bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Evolution Ontology
Authors: Goldstein Adam 
Published: August 2009

AbstractExisting ontologies model components of evolution, but none synthesize them or describe the framework of ideas used to conceptualize evolution. The Evolution Ontology (EO) aims to do just this. EO models processes (e.g. natural selection); contexts (e.g. habitats); the entities that undergo evolution; and the theories, methods, and disciplines of evolutionary science. Uses include data curation, data mining, and literature curation, EO’s developers working on the latter two for works of Darwin and the Biodiversity Heritage Library.
Developing a Mammalian Behaviour Ontology
Authors: Beck Tim , Hancock John , Mallon Ann-Marie 
Published: August 2009

AbstractThe use of the Entity + Quality (EQ) model in phenotypic descriptions is dependent on the use of specialised domain ontologies to define the entity under observation. A domain currently lacking a specialised ontology is mammalian behaviour, and so the Mammalian Behaviour Ontology is being constructed to address this. Top-level class distinctions are made between behavioural activities and behavioural functions of individuals, and those between two or more individuals. The ontology is manually developed and encourages contributions from domain experts.
Annotation-based meta-analysis of microarray experiments
Authors: Zheng Jie , Liu Junmin , Manduchi Elisabetta , Stoeckert, Christian 
Published: August 2009

AbstractWe are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments.
Interleukin‐1 β increases gap junctional communication among synovial fibroblasts via the extracellular‐signal‐regulated kinase pathway
Authors: Niger Corinne , Howell Floyd D. , Stains Joseph P. 
Published: August 2009

Background information. The gap junction protein, Cx43 (connexin 43), has been implicated in the aetiology of osteoarthritis. Studies have revealed that the size and number of gap junctions increase in synovial biopsies from patients with osteoarthritis. Furthermore, pharmacological inhibition of Cx43 function has been shown to reduce IL‐1β (interleukin‐1β)‐induced metalloproteinase production by synovial fibroblasts in vitro.Results. In the present study, we examined the link between IL‐1β and Cx43 function. We demonstrated that treatment of a rabbit synovial fibroblast cell line with IL‐1β markedly increased the level of the Cx43 protein in a concentration‐ and time‐dependent manner. The impact on Cx43 protein levels appeared to occur post‐transcriptionally, as mRNA levels are unaffected by IL‐1β administration. Additionally, we showed by fluorescence microscopy that IL‐1β alters the cellular distribution of Cx43 to cell–cell junctions and is concomitant with a striking increase in gap junction communication. Furthermore, we demonstrated that the increase in Cx43 protein, and the associated change in protein localization and gap junction communication following IL‐1β treatment, are dependent upon activation of the ERK (extracellular‐signal‐regulated kinase) signalling cascade.Conclusion. These data show that IL‐1β acts through the ERK signalling cascade to alter the expression and function of Cx43 in synovial fibroblasts.
La lecture des mots translinguistiques en français L3
Authors: Nilsson Anna 
Published: August 2009

Université, university, universitet, la lecture, a lecture « conférence », lektyr « lecture de détente », fromage de chèvre, citronfromage « mousse au citron »… Voici quelques mots qui paraissent translinguistiques aux yeux du lecteur trilingue suédois (L1), anglais (L2), français (L3). Le lecteur construit le sens à l’aide du contexte et de différentes connaissances linguistiques et encyclopédiques. Comprendre un texte ne va pas toujours de soi en langue première et le lecteur est souvent confronté à des mots ambigus comme les homographes. Selon l’hypothèse d’un accès lexical non sélectif, la lecture entraîne l’activation de plusieurs mots candidats, dans une, deux ou plusieurs langues selon les compétences du lecteur. Lire et comprendre dans une langue étrangère se présente alors comme un véritable tour de force.  	Nous chercherons à déterminer dans quelle mesure des facteurs comme le milieu d’apprentissage ou la langue des consignes des tâches, sont décisifs pour l’activation des mots translinguistiques chez les lecteurs pour lesquels le français est une langue étrangère en cours d’acquisition (L3). Le traitement des similitudes interlexicales constitue une pratique récurrente qui est plus ou moins contrôlée par les lecteurs, apprenants du français L3.
Immunization Programs for Infants, Children, Adolescents, and Adults: Clinical Practice Guidelines by the Infectious Diseases Society of America
Authors: Pickering Larry K. , Baker Carol J. , Freed Gary L. , Gall Stanley A. , Grogg Stanley E. , Poland Gregory A. , Rodewald Lance E. , Schaffner William , Stinchfield Patricia , Tan Litjen , Zimmerman Richard K. , Orenstein Walter A. 
Published: August 2009

AbstractEvidence-based guidelines for immunization of infants, children, adolescents, and adults have been prepared by an Expert Panel of the Infectious Diseases Society of America (IDSA). These updated guidelines replace the previous immunization guidelines published in 2002. These guidelines are prepared for health care professionals who care for either immunocompetent or immunocompromised people of all ages. Since 2002, the capacity to prevent more infectious diseases has increased markedly for several reasons: new vaccines have been licensed (human papillomavirus vaccine; live, attenuated influenza vaccine; meningococcal conjugate vaccine; rotavirus vaccine; tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis [Tdap] vaccine; and zoster vaccine), new combination vaccines have become available (measles, mumps, rubella and varicella vaccine; tetanus, diphtheria, and pertussis and inactivated polio vaccine; and tetanus, diphtheria, and pertussis and inactivated polio/Haemophilus influenzae type b vaccine), hepatitis A vaccines are now recommended universally for young children, influenza vaccines are recommended annually for all children aged 6 months through 18 years and for adults aged ⩾50 years, and a second dose of varicella vaccine has been added to the routine childhood and adolescent immunization schedule. Many of these changes have resulted in expansion of the adolescent and adult immunization schedules. In addition, increased emphasis has been placed on removing barriers to immunization, eliminating racial/ethnic disparities, addressing vaccine safety issues, financing recommended vaccines, and immunizing specific groups, including health care providers, immunocompromised people, pregnant women, international travelers, and internationally adopted children. This document includes 46 standards that, if followed, should lead to optimal disease prevention through vaccination in multiple population groups while maintaining high levels of safety.
Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model
Authors: Zhang Chen , Wu Chunguo , Blanzieri Enrico , Zhou You , Wang Yan , Du Wei , Liang Yanchun 
Published: August 2009

Abstract
Motivation: Mislabeled samples often appear in gene expression profile because of the similarity of different sub-type of disease and the subjective misdiagnosis. The mislabeled samples deteriorate supervised learning procedures. The LOOE-sensitivity algorithm is an approach for mislabeled sample detection for microarray based on data perturbation. However, the failure of measuring the perturbing effect makes the LOOE-sensitivity algorithm a poor performance. The purpose of this article is to design a novel detection method for mislabeled samples of microarray, which could take advantage of the measuring effect of data perturbations.
Results: To measure the effect of data perturbation, we define an index named perturbing influence value (PIV), based on the support vector machine (SVM) regression model. The Column Algorithm (CAPIV), Row Algorithm (RAPIV) and progressive Row Algorithm (PRAPIV) based on the PIV value are proposed to detect the mislabeled samples. Experimental results obtained by using six artificial datasets and five microarray datasets demonstrate that all proposed methods in this article are superior to LOOE-sensitivity. Moreover, compared with the simple SVM and CL-stability, the PRAPIV algorithm shows an increase in precision and high recall.
Availability: The program and source code (in JAVA) are publicly available at http://ccst.jlu.edu.cn/CSBG/PIVS/index.htm
Contact: blanzier@dit.unitn.it; ycliang@jlu.edu.cn
Depletion-corrected average catch: a simple formula for estimating sustainable yields in data-poor situations
Authors: MacCall Alec D. 
Published: August 2009

Abstract
MacCall, A. D. 2009. Depletion-corrected average catch: a simple formula for estimating sustainable yields in data-poor situations. – ICES Journal of Marine Science, 66: 2267–2271. The depletion-corrected average catch (DCAC) formula is an extension of the potential-yield formula, and it provides useful estimates of sustainable yield for data-poor fisheries on long-lived species. Over an extended period (e.g. a decade or more), the catch is divided into a sustainable yield component and an unsustainable “windfall” component associated with a one-time reduction in stock biomass. The size of the windfall is expressed as being equivalent to a number of years of sustainable production, in the form of a “windfall ratio”. The DCAC is calculated as the sum of catches divided by the sum of the number of years in the catch series and this windfall ratio. Input information includes the sum of catches and associated number of years, the relative reduction in biomass during that period, the natural mortality rate (M, which should be <0.2 year−1), and the assumed ratio of FMSY to M. These input values are expected to be approximate, and based on the estimates of their imprecision, the uncertainty can be integrated by Monte Carlo exploration of DCAC values.
Modulation of the Poly(ADP-ribosyl)ation Reaction via the Arabidopsis ADP-Ribose/NADH Pyrophosphohydrolase, AtNUDX7, Is Involved in the Response to Oxidative Stress
Authors: Ishikawa Kazuya , Ogawa Takahisa , Hirosue Eisuke , Nakayama Yasumune , Harada Kazuo , Fukusaki Eiichiro , Yoshimura Kazuya , Shigeoka Shigeru 
Published: August 2009

AbstractHere, we assessed modulation of the poly(ADP-ribosyl)ation (PAR) reaction by an Arabidopsis (Arabidopsis thaliana) ADP-ribose (Rib)/NADH pyrophosphohydrolase, AtNUDX7 (for Arabidopsis Nudix hydrolase 7), in AtNUDX7-overexpressed (Pro35S:AtNUDX7) or AtNUDX7-disrupted (KO-nudx7) plants under normal conditions and oxidative stress caused by paraquat treatment. Levels of NADH and ADP-Rib were decreased in the Pro35S:AtNUDX7 plants but increased in the KO-nudx7 plants under normal conditions and oxidative stress compared with the control plants, indicating that AtNUDX7 hydrolyzes both ADP-Rib and NADH as physiological substrates. The Pro35S:AtNUDX7 and KO-nudx7 plants showed increased and decreased tolerance, respectively, to oxidative stress compared with the control plants. Levels of poly(ADP-Rib) in the Pro35S:AtNUDX7 and KO-nudx7 plants were markedly higher and lower, respectively, than those in the control plants. Depletion of NAD+ and ATP resulting from the activation of the PAR reaction under oxidative stress was completely suppressed in the Pro35S:AtNUDX7 plants. Accumulation of NAD+ and ATP was observed in the KO-nudx7- and 3-aminobenzamide-treated plants, in which the PAR reaction was suppressed. The expression levels of DNA repair factors, AtXRCC1 and AtXRCC2 (for x-ray repair cross-complementing factors 1 and 2), paralleled that of AtNUDX7 under both normal conditions and oxidative stress, although an inverse correlation was observed between the levels of AtXRCC3, AtRAD51 (for Escherichia coli RecA homolog), AtDMC1 (for disrupted meiotic cDNA), and AtMND1 (for meiotic nuclear divisions) and AtNUDX7. These findings suggest that AtNUDX7 controls the balance between NADH and NAD+ by NADH turnover under normal conditions. Under oxidative stress, AtNUDX7 serves to maintain NAD+ levels by supplying ATP via nucleotide recycling from free ADP-Rib molecules and thus regulates the defense mechanisms against oxidative DNA damage via modulation of the PAR reaction.
A Bayesian model for estimating the effects of drug use when drug use may be under‐reported
Authors: McMillan Garnett P. , Bedrick Edward , C'deBaca Janet 
Published: August 2009

ABSTRACTAims  We present a statistical model for evaluating the effects of substance use when substance use might be under‐reported. The model is a special case of the Bayesian formulation of the ‘classical’ measurement error model, requiring that the analyst quantify prior beliefs about rates of under‐reporting and the true prevalence of substance use in the study population.Design  Prospective study.Setting  A diversion program for youths on probation for drug‐related crimes.Participants  A total of 257 youths at risk for re‐incarceration.Measurements  The effects of true cocaine use on recidivism risks while accounting for possible under‐reporting.Findings  The proposed model showed a 60% lower mean time to re‐incarceration among actual cocaine users. This effect size is about 75% larger than that estimated in the analysis that relies only on self‐reported cocaine use. Sensitivity analysis comparing different prior beliefs about prevalence of cocaine use and rates of under‐reporting universally indicate larger effects than the analysis that assumes that everyone tells the truth about their drug use.Conclusion  The proposed Bayesian model allows one to estimate the effect of actual drug use on study outcome measures.
Startle cue–reactivity differentiates between light and heavy smokers
Authors: Rehme Anne K. , Frommann Ingo , Peters Sandra , Block Verena , Bludau Julia , Quednow Boris B. , Maier Wolfgang , Schütz Christian , Wagner Michael 
Published: August 2009

ABSTRACTAims  It was assumed that the startle amplitude in smokers is reduced while viewing pictures of smoking, suggesting that smoking cues are appetitive. The goal of the present study was to investigate (i) whether smoking scenes induce appetitive cue effects in smokers, and (ii) whether smoking intensity is related to cue–reactivity.Design  Smokers and non‐smokers participated in a single session.Participants  A total of 62 individuals participated: 36 smokers and 26 non‐smokers.Measurements  Participants took part in an acoustic affective startle experiment using standardized pleasant, neutral and unpleasant scenes from the International Affective Picture System (IAPS), as well as pictures of smoking. The effect of smoking cues was assessed by comparing neutral and smoking scenes (termed cue‐related startle suppression, CSS).Findings  While there was no overall difference between smokers and non‐smokers regarding the CSS, light smokers showed significantly increased cue–reactivity towards smoking‐related cues, as compared with heavy smokers and non‐smokers. In addition, light smokers also displayed stronger appetitive responses towards positive stimuli.Conclusions  These data support recent theories which discriminate between habit‐based and incentive‐based drug abuse. This distinction may have consequences for the assessment and treatment of drug‐addicted subjects. Furthermore, incentive‐based light smoking seems to have general effects on the reward system.
First positive reactions to cannabis constitute a priority risk factor for cannabis dependence
Authors: Le Strat Yann , Ramoz Nicolas , Horwood John , Falissard Bruno , Hassler Christine , Romo Lucia , Choquet Marie , Fergusson David , Gorwood Philip 
Published: August 2009

ABSTRACTAim  To assess the association between first reactions to cannabis and the risk of cannabis dependence.Design  A cross‐sectional population‐based assessment in 2007.Setting  A campus in a French region (Champagne‐Ardennes).Participants  A total of 1472 participants aged 18–21 years who reported at least one life‐time cannabis consumption, of 3056 students who were screened initially [the Susceptibility Addiction Gene Environment (SAGE) study].Measurements  Positive and negative effects of first cannabis consumptions, present cannabis dependence and related risk factors were assessed through questionnaires.Findings  The effects of first cannabis consumptions were associated dose‐dependently with cannabis dependence at age 18–21 years, both according to the transversal approach of the SAGE study and to the prospective cohort of the Christchurch Health and Development Study (CHDS) assessed at the age of 25 years. Participants of the SAGE study who reported five positive effects of their first cannabis consumption had odds of life‐time cannabis dependence that were 28.7 (95% confidence interval: 14.6–56.5) higher than those who reported no positive effects. This association remains significant after controlling for potentially confounding factors, including individual and familial variables.Conclusions  This study suggests an association between positive reactions to first cannabis uses and risk of life‐time cannabis dependence, this variable having a central role among, and through, other risk factors.
Population pharmacokinetic analysis of varenicline in adult smokers
Authors: Ravva Patanjali , Gastonguay Marc R. , Tensfeldt Thomas G. , Faessel Hélène M. 
Published: August 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT? • Several clinical pharmacology studies have characterized the pharmacokinetics of varenicline in young adult and elderly smokers and subjects with impaired renal function.• Varenicline pharmacokinetics is linear over the recommended dose range.• Varenicline total clearance is linearly related to its renal clearance.• Both are progressively reduced as renal function declines, which results in a progressive increase in varenicline systemic exposure and prolonged half‐life. WHAT THIS STUDY ADDS? • This work provides an integrated model‐based analysis of varenicline pharmacokinetics across multiple studies in the target patient population.• The model describes the impact of patient‐specific covariates, such as renal function, and provides a rationale for dose adjustment.• The resulting model also provides a means to predict individual‐specific drug exposures to clinical responses in subsequent analyses.AIMSTo characterize the population pharmacokinetics of varenicline and identify factors leading to its exposure variability in adult smokers.METHODSData were pooled from nine clinical studies consisting of 1878 subjects. Models were developed to describe concentration–time profiles across individuals. Covariates were assessed using a full model approach; parameters and bootstrap 95% confidence intervals (CI) were estimated using nonlinear mixed effects modelling.RESULTSA two‐compartment model with first‐order absorption and elimination best described varenicline pharmacokinetics. The final population parameter estimates (95% CI) were: CL/F, 10.4 l h−1 (10.2, 10.6); V2/F, 337 l (309, 364); V3/F, 78.1 l (61.9, 98.9); Q/F, 2.08 l h−1 (1.39, 3.79); Ka, 1.69 h−1 (1.27, 2.00); and Alag, 0.43 h (0.37, 0.46). Random interindividual variances were estimated for Ka[70% coefficient of variation (CV)], CL/F (25% CV), and V2/F (50% CV) using a block covariance matrix. Fixed effect parameters were precisely estimated [most with % relative standard error < 10 and all with % relative standard error < 25], and a visual predictive check indicated adequate model performance. CL/F decreased from 10.4 l h−1 for a typical subject with normal renal function (CLcr = 100 ml min−1) to 4.4 l h−1 for a typical subject with severe renal impairment (CLcr = 20 ml min−1), which corresponds to a 2.4‐fold increase in daily steady‐state exposure. Bodyweight was the primary predictor of variability in volume of distribution. After accounting for renal function, there was no apparent effect of age, gender or race on varenicline pharmacokinetics.CONCLUSIONSRenal function is the clinically important factor leading to interindividual variability in varenicline exposure. A dose reduction to 1 mg day−1, which is half the recommended dose, is indicated for subjects with severe renal impairment.
Reduced incidence and severity of experimental autoimmune arthritis in mice expressing catalytically inactive A disintegrin and metalloproteinase 8 (ADAM8)
Authors: Zack M D , Melton M A , Stock J L , Storer C E , Barve R A , Minnerly J C , Weiss D J , Stejskal J A , Tortorella M D , Turk J R , Shevlin K M , Malfait A-M 
Published: August 2009

SummaryA disintegrin and metalloproteinase 8 (ADAM8), a catalytically active member of the ADAMs family of enzymes, is expressed primarily on immune cells and thus probably involved in inflammatory responses. ADAM8 is also produced by chondrocytes, and recombinant ADAM8 can induce cartilage catabolism. We therefore decided to test the role of ADAM8 in autoimmune inflammatory arthritis using transgenic mice expressing catalytically inactive ADAM8. Transgenic DBA/1J mice expressing an inactivating point mutation in the ADAM8 gene to change Glu330 to Gln330 (ADAM8EQ) were generated to evaluate the proteolytic function of ADAM8 in an lipopolysaccharide-synchronized collagen-induced arthritis (LPS-CIA) model of autoimmune arthritis. The systemic inflammatory reaction to LPS was also evaluated in these mice. Expression profiling of paw joints from wild-type mice revealed that ADAM8 mRNA levels increased at the onset of clinical arthritis and correlated well with cellular macrophage markers. When subjected to LPS-CIA, ADAM8EQ mice demonstrated decreased incidence and severity of clinical arthritis compared to wild-type mice. Histological examination of paw joints from ADAM8EQ mice confirmed marked attenuation of synovial inflammation, cartilage degradation and bone resorption when compared to wild-type mice. However, transgenic mice and wild-type mice responded similarly to LPS-induced systemic inflammation with regard to mortality, organ weights, neutrophil sequestration and serum cytokine/chemokine production. We conclude that ADAM8 proteolytic activity plays a key role in the development of experimental arthritis and may thus be an attractive target for the treatment of arthritic disorders while minimizing risk of immunocompromise.