Biomedical subjects

Jason C Cole

Publications and source records attributed to Jason C Cole.

17 recordsLinked to original sources

PubMed2006

Single-factor scoring validation for the Health Assessment Questionnaire-Disability Index (HAQ-DI) in patients with systemic sclerosis and comparison with early rheumatoid arthritis patients.

OBJECTIVE: Structural validity for the Health Assessment Questionnaire-Disability Index (HAQ-DI) has recently been provided for patients with rheumatoid arthritis (RA). The goal of the current study was to examine the structural validity of the HAQ-DI in patients with systemic sclerosis (SSc, scleroderma) and to compare its performance with that in patients with RA. METHODS: The HAQ-DI structural validity was first assessed in a sample of 100 scleroderma patients using confirmatory factor analysis. Second, the similarity of factor structures between SSc patients (n = 291) and RA patients (n = 278) was tested using a multigroup structural validity model to assure that comparison of scores between these two diagnostic groups is appropriate. RESULTS: Results yielded a single-factor HAQ-DI score which favored the current scoring system of the HAQ-DI (model fit was CFI = 0.99 and RMSEA = 0.04). Moreover, even the most stringent model of multigroup structural validity affirmed the similarity between SSc and RA patients on the HAQ-DI (model fit was CFI = 0.99 and RMSEA = 0.04) nor was it different from a model without any demands on group similarity: CFI difference = 0.007; chi(2) = 4.29, df = 26, p=0.99. CONCLUSION: The current results indicate that a single-factor HAQ-DI is appropriate for future clinical trials in scleroderma and, in addition, HAQ-DI scores among patients with SSc and early RA can be compared legitimately with one another.

Activities of Daily Living↗

PubMed2006

Comparative meta-analysis of behavioral interventions for insomnia and their efficacy in middle-aged adults and in older adults 55+ years of age.

Meta-analyses support the effectiveness of behavioral interventions for the treatment of insomnia, although few have systematically evaluated the relative efficacy of different treatment modalities or the relation of old age to sleep outcomes. In this meta-analysis of randomized controlled trials (k = 23), moderate to large effects of behavioral treatments on subjective sleep outcomes were found. Evaluation of the moderating effects of behavioral intervention type (i.e., cognitive-behavioral treatment, relaxation, behavioral only) revealed similar effects for the 3 treatment modalities. Both middle-aged adults and persons older than 55 years of age showed similar robust improvements in sleep quality, sleep latency, and wakening after sleep onset. A research agenda is recommended to examine the mechanisms of action of behavioral treatments on sleep with increased attention to the high prevalence of insomnia in older individuals.

Behavior Therapy↗

PubMed2006

Validation of a 3-factor scoring model for the Pittsburgh sleep quality index in older adults.

STUDY OBJECTIVES: The Pittsburgh Sleep Quality Index (PSQI) is widely used to assess subjective sleep disturbances in psychiatric, medical, and healthy adult and older adult populations. Yet, validation of the PSQI single-factor scoring has not been carried out. DESIGN: The PSQI was administered as a self-report questionnaire. Using a cross-validation approach, scores from the PSQI were analyzed with exploratory and confirmatory factor analyses. SETTING: San Diego, Denver, and Los Angeles community-based clinics. PARTICIPANTS: Community-dwelling depressed and nondepressed adults older that 60 years of age (N = 417) MEASUREMENTS AND RESULTS: Results yielded a 3-factor scoring model that obtained a measure of perfect fit and was significantly better fitted than either the original single-factor model or a 2-factor model. Components of the 3 factors were characterized by the descriptors sleep efficiency, perceived sleep quality, and daily disturbances. CONCLUSIONS: These findings validate the factor structure of the PSQI and demonstrate that a 3-factor score should be used to assess disturbances in three separate factors of subjective sleep reports.

Aged↗

PubMed2005

Modeling water molecules in protein-ligand docking using GOLD.

We implemented a novel approach to score water mediation and displacement in the protein-ligand docking program GOLD. The method allows water molecules to switch on and off and to rotate around their three principal axes. A constant penalty, sigma(p), representing the loss of rigid-body entropy, is added for water molecules that are switched on, hence rewarding water displacement. We tested the methodology in an extensive validation study. First, sigma(p) is optimized against a training set of 58 protein-ligand complexes. For this training set, our algorithm correctly predicts water mediation/displacement in approximately 92% of the cases. We observed small improvements in the quality of the predicted binding modes for water-mediated complexes. In the second part of this work, an entirely independent set of 225 complexes is used. For this test set, our algorithm correctly predicts water mediation/displacement in approximately 93% of the cases. Improvements in binding mode quality were observed for individual water-mediated complexes.

Algorithms↗

PubMed2005

Validation of single-factor structure and scoring protocol for the Health Assessment Questionnaire-Disability Index.

OBJECTIVE: The extensively used Health Assessment Questionnaire Disability Index (HAQ-DI) has been well received by the research and clinical community, notably because of its measurement strengths including reliability and stability of scores over time, utility in observational studies and clinical trials, predictive relationship with morbidity and mortality in rheumatoid arthritis (RA), and its translation for use in different countries. However, HAQ-DI scoring has not been validated. The purpose of this study was to examine the structural validity of the HAQ-DI and evaluate the latent factors underlying HAQ-DI scoring. METHODS: This study used a cross-validation approach on a total of 278 patients with RA. Exploratory and confirmatory factor analyses were performed. RESULTS: Results yielded a single-factor HAQ-DI score, which favored the current scoring system of the HAQ-DI. Additionally, modification indices suggested improved model fit with the secondary inclusion of correlated residual scores from a motor skills subdomain. CONCLUSION: The current study provides the first validation of the HAQ-DI scoring system as determined by its latent factor structure. In addition, the findings suggest some benefit from a secondary interpretation of the scores based on domains that measure motor skills.

Arthritis, Rheumatoid↗

PubMed2005

Comparing protein-ligand docking programs is difficult.

There is currently great interest in comparing protein-ligand docking programs. A review of recent comparisons shows that it is difficult to draw conclusions of general applicability. Statistical hypothesis testing is required to ensure that differences in pose-prediction success rates and enrichment rates are significant. Numerical measures such as root-mean-square deviation need careful interpretation and may profitably be supplemented by interaction-based measures and visual inspection of dockings. Test sets must be of appropriate diversity and of good experimental reliability. The effects of crystal-packing interactions may be important. The method used for generating starting ligand geometries and positions may have an appreciable effect on docking results. For fair comparison, programs must be given search problems of equal complexity (e.g. binding-site regions of the same size) and approximately equal time in which to solve them. Comparisons based on rescoring require local optimization of the ligand in the space of the new objective function. Re-implementations of published scoring functions may give significantly different results from the originals. Ostensibly minor details in methodology may have a profound influence on headline success rates.

Algorithms↗

PubMed2004

Development and validation of a Rasch-derived CES-D short form.

The current study presents a Rasch-derived short form of the Center for Epidemiologic Studies-Depression scale (CES-D) for use as a depression screening tool in the general population. In contrast to short forms developed with reliance on classical measurement techniques, those developed using techniques based on item response theory produce a measure that offers true interval scaling, provide enhanced information about responders with extreme scores, and expand understanding of the underlying latent structure. Cross-validation of the Rasch-derived CES-D short form supported its utility and structural validity across samples. Tests of structural validity using latent variable modeling methodology indicated that a hierarchical, single-factor model of depression had the best fit for the original full form and the Rasch-derived short form of the CES-D. This finding challenges depression researchers and theorists to reconsider the interfactor relationships in the study and assessment of depression.

Adult↗

PubMed2004

Latent relationships of fluid, visual, and simultaneous cognitive tasks.

Horn's 1989 fluid intelligence and Luria's 1966 simultaneous processing have been represented in various cognitive assessment batteries. Although related, these concepts are purported to measure distinct cognitive functions; fluid intelligence refers to deductive reasoning whereas simultaneous processing refers to understanding complex relationships among gestalts. The current study explored the factor structure of known fluid and simultaneous tests along with visually complex new tests. A total of 56 children in Grades 1 through 5 were administered tests from the Kaufman Assessment Battery for Children, Elliott's Differential Abilities Scales, and two experimental tasks. Findings suggest that (1) the two experimental subtests were psychometrically viable, (2) when analyzed as a two-factor structure, fluid and visual processing components were pronounced, and (3) when analyzed as a single-factor structure, simultaneous processing emerged. These findings indicate simultaneous processing may be a blend of fluid and visual components.

Child↗

PubMed2003

A database survey of molecular and crystallographic symmetry.

The point of contact between molecular and crystallographic symmetries is that of the Wyckoff position, the position at which a molecule resides in a crystal structure. These Wyckoff positions may have the same symmetry as the molecules, some symmetry in common with the molecules or no symmetry at all. Using CSDSymmetry [Yao et al. (2002). Acta Cryst. B58, 640-646], a relational database containing information pertaining to the symmetry of molecules and the crystal structures that play host to them, the distribution of molecules over Wyckoff positions and the occupancy of Wyckoff positions in crystal structures is presented. Analysis of these data has led to the characterization of some relationships between molecular and crystallographic symmetry.

Journal Article↗

PubMed2003

Improved protein-ligand docking using GOLD.

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol.

Algorithms↗

PubMed2003

Multimethod validation of the Beck Depression Inventory-II and Grossman-Cole Depression Inventory with an inpatient sample.

Psychometric examination of the Beck Depression Inventory-II has been adequate and varied for outpatient and nonclinical samples, but is still comparatively scant for inpatient psychiatric samples. In particular, important factor analytic questions have not been assessed on inpatient samples at all. Given that over time alone (regardless of symptom change) test scores on depression measures can spuriously drop, a convergent psychometric analysis of the Beck Depression Inventory-II was undertaken with a new measure of depression severity, the Grossman-Cole Depression Inventory. A sample of 101 psychiatric inpatients was administered both tests. Item and scale level psychometrics were reviewed for each measure. Results were highly consistent with previous findings, providing support for the use of the Beck Depression Inventory-II with inpatient samples. Moreover, the new inventory performed quite well, suggesting it has promise as another measure for self-reported depression symptom severity. The Beck Depression Inventory-II appears appropriately considered as a single-factor hierarchical measure of depression with the current inpatient sample. Moreover, the Grossman-Cole Depression Inventory is related enough to the Beck inventory to provide adequate similarity without being so similar the measures duplicate each other.

Adolescent↗

PubMed2002

A new test set for validating predictions of protein-ligand interaction.

We present a large test set of protein-ligand complexes for the purpose of validating algorithms that rely on the prediction of protein-ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein-ligand structures, and subsets are supplied for different protein-structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein-ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk).

Algorithms↗

PubMed2002

The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base.

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C(10)H(12)N(2)), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P2(1)2(1)2(1), a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) A, Z = 4, final reduced-chi(2) = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on chi(2) was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

Journal Article↗

PubMed2002

CSDSymmetry: the definitive database of point-group and space-group symmetry relationships in small-molecule crystal structures.

An algorithm that perceives molecular symmetry has been applied to ca. 200,000 entries from the Cambridge Structural Database (CSD). For each molecule, the perceived point group, together with crystallographic properties such as space group, occupied Wyckoff positions and number of residues in the asymmetric unit, have been placed in a relational database, CSDSymmetry, using Microsoft Access software. Database queries can be constructed easily to find occurrences of any combination of molecular or crystallographic attributes, and thereby to answer questions on relative distributions. Some typical example queries are given. The inclusion of CSD reference codes enables direct visualization of search results using the Cambridge Crystallographic Data Centre's three-dimensional structure visualizer, Mercury.

Journal Article↗

PubMed2002

New software for searching the Cambridge Structural Database and visualizing crystal structures.

Two new programs have been developed for searching the Cambridge Structural Database (CSD) and visualizing database entries: ConQuest and Mercury. The former is a new search interface to the CSD, the latter is a high-performance crystal-structure visualizer with extensive facilities for exploring networks of intermolecular contacts. Particular emphasis has been placed on making the programs as intuitive as possible. Both ConQuest and Mercury run under Windows and various types of Unix, including Linux.

Journal Article↗

PubMedDate not supplied

Retrieval of crystallographically-derived molecular geometry information.

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.

Journal Article↗

PubMedDate not supplied

Effects of a behavioral intervention, Tai Chi Chih, on varicella-zoster virus specific immunity and health functioning in older adults.

OBJECTIVE: Both the incidence and severity of herpes zoster (shingles) increase markedly with increasing age in association with a decline in varicella-zoster virus (VZV) specific cell-mediated immunity (CMI). This study examined whether a behavioral intervention, Tai Chi Chih (TCC), affects VZV specific immunity and health functioning in older adults who, on average, show impairments of health status and are at risk for shingles. METHODS: Thirty-six men and women (age > or =60 years) were assigned randomly to a 15-week program of TCC instruction (three 45 minute classes per week; N = 18) or a wait list control condition (N = 18). VZV-specific CMI was measured at baseline and at 1-week postintervention. Health functioning (Medical Outcome scale: SF-36) was assessed at baseline, and at 5, 10, and 15 weeks during the intervention, and at 1-week postintervention. RESULTS: In the intent-to-treat sample, VZV-specific CMI increased 50% from baseline to 1-week postintervention in the TCC group (p < 0.05) but was unchanged in the wait list control group. In those who completed the study, 1-week postintervention SF-36 scale scores for role-physical (p < 0.05) and physical functioning (p < 0.05) were higher in the TCC group (N = 14) as compared with controls (N = 17). Older adults who had impairments of physical status at baseline showed the greatest increases of SF-36 role-physical (p < 0.01) and physical functioning (p < 0.001) during the TCC intervention. CONCLUSIONS: Administration of TCC for 15 weeks led to an increase in VZV-specific CMI. Gains in health functioning were found in participants who received TCC and were most marked in those older adults who had the greatest impairments of health status.

Aged↗