bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genetic programming-based approach to the classification of multiclass microarray datasets
Authors: Liu Kun-Hong , Xu Chun-Gui 
Published: December 2008

Abstract
Motivation: Feature selection approaches have been widely applied to deal with the small sample size problem in the analysis of micro-array datasets. For the multiclass problem, the proposed methods are based on the idea of selecting a gene subset to distinguish all classes. However, it will be more effective to solve a multiclass problem by splitting it into a set of two-class problems and solving each problem with a respective classification system.
Results: We propose a genetic programming (GP)-based approach to analyze multiclass microarray datasets. Unlike the traditional GP, the individual proposed in this article consists of a set of small-scale ensembles, named as sub-ensemble (denoted by SE). Each SE consists of a set of trees. In application, a multiclass problem is divided into a set of two-class problems, each of which is tackled by a SE first. The SEs tackling the respective two-class problems are combined to construct a GP individual, so each individual can deal with a multiclass problem directly. Effective methods are proposed to solve the problems arising in the fusion of SEs, and a greedy algorithm is designed to keep high diversity in SEs. This GP is tested in five datasets. The results show that the proposed method effectively implements the feature selection and classification tasks.
Contact: lkhqz@163.com; khliu1977@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Histone H2B Deubiquitination Is Required for Transcriptional Activation of FLOWERING LOCUS C and for Proper Control of Flowering in Arabidopsis
Authors: Schmitz Robert Jeffrey , Tamada Yosuke , Doyle Mark Robert , Zhang Xiaoyu , Amasino Richard Mark 
Published: December 2008

Abstract
The spectrum of histone modifications at a given locus is a critical determinant for the correct output of gene expression. In Arabidopsis (Arabidopsis thaliana), many studies have examined the relationship between histone methylation and gene expression, but few studies exist on the relationship between other covalent histone modifications and gene expression. In this work, we describe the role of histone H2B deubiquitination in the activation of gene expression and the consequence of a perturbation of histone H2B deubiquitination in the timing of the floral transition in Arabidopsis. A mutation in a H2B deubiquitinase, UBIQUITIN-SPECIFIC PROTEASE26 (UBP26), results in an early-flowering phenotype. In the ubp26 mutant, mRNA levels of the floral repressor FLOWERING LOCUS C (FLC) and other related family members is decreased. Furthermore, this mutant accumulates H2B monoubiquitination, and has decreased levels of H3K36 trimethylation and increased levels of H3K27 trimethylation at the FLC locus. Thus, UBP26 is required for transcriptional activation of FLC through H2B deubiquitination and is consistent with a model in which deubiquitination is necessary for the accumulation of H3K36 trimethylation and the proper level of transcriptional activation.
Risk, resilience, and natural recovery: a model of recovery from alcohol abuse for Alaska Natives
Authors: Mohatt Gerald V. , Rasmus Stacy M. , Thomas Lisa , Allen James , Hazel Kelly , Marlatt G. Alan 
Published: December 2008

ABSTRACTAim  The People Awakening (PA) study explored an Alaska Native (AN) understanding of the recovery process from alcohol abuse and consequent sobriety.Design  PA utilized a cross‐sectional, qualitative research design and community‐based participatory research methods.Setting and participants  The study included a state‐wide convenience sample of 57 participants representing all five major AN groups: Aleut/Alutiiq, Athabascan, Inupiaq, Yup'ik/Cup'ik and Tlingit/Haida/Tsimshian. Participants were nominated and self‐identified as being alcohol‐abstinent at least five years following a period of problem drinking.Measurements  Open‐ended and semistructured interviews gathered extensive personal life histories. A team of university and community co‐researchers analyzed narratives using grounded theory and consensual data analysis techniques.Findings  A heuristic model of AN recovery derived from our participants' experiences describes recovery as a development process understood through five interrelated sequences: (i) the person entered into a reflective process of continually thinking over the consequences of his/her alcohol abuse; (ii) that led to periods of experimenting with sobriety, typically, but not always, followed by repeated cycling through return to drinking, thinking it over, and experimenting with sobriety; culminating in (iii) a turning point, marked by the final decision to become sober. Subsequently, participants engaged in (iv) Stage 1 sobriety, active coping with craving and urges to drink followed for some participants, but not all, by (v) Stage 2 sobriety, moving beyond coping to what one participant characterized as ‘living life as it was meant to be lived.Conclusions  The PA heuristic model points to important cultural elements in AN conceptualizations of recovery.
Effectiveness of ozone against endodontopathogenic microorganisms in a root canal biofilm model
Authors: Huth K. C. , Quirling M. , Maier S. , Kamereck K. , AlKhayer M. , Paschos E. , Welsch U. , Miethke T. , Brand K. , Hickel R. 
Published: December 2008

AbstractAim  To assess the antimicrobial efficacy of aqueous (1.25–20 μg mL−1) and gaseous ozone (1–53 g m−3) as an alternative antiseptic against endodontic pathogens in suspension and a biofilm model.Methodology  Enterococcus faecalis, Candida albicans, Peptostreptococcus micros and Pseudomonas aeruginosa were grown in planctonic culture or in mono‐species biofilms in root canals for 3 weeks. Cultures were exposed to ozone, sodium hypochlorite (NaOCl; 5.25%, 2.25%), chlorhexidine digluconate (CHX; 2%), hydrogen peroxide (H2O2; 3%) and phosphate buffered saline (control) for 1 min and the remaining colony forming units counted. Ozone gas was applied to the biofilms in two experimental settings, resembling canal areas either difficult (setting 1) or easy (setting 2) to reach. Time‐course experiments up to 10 min were included. To compare the tested samples, data were analysed by one‐way anova.Results  Concentrations of gaseous ozone down to 1 g m−3 almost and aqueous ozone down to 5 μg mL−1 completely eliminated the suspended microorganisms as did NaOCl and CHX. Hydrogen peroxide and lower aqueous ozone concentrations were less effective. Aqueous and gaseous ozone were dose‐ and strain‐dependently effective against the biofilm microorganisms. Total elimination was achieved by high‐concentrated ozone gas (setting 2) and by NaOCl after 1 min or a lower gas concentration (4 g m−3) after at least 2.5 min. High‐concentrated aqueous ozone (20 μg mL−1) and CHX almost completely eliminated the biofilm cells, whilst H2O2 was less effective.Conclusion  High‐concentrated gaseous and aqueous ozone was dose‐, strain‐ and time‐dependently effective against the tested microorganisms in suspension and the biofilm test model.
Benefits of fixed‐dose combination therapy with inhaled corticosteroids and long‐acting bronchodilators as initial maintenance therapy in the management of asthma
Authors: SEALE J. Paul , JENKINS Christine , WOOD‐BAKER Richard , NEVILLE A. Munro 
Published: December 2008

ABSTRACTBackground and objective:  Revised Australian guidelines for asthma management were released by the National Asthma Council (NAC) in 2006. One area where clinical opinion and trial data have changed recently concerns the place of fixed‐dose combination (FDC) therapy with inhaled corticosteroid (ICS) and long‐acting β2‐agonists as initial maintenance therapy.Methods:  A systematic review of the literature commissioned by the NAC and undertaken by the University of Tasmania addressed several questions, including whether there was evidence for the use of FDC therapy as first‐line asthma treatment in steroid‐naïve patients.Results:  Nineteen relevant studies were identified, from which 20 comparisons contributed to the analyses. The definition of steroid‐naïve ranged from no ICS therapy over the preceding 1 month to no ICS therapy ever. FDC therapy was effective in subjects who were steroid‐naïve and was more effective than an equivalent dose of ICS, irrespective of the definition of steroid‐naïvety. Compared with ICS alone, FDC therapy increased mean FEV1 by 140 mL, mean morning PEF by 21 L/min and mean evening PEF by 20 L/min. There was a mean increase of 9.8% in symptom‐free days, associated with a greater reduction in rescue medication use of −0.12 puff/24 h. FDC therapy was not superior to ICS alone for prevention of withdrawals or exacerbations requiring systemic corticosteroids. Adverse events were similar for FDC therapy and ICS, whether ICS were administered at the same or an increased dose.Conclusions:  FDC therapy is effective as first‐line treatment in steroid‐naïve subjects and is superior to ICS alone for most outcomes, irrespective of the period of time since last exposure to ICS.
Impact of Performance Obstacles on Intensive Care Nurses' Workload, Perceived Quality and Safety of Care, and Quality of Working Life
Authors: Gurses Ayse P. , Carayon Pascale , Wall Melanie 
Published: December 2008

Objectives. To study the impact of performance obstacles on intensive care nurses' workload, quality and safety of care, and quality of working life (QWL). Performance obstacles are factors that hinder nurses' capacity to perform their job and that are closely associated with their immediate work system.Data Sources/Study Setting. Data were collected from 265 nurses in 17 intensive care units (ICUs) between February and August 2004 via a structured questionnaire, yielding a response rate of 80 percent.Study Design. A cross‐sectional study design was used. Data were analyzed by correlation analyses and structural equation modeling.Principal Findings. Performance obstacles were found to affect perceived quality and safety of care and QWL of ICU nurses. Workload mediated the impact of performance obstacles with the exception of equipment‐related issues on perceived quality and safety of care as well as QWL.Conclusions. Performance obstacles in ICUs are a major determinant of nursing workload, perceived quality and safety of care, and QWL. In general, performance obstacles increase nursing workload, which in turn negatively affect perceived quality and safety of care and QWL. Redesigning the ICU work system to reduce performance obstacles may improve nurses' work.
Abrupt Termination of an Ethanol Regimen Provokes Ventricular Arrhythmia and Enhances Susceptibility to the Arrhythmogenic Effects of Epinephrine in Rats
Authors: Liu Jinyao , Fujimiya Tatsuya 
Published: December 2008

Background: Pathologists examining victims of sudden unexpected death encounter alcoholics more often than expected; alcohol may play a role in sudden arrhythmic death. Here we determine whether a pattern of alcohol consumption, chronic ethanol intake, and withdrawal increases the incidence of malignant ventricular arrhythmia and modulates susceptibility to the arrhythmogenic potential of sympathetic stimulation from an epinephrine test in rats.Methods: Male Wistar rats were treated with a continuous ethanol liquid diet for 7 weeks, and then subjected to 1‐day withdrawal or 21‐day abstinence. Ventricular ectopy was evaluated by 24‐hour electrocardiographic telemetry recording; whole‐body sympathetic activation, cardiac sympathovagal balance, and susceptibility to ventricular arrhythmia induced by sympathetic stimulation were evaluated based on blood noradrenalin metabolite concentrations, heart rate variability, and a 3‐step epinephrine test.Results: Ventricular arrhythmia and related death were observed only in rats at 1 day of withdrawal, but not in nonalcoholic, continuous ethanol intake or 21‐day abstinence rats. One‐day withdrawal after a 7‐week continuous ethanol regimen elevated circulating noradrenalin metabolite levels and induced cardiac sympathovagal imbalance. Deaths related to the epinephrine test and ventricular arrhythmia induced by low doses of epinephrine were observed only in 1‐day withdrawal rats. However, all anomalies were normalized by 21‐day abstinence.Conclusions: Abrupt termination of a 7‐week continuous ethanol regimen is sufficient to enhance the whole‐body sympathetic activation and cardiac sympathovagal imbalance that contribute to ventricular arrhythmia and sudden death in alcoholic rats. Those providing medical care for alcoholics, including in cases of legal imprisonment, should be aware of the possibility of enhanced susceptibility to sudden arrhythmic death due to the abrupt termination of a chronic ethanol regimen.
A Product‐Level Approach to Historical Material Flow Analysis
Authors: Harper Ermelinda M. 
Published: December 2008

SummaryStudies of material cycles, which have a solid history in biogeochemistry, include characterization of technological materials cycles that quantify the way in which materials move through the economy and environment of a region. One of the most important aspects of historical technological materials cycles is determining how much material goes into various uses over time and modeling its lifetime in each use. A material flow analysis methodology is presented by which a historical (i.e., 1975 to 2000) study of tungsten use in the United States was constructed. The approach utilized in this study is twofold: the traditional approach by which material going into end‐use sectors is approximated (the “end‐use sector model”), and a second approach by which end‐use products are specifically addressed (the “finished product model”). By virtue of the latter method, a detailed historical account of a material's end uses was developed. This study shows that (1) both models present a detailed treatment of trade of finished products over time for a variety of highly disaggregated products, (2) the end‐use sector model provides a method to combine quantitative and qualitative data about products in various sectors to estimate domestic production for a metal about which little is known in terms of its end uses, and (3) the finished product model produces detailed estimates of domestic production for a large number of highly disaggregated products.
The role of CCAAT/enhancer binding protein (C/EBP)‐α in osteogenesis of C3H10T1/2 cells induced by BMP‐2
Authors: Fan Qiming , Tang Tingting , Zhang Xiaoling , Dai Kerong 
Published: December 2008

AbstractThe balance between osteogenesis and adipogenesis of mesenchymal stem cells is disrupted in various human diseases. Investigating the mechanisms that fine‐tune this balance is of medical importance. Identification of potential target gene which can be used to study the relationship between them could be really helpful for this purpose. In the current study, we used C3H10T1/2 as model cells and through which two models of both osteogenesis induced by bone‐morphogenetic protein (BMP)‐2 and transdifferentiation from osteogenesis to adipogenesis were established. We investigated the role of CCAAT/enhancer binding protein (C/EBP)‐α in these two systems. Then from epigenetic point of view, we elucidated the underlying molecular mechanisms preliminarily. The results showed that down‐regulations of both C/EBP‐α expression and its inducibility in response to insulin, fetal bovine serum, methylisobutylxanthine and dexamethasone (IFMD) adipogenic hormonal cocktail were observed in terminal stage of osteogenesis of C3H10T1/2 cells induced by BMP‐2. And overexpression of C/EBP‐α could lead to inhibition of osteogenesis differentiation and rescue attenuation of potential of adipogenic conversion in this process. Furthermore, we provided evidence that remarkable DNA hypermethylation and histones 3 and 4 hypoacetylation in –1286 bp/−1065 bp promoter region of C/EBP‐α were involved in both of down‐regulations. Our data suggest that C/EBP‐α functions as regulator in the balance between osteogenesis and adipogenesis of C3H10T1/2 cells and may be a therapeutic target.
Beyond Westminster governance: Bringing politics and public service into the networked era
Authors: Roy Jeffrey 
Published: December 2008

Abstract: The underlying premise of this article stems from the following question: is our Westminster, parliamentary model of democratic governance and administration adaptable for contemporary realities and emerging challenges? By way of response, the author attempts to expose what is wrong with the current model and sketches what changes to our governing institutions must be envisioned in order to safeguard political legitimacy and administrative competence in a world that is increasingly networked. Central to this discussion is the doctrine of ministerial responsibility and accountability and an appropriate parcelling of roles and authorities to public servants and politicians. Equally important is the rise of the Internet and new forms of political mobilization outside of government, on the one hand, and the potential for more direct mechanisms of public engagement, on the other hand. Without significant innovation and reform, Parliament and the federal government instead face a steady erosion of political and human capital that cannot be reversed until the country is convinced that 1) a new approach to governing is a realistic proposition, and 2) citizens will play an important role in designing this new approach.Sommaire: La prémisse sous‐jacente du présent article découle de la question suivante : est‐ce que notre modèle de Westminster de gouvernance et d'administration démocratique parlementaire peut s'adapter aux réalités contemporaines et aux défis émergents? En guise de réponse, l'article essaie d'exposer ce qui ne ne fonctionne pas dans le modèle actuel et donne un aperçu du genre de changements que nous devons envisager pour nos institutions dirigeantes afin de sauvegarder la légitimité politique et la compétence administrative dans un monde de plus en plus réseauté. Au centre de cette discussion se trouvent la doctrine de la responsabilité et de l'imputabilité ministérielle et une répartition appropriée des rôles et des pouvoirs des fonctionnaires et des responsables politiques. Tout aussi importants sont le rôle accru d'Internet et de nouvelles formes de mobilisation politique en dehors du gouvernement d'une part, et la possibilité de recourir à des mécanismes de participation publique plus directe, d'autre part. Par contre, à défaut d'innovations et de réformes importantes, le Parlement et le gouvernement fédéral font face à une érosion continue du capital politique et humain qui ne peut être inversée tant que le pays ne sera pas convaincu : a) qu'une nouvelle manière de gouverner est une proposition réaliste; et b) que les citoyens joueront un rôle important en concevant cette nouvelle démarche.
Les relations de collaboration entre le secteur public et les organismes communautaires du secteur jeunesse‐enfance‐famille : Entre la sous‐traitance et la coconstruction
Authors: Savard Sébastien , Harvey Benoît , Tremblay Sabrina 
Published: December 2008

Sommaire: L'État incite les établissements publics et les organismes communautaires à développer et à augmenter la fréquence de leurs relations interorganisationnelles. L'État veut ainsi favoriser une intégration des services permettant une meilleure réponse aux besoins sociaux de la population. Cette étude propose une typologie permettant d'analyser les modèles de relation qui se mettent en place entre ces deux groupes d'acteurs. La recherche s'est intéressée aux interfaces dans le secteur des services sociaux à l'enfance, à la jeunesse et aux familles québécoises. Au total, 111 gestionnaires ont répondu à un questionnaire leur permettant d'évaluer leurs rapports en fonction de quatre dimensions proposées par Coston pour situer les relations entre l'État et les organismes du tiers secteur. Le modèle de relation rapporté par les répondants est celui de la coexistence. Quoique le modèle de relation rapporté par les organismes communautaires et par les établissements publics soit le même, une analyse plus nuancée des résultats permet de constater que les organismes communautaires se perçoivent appartenir à un système plus socio‐étatique (dominé par les établissements de réseau) que les répondants des établissements publics.Abstract: The government encourages public institutions and community organizations to develop and increase the frequency of their inter‐organizational relationships. In doing so, the government seeks the integration of their services in order to meet the social needs of the population more effectively. This study aims to develop a typology for analysing patterns in the relationships being established between these two groups of stakeholders. The research focused on the interfaces in the social service sector for children, youth and families in Quebec. In total, 111 managers responded to a survey that enabled them to assess their relationships on the basis of four dimensions proposed by Coston for analysing relationships between the government and third‐sector organizations. The respondents identified “coexistence” as the most common type of relationships. Although the community organizations and the public institutions identified the same type of relationships, a more nuanced analysis of the survey results reveals that community organizations see themselves as part of a system that is more “socio‐governmental” in nature (i.e., dominated by the institutions in the network) rather than “public.”
Inhibition of Lassa and Marburg Virus Production by Tetherin
Authors: Sakuma Toshie , Noda Takeshi , Urata Shuzo , Kawaoka Yoshihiro , Yasuda Jiro 
Published: December 2008

ABSTRACT
Recently, tetherin has been identified as an effective cellular factor that prevents the release of human immunodeficiency virus type 1. Here, we show that the production of virus-like particles induced by viral matrix proteins of Lassa virus or Marburg virus was markedly inhibited by tetherin and that N-linked glycosylation of tetherin was dispensable for this antiviral activity. Our data also suggest that viral matrix proteins or one or more components that originate from host cells are targets of tetherin but that viral surface glycoproteins are not. These results suggest that tetherin inhibits the release of a wide variety of enveloped viruses from host cells by a common mechanism.
Structural Characterization of the Rous Sarcoma Virus RNA Stability Element
Authors: Weil Jason E. , Hadjithomas Michalis , Beemon Karen L. 
Published: December 2008

ABSTRACT

In eukaryotic cells, an mRNA bearing a premature termination codon (PTC) or an abnormally long 3′ untranslated region (UTR) is often degraded by the nonsense-mediated mRNA decay (NMD) pathway. Despite the presence of a 5- to 7-kb 3′ UTR, unspliced retroviral RNA escapes this degradation. We previously identified the Rous sarcoma virus (RSV) stability element (RSE), an RNA element downstream of the
gag
natural translation termination codon that prevents degradation of the unspliced viral RNA. Insertion of this element downstream of a PTC in the RSV
gag
gene also inhibits NMD. Using partial RNase digestion and selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, we determined the secondary structure of this element. Incorporating RNase and SHAPE data into structural prediction programs definitively shows that the RSE contains an AU-rich stretch of about 30 single-stranded nucleotides near the 5′ end and two substantial stem-loop structures. The overall secondary structure of the RSE appears to be conserved among 20 different avian retroviruses. The structural aspects of this element will serve as a tool in the future design of
cis
mutants in addressing the mechanism of stabilization.