Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computing Methodologies”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,135 records · Page 63Linked to original sources
PubMed2006

FT-IR, FT-Raman spectra and scaled quantum mechanical study of 2,3-dihydroxy pyridine and 2,4-dihyroxy-3-nitropyridine.

The vibrational spectra of 2,3-dihydroxy pyridine (DHP) and 2,4-dihyroxy-3-nitropyridine (DHNP) have been computed using B3LYP methodology and 6-31G** basis set. The solid phase FTIR and FT Raman spectra were recorded in the region 4000-400 and 3500-100 cm(-1), respectively. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors.

Molecular Structure↗
PubMed1996

Heart rate variability in the early hours of an acute myocardial infarction.

The occurrence of an autonomic disturbance early in acute myocardial infarction (AMI) has been reported: signs of sympathetic activation were mainly observed in relation to an anterior localization, whereas signs of vagal overactivity were more frequent in inferior wall AMI. Information is limited in relation to the persistence of these alterations during the early hours of AMI. We studied 33 patients with an AMI within 188 +/- 16 minutes from the onset of symptoms and 1 week after hospital admission. From a 20-minute Holter recording, we computed with autoregressive methodology, time and frequency domain indexes of heart rate variability. At admission, patients with an anterior wall AMI exhibited a smaller RR variance (593 +/- 121 ms2) than did those with an inferior wall AMI (1,122 +/- 191 ms2). In both groups the spectral profile was characterized by a predominant (73 +/- 4 and 61 +/- 4 normalized units) low frequency and by a small (13 +/- 2 and 22 +/- 3 normalized units) high-frequency component, indicating the presence of a sympathetic excitation and of a diminished vagal modulation. Although signs of sympathetic activation were more evident in patients with anterior wall AMI, no evidence of a vagal hyperactivity was observed in patients with inferior wall AMI. In the latter group, we noticed 1 week after the acute event an increase in the low-frequency component, which reached the values observed in patients with anterior wall AMI. Thrombolysis did not affect heart rate variability parameters. Thus, this study suggests the presence of an autonomic disturbance characterized by signs of sympathetic excitation and of a reduced vagal modulation, which was more evident in patients with an anterior localization early after AMI.

Electrocardiography, Ambulatory↗
PubMed1999

Concordancing: use of language-based research in medical communication.

BACKGROUND: The available literature on medical communication reports almost exclusively on observational, qualitative studies. We aimed to apply a novel approach to the analysis of doctor-patient consultation by means of computer concordancing. This methodology, established in linguistic research but rarely applied to professional language, allows both the quantitative and qualitative study of language. METHODS: We analysed the language of 40 doctors and their patients during 373 complete primary-care consultations. We examined the use of jargon by doctors, the language of power and absence of power, and ways in which language was used to diminish the potential threat of the presenting disorder. FINDINGS: There was no evidence that the doctors used medical jargon. Some doctors used language associated with social power, and some patients used language associated with absence of power. There was substantial evidence that the doctors used language to express emotions (eg, anxiety), to diminish threats (eg, words such as "little"), and to reassure patients. INTERPRETATION: Concordancing is a valuable resource to study the consultation. The finding that doctors do not use jargon suggests that they are aware of the need to avoid it, but it does not follow that they are easily understood by patients. The use of some elements of the language of power may imply that consultations may be less democratic than is appropriate. The language of emotion and diminution is a major part of the primary-care doctor's repertoire and denotes a therapeutic use of language.

Dominance-Subordination↗
PubMed1986

Guidelines for use of lumbar spine radiography.

In deciding whether to obtain lumbosacral spine films, the emergency physician must not ask whether a diagnosis can be established, but whether obtaining films will affect management. Low back pain is a considerable problem for society with cost in billions of dollars. Gonadal radiation from lumbosacral radiographs is significant, and thus ordering films should be minimized. Plain radiographs are rarely indicated in otherwise healthy patients 20 to 50 years old with mechanical or root pain on initial presentation. In other patients alternative diagnostic methodologies such as computed tomography may be superior, with less radiation risk. Specific recommendations for emergency radiographic evaluation of the lumbosacral spine are offered.

Adult↗
PubMed2003

Language evolution: consensus and controversies.

Why is language the way it is? How did language come to be this way? And why is our species alone in having complex language? These are old unsolved questions that have seen a renaissance in the dramatic recent growth in research being published on the origins and evolution of human language. This review provides a broad overview of some of the important current work in this area. We highlight new methodologies (such as computational modeling), emerging points of consensus (such as the importance of pre-adaptation), and the major remaining controversies (such as gestural origins of language). We also discuss why language evolution is such a difficult problem, and suggest probable directions research may take in the near future.

Journal Article↗
PubMed1991

An integrated approach to three-dimensional information management with MACCS-3D.

In the past decade, the scientific community has realized the value of three-dimensional (3D) structural information and '3D searching' has started to become an important new methodology for computer-aided drug design. During this time, molecular modeling information generated from various sources has proliferated due to the growing availability of software and hardware and the increasing use of crystallographic and spectroscopic techniques. This information needs to be organized to allow for its effective storage and retrieval. This paper presents an approach to address this problem with a recently introduced program, MACCS-3D. In particular, this approach utilizes MACCS-3D's capability of handling data specific for atoms and atom pairs. With this software, various biological, computational, and spectroscopic data can be merged, allowing scientists from different disciplines to access and use this information more efficiently.

Chemistry, Organic↗
PubMed2006

De novo structure-based design of bisurea hosts for tetrahedral oxoanion guests.

This paper presents a computational approach to the deliberate design of improved host architectures. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential structures. The efficacy of this computer-aided design methodology is illustrated with a search for bisurea podands that are structurally organized for complexation with tetrahedral oxoanions.

Journal Article↗
PubMed2005

Theoretical calculations of refractive indices and optical effects in spectra of nitric acid and nitric acid monohydrate crystals.

The theoretical infrared refractive indices of two systems related to atmospheric research, nitric acid (NA) and nitric acid monohydrate (NAM) crystals, have been computed using a methodology based on first-principles. The effects of lack of coherence in the infrared beam in RAIR and transmission spectra have also been treated using a model based on classical optics. The optical constants of NA crystals are presented for the first time; the results on NAM are compared to empirical values previously published with good general agreement. With the optical constants of NA, polarized reflection-absorption infrared spectra are predicted and compared to experimental spectra recorded also for the first time, for a set of varying film thickness. The global agreement is satisfactory. The effects of a number of experimental factors in transmission spectra of NAM are assessed, in an attempt to explain observed differences among experimental spectra. It is concluded that the spectral disparities are probably due to differences in the nature of the samples.

Journal Article↗
PubMed2005

Challenges of crystal structure prediction of diastereomeric salt pairs.

A methodology for the computational prediction of the crystal structures and resolution efficiency for diastereomeric salt pairs is developed by considering the polymorphic system of the diastereomeric salt pair (R)-1-phenylethylammonium (R/S)-2-phenylpropanoate. To alleviate the mathematical complexity of the search for minima in the lattice energy due to the presence of two flexible entities in the asymmetric unit, the range of rigid-body lattice energy global optimizations was guided by a statistical analysis of the Cambridge Structural Database for common ion-pair geometries and ion conformations. A distributed multipole model for the dominant electrostatic interactions and high-level ab initio calculations for the intramolecular energy penalty for conformational distortions are used to quantify the relative stabilities of the p- and n-salt forms. While the ab initio prediction of the known structure of the p-salt as the most stable structure was insensitive to minor changes in the rigid-ion conformations considered, the relative stabilities of the known polymorphs and hypothetical structures of the n-salt were very sensitive. Although this paper provides a significant advance over traditional search algorithms and empirical force fields in determining the structures and relative stabilities of diastereomeric salt pairs, the sensitivity of the computed lattice energies to the fine details of the ion conformations overtaxes current computational models and renders the design of diastereomeric resolution processes by computational chemistry a challenging problem.

Algorithms↗
PubMed2002

Revisiting field experimentation: field notes for the future.

Field experiments in the social sciences were increasingly used in the 20th century. This article briefly reviews some important lessons in design, analysis, and theory of field experiments emerging from that experience. Topics include the importance of ensuring that selection into experiments and assignment to conditions occurs properly, how to prevent and analyze attrition, the need to attend to power and effect size, how to measure and take partial treatment implementation into account in analyses, modern analyses of quasi-experimental and multilevel data, Rubin's model, and the role of internal and external validity. The article ends with observations on the computer revolution in methodology and statistics, convergences in theory and methods across disciplines, the need for an empirical program of methodological research, the key problem of selection bias, and the inevitability of increased specialization in field experimentation in the years to come.

Forecasting↗
PubMed1998

Body mass and 26 y risk of mortality among men who never smoked: a re-analysis among men from the Adventist Mortality Study.

OBJECTIVE: To re-analyse the previously reported linear relation between Quetelet's body mass index (BMI) and mortality, among men from the Adventist Mortality Study after accounting for effects due to age at measurement of BMI, smoking history and race. DESIGN: Prospective cohort study. To specifically account for effects due to age at measurement of BMI, smoking history and race, our methodology includes: 1, computing hazard ratios for BMI quintiles from a proportional hazard regression, with 'time on study' as the time variable, and age at baseline as a covariate; 2, conducting separate analyses of middle-aged (age 30-54y) and older (age 55-74y) men; and 3, restriction of the analyses to never-smoking, non-Hispanic white males. SUBJECTS: 5062 men (age: 30-74 y, BMI: 14-44 kg/m2) from the Adventist Mortality Study. MEASUREMENTS: Subjects reported data on anthropometric, demographic, medical, dietary and lifestyle characteristics at baseline and were enrolled in mortality surveillance during a 26y study period (1960-1985). RESULTS: During the early years of follow-up (years 1-8, 9-14), we found some evidence of excess risk among the leanest men that was probably due to the effects of antecedent illness. During the later years of follow-up (years 15-26), effects due to antecedent illness were not apparent and a significant positive, linear relation between BMI and all-cause mortality was consistently found among middle-aged (30-54 y) and older (55-74 y) men. Disease-specific analyses of the later follow-up (years 15-26) revealed that the positive linear trends with all-cause mortality, were primarily due to excess risk of cardiovascular disease and cancer among the heavier men. Among older men, a significant inverse relation between BMI and respiratory disease mortality risk was identified during later follow-up (years 15-26), but this effect attenuated after restriction of the analyses to men with no baseline history of respiratory disease. CONCLUSIONS: The re-analysis confirms the findings of a positive, linear relation between BMI and all-cause mortality, reported in the original study.

Adult↗
PubMed2006

An adaptive clinical test of temporal resolution.

PURPOSE: It has been recommended that diagnostic and screening test batteries for auditory processing disorder (APD) include a measure of temporal gap detection using broadband noise stimuli. Although psychophysical laboratory procedures exist for the measurement of temporal resolution, none are clinically feasible. This study was designed to obtain preliminary data on a new clinical measure of gap detection, the Adaptive Test of Temporal Resolution (ATTR). METHOD: The ATTR, a currently available clinical test (Random Gap Detection Test), and a standard psychophysical laboratory procedure were used to measure gap detection thresholds (GDTs) from a group of 30 young adults with normal hearing. RESULTS: Mean ATTR GDTs were 2.2 ms, consistent with GDTs measured using the psychophysical laboratory procedure (3.2 ms) and significantly smaller than those measured using the Random Gap Detection Test (7.0 ms). CONCLUSIONS: Because it incorporates standard adaptive psychophysical methodology in a computer application that can be used on any desktop computer but does not depend on specialized hardware for application, the ATTR promises to be a clinically feasible addition to the APD test battery.

Acoustic Stimulation↗
PubMed2005

A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution.

The free energy change associated with the isomerization reaction of glycine in water solution has been studied by a hybrid quantum mechanical/molecular mechanical (QM/MM) approach combined with the theory of energy representation (QM/MM-ER) recently developed. The solvation free energies for both neutral and zwitterionic form of glycine have been determined by means of the QM/MM-ER simulation. The contributions of the electronic polarization and the fluctuation of the QM solute to the solvation free energy have been investigated. It has been found that the contribution of the density fluctuation of the zwitterionic solute is estimated as -4.2 kcal/mol in the total solvation free energy of -46.1 kcal/mol, while that of the neutral form is computed as -3.0 kcal/mol in the solvation free energy of -15.6 kcal/mol. The resultant free energy change associated with the isomerization of glycine in water has been obtained as -7.8 kcal/mol, in excellent agreement with the experimental data of -7.3 or -7.7 kcal/mol, implying the accuracy of the QM/MM-ER approach. The results have also been compared with those computed by other methodologies such as the polarizable continuum model and the classical molecular simulation. The efficiency and advantage of the QM/MM-ER method has been discussed.

Journal Article↗
PubMed2000

Pilot testing standardized surveillance: Hospital Infection Standardised Surveillance (HISS). On behalf of the HISS Reference Group.

In Australia the time-consuming nature of double handling of surveillance data has meant that surveillance methodology rarely included prospective monitoring of patients at risk for the acquisition of a nosocomial infection. To streamline surveillance activities, infection control professionals favored the collection of case data either from the ward or pathology laboratories. By default, this method introduced a variety of definitions resulting in inconsistencies across health care facilities and artificial fluctuations in the magnitude of infection. In June 1998, the New South Wales Health Department funded its first attempt to develop and implement a standardized approach to collection of nosocomial infection data-Hospital Infection Standardized Surveillance (HISS). Six months later, in December 1998, 10 public acute care hospitals pilot tested the content and methodology of HISS. HISS members tested the application of the National Nosocomial Infection Surveillance system definitions for infection, active and passive surveillance methodology, the handheld computer for data collection, and the Electronic Infection Control Automated Technology (eICAT) version for HISS software and analysis. HISS member hospitals selected from several sentinel monitoring programs such as intravascular device-related bacteremia and nonintravascular device-related bacteremia infections, surgical site infections, respiratory syncytial virus infections, and rotavirus infections. Hospitals continued to perform active surveillance in the first 12 months, collecting demographic variables, risk factors, and outcomes. The completeness of the data sets for the two most frequently monitored programs, surgical site infections and intravascular device-related bacteremia, was high, with 99.6% of the required 36, 372 surgical site infection data fields and 99.4% of the 572,717 intravascular device-related bacteremia data fields completed.

Acute Disease↗
PubMed2006

First-principles, quantum-mechanical simulations of electron solvation by a water cluster.

Despite numerous experiments and static electronic structure calculations, the nature of hydrated-electron clusters, (H2O)(n)(-), remains poorly understood. Here, we introduce a hybrid ab initio molecular dynamics scheme, balancing accuracy against feasibility, to simulate vibrational and photoelectron spectra of (H(2)O)(n)(-), treating all electrons quantum-mechanically. This methodology provides a computational tool for understanding the spectra of weakly bound and supramolecular anions and for elucidating the fingerprint of dynamics in these spectra. Simulations of (H2O)(4)(-) provide quantitative agreement with experimental spectra and furnish direct evidence of the nonequilibrium nature of the cluster ensemble that is probed experimentally. The simulations also provide an estimate of the cluster temperature (T approximately 150-200 K) that is not available from experiment alone. The "double acceptor" electron-binding motif is found to be highly stable with respect to thermal fluctuations, even at T = 300 K, whereas the extra electron stabilizes what would otherwise be unfavorable water configurations.

Journal Article↗
PubMed2004

A free energy based computational pathway from chemical templates to lead compounds: a case study of COX-2 inhibitors.

Automation of lead compound design in silico given the structure of the protein target and a definition of its active site vies for the top of the wish list in any drug discovery programme. We present here an enumeration of steps starting from chemical templates and propose a solution at the state of the art, in the form of a system independent comprehensive computational pathway. This methodology is illustrated with cyclooxygenase-2 (COX-2) as a target. We built candidate molecules including a few Non Steroidal Anti-inflammatory Drugs (NSAIDs) from chemical templates, passed them through empirical filters to assess drug-like properties, optimized their geometries, derived partial atomic charges via quantum calculations, performed Monte Carlo docking, carried out molecular mechanics and developed free energy estimates with Molecular Mechanics Generalized Born Solvent Accessibility (MMGBSA) methodology for each of the candidate molecules. For the case of aspirin, we also conducted molecular dynamics on the enzyme, the drug and the complex with explicit solvent followed by binding free energy analysis. Collectively, the results obtained from the above studies viz. sorting of drugs from non-drugs, semi-quantitative estimates of binding free energies, amply demonstrate the viability of the strategy proposed for lead selection/design for biomolecular targets.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2005

Contemporary measurement techniques for rehabilitation outcomes assessment.

In this article, we review the limitations of traditional rehabilitation functional outcome instruments currently in use within the rehabilitation field to assess Activity and Participation domains as defined by the International Classification of Function, Disability, and Health. These include a narrow scope of functional outcomes, data incompatibility across instruments, and the precision vs feasibility dilemma. Following this, we illustrate how contemporary measurement techniques, such as item response theory methods combined with computer adaptive testing methodology, can be applied in rehabilitation to design functional outcome instruments that are comprehensive in scope, accurate, allow for compatibility across instruments, and are sensitive to clinically important change without sacrificing their feasibility. Finally, we present some of the pressing challenges that need to be overcome to provide effective dissemination and training assistance to ensure that current and future generations of rehabilitation professionals are familiar with and skilled in the application of contemporary outcomes measurement.

Activities of Daily Living↗
PubMed2005

Assessing reliable and clinically significant change on Health of the Nation Outcome Scales: method for displaying longitudinal data.

OBJECTIVE: Many authors recommended that reliable and clinically significant change (RCSC) should be calculated when reporting results of interventions. To test the reliability of the Health of the Nation Outcome Scales (HoNOS) in identifying RCSC, we applied the Jacobson and Truax model to two HoNOS assessments in a large group of people evaluated in 10 community mental health services in Lombardy, Italy, in 2000. METHOD: The HoNOS was administered to 9817 patients; of these, 4759 (48%) were re-assessed. Reliable change (RC) was calculated using Cronbach's alpha (alpha), as a parameter of the reliability of the measure. Clinical significance cut-offs were calculated using a classification of severity based on HoNOS items. RESULTS: In the whole sample, the clinical improvement cut-off was 11 and the remission cut-off was 5. Considering the severe patients, the clinical improvement cut-off was 12. The RC index calculated on the whole group and on the subgroup of severe patients indicated that eight-point and seven-point changes, respectively, were needed to be confident that a real change had occurred. Longitudinal changes were depicted on two-dimensional graphs as examples of reporting RCSC on HoNOS total scores in a routine data collection: 91.6% of the whole sample (4361) was stable, 5.6% (269) improved and 1.8% (129) worsened. CONCLUSION: Our study proposes a methodological framework for computing RCSC normative data on a widely used outcome scale and for identifying different degrees of clinical change.

Follow-Up Studies↗