthy cartilage, a low turnover of extracellular matrix molecules occurs. Proper balance of anabolic and catabolic activities is thus crucial for the maintenance of cartilage tissue integrity and for the repair of molecular damages sustained during daily usage. In persons with degenerative diseases such as osteoarthritis, this balance of anabolic and catabolic activities is compromised, and the extent of tissue degradation predominates over the capacity of tissue repair. This mismatch eventually results in cartilage loss in persons with osteoarthritis. Tissue homeostasis is controlled by coordinated actions and crosstalk among a number of proanabolic and antianabolic and procatabolic and anticatabolic factors. In osteoarthritis, an elevation of antianabolic and catabolic factors occurs. Interestingly, anabolic activity is also increased, but this response fails to repair the tissue because of both quantitative and qualitative insufficiency. This review presents an overview of the anabolic and catabolic activities involved in cartilage degeneration and the interplay among different signaling and metabolic factors. Understanding the basic molecular mechanisms responsible for tissue degeneration is critical to identifying and developing means to efficiently block or reverse the pathobiological symptoms of osteoarthritis.
A resonance method for measuring permeability
Authors: Dorovsky V.N. , Romensky E.I. , Fedorov A.I. , Perepechko Yu.V. 
Published: June 2011

Abstract
A physically simple method is suggested to measure the permeability of porous reservoirs on the basis of resonance radial oscillations of borehole fluid. The interfacial velocity difference between the porous solid and the fluid is highly sensitive to the permeability of the formation outside the borehole at the resonance frequency. Thus, the permeability can be inferred from the instrumentally measured velocity difference. The instrumental measurements have technological limitations due to the finite size of the source. The two-velocity acoustic data from saturated porous media can be processed using the high-performance and high-order accurate WENO/Runge–Kutta 2D finite-difference scheme.
Thirty Years of Multiple Sequence Codes
Authors: Trifonov Edward N. 
Published: June 2011

Abstract
An overview is presented on the status of studies on multiple codes in genetic sequences. Indirectly, the existence of multiple codes is recognized in the form of several rediscoveries of Second Genetic Code that is different each time. A due credit is given to earlier seminal work related to the codes often neglected in literature. The latest developments in the field of chromatin code are discussed, as well as perspectives of single-base resolution studies of nucleosome positioning, including rotational setting of DNA on the surface of the histone octamers.
A comparison between patient self-report and radiation therapists’ ability to identify anxiety and distress in head and neck cancer patients requiring immobilization for radiation therapy
Authors: Oultram S. , Findlay N. , Clover K. , Cross L. , Ponman L. , Adams C. 
Published: June 2011

AbstractPurpose: The purpose of this study is to identify the incidence of anxiety and distress among patients requiring immobilization during radiation therapy to the head and neck region; then to compare this with radiation therapists’ ability to identify anxiety in the same group of patients.Materials and methods: Data from a sample of 70 patients requiring an immobilization mask participated in this study. Patient self-report assessments and radiation therapists’ ratings were recorded at two time points, CT-Simulation and fraction 1 of treatment. Self-reported patient anxiety was assessed with the Brief Symptom Inventory-18. To determine radiation therapists’ ratings of patient anxiety, two rating scales were developed.Results: Patient self-report identified anxiety in 16% and 14% of patients at CT Simulation and fraction 1 of treatment, respectively. Radiation therapists identified anxiety in 24% patients at time point one and in 44% of patients at time point two.Conclusion: There was slight agreement between patient self-reported levels of anxiety and radiation therapists’ ratings of patient anxiety. This study suggests that there is scope for further investigation into the identification and management of anxiety and distress in head and neck cancer patients requiring immobilization.
China, Economic Regionalism, and East Asian Integration
Authors: YUZHU WANG 
Published: June 2011

AbstractAs a rising power, China has become actively involved in regional bilateral/multilateral arrangements in the post-Cold War, especially post-crisis (1997– 98 financial crises) era, and this has attracted much attention from within and outside East Asia. Diverse understandings of China's regional ambition have appeared, especially since the launch of the China-ASEAN free trade agreement (FTA). Aiming at deciphering the ideas behind China's regional thinking, this paper argues that China's perspective on regionalism is a broadened economic regionalism, which is basically economic-centered, because economic performance is vital both to its long-term strategic target and to its internal social stability. This economic regionalism will last for some time because China will be a developing country at least in the mid-term, which means China will have to focus more on its economic performance. In practice, China will engage bilaterally or multilaterally with others through its FTA strategy. Thus, China cannot be a main contributor to East Asian integration as expected, owing to the inward-looking nature of its economic regionalism. Also, the institutional integration of East Asia needs the effort of all the players in the region.
Ideas of Regionalism: The European Case
Authors: MURRAY PHILOMENA B. 
Published: June 2011

AbstractThis article traces the development of major ideas about integration in Europe. It examines the historical development of, and competition between, ideas about the EU, exploring the clash of integration models and ideals. It draws on the visions of European unity that led to the creation and development of the EU. Regional integration in the EU is distinctive and not necessarily ‘exportable’. The article examines governing norms, material interests, power, and security. It demonstrates that the narrative of shared experience and history formed part of a need to both overcome hyper-nationalism and to share sovereignty, while also privileging some memories. EU norms are also enshrined in a distinctive institutionalized structure, based on a co-existence of national and EU interests and a balancing among often competing interests.
Gaia: automated quality assessment of protein structure models
Authors: Kota Pradeep , Ding Feng , Ramachandran Srinivas , Dokholyan Nikolay V. 
Published: June 2011

Abstract
Motivation: Increasing use of structural modeling for understanding structure–function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.
Results: In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement.
Availability and Implementation: We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures.
Contact: dokh@unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
Authors: Wrzodek Clemens , Dräger Andreas , Zell Andreas 
Published: June 2011

Abstract
Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms.
We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those.
Availability: KEGGtranslator is freely available as a Java™ Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application.
Contact: clemens.wrzodek@uni-tuebingen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize
Authors: Eichten Steven R. , Foerster Jillian M. , de Leon Natalia , Kai Ying , Yeh Cheng-Ting , Liu Sanzhen , Jeddeloh Jeffrey A. , Schnable Patrick S. , Kaeppler Shawn M. , Springer Nathan M. 
Published: June 2011

Abstract
Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.
CESA5 Is Required for the Synthesis of Cellulose with a Role in Structuring the Adherent Mucilage of Arabidopsis Seeds
Authors: Sullivan Stuart , Ralet Marie-Christine , Berger Adeline , Diatloff Eugene , Bischoff Volker , Gonneau Martine , Marion-Poll Annie , North Helen M. 
Published: June 2011

Abstract
Imbibed Arabidopsis (Arabidopsis thaliana) seeds are encapsulated by mucilage that is formed of hydrated polysaccharides released from seed coat epidermal cells. The mucilage is structured with water-soluble and adherent layers, with cellulose present uniquely in an inner domain of the latter. Using a reverse-genetic approach to identify the cellulose synthases (CESAs) that produce mucilage cellulose, cesa5 mutants were shown to be required for the correct formation of these layers. Expression of CESA5 in the seed coat was specific to epidermal cells and coincided with the accumulation of mucilage polysaccharides in their apoplast. Analysis of sugar composition showed that although total sugar composition or amounts were unchanged, their partition between layers was different in the mutant, with redistribution from adherent to water-soluble mucilage. The macromolecular characteristics of the water-soluble mucilage were also modified. In accordance with a role for CESA5 in mucilage cellulose synthesis, crystalline cellulose contents were reduced in mutant seeds and birefringent microfibrils were absent from adherent mucilage. Although the mucilage-modified5 mutant showed similar defects to cesa5 in the distribution of sugar components between water-soluble and adherent mucilage, labeling of residual adherent mucilage indicated that cesa5 contained less cellulose and less pectin methyl esterification. Together, the results demonstrate that CESA5 plays a major and essential role in cellulose production in seed mucilage, which is critical for the establishment of mucilage structured in layers and domains.
Severe adverse cutaneous drug eruptions: epidemiological and clinical features
Authors: Zaraa Inès , Jones Meriem , Trojjet Sondes , Cheikh Rouhou Rym , El Euch Dalenda , Mokni Mourad , Ben Osman Amel 
Published: June 2011

AbstractIntroduction  Adverse cutaneous drug reactions (ACDR) are common, and some can be lethal. The aim of our study was to discuss the epidemiological and clinical features of severe ACDR.Materials and methods  We retrospectively analyzed 100 cases of ACDR from 1981 to 2007, collected in the Department of Dermatology of the La Rabta Hospital in Tunis, which is located in the north of Tunisia. Severity was defined on three criteria: hospitalization; visceral involvement; and severity markers.Results  Characteristics of the 54 included cases were: women (70%); mean age: 44.8 years; responsible drugs: anticonvulsants (28%), antibiotics (28%), and nonsteroidal anti‐inflammatory drugs (15%). The most common dermatoses were maculopapular rash (50%). We observed fever (76%), lymphadenopathy (31.5%), eosinophilia (35%), and visceral involvement (50%). Twelve patients died directly related to the ACDR.Conclusion  This study underlines the polymorphous clinical presentation of ACDR and the importance of researching some severity markers, which have important practical implications.
Stress and quality of life in psoriasis: an update
Authors: Basavaraj Kabbur H. , Navya Mysore Ashok , Rashmi Ramesh 
Published: June 2011

AbstractPsoriasis is a chronic, relapsing, cutaneous condition with 1–2% prevalence in the general population. There are many factors involved in the induction and/or exacerbation of psoriasis of which stress is a well‐known trigger factor in the appearance or exacerbation of psoriasis. Stress reaction in patients with psoriasis is probably mediated by the hypothalamic–pituitary–adrenal relationship with immunologic effects. Stress response involves increased levels of neuroendocrine hormones and autonomic neurotransmitters. Psychological stress or an abnormal response to stressors has been found to modify the evolution of skin disorders such as psoriasis. It can also have substantial psychological, and psychosocial impact on a patient’s quality of life. Treatment regimens include stress‐reduction strategies, such as biofeedback, meditation, yoga, and self‐help approaches. This review focuses the relationship between psoriasis and stress, especially relating to psychosocial, psychological, and emotional stress aspects.
Serum markers for necroinflammatory activity in patients with chronic viral hepatitis and normal or mildly elevated aminotransferase levels
Authors: Cheong Jae Y. , Kim Dong J. , Hwang Seong G. , Yang Jin M. , Kim Young B. , Park Young N. , Cho Sung W. 
Published: June 2011

Abstract
Background: Reports on the usefulness of serum markers for predicting liver necroinflammation are limited. The aim of this study was to determine the serum markers that predict significant inflammation in patients with chronic hepatitis B (CHB) and C (CHC) and normal or mildly elevated serum aminotransferase levels.
Methods: Two hundred twenty‐seven patients with CHB or CHC with normal or mildly elevated serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels (≤60 IU/L) were enrolled in this study. Significant inflammation was defined as inflammatory grade ≥3 activities using the Batt–Ludwig scoring system. The correlation between liver histology and serum markers of liver inflammation was analysed.
Results: Forty‐eight (21.1%) and eight patients (3.5%) had grade 3 and 4 inflammation respectively. Univariate analysis revealed that age, platelet coun, and AST, ALT, γ‐glutamyl transpeptidase, alkaline phosphatase, hyaluronic acid, haptoglobin, apolipoprotein A1 and procollagen III N‐terminal peptide levels were significantly different between the patients with and without significant inflammation. There were no significant differences in the cytokeratin‐18 fragment levels between the two groups. On the basis of multivariate analysis, the AST and apolipoprotein A1 levels and stage of fibrosis were highly predictive of significant inflammation. Using AST and apolipoprotein cut‐off values ≥44 IU/L and ≤100 ng/ml, respectively, the presence of significant inflammation was predicted with high specificity (96.5%) and with a negative predictive value of 76.3%.
Conclusion: The AST and apolipoprotein A1 levels were shown to be independent predictors of significant inflammatory activities in patients with CHB and CHC and normal or mildly elevated aminotransferase levels.