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Latin hypercube sampling and the sensitivity analysis of a Monte Carlo epidemic model.

Discrete, algorithmic simulation and Monte Carlo methodologies are currently used in population biology, connectionist cognitive modeling, and physics. However, little is typically known about the sensitivity of such models to changes in the values of the model features. Traditional methods of sensitivity analysis for systems of differential equations do not apply. Sometimes, one or two parameters are modified at a time in an ad hoc fashion in an attempt to assess sensitivity. To include more model features and their interactions in a sensitivity study, while limiting computer utilization, various sampling methods have been suggested. In this article, a sensitivity study based on a Latin hypercube (LH) sampling design is compared with a similar study using a full factorial (FF), fixed-point sample. A discrete, Monte Carlo model of epidemics of influenzavirus infections in a human community is used for illustrative purposes. Although the FF scheme used over 14 times as many samples as the LH sampling one, both provided comparable predictive ability and comparable information about simulation sensitivity to model features.

Adolescent↗

Testing equivalence between two laboratories or two methods using paired-sample analysis and interval hypothesis testing.

A modified interval hypothesis testing procedure based on paired-sample analysis is described, as well as its application in testing equivalence between two bioanalytical laboratories or two methods. This testing procedure has the advantage of reducing the risk of wrongly concluding equivalence when in fact two laboratories or two methods are not equivalent. The advantage of using paired-sample analysis is that the test is less confounded by the intersample variability than unpaired-sample analysis when incurred biological samples with a wide range of concentrations are included in the experiments. Practical aspects including experimental design, sample size calculation and power estimation are also discussed through examples.

Laboratories↗

Design of a sampling plan to detect ochratoxin A in green coffee.

The establishment of maximum limits for ochratoxin A (OTA) in coffee by importing countries requires that coffee-producing countries develop scientifically based sampling plans to assess OTA contents in lots of green coffee before coffee enters the market thus reducing consumer exposure to OTA, minimizing the number of lots rejected, and reducing financial loss for producing countries. A study was carried out to design an official sampling plan to determine OTA in green coffee produced in Brazil. Twenty-five lots of green coffee (type 7 - approximately 160 defects) were sampled according to an experimental protocol where 16 test samples were taken from each lot (total of 16 kg) resulting in a total of 800 OTA analyses. The total, sampling, sample preparation, and analytical variances were 10.75 (CV = 65.6%), 7.80 (CV = 55.8%), 2.84 (CV = 33.7%), and 0.11 (CV = 6.6%), respectively, assuming a regulatory limit of 5 microg kg(-1) OTA and using a 1 kg sample, Romer RAS mill, 25 g sub-samples, and high performance liquid chromatography. The observed OTA distribution among the 16 OTA sample results was compared to several theoretical distributions. The 2 parameter-log normal distribution was selected to model OTA test results for green coffee as it gave the best fit across all 25 lot distributions. Specific computer software was developed using the variance and distribution information to predict the probability of accepting or rejecting coffee lots at specific OTA concentrations. The acceptation probability was used to compute an operating characteristic (OC) curve specific to a sampling plan design. The OC curve was used to predict the rejection of good lots (sellers' or exporters' risk) and the acceptance of bad lots (buyers' or importers' risk).

Coffee↗

Association between use of unconventional therapies and conventional medical services.

CONTEXT: The terms alternative and complementary medicine suggest 2 contradictory possibilities. Whether individuals use unconventional therapies as a substitute for or as an "add on" to conventional medical treatments is uncertain. OBJECTIVE: To determine the association between use of unconventional therapies and conventional medical care in a national sample. DESIGN, SETTING, AND PARTICIPANTS: The 1996 Medical Expenditure Panel Survey was distributed to a probability sample of the noninstitutionalized civilian US population. Of 24676 individuals responding (77.7% response rate), 16068 adults 18 years or older were included in the analysis. MAIN OUTCOME MEASURES: Visits to practitioners for unconventional therapies and conventional medical services, including number of inpatient, outpatient, and emergency department visits and use of 8 types of preventive medical services (blood pressure, cholesterol level, physical examination, influenza vaccination, prostate examination, breast examination, mammography, and Papanicolaou test). RESULTS: During 1996, an estimated 6.5% of the US population had visits for both unconventional therapies and conventional medical care; 1.8% used only unconventional services; 59.5% used only conventional care; and 32.2% used neither. Compared with those with only conventional visits, those who used both types of care had significantly more outpatient physician visits (7.9 vs 5.4; P<.001), and used more of all types of preventive services except mammography. These groups did not differ significantly in inpatient care, prescription drug use, or number of emergency department visits. Individuals in the top quartile of number of physician visits were more than twice as likely as those in the bottom quartile to have used unconventional therapies in the past year (14.5% vs 6.4%; P<.001). The association between unconventional treatments and physician visits remained after adjusting for potential confounders and across different types of unconventional treatment. CONCLUSIONS: In this sample, use of unconventional therapies was substantially lower than has been reported in previous national surveys, but was associated with increased use of physician services. From a health services perspective, practitioner-based unconventional therapies appear to serve more as a complement than an alternative to conventional medicine.

Adult↗

Estimation of the three-dimensional wall thickness of completed remodeling sites in iliac trabecular bone.

The wall thickness of completed remodeling sites in trabecular bone was estimated in 25 normal individuals and 5 patients with arthrosis of the knee, using 7 micron sections of undecalcified iliac crest bone. A systematic sampling procedure which gives a surface referent estimate of the thickness was applied. The efficiency of the sampling design was optimized by means of a cost-variance analysis. The proposed method of sampling which eliminates a common bias in bone histomorphometry is recommended for determinations of wall thickness, osteoid thickness, lamellar thickness, and distance between fluorochrome markers in trabecular bone. The intraindividual distributions of three-dimensional wall thickness were reconstructed from the measurements of apparent width by an unfolding procedure based on the geometric probability density function pertaining to randomly sectioned plates. Distributions of true wall thickness for the young normal individuals were unimodal and resembled normal distributions. The three-dimensional mean wall thickness was 61.4 +/- 4.4 micron (+/- SD). It was demonstrated that the conventionally applied stereological transformation, which calculates the three-dimensional mean wall thickness from the mean apparent width by multiplying the latter by pi/4, underestimates the three-dimensional mean wall thickness. An improved transformation is illustrated and is recommended for estimating three-dimensional mean thickness of plates from two-dimensional measurements in trabecular bone.

Adult↗

Physician response rates to a mail survey by specialty and timing of incentive.

BACKGROUND: Historically, achieving a high response rate on physician surveys has been a challenging task. Given such concerns, understanding research strategies that facilitate adequate response rates is important. Primary care physician responses to a mail survey on smoking cessation are summarized by physician specialty and timing of incentive. METHODS: A stratified random-sample design, stratified by patient populations-adults, adolescents, and pregnant women-was used. The sampling frame included New Jersey internists, general practitioners, family physicians, pediatricians, and obstetrician-gynecologists. A total of 2100 physicians, 700 physicians from each patient strata, were sampled and mailed a smoking-cessation survey in summer 2002. The sample was randomized by incentive timing: Half received the incentive (i.e., 25 dollars gift card) with the first survey mailing, and half received the incentive on receipt of their completed survey. RESULTS: The promised-incentive group achieved a significantly lower response rate (56%) compared with the up-front-incentive group (71.5%). Response rates by medical specialty varied overall and within incentive groups. The difference between the incentive groups was greatest among obstetrician-gynecologists (i.e., 20.2 percentage points) and was least among pediatricians (i.e., 5.8 percentage points). CONCLUSIONS: Physician response rates to mail surveys are greatly improved, especially among certain medical specialties, by using up-front incentives.

Adolescent↗

Use of nutrition facts panels among adults who make household food purchasing decisions.

OBJECTIVE: To identify sociodemographic variables and beliefs about the causes of obesity associated with reported use of Nutrition Facts panel (NFP) information. DESIGN/SETTING: Nationally representative, cross-sectional survey of 1139 adults. Data collection employed a single-stage, equal-probability sampling design with random-digit dialing across 50 states and the District of Columbia. Analysis sample consisted of 390 adults living with one or more children who reported making food purchasing decisions. MAIN OUTCOME MEASURE: Respondents provided self-reported information on their use of NFP information when making food purchasing decisions for their household. ANALYSIS: Chi-square and analysis of variance (ANOVA) tests compared the analysis sample to the broader population. Logistic regression analyses identified the sociodemographic and beliefs about obesity variables related to NFP use. RESULTS: Fifty-three percent of the sample reported using NFP information on a consistent basis. Females, those with more education, and those currently married were more likely to use NFP labels. The importance of knowledge in order to maintain healthy body weight was the only belief variable associated with use of NFP information. IMPLICATIONS FOR RESEARCH AND PRACTICE: Nutrition educators interested in changing dietary behaviors should begin by identifying levels of nutritional literacy and beliefs about the importance of nutrition to motivate use of NFP labels.

Adult↗

Secular trends in diet and risk factors for cardiovascular disease: the Framingham Study.

OBJECTIVE: In this study we examined changes in dietary intake and risk factors for cardiovascular disease that occurred over three decades in a US-population-based sample. DESIGN: Secular trends in dietary profiles and risk factors were studied in cross-sectional samples of subjects from the Framingham Study in 1957-1960, 1966-1969, and 1984-1988. RESULTS: Dietary levels of cholesterol appeared to have declined considerably, whereas macronutrient and fatty acid intakes appeared to change only slightly. Men appeared to increase their saturated fat intakes from 16.4% in 1966-1969 to 17.0% in 1984-1988 (P < .01). In spite of relatively stable mean total fat intake levels, 35% to 60% of Framingham Study men and women reported decreased consumption of higher-fat animal products over the 10-year period between 1974-1978 and 1984-1988. Framingham subjects who reported modifying their diets by substituting lower-fat foods for high-fat items between 1974-1978 and 1984-1988 were more likely to achieve the guidelines of the National Cholesterol Education Program and Healthy People 2000 for dietary fat and cholesterol intake and for serum total cholesterol level. Levels of systolic and diastolic blood pressure, total and low-density lipoprotein cholesterol, and cigarette smoking were also lower in 1984-1988 than in earlier times. Compared with 1957-1960, mean body mass index and prevalence rates of overweight and hypertension were higher in 1984-1988, despite higher levels of reported physical activity. CONCLUSIONS: The observed secular trends in diet and risk factor levels for cardiovascular disease in the Framingham population are important to guide the development and implementation of population-based strategies for promoting cardiovascular health, including nutrition interventions.

Adult↗

Prospective use of optimal sampling theory: steady-state ciprofloxacin pharmacokinetics in critically ill trauma patients.

We examined the use of optimal sampling theory to determine a sparse sampling design to estimate pharmacokinetic parameters of ciprofloxacin in patients who had sustained trauma. Two serum sampling strategies, consisting of six sampling times each, were derived on the basis of the patient's renal function (patients with creatinine clearance greater than or equal to 6 L/hr/1.73 m2 and patients with creatinine clearances less than 6 L/hr/1.73 m2). Two additional serum samples were obtained for other aspects to the study. A timed urine collection was also obtained. Pharmacokinetic parameter estimates were determined by comodeling the serum and urine data with a three-compartment open model (parameterized as microconstants) with a bayesian algorithm and by noncompartmental analysis. Bayesian-derived parameter estimates were total body clearance of drug from plasma, 29.8 L/hr/1.73 m2; renal clearance, 17.0 L/hr/1.73 m2; and nonrenal clearance, 12.7 L/hr/1.73 m2 and were not significantly different from noncompartmentally derived parameters (p = 0.80, p = 0.65 and p = 0.333, respectively). The study demonstrates the use of optimal sampling theory to determine an informative yet relatively sparse sampling strategy for a drug with a complex pharmacokinetic model.

Adult↗

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription.

We describe an integrative data-driven mathematical framework that formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the "basis" set. By using pseudoinverse projection, the molecular biological profiles of the data samples are least-squares-approximated as superpositions of the basis profiles. Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. We illustrate this framework with an integration of yeast genome-scale proteins' DNA-binding data with cell cycle mRNA expression time course data. Novel correlation between DNA replication initiation and RNA transcription during the yeast cell cycle, which might be due to a previously unknown mechanism of regulation, is predicted.

Cell Cycle↗

Sampling problems in an heterogeneous organ: quantitation of relative and total volume of pancreatic islets by light microscopy.

In stereological studies analysis of sampling variances is used for optimizing the sampling design. In organs with a heterogeneous distribution of the phase of interest the analysis of sampling variances can be undertaken only if the observed variance between sections is distributed into the fraction which is due to random variation and the fraction which is due to the heterogeneity. In the present example (pancreatic islet volume estimated by light microscopic point-counting) the density of islets showed a linear increase along the axis of the organ. By analysis of sampling variances it was calculated that the most efficient number of sections (cut perpendicular to the organ) was considerably lower when the isolated contribution from the random variation was considered. The total islet volume was obtained by the product of the fractional islet volume and the pancreatic weight. Analysis of sampling variances of the total islet volume was performed by including the variance contribution from the individual pancreatic weights to the variance of the group mean total islet volume. Due to a negative correlation between the fractional volume and organ weight the total islet volume in the group of animals was more precisely estimated than the fractional islet volume. The methods used for dealing with the heterogeneity of the organ and for estimating sampling variances of total structural quantities generalize to a large number of stereological studies in biology.

Analysis of Variance↗

Choice of time for urine collection for detecting early kidney abnormalities in hypertensives.

The aim of this study was to determine the most appropriate urine collection for detecting differences in the excretion rates of albumin, gamma glutamyl transpeptidase (GGT) and N-acetyl-beta-D-glucosaminidase (NAGA) between normotensive subjects and hypertensive patients on treatment. Twenty treated hypertensive patients, mean (SEM, standard error of mean) age; 52.2 (6.2) years and 20 normotensive subjects, mean age 49.2 (4.2) years, were studied in a consecutive sampling design. Urinary excretion rates of albumin, GGT and NAGA were determined in consecutive timed urine samples collected overnight and during 3-5 h the next morning. Mean (SEM) overnight excretion rates for albumin, GGT and NAGA for normotensive subjects were 11.05 (1.18) micrograms/min, 17.00 (2.20) mU/min and 6.55 (0.39) mU/min, respectively, which were significantly lower than those of hypertensive subjects which were 20.77 (2.14) micrograms/min, 21.84 (1.65) mU/min and 10.92 (0.87) mU/min, respectively (P < 0.05). The mean (SEM) percentage increases in urinary albumin, GGT and NAGA in morning urine collections of normotensive subjects of 15.22 (3.88)%, 34.04 (6.45)% and 11.54 (3.63)%, respectively were significantly lower than 107.03 (15.04)%, 121.96 (16.71)% and 72.75 (7.50)% found in hypertensive patients (P < 0.05). These data suggest that were urinary albumin and tubular enzyme excretion to be used as correlates of hypertensive renal damage, ambulatory urine collections may be more sensitive than overnight collections.

Adult↗

[Systematic home screening for Chlamydia trachomatis infections of asymptomatic men and women in family practice by means of mail-in urine samples].

OBJECTIVE: To determine the prevalence and determinants of Chlamydia trachomatis (CT) infections among asymptomatic men and women in general practice. To determine participation rates in a systematic screening programme in general practice, using home obtained mailed urine samples. DESIGN: Cross-sectional study. METHODS: In 15 general practices in Amsterdam, the Netherlands, a sample of 11,005 persons (5541 women and 5464 men), aged 15-40 were invited to send in a urine sample and a completed questionnaire by mail. The urine samples were tested using the ligase chain reaction for DNA amplification. Patients diagnosed with CT were treated and partner notification was performed. RESULTS: 33% of invited males (1809/5464) and 50% of females (2751/5541) sent in the study material. Older patients participated more frequently than younger patients. Participation rates among persons with a Dutch background were higher than rates among persons from other ethnic groups. In 42 men and 79 women a CT infection was identified (2.3% and 2.9% respectively). Infections were more prevalent in patients from Surinam and the Dutch Antilles and in the age category 21-25 years. Type of health insurance as a proxy measure of socioeconomic status was not an indicator of infection. CONCLUSION: The participation in this systematic screening using mail-sent urine samples was 33% in men and 50% in women. The CT prevalences among asymptomatic men and women were 2.3% and 2.9% respectively.

Adolescent↗

Comparison of an immunochromatographic card test with night blood smear examination for detection of Wuchereria bancrofti microfilaria carriers.

BACKGROUND: At present, two diagnostic tests--Og4C3 ELISA and an immunochromatographic card test (ICT)--are available to detect circulating filarial antigens of Wuchereria bancrofti in serum/whole blood samples collected during the day. We aimed to assess the sensitivity of the new format card test 'NOW ICT Filariasis' in detecting microfilaria carriers of W. bancrofti in comparison with conventional microscopic techniques and Og4C3 ELISA. METHODS: A total of 200 persons were selected from two villages following a quota sampling design (100 in each village). The required number of houses was selected using a systematic sampling procedure with a random start of the first household. Blood samples were taken from all the available persons in each selected house until the quota of 100 was reached. The new format ICT test, Og4C3 ELISA and night blood smear examination for microfilaria were carried out following standard procedures. RESULTS: The sensitivity of the new format ICT test was 100% among microfilaria carriers (detected by both early and late readings). The kappa statistic measure of agreement between the two readings of all the samples (n =200) tested was 0.811 (p<0.05). The new format test also reported 25% of microfilaria-negative individuals as being positive for circulating filarial antigens. However, the diagnostic lines were not stable beyond 10 minutes (particularly in the case of amicrofilaraemic persons). Though there was an overall agreement between the results of ICT and Og4C3 tests (kappa =0.612; p< 0.05), the sensitivity of the Og4C3 test was lower than that of ICT. CONCLUSION: The new format ICT test is highly sensitive in detecting microfilaria carriers in endemic communities. Improvement in the format to provide stable diagnostic lines, specificity of the format and cost of the test kit are to be considered before its large-scale use.

Adult↗

ROC curves in clinical chemistry: uses, misuses, and possible solutions.

BACKGROUND: ROC curves have become the standard for describing and comparing the accuracy of diagnostic tests. Not surprisingly, ROC curves are used often by clinical chemists. Our aims were to observe how the accuracy of clinical laboratory diagnostic tests is assessed, compared, and reported in the literature; to identify common problems with the use of ROC curves; and to offer some possible solutions. METHODS: We reviewed every original work using ROC curves and published in Clinical Chemistry in 2001 or 2002. For each article we recorded phase of the research, prospective or retrospective design, sample size, presence/absence of confidence intervals (CIs), nature of the statistical analysis, and major analysis problems. RESULTS: Of 58 articles, 31% were phase I (exploratory), 50% were phase II (challenge), and 19% were phase III (advanced) studies. The studies increased in sample size from phase I to III and showed a progression in the use of prospective designs. Most phase I studies were powered to assess diagnostic tests with ROC areas >/=0.70. Thirty-eight percent of studies failed to include CIs for diagnostic test accuracy or the CIs were constructed inappropriately. Thirty-three percent of studies provided insufficient analysis for comparing diagnostic tests. Other problems included dichotomization of the gold standard scale and inappropriate analysis of the equivalence of two diagnostic tests. CONCLUSION: We identify available software and make some suggestions for sample size determination, testing for equivalence in diagnostic accuracy, and alternatives to a dichotomous classification of a continuous-scale gold standard. More methodologic research is needed in areas specific to clinical chemistry.

Chemistry, Clinical↗

Public knowledge and attitudes toward organ donation and transplantation: a cross-cultural study.

OBJECTIVE: The aim of this study was to determine the knowledge, attitudes, awareness, and determinants of organ donation and transplantation in a Qatari population. DESIGN: This is a cross-sectional study to determine the knowledge and attitude toward organ donation in a Peninsula Arabian Gulf country. SETTING: The setting was Primary Health Care (PHC) Centers and community-based study in Qatar. SUBJECTS: A multistage sampling design was used in a representative sample of 1600 Qataris and non-Qataris, including males and females of at least 17 years of age, from October 2003 to May 2004. In this study a 1305 (81.5%) subjects participated, each giving consent for the study. MEASUREMENTS: Participants completed a questionnaire assessing their knowledge, attitudes, and awareness for organ donation. RESULTS: Of 1305 samples, 637 (48.8%) males and 668 females (51.2%) living in urban and semiurban areas agreed to participate and complete the questionnaire. Of these, 762 (58.4%) were Qataris. There was a significant difference between Qataris and non-Qataris with respect to their age, educational level, monthly income, and occupation. In this study, 31.6% of Qataris and 29.8% of non-Qataris had no idea about the organ donation; 37.8% of Qataris and 32.8% of non-Qataris were willing to donate their organs. The majority of subjects preferred donating organs to their close relatives and friends. However, 83.8% of the studied subjects did not agree with an incentive-based approach for donating organs. CONCLUSION: This study showed that people should not be blamed for not being willing to participate in organ donation, but the health system and health education providers are responsible. A more effective approach should be tried regarding health education.

Cross-Cultural Comparison↗

Betel nut chewing and other risk factors associated with obesity among Taiwanese male adults.

OBJECTIVE: The research aimed at examining betel nut chewing and other risk factors associated with obesity among Taiwanese male adults. DESIGN: The research analyzed the data obtained by the 2001 National Health Interview Survey in Taiwan that covered all the administrative divisions in Taiwan. Multistage stratified systematic sampling design was adopted for survey. All members of a sampled household received the interview. SUBJECTS: The research analyzed questionnaires answered by nonaboriginal male respondents aged between 20 and 59 years old, and the total number of samples analyzed read 6126. Since very few female subjects chewed betel nut, they were excluded from the analysis. MEASUREMENTS: Criteria of obesity was defined as body mass index > or = 27 kg/m2. The variables incorporated for analysis included the respondents' status of betel nut chewing, age, educational background, presence of hypertension and diabetes mellitus, drinking and smoking status, exercise status, and demand for physical strength at job. Generalized estimating equations model was employed to estimate the odd ratios (with 95% CI) of obesity of each independent variable. RESULTS: Approximately 16.2% of respondents were obese. The distribution of betel nut chewing was current chewers 15.9%, ex-chewers 4.3%, and nonchewers 79.8%. After controlling above-mentioned independent variables, hypertension, diabetes mellitus, betel nut chewing, never exercising, and sedentary jobs were closely associated with obesity. CONCLUSION: The research found that betel nut chewing closely associated with obesity. The increased appetite of betel nut chewers is speculated as the underlying cause. The prospective study is needed to clarify this issue. In addition to increasing the risk of developing oral cancer, betel nut chewing seemed to be related with another health hazard: obesity.

Adult↗

An international study of the exposure of children to traffic.

OBJECTIVES: To examine the extent of international differences in children's exposure to traffic as pedestrians or bicyclists. DESIGN: Children's travel patterns were surveyed using a parent-child administered questionnaire. Children were sampled via primary schools, using a probability cluster sampling design. SETTING: Six cities in five countries: Melbourne and Perth (Australia), Montreal (Canada), Auckland (New Zealand), Umeå (Sweden), and Baltimore (USA). SUBJECTS: Children aged 6 and 9 years. MAIN OUTCOME MEASURES: Modes of travel on the school-home journey, total daily time spent walking, and the average daily number of roads crossed. MAIN FINDINGS: Responses were obtained from the parents of 13423 children. There are distinct patterns of children's travel in the six cities studied. Children's travel in the three Australasian cities, Melbourne, Perth and Auckland, is characterised by high car use, low levels of bicycling, and a steep decline in walking with increasing car ownership. In these cities, over a third of the children sampled spent less than five minutes walking per day. In Montreal, walking and public transport were the most common modes of travel. In Umeå, walking and bicycling predominated, with very low use of motorised transport. In comparison with children in the Australasian and North American cities, children in Umeå spend more time walking, with 87% of children walking for more than five minutes per day. CONCLUSIONS: There are large international differences in the extent to which children walk and cycle. These findings would suggest that differences in 'exposure to risk' may be an important contributor to international differences in pedestrian injury rates. There are also substantial differences in pedestrian exposure to risk by levels of car ownership-differences that may explain socioeconomic differentials in pedestrian injury rates.

Australia↗