bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Magnetic Resonance Imaging and Multiple Sclerosis: The Evidence for Neuronal Plasticity
Authors: Buckle Guy J. 
Published: December 2005

ABSTRACTBlood oxygen level–dependent (BOLD) functional magnetic resonance imaging (fMRI) has emerged as a powerful technique to visualize the localization of cerebral activity in both healthy and diseased brains. BOLD fMRI has been used to assess brain function in a variety of diseases, including multiple sclerosis (MS), and has shown that altered patterns of connectivity are used to recruit more widespread eloquent brain networks engaged in tasks relating to motor activity, sensory and cognitive function, and memory when compared to normal controls. This review will examine the evidence that functional reorganization is a consequence of demyelination and tissue loss in MS that may serve as an adaptive response to limit clinical disability. It remains unclear whether cerebral plasticity is a marker of permanent functional restructuring or a short‐term compensatory response to injury. Long‐term longitudinal studies that correlate fMRI activity with other MRI markers of disease burden and activity, as well as with clinical measures of disease activity and progression, are badly needed to determine fMRI's relevance to clinical practice and its place as a surrogate outcome measure in MS.
Magnetic Resonance Spectroscopy in the Monitoring of Multiple Sclerosis
Authors: Narayana Ponnada A. 
Published: December 2005

ABSTRACTIn addition to providing information on tissue structure, magnetic resonance (MR) technology offers the potential to investigate tissue metabolism and function. MR spectroscopy (MRS) offers a wealth of data on the biochemistry of a selected brain tissue volume, which represent potential surrogate markers for the pathology underlying multiple sclerosis (MS). In particular, the N‐acetylaspartate peak in an MR spectrum is a putative marker of neuronal and axonal integrity, and the choline peak appears to reflect cell‐membrane metabolism. On this basis, a diminished N‐acetylaspartate peak is interpreted to represent neuronal/axonal dysfunction or loss, and an elevated choline peak represents heightened cell‐membrane turnover, as seen in demyelination, remyelination, inflammation, or gliosis. Therefore, MRS may provide a unique tool to evaluate the severity of MS, establish a prognosis, follow disease evolution, understand its pathogenesis, and evaluate the efficacy of therapeutic interventions, which complements the information obtained from the various forms of assessment made by conventional MR imaging.
Greater risk of incident asthma cases in adults with Allergic Rhinitis and Effect of Allergen Immunotherapy: A Retrospective Cohort Study
Authors: Polosa Riccardo , Al-Delaimy Wael K , Russo Cristina , Piccillo Giovita , Sarvà Maria 
Published: December 2005

AbstractAsthma and rhinitis are often co-morbid conditions. As rhinitis often precedes asthma it is possible that effective treatment of allergic rhinitis may reduce asthma progression.The aim of our study is to investigate history of allergic rhinitis as a risk factor for asthma and the potential effect of allergen immunotherapy in attenuating the incidence of asthma.Hospital-referred non-asthmatic adults, aged 18–40 years between 1990 and 1991, were retrospectively followed up until January and April 2000. At the end of follow up, available subjects were clinically examined for asthma diagnosis and history of allergen specific immunotherapy, second-hand smoking and the presence of pets in the household. A total of 436 non-asthmatic adults (332 subjects with allergic rhinitis and 104 with no allergic rhinitis nor history of atopy) were available for final analyses.The highest OR (odds ratio) associated with a diagnosis of asthma at the end of follow-up was for the diagnosis of allergic rhinitis at baseline (OR, 7.8; 95%CI, 3.1–20.0 in the model containing the covariates of rhinitis diagnosis, sex, second-hand smoke exposure, presence of pets at home, family history of allergic disorders, sensitization toParietaria judaica; grass pollen; house dust mites;Olea europea: orchard; perennial rye; and cat allergens). Female sex, sensitization toParietaria judaicaand the presence of pets in the home were also significantly predictive of new onset asthma in the same model. Treatment with allergen immunotherapy was significantly and inversely related to the development of new onset asthma (OR, 0.53; 95%CI, 0.32–0.86).In the present study we found that allergic rhinitis is an important independent risk factor for asthma. Moreover, treatment with allergen immunotherapy lowers the risk of the development of new asthma cases in adults with allergic rhinitis.
Comparison of normalization methods for CodeLink Bioarray data
Authors: Wu Wei , Dave Nilesh , Tseng George C , Richards Thomas , Xing Eric P , Kaminski Naftali 
Published: December 2005

AbstractBackgroundThe quality of microarray data can seriously affect the accuracy of downstream analyses. In order to reduce variability and enhance signal reproducibility in these data, many normalization methods have been proposed and evaluated, most of which are for data obtained from cDNA microarrays and Affymetrix GeneChips. CodeLink Bioarrays are a newly emerged, single-color oligonucleotide microarray platform. To date, there are no reported studies that evaluate normalization methods for CodeLink Bioarrays.ResultsWe compared five existing normalization approaches, in terms of both noise reduction and signal retention: Median (suggested by the manufacturer), CyclicLoess, Quantile, Iset, and Qspline. These methods were applied to two real datasets (a time course dataset and a lung disease-related dataset) generated by CodeLink Bioarrays and were assessed using multiple statistical significance tests. Compared to Median, CyclicLoess and Qspline exhibit a significant and the most consistent improvement in reduction of variability and retention of signal. CyclicLoess appears to retain more signal than Qspline. Quantile reduces more variability than Median in both datasets, yet fails to consistently retain more signal in the time course dataset. Iset does not improve over Median in either noise reduction or signal enhancement in the time course dataset.ConclusionMedian is insufficient either to reduce variability or to retain signal effectively for CodeLink Bioarray data. CyclicLoess is a more suitable approach for normalizing these data. CyclicLoess also seems to be the most effective method among the five different normalization strategies examined.
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
Authors: Xue Chenghai , Li Fei , He Tao , Liu Guo-Ping , Li Yanda , Zhang Xuegong 
Published: December 2005

Abstract
Background
MicroRNAs (miRNAs) are a group of short (~22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology.

Results
A set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM) is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information.

Conclusion
The local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.
Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis
Authors: Magnusson Nils E , Cardozo Alessandra K , Kruhøffer Mogens , Eizirik Decio L , Ørntoft Torben F , Jensen Jens L 
Published: December 2005

Abstract
Background
Type 1 diabetes mellitus (T1DM) is a autoimmune disease caused by a long-term negative balance between immune-mediated beta-cell damage and beta-cell repair/regeneration. Following immune-mediated damage the beta-cell fate depends on several genes up- or down-regulated in parallel and/or sequentially. Based on the information obtained by the analysis of several microarray experiments of beta-cells exposed to pro-apoptotic conditions (e.g. double stranded RNA (dsRNA) and cytokines), we have developed a spotted rat oligonucleotide microarray, the APOCHIP, containing 60-mer probes for 574 genes selected for the study of beta-cell apoptosis.

Results
The APOCHIP was validated by a combination of approaches. First we performed an internal validation of the spotted probes based on a weighted linear regression model using dilution series experiments. Second we profiled expression measurements in ten dissimilar rat RNA samples for 515 genes that were represented on both the spotted oligonucleotide collection and on the in situ-synthesized 25-mer arrays (Affymetrix GeneChips). Internal validation showed that most of the spotted probes displayed a pattern of reaction close to that predicted by the model. By using simple rules for comparison of data between platforms we found strong correlations (rmedian= 0.84) between relative gene expression measurements made with spotted probes and in situ-synthesized 25-mer probe sets.

Conclusion
In conclusion our data suggest that there is a high reproducibility of the APOCHIP in terms of technical replication and that relative gene expression measurements obtained with the APOCHIP compare well to the Affymetrix GeneChip. The APOCHIP is available to the scientific community and is a useful tool to study the molecular mechanisms regulating beta-cell apoptosis.
Functional studies of signaling pathways in peri-implantation development of the mouse embryo by RNAi
Authors: Soares Miguel L , Haraguchi Seiki , Torres-Padilla Maria-Elena , Kalmar Tibor , Carpenter Lee , Bell Graham , Morrison Alastair , Ring Christopher JA , Clarke Neil J , Glover David M , Zernicka-Goetz Magdalena 
Published: December 2005

Abstract

Background
Studies of gene function in the mouse have relied mainly on gene targeting via homologous recombination. However, this approach is difficult to apply in specific windows of time, and to simultaneously knock-down multiple genes. Here we report an efficient method for dsRNA-mediated gene silencing in late cleavage-stage mouse embryos that permits examination of phenotypes at post-implantation stages.

Results
We show that introduction of Bmp4 dsRNA into intact blastocysts by electroporation recapitulates the genetic Bmp4 null phenotype at gastrulation. It also reveals a novel role for Bmp4 in the regulation the anterior visceral endoderm specific gene expression and its positioning. We also show that RNAi can be used to simultaneously target several genes. When applied to the three murine isoforms of Dishevelled, it leads to earlier defects than previously observed in double knock-outs. These include severe delays in post-implantation development and defects in the anterior midline and neural folds at headfold stages.

Conclusion
Our results indicate that the BMP4 signalling pathway contributes to the development of the anterior visceral endoderm, and reveal an early functional redundancy between the products of the murine Dishevelled genes. The proposed approach constitutes a powerful tool to screen the functions of genes that govern the development of the mouse embryo.
The Academic Medical Center Linear Disability Score (ALDS) item bank: item response theory analysis in a mixed patient population
Authors: Holman Rebecca , Weisscher Nadine , Glas Cees AW , Dijkgraaf Marcel GW , Vermeulen Marinus , de Haan Rob J , Lindeboom Robert 
Published: December 2005

Abstract

Background
Currently, there is a lot of interest in the flexible framework offered by item banks for measuring patient relevant outcomes. However, there are few item banks, which have been developed to quantify functional status, as expressed by the ability to perform activities of daily life. This paper examines the measurement properties of the Academic Medical Center linear disability score item bank in a mixed population.

Methods
This paper uses item response theory to analyse data on 115 of 170 items from a total of 1002 respondents. These were: 551 (55%) residents of supported housing, residential care or nursing homes; 235 (23%) patients with chronic pain; 127 (13%) inpatients on a neurology ward following a stroke; and 89 (9%) patients suffering from Parkinson's disease.

Results
Of the 170 items, 115 were judged to be clinically relevant. Of these 115 items, 77 were retained in the item bank following the item response theory analysis. Of the 38 items that were excluded from the item bank, 24 had either been presented to fewer than 200 respondents or had fewer than 10% or more than 90% of responses in the category 'can carry out'. A further 11 items had different measurement properties for younger and older or for male and female respondents. Finally, 3 items were excluded because the item response theory model did not fit the data.

Conclusion
The Academic Medical Center linear disability score item bank has promising measurement characteristics for the mixed patient population described in this paper. Further studies will be needed to examine the measurement properties of the item bank in other populations.
Changes in microRNA expression profiles in HIV-1-transfected human cells
Authors: Yeung Man Lung , Bennasser Yamina , Myers Timothy G , Jiang Guojian , Benkirane Monsef , Jeang Kuan-Teh 
Published: December 2005

Abstract
MicroRNAs (miRNAs) are small RNAs of 18–25 nucleotides (nt) in length that play important roles in regulating a variety of biological processes. Recent studies suggest that cellular miRNAs may serve to control the replication of viruses in cells. If such is the case, viruses might be expected to evolve the ability to modulate the expression of cellular miRNAs. To ask if expression of HIV-1 genes changes the miRNA profiles in human cells, we employed a high throughput microarray method, termed the RNA-primed Array-based Klenow Enzyme (RAKE) assay. Here, we describe the optimization of this assay to quantify the expression of miRNAs in HIV-1 transfected human cells. We report distinct differences in miRNA profiles in mock-transfected HeLa cells versus HeLa cells transfected with an infectious HIV-1 molecular clone, pNL4-3.
IX international conference on Salt Lake research: Research opportunities and management challenges
Authors: Jellison Robert 
Published: December 2005

Abstract
The 9th International Conference on Salt Lake Research was held 26–30 September 2005 in Western Australia at the Curtin University of Technology, Perth, Australia. One hundred scientists from 10 countries presented research on a diverse array of topics highlighting research findings and opportunities, and management challenges associated with inland saline waters. Major emergent themes of the conference included modeling of ecosystem processes, microbial communities, and features of Western Australian inland saline environments, including current threats, conservation and management.
Double Acting Tanker: Experiences from Model Tests and Sea Trials
Authors: Trägärdh P , Lindell P , Sasaki N 
Published: December 2005

The acronym DAT stands for double acting tanker, a concept where the ship is designed to run astern in heavy ice conditions while remaining hydrodynamically efficient for ahead propulsion in open water conditions. Two large aframax DATs - 106.000 dwt (deadweight tons) each - have been delivered by Sumitomo Heavy Industries to Fortum Oil and Gas OY. They are the first crude carriers built according to the DAT principle and also the first using pod propulsion from the beginning (Fig. 1). They will also be the world's largest crude carriers with ice class 1A super and are primarily intended for year-round transportation of North Sea crude to Fortum's refineries in the Gulf of Finland. The ships were appointed ‘ship of the year’ in Japan in 2003. SSPA was contracted by Sumitomo Heavy Industries to perform model tests. A comprehensive open water model test programme was used to investigate aspects of resistance and propulsion, manoeuvring, and cavitation performance. As the ship is designed to operate both in ahead and astern conditions for prolonged periods of time, most tests were performed both ahead and astern. Also, a simulation study of dynamic positioning at buoy or floating production, storage offshore (FPSO) loading was made by SSPA. Comprehensive tests of the ship's performance in ice were performed in the ice tank at MARC (Masa-Yards Artic Research Centre). The eight-month model testing and development campaign resulted in a ship with excellent propulsion and manoeuvring performance, especially with regard to the high ice class. Sea trials carried out with ship in August 2002 confirmed the results of the model test. Interesting experiences of the model test campaign and comparison between model test and sea trial results are presented, as well as some examples of single-point mooring simulations.
Removal of Some Heavy Metal Cations from Aqueous Solution by Adsorption onto Natural Kaolin
Authors: Ceylan H. , Şahan T. , Gürkan R. , Kubilay Ş. 
Published: December 2005

The adsorption removal of some heavy metal cations such as Cu(II), Zn(II) and Co(II) from aqueous solution onto kaolin has been studied using the batch method with initial metal ion concentrations within the range 15–70 mg/l. The percentage adsorption and equilibrium concentrations were determined by means of atomic absorption flame photometry as a function of adsorbate concentration, pH and temperature. Ion-exchange studies showed that over the complete concentration range studied the adsorption ratios for metal cations adsorbed onto kaolin correlated with the linear forms of the Langmuir, Freundlich and Dubinin—Kaganer—Radushkevich (DKR) adsorption isotherms. The cationexchange capacity of kaolin towards each metal ion studied was evaluated. It was found that the adsorption phenomena depended on the charge density and diameter of the hydrated ion. The equilibrium studies demonstrated that the selectivity of the ions followed the sequence Zn(II) > Cu(II) > Co(II) at pH 7.0. Calculation of thermodynamic parameters such as the standard enthalpy (ΔH0), Gibbs free energy (ΔG0) and entropy (ΔS0) showed that the adsorption of the heavy metal ions studied onto kaolin was an endothermic process which was favoured at higher temperatures. These results show that natural kaolin has a considerable potential for the removal of heavy metal cationic species from aqueous solution and wastewater.
Effect of Ring Beam Stiffness on Behaviour of Reticulated Timber Domes
Authors: Pan Dan H. , Girhammar Ulf Arne 
Published: December 2005

Domes are efficient structural systems for long clear-span buildings. The introduction of laminated timber highlighted the economic advantages of this material and led to the use of timber domes even for very large spans. In this paper, reticulated timber domes of triangular network shape with decking and bottom tension ring are considered. These types of domes have high stiffness in all directions along the surface and are kinematically stable. The dome is subjected to uniformly distributed load over the entire structure. The dome model is generated with a preprocessor program called DOME-IN and analysed with ABAQUS. The focus of this paper is to evaluate the behaviour of reticulated timber domes with respect to different stiffnesses of the bottom ring beam, here defined as a non-dimensional ring beam area parameter Ar*, which is shown to be a very well adapted design parameter for the ring beam. As far as global buckling is concerned, the critical pressure is sensitive to the bottom ring beam stiffness only if the latter is within a certain range. In terms of design, the stiffness of the ring beam should exceed A* > 2 in order to utilise the full buckling load capacity of the dome system itself. The maximum deflection, normal forces and bending moments versus the ring beam area parameter are also evaluated. The maximum values of the deflection and the internal actions next to the bottom ring are very sensitive to the bottom ring beam stiffness only if the latter is less than about Ar* < 10. A recommended value for the design of the bottom ring beam is A* > 20.
Interpreting the course of privatisation in the Czech Republic: a path-dependency approach
Authors: McMaster Irene 
Published: December 2005

English
This article focuses on the path-dependency approach and explores whether it could be used to account for the distinctive course of Czech privatisation. The approach offers a constructive understanding of the processes. However, shortcomings in existing applications of the approach are highlighted. The conclusion is reached that interactions of resources, constraints and strategic actors resulted in a distinct course of privatisation. However, the relative weight and number of constraints is open to debate. In the case of Czech privatisation, limited constraints on policy makers combined with complex institutional legacies in the economic realm are key factors that shaped the process.
Social capital, community empowerment and public health: policy developments in the UK since 1997
Authors: Bridgen Paul 
Published: December 2005

English
The use made of social capital in UK health policy by New Labour has been criticised as evidence of an ideological retreat away from traditional social democracy. This article argues that the influence of the concept on policy development in the public health field has, in fact, the potential to complement, rather than provide an alternative to, social democratic approaches. Its operationalisation in the establishment of local health initiatives, when combined with the broader policy framework, appears to reinforce the gradual shift in UK primary care towards a more public health orientation, a shift generally regarded as vital for the secure establishment of health inequalities on the UK health agenda.
What is to be done about undeclared work? Evaluating the policy options
Authors: Williams Colin C. 
Published: December 2005

English
Grounded in the view that undeclared work is conducted under work relations akin to employment and motivated primarily by monetary gain, the thrust of public policy has been to deter this work by seeking to ensure that the expected cost of being caught and punished is greater than the potential economic benefits. This article reviews recent research that reveals that, although some undeclared work is marketlike and conducted for monetary gain, a large proportion is carried out under relations more akin to unpaid mutual aid. It then critically evaluates the implications of pursuing deterrence as well as other approaches. The result is a proposal for a new policy approach that recognises the heterogeneous nature of undeclared work and actively seeks to facilitate its legitimisation.