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PubMed2001

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study.

The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.

Body Water↗
PubMed2003

Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations.

Genome-wide measurements of multiple experimental samples yield rich fingerprints for comparison and interpretation. Here, a two-dimensional matrix of the cellular effects of all possible pairwise combinations of 24 small molecules, each with a different structure and bioactivity, was used to profile otherwise isogenic deletion strains of the yeast Saccharomyces cerevisiae. Using principles from graph theory, we derived a discrete model of the data for each strain by encoding the information in the form of a binary adjacency matrix. This matrix was used to construct a graph composed of nodes representing small molecules and edges connecting combinations that inhibited cell cycle progression. Computation of a set of graph theoretic descriptors for each chemical genetic network provided a topological fingerprint that showed genotype-dependent fluctuations. Because the structure of the genetic network determines the structure of the chemical genetic network, multidimensional chemical genomic profiling can be used for the characterization of perturbations in biological networks or the networks themselves. This application of small molecules could be useful for discerning the molecular basis of highly complex biological phenotypes, including those involved in the susceptibility to or etiology of human disease.

Computer Graphics↗
PubMed1987

Cluster significance analysis contrasted with three other quantitative structure-activity relationship methods.

Cluster significance analysis (CSA), a new statistical method to analyze structure-activity relationships in graphically displayed data, is contrasted with linear discriminant analysis, SIMCA, and the method of "relative odds". The data sets evaluated are as follows: antibacterial lasalocid derivatives, antimalarial naphthoquinones, and carcinogenic polycyclic aromatic hydrocarbons. CSA gives results comparable to these other methods, involves fewer assumptions, can be more reliable, and in general is easier to understand.

Antimalarials↗
PubMed2005

Pharmacophore-guided drug discovery investigations leading to bioactive 5-aminotetrahydropyrazolopyridines. Implications for the binding mode of heterocyclic dopamine D3 receptor agonists.

Taking advantage of a 3D-QSAR based pharmacophore hypothesis, synthesis and biological evaluation of dopaminergic 5-aminotetrahydropyrazolo[1,5-a]pyridines are described. The data displayed substantial and selective D3 receptor affinity for the heterocyclic test compound (+/-)-1 when the enantiomer (S)-1 turned out to be responsible for the D3 binding (K(i) (high) = 4.0 nM). (S)-1 exhibited binding affinity and ligand efficacy comparable to those of our previously described D3 agonist FAUC 54, when subtype selectivity could be significantly improved. The results indicate that the sp(2) nitrogens of the pyrazole and thiazole rings of the dopaminergics (S)-1 and pramipexole, respectively, are pharmacophoric elements of major importance. To provide putative explanations for the high affinity of (S)-1, computational studies were performed employing an active state D3 model.

Animals↗
PubMed1999

Lamellarin alpha 20-sulfate, an inhibitor of HIV-1 integrase active against HIV-1 virus in cell culture.

HIV-1 integrase is an attractive target for anti-retroviral chemotherapy, but to date no clinically useful inhibitors have been developed. We have screened diverse marine natural products for compounds active against integrase in vitro and found a series of ascidian alkaloids, the lamellarins, that show selective inhibition. A new member of the family named lamellarin alpha 20-sulfate (1), the structure of which was determined from spectroscopic data, displayed the most favorable therapeutic index. The site of action of lamellarin alpha 20-sulfate on the integrase protein was mapped by testing activity against deletion mutants of integrase. Inhibition of isolated catalytic domain was detectable though weaker than inhibition of full length integrase; possibly lamellarin alpha 20-sulfate binds a site composed of multiple integrase domains. Lamellarin alpha 20-sulfate also inhibited integration in vitro by authentic HIV-1 replication intermediates isolated from infected cells. Lamellarin alpha 20-sulfate was tested against wild type HIV using the MAGI indicator cell assay and found to inhibit early steps of HIV replication. To clarify the inhibitor target, we tested inhibition against an HIV-based retroviral vector bearing a different viral envelope. Inhibition was observed, indicating that the HIV envelope cannot be the sole target of lamellarin alpha 20-sulfate in cell culture. In addition, these single round tests rule out action against viral assembly or budding. These findings provide a new class of compounds for potential development of clinically useful integrase inhibitors.

Animals↗
PubMed2006

[Neuroimaging data of ADHD, tic-disorder and obsessive-compulsive-disorder in children and adolescents].

ADHD, Tic Disorder, Tourette's Syndrome, and Obsessive-Compulsive Disorder are all characterised by an impairment of executive functioning and often occur together. There are thus indications of a similar neurobiological basis. This review presents an overview of neuroimaging studies of these disorders in childhood and adolescence, focusing thereby on magnet resonance imaging data. Studies provide concurring data about structural changes in the basal ganglia and the prefrontal cortex, and abnormal activation in the fronto-striatal circuitry in patients as compared to healthy controls. ADHD and Tourette's Syndrome are both associated with prefrontal aberrations. However, variances in Tourette's Syndrome are less pronounced, which might be due to compensation mechanisms. ADHD children show small, but more global, morphological alterations in the cortex and cerebellum, while Tourette's Syndrome seems to be linked additionally to differences in the occipital cortex. Furthermore, structural and functional data for obsessive-compulsive disorder indicate aberrations in the amygdala and thalamus, and functional changes in the orbito-frontal cortex. By comparison, findings in children with ADHD point towards abnormal activity in the ventral prefrontal cortex. To summarise, the data display an impairment of cortico-striato-thalamic circuits which appears to be associated with dysfunctioning motor inhibition, and impulsive behaviour and objectionable thoughts. Since the majority of the studies reviewed are characterised by small and heterogeneous samples, and since the studies differ in their methods, comparability is limited and general conclusions can not be drawn.

Adolescent↗
PubMed2005

Psychological distress of patients undergoing intensified conditioning with radioimmunotherapy prior to allogeneic stem cell transplantation.

This is a pilot study comparing the emotional distress of patients receiving an intensified conditioning regimen (radioimmunotherapy=RIT) with patients receiving conventional conditioning for allogeneic stem cell transplantation. In total, 53 patients (18 received RIT) were given two questionnaires designed to measure emotional distress (HADS, POMS) before starting conditioning (t1) and at discharge (t2). During the in-patient period, patients answered questions daily relating to physical distress, psychological distress, and how they were "coping with the situation". At t2, the transplant team assessed the manner in which the patients were coping. The data displayed no relevant differences with regard to emotional distress between the two groups, both at t1 and t2. For both groups, anxiety and vigor decreased and fatigue increased between t1 and t2. On average, perceived distress was higher for those patients being treated with RIT during the in-patient time, but the differences between both groups were significant only regarding physical distress during the recovery period. No difference was found for the transplant team's assessment. We hypothesize that an intensified conditioning regimen with RIT per se has only a small distressing effect on the patients' psyche during their stay at the hospital. Differences between both groups probably result from independent factors such as, for example, the patients' pre-existing health conditions.

Adult↗
PubMed1991

Effects of thermal application on dysphagia after stroke.

The influence of thermal application on dysphagia for liquid boluses after multiple cerebrovascular accidents was measured. A month-long trial of thermal application organized according to the guidelines of a single-subject withdrawal or ABAB design was replicated across 7 male subjects. After baseline testing, 6 subjects were randomly assigned to begin the study with a week-long period of thermal application (B stage), and 1 subject was randomly assigned to begin the study with a week-long period of no thermal application (A stage). Subsequent week-long A and B stages were then alternated until each subject had completed the 4-week interval of this study. Progress testing occurred at the end of each stage and at follow-up testing 1 month after the study's completion. The influence of thermal application on eight duration and four descriptive measures was determined by three judges using visual inspection of data displays. Two of three judges agreed that 2 of the subjects demonstrated decreased Duration of Stage Transition in the absence of any change in the occurrence of aspiration or penetration. Overall, this study failed to reveal strong evidence that 2 weeks of thermal application alternating with 2 weeks of no thermal application improves dysphagia following multiple strokes. Further replications are needed.

Aged↗
PubMed2002

Application of a computerized nursing care plan system in one hospital: experiences of ICU nurses in Taiwan.

AIM OF THE STUDY: The purpose of this paper is to present ICU nurses' experiences with a computerized nursing care plan system at a medical centre in Taiwan. BACKGROUND: Computerized nursing care plans have been implemented in recent years, but users' perceptions of this technology have not been comprehensively explored. It is believed that by taking into consideration users' experiences with computer use, strategies and programs can be developed to help users adapt to new systems. METHODS: A qualitative study, involving one-to-one interviews, was conducted with 12 Registered Nurses. Data were analysed according to Miles and Huberman's data reduction, data display and conclusion verification process. FINDINGS: Themes related to the clinical impact of system use were: 'saves paper/time', 'time-consuming for print-outs', 'de-individualization of care plan', 'routine/paperwork requirement', 'no consensus for nursing diagnoses', and 'guidelines for the novice'. CONCLUSIONS: Nurses prefer tools that can help them save time with paperwork and focus on targeting patient problems. With careful assessment and evaluation of nurses' experiences in the use of clinical computer systems, the success of computer implementation can be enhanced.

Attitude to Computers↗
PubMed2004

Sound attenuation, shear viscosity, and mutual diffusivity behavior in the nitroethane-cyclohexane critical mixture.

The shear viscosity eta(s), mutual diffusion coefficient D, and ultrasonic attenuation spectra of the nitroethane-cyclohexane mixture of critical composition have been measured at various temperatures near the critical temperature T(c). The relaxation rate of order parameter fluctuations resulting from a combined evaluation of the eta(s) and D data follows power law behavior with the theoretical exponent and with the large amplitude Gamma(o)=(156+/-2)x10(9) s(-1). The ultrasonic spectra have been evaluated in terms of a critical contribution and a noncritical background contribution. The amplitude of the former exhibits a temperature dependence, in conformity with a temperature dependence in the adiabatic coupling constant (|g| = 0.064 near T(c) and 0.1 at T-T(c)=3 K). If the variation of the critical amplitude with T is taken into account the experimental attenuation coefficient data display a scaling function which nicely fits to the theoretical prediction from the Bhattacharjee-Ferrell dynamic scaling model [R. A. Ferrell and J. K. Bhattacharjee, Phys. Rev. A 31, 1788 (1985)].

Journal Article↗
PubMed2005

Combined metabolic gas analyser and dGPS analysis of performance in cross-country skiing.

The purpose of this study was to provide a more detailed analysis of performance in cross-country skiing by combining findings from a differential global positioning system (dGPS), metabolic gas measurements, speed in different sections of a ski-course and treadmill threshold data. Ten male skiers participated in a freestyle skiing field test (5.6 km), which was performed with dGPS and metabolic gas measurements. A treadmill running threshold test was also performed and the following parameters were derived: anaerobic threshold, threshold of decompensated metabolic acidosis, respiratory exchange ratio = 1, onset of blood lactate accumulation and peak oxygen uptake (VO2peak). The combined dGPS and metabolic gas measurements made detailed analysis of performance possible. The strongest correlations between the treadmill data and final skiing field test time were for VO2peak (l x min(-1)), respiratory exchange ratio = 1 (l x min(-1)) and onset of blood lactate accumulation (l x min(-1)) (r = -0.644 to - 0.750). However, all treadmill test data displayed stronger associations with speed in different stretches of the course than with final time, which stresses the value of a detailed analysis of performance in cross-country skiing. Mean oxygen uptake (VO2) in a particular stretch in relation to speed in the same stretch displayed its strongest correlation coefficients in most stretches when VO2 was presented in units litres per minute, rather than when VO2 was normalized to body mass (ml x kg(-1) x min(-1) and ml x min(-1) x kg(-2/3)). This suggests that heavy cross-country skiers have an advantage over their lighter counterparts. In one steep uphill stretch, however, VO2 (ml x min(-1) x kg(-2/3)) displayed the strongest association with speed, suggesting that in steep uphill sections light skiers could have an advantage over heavier skiers.

Adolescent↗
PubMed2000

Computer-aided video exposure monitoring.

A computer-aided video exposure monitoring system was used to record exposure information. The system comprised a handheld camcorder, portable video cassette recorder, radio-telemetry transmitter/receiver, and handheld or notebook computers for remote data logging, photoionization gas/vapor detectors (PIDs), and a personal aerosol monitor. The following workplaces were surveyed using the system: dry cleaning establishments--monitoring tetrachoroethylene in the air and in breath; printing works--monitoring white spirit type solvent; tire manufacturing factory--monitoring rubber fume; and a slate quarry--monitoring respirable dust and quartz. The system based on the handheld computer, in particular, simplified the data acquisition process compared with earlier systems in use by our laboratory. The equipment is more compact and easier to operate, and allows more accurate calibration of the instrument reading on the video image. Although a variety of data display formats are possible, the best format for videos intended for educational and training purposes was the review-preview chart superimposed on the video image of the work process. Recommendations for reducing exposure by engineering or by modifying work practice were possible through use of the video exposure system in the dry cleaning and tire manufacturing applications. The slate quarry work illustrated how the technique can be used to test ventilation configurations quickly to see their effect on the worker's personal exposure.

Aerosols↗
PubMed2006

Development of a spreadsheet for the calculation of new tools to improve the reporting of the results of medical research.

PRIMARY OBJECTIVE: Confidence levels, clinical significance curves and risk - benefit contours have recently been developed with the aim of improving the interpretation of clinical studies. It has been suggested that their use may complement traditional methods of result reporting (i.e. p values and 95% confidence intervals), and subsequently improve medical decision-making. These new methods have been used to report study results; however, widespread use may be hampered by the lack of available computer software. Our objective was to design user-friendly software to enable researchers to use these statistical methods. RESEARCH DESIGN: A spreadsheet was designed to calculate these statistics for the assessment of two arm medical studies. The spreadsheet was tested using a wide range of input data and operating systems. User-friendliness was tested by researchers who had no background in statistics. MAIN OUTCOMES AND RESULTS: The confidence calculator was successfully designed, and found to be user-friendly. The spreadsheet is MS Excel-based to allow wide usage. The spreadsheet is freely available from the author and from the web site http://www.primercollaboration.com/Tools/tools.html. CONCLUSIONS: We have successfully designed a spreadsheet that is simple to use and freely accessible for researchers. This is the first such software that calculates confidence levels, clinical significance curves, and risk - benefit contours.

Biomedical Research↗
PubMed2006

Tympanometric norms for Chinese schoolchildren.

Current tympanometric norms have acknowledged the relevance of age as an influencing factor. However, little attention has been afforded to other potentialities such as the non-pathological effects of gender, ear asymmetry, and racial heritage. This study aimed to examine normative tympanometric findings in a large sample of Chinese schoolchildren. Using a Madsen 901 Middle Ear Analyzer, data was collected from 269 children (538 ears), ranging in age from 6.2 12.7 years (mean = 9.4 years, SD = 1.7), in Jiangsu province. Descriptive statistics were calculated for the parameters of equivalent ear canal volume (chi = 1.03, SD = 0.25, 90% = 0.68 1.46), peak compensated static acoustic admittance (chi = 0.58, SD = 0.34, 90%=0.26 1.13), tympanometric width (chi = 112, SD = 36, 90% = 62-156), and peak pressure (chi = -25, SD = 30, 90% = -85 -/+ 10). Statistically significant ear asymmetry and grade/age effects were established, although differences found were minor. In comparison with past studies in Caucasian paediatric populations, the Chinese normative data displayed minimal disparities.

Acoustic Impedance Tests↗
PubMed1996

Exploratory data analysis: data visualization or torture?

Exploratory Data Analysis offers a set of graphical and statistical tools to find the full meaning from data sets. The user visualizes, analyzes, and transforms data distributions with these tools. Graphs reveal relationships between variables; the residuals left after fitting data show the adequacy of the model. Without this careful examination and understanding of the data, rote data analysis using standard statistical tests can give misleading results. Exploratory Data Analysis has its own set of pitfalls and must be used with confirmatory statistics and studies. Increasing power and resolution in personal computers enables modern statistical software to make these methods widely accessible. By easily moving between data and their graphic representation, analysis can be comprehensive without being tedious. Exploratory Data Analysis can add an exciting and useful tool to the epidemiologist's repertoire. This article illustrates several tools from an evolving list.

Computer Graphics↗