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Biomedical subjects

R Stevens

Publications and source records attributed to R Stevens.

At least 19 recordsLinked to original sources
PubMed2006

Phonons and thermodynamics of unmixed and disordered Li0.6FePO4.

The lithium-storage material Li(0.6)FePO(4) was studied by inelastic neutron scattering and differential scanning calorimetry. Li(0.6)FePO(4) undergoes a transformation from a two-phase mixture (heterosite and triphylite) to a disordered solid-solution at 200 degrees C. Phonon densities of states (DOS) obtained from the inelastic neutron scattering were similar for the two-phase sample measured at 180 degrees C and the disordered sample measured at 220 degrees C. The vibrational entropy of transformation is 1.8 +/-0.9 J/(K mol), which is smaller than the configurational entropy difference of approximately 3.1 J/(K mol). The measured enthalpy of the disordering transition was estimated as 2.5 kJ/mol. The phonon data show a small change in lattice dynamics upon disordering.

Journal Article↗
PubMed2006

Absence of magnetism in hcp iron-nickel at 11 K.

Synchrotron Mössbauer spectroscopy (SMS) was performed on an hcp-phase alloy of composition Fe92Ni8 at a pressure of 21 GPa and a temperature of 11 K. Density functional theoretical calculations predict antiferromagnetism in both hcp Fe and hcp Fe-Ni. For hcp Fe, these calculations predict no hyperfine magnetic field, consistent with previous experiments. For hcp Fe-Ni, however, substantial hyperfine magnetic fields are predicted, but these were not observed in the SMS spectra. Two possible explanations are suggested. First, small but significant errors in the generalized gradient approximation density functional may lead to an erroneous prediction of magnetic order or of erroneous hyperfine magnetic fields in antiferromagnetic hcp Fe-Ni. Alternately, quantum fluctuations with periods much shorter than the lifetime of the nuclear excited state would prohibit the detection of moments by SMS.

Journal Article↗
PubMed2006

Protein classification using ontology classification.

MOTIVATION: The classification of proteins expressed by an organism is an important step in understanding the molecular biology of that organism. Traditionally, this classification has been performed by human experts. Human knowledge can recognise the functional properties that are sufficient to place an individual gene product into a particular protein family group. Automation of this task usually fails to meet the 'gold standard' of the human annotator because of the difficult recognition stage. The growing number of genomes, the rapid changes in knowledge and the central role of classification in the annotation process, however, motivates the need to automate this process. RESULTS: We capture human understanding of how to recognise members of the protein phosphatases family by domain architecture as an ontology. By describing protein instances in terms of the domains they contain, it is possible to use description logic reasoners and our ontology to assign those proteins to a protein family class. We have tested our system on classifying the protein phosphatases of the human and Aspergillus fumigatus genomes and found that our knowledge-based, automatic classification matches, and sometimes surpasses, that of the human annotators. We have made the classification process fast and reproducible and, where appropriate knowledge is available, the method can potentially be generalised for use with any protein family. AVAILABILITY: All components described in this paper are freely available. OWL ontology http://www.bioinf.man.ac.uk/phosphabase myGrid http://www.mygrid.org.uk Instance Store http://instancestore.man.ac.uk.

Algorithms↗
PubMed2006

MRI protocols for whole-organ assessment of the knee in osteoarthritis.

One of the critical challenges in developing structure-modifying therapies for arthritis, especially osteoarthritis (OA), is measuring changes in progression of joint destruction. Magnetic resonance imaging (MRI) offers considerable promise in this regard. Not only can MRI quantify articular cartilage volume and morphology with high precision and accuracy, but it can also examine several other important articular components, and thus offer a unique opportunity to evaluate the knee and other joints as whole organs. On December 5 and 6, 2002, OMERACT (Outcome Measures in Rheumatology Clinical Trials) and OARSI (Osteoarthritis Research Society International), with support from various pharmaceutical companies listed at the beginning of this supplement, held a Workshop for Consensus on Osteoarthritis Imaging in Bethesda, MD. The aim of the Workshop was to provide a state-of-the-art review of imaging outcome measures for OA of the knee to help guide scientists and pharmaceutical companies who want to use MRI in multi-site studies of OA. Applications of MRI were initially reviewed by a multidisciplinary, international panel of expert scientists and physicians from academia, the pharmaceutical industry and regulatory agencies. The findings of the panel were then presented to a wider group of participants for open discussion. The following report summarizes the results of these discussions with respect to MRI acquisition techniques for whole-organ assessment of the knee in OA. The discussion reviews the selection and qualification of imaging sites for clinical trials, designing imaging protocols for whole-organ assessment of OA, and key considerations in image quality (IQ) control and data management.

Bone Marrow↗
PubMed2006

Comparison of fixed flexion, fluoroscopic semi-flexed and MTP radiographic methods for obtaining the minimum medial joint space width of the knee in longitudinal osteoarthritis trials.

OBJECTIVE: To compare three radiographic techniques (fluoroscopic semi-flexed [Fluoro], fixed flexion [FF], and semi-flexed metatarsophalangeal joint [MTP] views) for measuring medial joint space width (JSW) of the knee in longitudinal osteoarthritis (OA) trials and to identify the percentage of patients with detectable progression. DESIGN: Retrospective summary of the progression and variability of the change in JSW in knee OA. MATERIAL AND METHODS: Data from the placebo arms of three separate, structure modifying, knee OA trials were compared including gender, age, baseline JSW, change from baseline in JSW, duration of observation, and number and percent of patients with joint space narrowing of various degrees. Computer evaluation of the joint space at its narrowest point in the medial compartment was used in the studies. It is important to note that the narrowest joint space at baseline may not be in the same anatomic location at subsequent evaluations. No statistical tests were performed. RESULTS: The average observation times were 0.98, 0.68 and 0.82 years for the Fluoro, FF, and MTP studies, respectively. The amount of progression was different among the three studies. The Fluoro study showed the greatest magnitude of OA structural progression and the lowest variability. The Fluoro study was expected to show the greatest magnitude of structural progression since it was conducted for the longest duration. For all patients, the standard deviation of the change in JSW was 0.42, 0.63, and 0.53 mm for the Fluoro, FF, and MTP studies, respectively. The percent of patients with detectable progression was similar across studies. CONCLUSION: With these data, information was not sufficient to control for duration of observation and differences in inclusion criteria for the three study populations. Therefore, no definitive conclusions can be made regarding the degree of progression of OA over specific time intervals. However, the data indicate that all three studies contain a cohort of patients that exhibit detectable progression.

Clinical Trials as Topic↗
PubMed2006

Responsiveness, effect size, and smallest detectable difference of Magnetic Resonance Imaging in knee osteoarthritis.

OBJECTIVE: The aim of this study was to determine the responsiveness, effect size (ES) and smallest detectable difference (SDD) of two Magnetic Resonance Imaging (MRI) measures for osteoarthritis (OA) of the knee: a whole-organ semiquantitative evaluation and cartilage volume. DESIGN: This analysis was performed on a dataset from a randomized, double-blind trial (Roche NI-15713) conducted in 1998 of a novel therapy in subjects with mild-moderate knee OA, with MRI at baseline and 6-month follow-up. The trial measurements included (1) cartilage volume measured using a proprietary software method; and (2) semiquantitative scoring of other parameters important for "whole organ" evaluation of OA knee joint pathology, using the Whole-Organ MRI Score (WORMS). The analysis initially examined the distributional characteristics of WORMS items, such as cartilage morphology. Standardized response mean (SRM), ES, and SDD between baseline and 6-month follow-up were then calculated in the whole group and the placebo group alone. RESULTS: In general, the differences were small and this was reflected in the small ESs and SRMs. There was also a suggestion of a treatment effect with reduction in differences between baseline and follow-up in the treatment group. CONCLUSION: Of the MRI semiquantitative measures, cartilage morphology, synovitis and osteophytes appeared to be responsive to change and the focus of repeat measures should highlight these articular features. In general, the ESs and SRMs were small.

Adult↗
PubMed2006

Examining a whole-organ magnetic resonance imaging scoring system for osteoarthritis of the knee using Rasch analysis.

OBJECTIVE: The ability to reliably quantify all the structural abnormalities in osteoarthritis (OA) of the knee is a long-standing goal of OA research. On December 5 and 6, 2002, Outcome Measures in Rheumatology Clinical Trials and Osteoarthritis Research Society, International held a Workshop for Consensus on Osteoarthritis Imaging in Bethesda, MD, with the aim of providing a state-of-the-art review of imaging outcome measures for OA of the knee. As part of the Workshop, data from previous clinical trials and epidemiological studies of OA were analysed with respect to the metrological properties of the measurement methods used. The following report outlines the results of analyses aimed at evaluating the internal construct validity of a whole-organ, ordinal (semi-quantitative) magnetic resonance imaging score (WORMS) using Rasch analysis. The fit of data to the Rasch model offers a measure of the validity of summing different items into a subscale score and the degree to which this score behaves as a unidimensional, interval level measurement tool. METHODS: The Rasch model was applied in two OA studies. The first was a clinical cohort comprising OA knee subjects entering a clinical trial; study entry criteria included patients with at least moderate pain, radiographic osteophytes and a minimum of 1.5mm tibiofemoral joint-space width. The second cohort was from the Boston Osteoarthritis Knee Study, an observational cohort of subjects with symptomatic knee OA with pain on most days and a definite osteophyte in either the tibiofemoral or patellofemoral joints. Baseline WORMS scores from both studies were used for the Rasch analysis, performed with RUMM 2020 software. RESULTS: There was a substantial proportion of subjects in both study populations with zero scores in several of the subscales of WORMS. Few of the subscales met the requirements of the Rasch measurement model when summated across all sites, and summations of some postulated compartmentally based sites also failed to fit the Rasch model. The existing scoring categories also required rescoring at many sites. CONCLUSION: There remain important issues in constructing outcome measurements that summate different features across multiple anatomical sites. The whole-organ scoring system evaluated here is no exception. Resolving these issues will improve the ability of imaging studies to assess complex pathological structural change.

Adult↗
PubMed2006

PROactive study.

Explore the source record for details and available documents.

Diabetes Mellitus, Type 2↗
PubMed2006

In-vitro dynamic micro-probing and the mechanical properties of human prostate tissues.

In vitro macro- and micro-indentation test systems have been designed to measure the dynamic micro-mechanical properties of human prostate tissues at actuation frequencies between 5 Hz and 30 Hz, and 0.5 Hz and 20 Hz, respectively. The development of in vitro test systems was aimed at assessing the capacity of such an in vivo medical probe to provide information useful for the diagnosis of various prostate diseases. The macro-indentation test system is an established one, which we have used to determine structure-property relationships in human and canine prostate tissues and here we use it to validate a newly-developed micro-indentation test system using a tissue phantom. Mechanical testing was also carried out on sections of prostate tissue harvested from cystectomy and radical prostatectomy, diagnosed with bladder cancer and benign prostatic hyperplasia. Dynamic probing under displacement control was carried at pre-strains between 5% and 8% for macro-probing and at 5% pre-strain for micro-probing, and the general effect of pre-strain on the dynamic mechanical properties (described by the amplitude ratio between stress and strain, and the phase lag between strain and stress) of phantom and prostate tissues is presented. Specific point probing on epithelial and stromal histological components was also carried out showing a significant difference between the amplitude ratios of epithelial and stromal components for actuation frequencies exceeding 5 Hz. However, no significant difference was found between phase lags for epithelial and stromal tissues.

Biomechanical Phenomena↗
PubMed2005

Infliximab leads to a rapid but transient improvement in endothelial function in patients with primary systemic vasculitis.

OBJECTIVE: To assess the immediate effects of tumour necrosis factor alpha (TNFalpha) blockade on endothelial function in systemic vasculitis. METHODS: Endothelial function was assessed by laser Doppler flowmetry in patients with active vasculitis after 10 infusions of infliximab. For comparison endothelial responses were assessed after five infusions of cyclophosphamide plus methylprednisolone. RESULTS: Endothelial dependent vasodilatation (EDV) improved significantly within 24 hours of infliximab infusion. The median change in red blood cell flux (interquartile range) was 5.7 (4.3-8.2) before infusion v 8.4 (7.5-10.9) at 24 hours; p=0.027. This was not maintained at day 14. No improvement was seen in EDV after cyclophosphamide plus methylprednisolone infusion. CONCLUSION: The rapid but transient improvement in EDV after TNFalpha inhibition suggests that TNFalpha may have a direct role in the impairment of endothelial function.

Adult↗
PubMed2005

PhosphaBase: an ontology-driven database resource for protein phosphatases.

PhosphaBase is an ontology-driven database resource containing information on the protein phosphatase family. It is the first public resource dedicated to protein phosphatases, which are enzymes that perform dephosphorylation reactions. In conjunction with the phosphorylation action of protein kinases, phosphatases are involved in important control and communication mechanisms in the cell. They have also been implicated in many human diseases, including diabetes and obesity, cancers, and neurodegenerative conditions. PhosphaBase aims to centralize the growing base of knowledge in the phosphatase research domain. The resource is built around a formal, domain-specific DAML+OIL ontology, and the data are collected from heterogeneous biological sources using Gene Ontology terms as a means of data extraction. The overall ontology-driven architecture provides a robust structure with distinct advantages for sustainability and provides the potential for the development of diagnostic tools, as well as a data repository.

Animals↗
PubMed2004

Constructing ontology-driven protein family databases.

MOTIVATION: Protein family databases provide a central focus for scientific communities as well as providing useful resources to aide research. However, such resources require constant curation and often become outdated and discontinued. We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability. RESULTS: Using protein phosphatases and ABC transporters as model protein families, we constructed two protein family database resources around a central DAML+OIL ontology. Each resource contains specialist information about each protein family, providing specialized domain-specific resources based on the same template structure. The formal structure, combined with the extraction of biological data using GO terms, allows for automated update strategies. Despite the functional differences between the two protein families, the ontology model was equally applicable to both, demonstrating the generic nature of the system. AVAILABILITY: The protein phosphatase resource, PhosphaBase, is freely available on the internet (http://www.bioinf.man.ac.uk/phosphabase). The DAML+OIL ontology for the protein phosphatases and the ABC transporters is available on request from the authors. CONTACT: kwolstencroft@cs.man.ac.uk.

ATP-Binding Cassette Transporters↗
PubMed2004

Differential propagation of the metazoan parasite Myxobolus cerebralis by Limnodrilus hoffmeisteri, Ilyodrilus templetoni, and genetically distinct strains of Tubifex tubifex.

Whirling disease, caused by the parasite Myxobolus cerebralis, has infected rainbow trout (Oncorhynchus mykiss) and other salmonid fish in the western United States, often with devastating results to native populations but without a discernible spatial pattern. The parasite develops in a complex 2-host system in which the aquatic oligochaete Tubifex tubifex is an obligate host. Because substantial differences in whirling disease severity in different areas of North America did not seem explainable by environmental factors or features of the parasite or its fish host, we sought to determine whether ecological or genetic variation within oligochaete host populations may be responsible. We found large differences in compatibility between the parasite and various laboratory strains of T. tubifex that were established from geographic regions with different whirling disease histories. Moreover, 2 closely related species of tubificids, Limnodrilus hoffmeisteri and Ilyodrilus templetoni, which occur naturally in mixed species assemblages with T. tubifex, were incompatible with M. cerebralis. Virulence of the parasite was directly correlated with the numbers of triactinomyxon spores that developed within each strain of T. tubifex. Thus, the level of virulence was directly related to the compatibility between the host strain and the parasite. Genetic analyses revealed relationships that were in agreement with the level of parasite production. Differences in compatibilities between oligochaetes and M. cerebralis may contribute to the spatial variance in the severity of the disease among salmonid populations.

Analysis of Variance↗
PubMed2003

The comparative sealing ability of hydroxyapatite cement, mineral trioxide aggregate, and super ethoxybenzoic acid as root-end filling materials.

A comparison was made of the ability of hydroxyapatite cement, mineral trioxide aggregate, and super ethoxybenzoic acid to prevent the leakage of bacteria from root canals, when used as root-end filling materials. The materials were tested in a double-chamber device in which a root segment connects the upper (delivery) chamber and the lower (receiving) chamber. The root segment was prepared by having the root canal instrumented to a #45 file, and a 3-mm-deep, root-end preparation placed at the apical foramen. The canal of each root segment was filled with gutta-percha, and the root-end preparation was filled with one of three test materials, mixed according to the manufacturer's directions. Negative controls were constructed with sticky wax sealing the apical foramen. A titered suspension of radioactively (3H-thymidine)-labeled bacteria (Enterococcus fecalis) was placed into the delivery chamber, and sterile saline was placed into the receiving chamber such that the apical third of each root section was immersed. At various time points, samples were taken from the receiving chamber, and measured for 3H activity. The results indicated that (a) all the test materials leaked significantly compared with the negative controls; and (b) there was no significant difference found between the leakage rates of the three materials tested.

Aluminum Compounds↗
PubMed2003

A methodology to migrate the gene ontology to a description logic environment using DAML+OIL.

The Gene Ontology Next Generation Project (GONG) is developing a staged methodology to evolve the current representation of the Gene Ontology into DAML+OIL in order to take advantage of the richer formal expressiveness and the reasoning capabilities of the underlying description logic. Each stage provides a step level increase in formal explicit semantic content with a view to supporting validation, extension and multiple classification of the Gene Ontology. The paper introduces DAML+OIL and demonstrates the activity within each stage of the methodology and the functionality gained.

Classification↗
PubMed2002

AtE2F-a and AtDP-a, members of the E2F family of transcription factors, induce Arabidopsis leaf cells to re-enter S phase.

In eukaryotes, transcription factors of the E2F family, in addition to having a role in cell proliferation, participate in regulating apoptosis, differentiation and development. In Arabidopsis thaliana, eight gene sequences have been identified as encoding E2F or DP homologues. DP proteins form heterodimers with E2Fs. The aim of this work was to characterize the functions of three of these factors: AtE2F-a, AtE2F-b and AtDP-a. Here we report that AtE2F-a and AtE2F-b transactivate a reporter gene via an E2F consensus cis-acting element in Arabidopsis protoplasts. AtE2F-a is a more potent activator than AtE2F-b. Furthermore, co-expression of the E2F partner AtDP-a, or the DNA binding protein AtPur alpha, modulates the activation of AtE2F-a. Taken together, these results suggest that AtE2F-a, AtE2F-b and AtDP-a share features characteristic of members of the E2F family of transcription factors. Moreover, over-expression of AtE2F-a and AtDP-a can induce differentiated, non-dividing, leaf cells to re-enter S-phase. We conclude that the transcription factor AtE2F-a plays an important role in progression into S phase, which probably correlates with its capacity to stimulate transcription.

Arabidopsis↗