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PubMed1998

Advances in HIV/AIDS statistical methodology over the past decade.

This review provides a synopsis of the developments over the past decade in mathematical and statistical methodology in response to the AIDS epidemic. This review includes highlights of the development of epidemic models, approaches to describing the natural history of HIV infection, and the methods developed for HIV therapeutic or prevention research. A bibliography, which is extensive but purposely not intended to be comprehensive, is included. The intention is to provide a historical perspective on the methodologic developments and a framework for identifying HIV/AIDS-related needs for the future.

Anti-HIV Agents↗

PubMed1996

New theoretical methodology for elucidating the solution structure of peptides from NMR data. II. Free energy of dominant microstates of Leu-enkephalin and population-weighted average nuclear Overhauser effects intensities.

A small linear peptide in solution may populate several stable states (called here microstates) in thermodynamic equilibrium; elucidating its dynamic three dimensional structure by multi- dimensional nmr is complex since the experimentally measured nuclear Overhauser effect intensities (NOEs) represent averages over the individual contributions. We propose a new methodology based on statistical mechanical considerations for analyzing nmr data of such peptides. In a previous paper (called paper I, H. Meirovitch et al. (1995) Journal of Physical Chemistry, 99, 4847-4854] we have developed theoretical methods for determining the contribution to the partition function Z of the most stable microstates, i.e. those that pertain to a given energy range above the global energy minimum (GEM). This relatively small set of dominant microstates provides the main contribution to medium- and long-range NOE intensities. In this work the individual populations and NOEs of the dominant microstates are determined, and then weighted averages are calculated and compared with experiment. Our methodology is applied to the pentapeptide Leu-enkephalin H-Tyr-Gly-Gly-Phe-Leu-OH, described by the potential energy function ECEPP. Twenty one significantly different energy minimized structures are first identified within the range of 2 kcal/mol above the GEM by an extensive conformational search; this range has been found in paper I to contribute 0.6 of Z. These structures then become "seeds" for Monte Carlo (MC) simulations designed to keep the molecule relatively close to its seed. Indeed, the MC samples (called MC microstates) illustrate what we define as intermediate chain flexibility; some dihedral angles remain in the vicinity of their seed value, while others visit the full range of [-180 degrees, 180 degrees]. The free energies of the MC microstates (which lead to the populations) are calculated by the local states method, which (unlike other techniques) can handle any chain flexibility. The NOE of MC microstate i is calculated as the average <1/r(3)>i(2), and an effective interatomic distance ri(eff) is defined as ri(eff) = i(-1/3), where r is the distance between two protons. Under "initial rate approximation," and neglecting angular modulations, the overall I is the average over ri(eff-6), weighted by the populations of the MC microstates. This treatment is justified under the assumption that the rates at which conformations interconvert within, and among, microstates are faster and slower, respectively, than the rotational reorientation of the molecule. I(-6) leads to the virtual theoretical distances, compared to the corresponding virtual experimental distances, which were obtained previously from a cryoprotective solution of Leu-enkephalin at 280 K. A reasonable fit is found between theory and experiment. Future research directions are outlined.

Computers↗

PubMed1982

A, B, H antigen detectability in normal and neoplastic urothelium. Influence of methodologic factors.

Markedly reduced or absent reactivity for the normally expressed A B H antigens in transitional cell carcinomas (TCCs) of the human urinary bladder appears to correlate with an aggressive clinical course. To evaluate the clinical applicability of this observation, the authors investigated the influence of methodologic variants as well as certain patient characteristics on urothelial A, B, H reactivity. Biopsy-obtained TTCs and/or normal mucosae from 104 patients were examined for the effect of fixation, paraffinization, and alcohol treatment. Variability due to the secretor status and blood group of the patient was evaluated in conjunction with methodologic factors. In the fresh-frozen state, the expected antigen was always detectable in normal mucosas but only in 69% of TCCs regardless of patient's secretor status and blood group (BG). Few normal mucosae (12%) but a large number of TTCs (46%) converted to negative after paraffin processing. Similar reduction in A, B, H reactivity was also noted when the tissues were treated with concentrations of alcohol comparable to those used in the paraffin procedure. Tumor antigens were more sensitive to alcohol. This suggested that in neoplastic cells ABH determinants are not only fewer but also disproportionately represented in polar (alcohol-soluble) molecules. Alcohol more profoundly affected tissues from nonsecretors probably because the proportion of alcohol-soluble A, B, H substances differs in secretors and nonsecretors. In the fresh-frozen state, the H antigen was detectable with the Ulex Europeus lectin in the majority of TCCs from BGO patients (79%) as well as in most tumors from BGA or B patients (90%) even in the absence of the expected A or B antigen. Alcohol treatment, however, more potently reduced reactivity for H rather than the other antigens, a phenomenon that also points to the significance of glycolipid extraction and explains the marked differences in the detectability of this antigen between fresh-frozen and paraffin-processed TCCs.

ABO Blood-Group System↗

PubMed1978

Methodological advances in the validation of inventory items, scales, profiles and interpretations.

Factor analytic research is still in its infancy--theoretically, methodologically, and interpretively. Definitive research has not yet been done on problems of (a) item design and selection of items suitable for factor analysis; (b) identification of highly significant marker items; (c) tracings of item response distributions across scales, populations, occasions and other relevant variables; (d) determination of the number of items with different loadings necessary to obtain valid scale scores for psychological state measurements; (e) questions about the validity of summating factorially heterogeneous lowly correlated items in arriving at scale scores; (f) the use of clinical judgment to evaluate the possibly differing significances of the same item responses across populations and occasions; i.e., does the same factored item response have the same significance across scales?; (g) how to interpret scales with factorially mixed item compositions; (h) clinical judgement decisions in evaluating and interpreting scale meanings; and (i) the comparison of the results of analyzing data by different scaling methods. This study makes a start toward clarifying these methodological issues by analyzing the results of applying different methods of scale construction that utilized 146,000 item responses made by 730 Ss on the Personal Health Survey, a 200-item inventory designed to measure organ system functioning that contributes to physical and mental health.

Evaluation Studies as Topic↗

PubMed2001

Gross anatomy course content and teaching methodology in allied health: clinicians' experiences and recommendations.

The purpose of this study was to sample the experiences and recommendations of clinicians in allied health fields about gross anatomy courses. The objective was to determine if practicing clinicians recommended a course in gross anatomy, and, if so, their recommendations for course content and teaching methodology. Questionnaires were mailed to a random selection of occupational therapists (OTs), physician assistants (PAs), and physical therapists (PTs) licensed in the state of Texas. In addition to demographics, the survey asked 14 questions regarding the experiences and recommendations in seven areas of interest about gross anatomy courses. The responding sample appeared to be representative of the target population. A course in human gross anatomy during professional school was recommended by 96% of OTs, and 100% of PAs and PTs. The single most recommended teaching method was student dissection of human cadavers. Although significant differences were found regarding primary course orientation, a majority favored some form of combined systems and regional oriented courses. A majority of clinicians in each field recommended a gross anatomy course at the beginning of professional training. Specific recommendations were given for content of systems and regional oriented gross anatomy courses. We recommend that the gross anatomy course content and teaching methodologies in allied health areas be responsive to the specific needs of each clinical specialty.

Adult↗

PubMed2005

The global burden of selected occupational diseases and injury risks: Methodology and summary.

BACKGROUND: Around the globe, work has a heavy impact on health. To better advise policy makers, we assessed the global burden of disease and injury due to selected occupational hazards. This article presents an overview, and describes the methodology employed in the companion studies. METHODS: Using the World Health Organization (WHO) Comparative Risk Assessment methodology, we applied relative risk measures to the proportions of the population exposed to selected occupational hazards to estimate attributable fractions, deaths, and disability-adjusted life years (DALYs). Numerous occupational risk factors had to be excluded due to inadequate global data. RESULTS: In 2000, the selected risk factors were responsible worldwide for 37% of back pain, 16% of hearing loss, 13% of chronic obstructive pulmonary disease (COPD), 11% of asthma, 8% of injuries, 9% of lung cancer, and 2% of leukemia. These risks at work caused 850,000 deaths worldwide and resulted in the loss of about 24 million years of healthy life. Needlesticks accounted for about 40% of Hepatitis B and Hepatitis C infections and 4.4% of HIV infections in health care workers. CONCLUSIONS: Exposure to occupational hazards accounts for a significant proportion of the global burden of disease and injury, which could be substantially reduced through application of proven risk prevention strategies.

Accidents, Occupational↗

PubMed1990

Beyond surveillance: methodologic considerations in analytic studies of agricultural injuries.

A major impediment to current efforts to lower the toll of injuries in agricultural workers is a fundamental lack of knowledge of the causes and risk factors associated with these injuries. Surveillance systems and other descriptive efforts can provide useful information on the scope and spectrum of agricultural injuries but can seldom identify specific factors, such as faulty machinery, risky behaviors, or particularly hazardous environments, which can be the focus of preventive efforts. Since few analytic epidemiologic studies of the causes of agricultural injuries have been conducted to date, a large number of focused, carefully designed studies, of both cohort and case-control design, will be needed to develop the information on which effective interventions can be based. This paper highlights certain methodologic barriers to effective analytic studies of agricultural injuries and suggests approaches to addressing these methodologic concerns.

Accidents, Occupational↗

PubMed2006

Methodology of detailed dosimetry and treatment of uncertainty and variations for in vivo studies.

Detailed and accurate dosimetric information is a basic precondition for acquiring adequate interpretations and valuations of in vivo studies testing radiofrequency (RF) electromagnetic fields (EMF). Instantaneous locally induced fields depend on many parameters, for example, orientation of the animal with respect to the incident field, animal size and posture, and tissue distribution. These parameters are often constrained, resulting in significant uncertainties in the dosimetric assessment of the exposure, averaged over all animals and the entire experimental phase, as well as in significant variations of the local exposures during the experiment. A sufficient analysis should therefore include (1) average and peak spatial specific absorption rate (SAR) values for the whole body and specific organs, (2) the uncertainty of each assessed SAR value, and (3) the short term and long term SAR variations between the tissues of individual animals. A methodology to obtain this pertinent information is developed and proposed in this paper. Using this methodology the dosimetry of a rat exposure apparatus operating at the carrier frequency of 1747 MHz, previously developed for a 2-year bioassay study within the European Union project PERFORM, was obtained. We have demonstrated that comprehensive dosimetric data can be obtained with reasonable effort using the proposed method, providing that the exposure setup is soundly formulated.

Animals↗

PubMed2002

Hybrid model building methodology using unsupervised fuzzy clustering and supervised neural networks.

This paper suggests a model building methodology for dealing with new processes. The methodology, called Hybrid Fuzzy Neural Networks (HFNN), combines unsupervised fuzzy clustering and supervised neural networks in order to create simple and flexible models. Fuzzy clustering was used to define relevant domains on the input space. Then, sets of multilayer perceptrons (MLP) were trained (one for each domain) to map input-output relations, creating, in the process, a set of specified sub-models. The estimated output of the model was obtained by fusing the different sub-model outputs weighted by their predicted possibilities. On-line reinforcement learning enabled improvement of the model. The determination of the optimal number of clusters is fundamental to the success of the HFNN approach. The effectiveness of several validity measures was compared to the generalization capability of the model and information criteria. The validity measures were tested with fermentation simulations and real fermentations of a yeast-like fungus, Aureobasidium pullulans. The results outline the criteria limitations. The learning capability of the HFNN was tested with the fermentation data. The results underline the advantages of HFNN over a single neural network.

Biotechnology↗

PubMed2006

A methodology for centrifuge selection for the separation of high solids density cell broths by visualisation of performance using windows of operation.

Expression systems capable of growing to high cell densities are now readily available and are popular due to the benefits of increased product concentration. However, such high solids density cultures pose a major challenge for bioprocess engineers as choosing the right separation equipment and operating it at optimal conditions is crucial for efficient recovery. This study proposes a methodology for the rapid determination of suitable operating conditions for the centrifugal recovery of high cell density fermentation broths. An ultra scale-down (USD) approach for the prediction of clarification and dewatering levels achieved in a range of typical high-speed centrifuges is presented. Together with a visualisation tool, a Window of Operation, this provides for the rapid analysis of separation performance and evaluation of the available operating conditions, as an aid in the selection of the centrifuge equipment most appropriate for a given process duty. A case study examining centrifuge selection for the processing of a high cell density Pichia pastoris culture demonstrates the method. The study examines semi-continuous disc-stack centrifuges and batch-operated machines such as multi-chamber bowls and Carr Powerfuges. Performance is assessed based on the variables of clarification, dewatering and product yield. Inclusion of limits imposed by the centrifuge type and design, and operation itself, serve to constrain the process and to define the Windows of Operation. The insight gained from the case study provides a useful indication of the utility of the methodology presented and illustrates the challenges of centrifuge selection for the demanding case of high solids concentration feed streams.

Biotechnology↗

PubMed1991

Statistical aspects of research methodology.

Many reports in the medical literature are flawed through poor presentation of numerical results, or, more seriously, by the use of inadequate or inappropriate statistical methodology. This article expands on the more complex methodological issues. The main emphasis is on discussing key aspects of experimental design, and the idea of reporting results in terms of confidence intervals rather than P values.

Confidence Intervals↗

PubMed1982

Methodology for the identification of the urinary metabolites of the analgesic-narcotic antagonist, codorphone, by gas chromatography mass spectrometry.

Methodology is presented for the identification of codorphone and its metabolites in urine samples using gas chromatography mass spectrometry. The procedure focuses on the clean-up of biological samples and a derivatization technique suitable for these samples. Sep-Pak C-18 cartridges were employed in the clean-up procedure permitting the biological sample to be derivatized in a relatively small volume of reagents. The derivatization procedure incorporated a one-step trimethylsilyloxime reaction to prevent enol formation while simultaneously derivatizing free hydroxyl groups with the excess trimethylsilylimidazole present in the reaction mixture. This was followed by the addition of BSTFA directly to this reaction mixture to complete derivatization of any metabolites possessing dealkylation of the nitrogen. Using this derivatization scheme, synthetic metabolites were analyzed by gas chromatography mass spectrometry, and their mass spectra were characterized emphasizing the diagnostic fragment ions observed in the spectra. To illustrate the usefulness of this methodology, a urine sample obtained from a dog that had been dosed with codorphone was analyzed by gas chromatography mass spectrometry, and the metabolites were identified by comparison to the mass spectra of the synthetic derivatives.

Analgesics, Opioid↗

PubMed1979

Retrieving information on clinical methodology.

Evidence derived from several simple searchers of the literature suggests that one interested in identifying papers which discuss the methodologies of clinical trials will have reasonable success. However, the retrieval of a meaningful methodologic duscussion of any actual trial is unlikely because very little of this information has been published. Some suggestions to remedy this deficiency are given.

Clinical Trials as Topic↗

PubMed2005

Association mapping: methodologies, strategies, and issues.

Recent advances in molecular genetic technology allow for detailed characterization of genetic variation and easy cost-efficient accumulation of such data, even for large human samples. One such advance that presents incredible opportunities for identifying associations between genetic polymorphisms and disease-related phenotypes is the ability to quickly type a large number of single-nucleotide polymorphisms (SNPs). Contributors to Group 10 of Genetic Analysis Workshop 14 explored the potential of SNP genotypes for the association mapping of disease-related genes in family-based studies. Using both real data involving alcoholism susceptibility, made available by the Collaborative Study on the Genetics of Alcoholism (COGA), and simulated data involving personality-disorder susceptibility, group members investigated specific methodological issues involved in association mapping, such as multiple testing, single SNPs vs. combinations and haplotypes, and the effect of linkage disequilibrium on SNP-based linkage; evaluated existing methodologies for association mapping using SNPs, short-tandem repeats (STRs), or a combination of the two; and introduced new or modified association-mapping methods, including a gamma random effects (GRE) model and the quantitative trait linkage disequilibrium (QTLD) test. These papers are unified by the application of association-based methods to analyze SNPs, microsatellite markers, or both, to identify chromosomal regions harboring genes that contribute to quantitative endophenotype variation, and thus to disease risk. Their diversity attests to the breadth and flexibility of association-mapping approaches to the genetics of complex disease.

Alcoholism↗

PubMed2005

Methodological issues relating to in vivo cortical myelography using MRI.

The relationship between neocortical structure and function is a key area of research in neuroscience. Most studies of neural function, whether using neurophysiology or neuroimaging methods, are interpreted with relation to the underlying cortical myelo- and cytoarchitecture. For functional neuroimaging studies this often means using cytoarchitectonic maps based on the study of a limited number of brains, despite evidence for substantial interindividual variation. Improvements in MR technology, resulting in wider availability of high-field MRI systems, have led to an increase in the achievable resolution in MR scans. Several groups have reported the in vivo detection of myelination patterns within the cortex, consistent with those observed in postmortem tissue. This leads to the possibility of predefining areas for fMRI analysis based on the cortical architecture. To do this it is essential to know, in a quantitative way, how reliably myeloarchitectonic areas and boundaries can be detected using MRI. Here we investigate the striate cortex, known to be coincident with V1, to assess the detectability of the stria of Gennari across V1 and across subjects. Under optimal conditions, 80% of the stria of Gennari was visualized using our methodology, although there was considerable variability in the level of detection across subjects. We discuss the limitations of the methodology and propose ways to improve the detection level of cortical myeloarchitecture more generally.

Adult↗

PubMed2001

Methodological limitations of economic evaluations of antenatal screening.

A review of recent economic studies of antenatal screening reveals widespread violation of accepted economic evaluation methodology. In particular, the costs and benefits of antenatal screening are often misclassified and conflated, and the non-resource effects of averted costs are often excluded from the evaluation process. The result is a widespread violation of the explicit and systematic approaches taken by economic analysts more generally, and conclusions that may be described as misleading. This letter calls for economic analysts to be consistent in their application of economic evaluation methodology to antenatal screening programmes.

Abortion, Legal↗

PubMed2003

Methodological issues raised by preference-based approaches to measuring the health status of children.

This paper identifies and discusses a number of methodological issues that require consideration when applying preference-based approaches to the measurement of the health status of children. It is argued that the decision about which dimensions of health status to incorporate into health state descriptions or classifications should depend, in part, upon whether the measure will be used to inform resource allocation within or across age groups. In addition, the paper identifies and discusses a number of methodological issues surrounding the appropriate respondents for descriptions and valuations of health status in different contexts; potential sources of bias in the description and valuation processes; and the psychometric integrity of alternative measurement approaches.

Child↗

PubMed2005

Are QALYs based on time trade-off comparable?--A systematic review of TTO methodologies.

A wide range of methods is used to elicit quality-of-life weights of different health states to generate 'Quality-adjusted life years' (QALYs). The comparability between different types of health outcomes at a numerical level is the main advantage of using a 'common currency for health' such as the QALY. It has been warned that results of different methods and perspectives should not be directly compared in QALY league tables. But do we know that QALYs are comparable if they are based on the same method and perspective?The Time trade-off (TTO) consists in a hypothetical trade-off between living shorter and living healthier. We performed a literature review of the TTO methodology used to elicit quality-of-life weights for own, current health. Fifty-six journal articles, with quality-of-life weights assigned to 102 diagnostic groups were included. We found extensive differences in how the TTO question was asked. The time frame varied from 1 month to 30 years, and was not reported for one-fourth of the weights. The samples in which the quality-of-life weights were elicited were generally small with a median size of 53 respondents. Comprehensive inclusion criteria were given for half the diagnostic groups. Co-morbidity was described in less than one-tenth of the groups of respondents. For two-thirds of the quality-of-life weights, there was no discussion of the influence of other factors, such as age, sex, employment and children. The different methodological approaches did not influence the TTO weights in a predictable or clear pattern. Whether or not it is possible to standardise the TTO method and the sampling procedure, and whether or not the TTO will then give valid quality-of-life weights, remains an open question.This review of the TTO elicited on own behalf, shows that limiting cost-utility analysis to include only quality life weights from one method and one perspective is not enough to ensure that QALYs are comparable.

Attitude to Health↗