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PubMed2004

Estimation of particle number by stereology: an update.

Sampling designs dictated by stereology have proven very useful in recent years to estimate in situ the total number of deposited particles, or of macrophages, in different lung compartments at the light microscopical level. The sampling methods are based on parallel slabs which are subsequently subsampled by disectors. The resulting number estimators are unbiased irrespective of tissue shrinkage or swelling, and they are readily applicable in other contexts (notably in neuroscience). Several variants of the design are available, however, and, although they all yield the same number estimates, their precision, and the mathematical prediction of it, vary among the different estimators and are subjected to theoretical improvement. The present paper constitutes a detailed survey of the latest advances, and it illustrates methods and formulae alike by way of a real example stemming from an earlier study on particle retention and clearance.

Animals↗
PubMed1996

Time-of-flight Laue fiber diffraction studies of perdeuterated DNA.

The diffractometer SXD at the Rutherford Appleton Laboratory ISIS pulsed neutron source has been used to record high resolution time-of-flight Laue fiber diffraction data from DNA. These experiments, which are the first of their kind, were undertaken using fibers of DNA in the A conformation and prepared using deuterated DNA in order to minimise incoherent background scattering. These studies complement previous experiments on instrument D19 at the Institut Laue Langevin using monochromatic neutrons. Sample preparation involved drawing large numbers of these deuterated DNA fibers and mounting them in a parallel array. The strategy of data collection is discussed in terms of camera design, sample environment and data collection. The methods used to correct the recorded time-of-flight data and map it into the final reciprocal space fiber diffraction dataset are also discussed. Difference Fourier maps showing the distribution of water around A-DNA calculated on the basis of these data are compared with results obtained using data recorded from hydrogenated A-DNA on D19. Since the methods used for sample preparation, data collection and data processing are fundamentally different for the monochromatic and Laue techniques, the results of these experiments also afford a valuable opportunity to independently test the data reduction and analysis techniques used in the two methods.

Crystallography↗
PubMedDate not supplied

Chemical library subset selection algorithms: a unified derivation using spatial statistics.

If similar compounds have similar activity, rational subset selection becomes superior to random selection in screening for pharmacological lead discovery programs. Traditional approaches to this experimental design problem fall into two classes: (i) a linear or quadratic response function is assumed (ii) some space filling criterion is optimized. The assumptions underlying the first approach are clear but not always defendable; the second approach yields more intuitive designs but lacks a clear theoretical foundation. We model activity in a bioassay as realization of a stochastic process and use the best linear unbiased estimator to construct spatial sampling designs that optimize the integrated mean square prediction error, the maximum mean square prediction error, or the entropy. We argue that our approach constitutes a unifying framework encompassing most proposed techniques as limiting cases and sheds light on their underlying assumptions. In particular, vector quantization is obtained, in dimensions up to eight, in the limiting case of very smooth response surfaces for the integrated mean square error criterion. Closest packing is obtained for very rough surfaces under the integrated mean square error and entropy criteria. We suggest to use either the integrated mean square prediction error or the entropy as optimization criteria rather than approximations thereof and propose a scheme for direct iterative minimization of the integrated mean square prediction error. Finally, we discuss how the quality of chemical descriptors manifests itself and clarify the assumptions underlying the selection of diverse or representative subsets.

Journal Article↗
PubMed2002

A population-based study of cigarette smoking among illicit drug users in the United States.

AIMS: People who use illicit drugs are thought to have high rates of cigarette smoking; however, few population-based studies have been reported. We describe smoking patterns among illicit drug users, assess whether cigarette smoking is more prevalent among illicit drug users than it is among non-users and explore how smoking relates to level and type of drug use. DESIGN, SETTING, PARTICIPANTS: We used adult responses to the 1997 National Household Survey on Drug Abuse (n = 16 661). Multivariate analyses used SUDAAN to adjust standard errors for the sampling design and controlled for age, race, sex, education, depression, treatment history and alcohol. MEASUREMENTS: Smoking rates, cessation rates and smoking levels. FINDINGS: Seventy-one per cent of recent illicit drug users smoked cigarettes at least once in the past month. Their adjusted odds of being a smoker were much greater than for the general population (OR = 3.07, P < 0.0001). Their quit rate, although substantial, was half that of non-users (23% versus 56%, P=0.0001). Odds of being a smoker were higher for poly- versus monodrug users (OR = 2.35, P=0.0020) and rose with increased drug use (OR = 1.36, P=0.0374). Illicit drug users who perceived smoking to be risky were four times less likely to smoke (OR = 0.23, P=0.0008). CONCLUSIONS: Although most recent illicit drug users smoke, some are able to quit. Better understanding of concurrent cigarette and illicit drug use may provide impetus for policy change and shed light on underlying mechanisms of addiction. Clinicians, policy makers and user advocates should address tobacco use in drug treatment and in harm reduction interventions.

Adolescent↗
PubMed2002

Differences in arterial and venous thromboelastography parameters: potential roles of shear stress and oxygen content.

OBJECTIVE: To investigate potential mechanisms for the differences in thromboelastography variables observed between arterial blood samples and venous blood samples. DESIGN: Prospective cohort study. SETTING: University hospital. PARTICIPANTS: Patients undergoing cardiac surgery (n = 33). INTERVENTIONS: After the withdrawal of 10 mL of discarded blood (>3 deadspace volumes), 3 blood samples were withdrawn simultaneously from the central venous port of the pulmonary artery catheter (CVP), the radial arterial catheter (ART), and the side port of the 9F sheath introducer (SI). MEASUREMENTS AND MAIN RESULTS: Thromboelastography was done simultaneously on each sample. All thromboelastography analyses were performed with 1% celite and heparinase according to the manufacturer's guidelines. A total of 80 ART, SI, and CVP comparisons were obtained. Mean hematocrit values were not different between sampling sites (27 +/- 4 v 27 +/- 4 v 27 +/- 3). Thromboelastography R time values (mean +/- SD) were CVP, 8 +/- 3; ART, 10 +/- 3; and SI, 13 +/- 5 (p = 0.004). Thromboelastography maximal amplitude (MA) values (mean +/- SD) were CVP, 60.4 +/- 11.7; ART, 56.2 +/- 11.4; and SI, 50.5 +/- 13.2 (p = 0.008). Calculated maximal shear stresses were CVP, 48 dyne/cm(2); ART, 36 dyne/cm(2); and SI, 0.3 dyne/cm(2). Blood samples obtained from the CVP (highest shear stress) resulted in faster (shorter R) and stronger (larger MA) coagulation compared with the arterial site (intermediate shear stress) and sheath introducer (lowest shear stress). CONCLUSION: These data show that differences exist in thromboelastography values between arterial and venous blood samples and, more importantly, show that the differences observed are not related to differences in oxygen content. These differences seem to be related to differences in catheter lumen diameter and, presumably, shear forces.

Adult↗
PubMed1986

Prolonged service intervals in cattle.

A trial based on progesterone radioimmunoassay of milk samples is described. Samples from 2274 cows in 14 herds were collected on the day of insemination and 7, 23 and 30 days later, unless a return to service occurred before the designated sample date. Two additional samples were collected from cows which returned to service more than 35 days after the first service, one on the day of the return and another seven days later. All six samples from these cows were assayed for progesterone concentration. Late returns, defined as returns to oestrus 36 or more days after mating, occurred in 8.6% of the cows. Milk progesterone assay results indicate that of these apparently late-returning cows, 55.9% suffered a loss of the conceptus, 22.1% had not been detected in oestrus around 21 days after first insemination, 11.8% were in anoestrus at insemination, 5.6% conceived to the insemination and were pregnant when thought to have had a late return, 2.6% were in prooestrus or dioestrus at insemination and 2.1% went into anoestrus after an oestrus insemination. The average prevalence of late returns after the 35th day (8.6%) and the estimated incidence of losses of concepta (4.8%) are lower than those reported in comparable studies elsewhere. Although many of the late-return cows were mated again and conceived, this syndrome nevertheless contributes significantly to the wastage rate, at least in New Zealand dairy herds with their strictly seasonal calving pattern. The implications of these findings are discussed and recommendations for their prevention are made where appropriate.

Journal Article↗
PubMed1992

Well shaped ST segment and risk of cardiovascular mortality.

OBJECTIVE: To investigate the prognostic value of frequently occurring slight variations in the ST segment for cardiovascular mortality in healthy subjects. DESIGN: Follow up study of mortality in relation to variations in ST segment level in a cohort over the 28 years from 1953 to 1981. A case-cohort sampling design was applied to limit the number of electrocardiograms that had to be coded by hand. SETTING: General health examination carried out in 1953 of civil servants in Amsterdam and assessment of subsequent mortality. SUBJECTS: Apparently healthy civil servants aged 40 to 65 years: 1583 men and 1508 women. MAIN OUTCOME MEASURES: Relative risk of variations in ST segment level for mortality from all causes, cardiovascular disease, and coronary heart disease. RESULTS: In men the multivariate relative risks of 15 year mortality from cardiovascular disease and coronary heart disease of slight ST elevation at 80 ms past the J point (compared with isoelectric ST segment) were 0.5 (95% confidence interval 0.3 to 0.9) and 0.4 (0.2 to 0.8), respectively. As expected, ST segment depression (greater than 0.25 mm) was associated with increased risk: 1.9 (1.1 to 3.0) and 2.2 (1.2 to 3.9), respectively. In women associations were weaker. The full 28 year period showed a similar pattern of somewhat weaker associations for men; among women, however, no predictive value was apparent. CONCLUSION: These results are empirical evidence for the intuitive opinion among doctors that a curved, upward sloping ST segment, resulting in slight ST elevation at 80 ms, indicates low risk compared with the isoelectric flat, stretched ST segment.

Adult↗
PubMed2004

Frequency of M-cadherin-stained satellite cells declines in human muscles during aging.

To answer the question of whether the satellite cell pool in human muscle is reduced during aging, we detected satellite cells in 30- microm-thick transverse sections under the confocal microscope by binding of M-cadherin antibody. The basal lamina was detected with laminin. Nuclei were stained with bisbenzimide or propidium iodide. Satellite cells were counted by applying the disector method and unbiased sampling design. To determine if there are age-related differences in muscle fiber types, morphometric characteristics of muscle fibers were examined on thin sections stained for myofibrillar ATPase. Autopsy samples of vastus lateralis muscle from six young (28.7 +/- 2.3 years) and six old (70.8 +/- 1.3 years) persons who had suffered sudden death were analyzed. Numbers of satellite cells per fiber length (Nsc/Lfib) and number of satellite cells per total number of nuclei (satellite cell nuclei + myonuclei) (Nsc/Nnucl) were significantly lower in the old group (p < 0.05). We demonstrate the importance of proper sampling and counting in estimation of sparsely distributed structures such as satellite cells. Our results support the hypothesis that the satellite cell fraction declines during aging.

Adult↗
PubMed2005

Psychosocial impact of sickle cell disease in children seen at University of Ilorin Teaching Hospital, Ilorin, Nigeria.

BACKGROUND: The increased risk of psychological disorders constitutes one of the complications of sickle cell disease (SCD) in Nigeria. This subject has received insufficient attention. OBJECTIVES: To assess the psychosocial impact of SCD on affected children and two control samples. DESIGN: A cross-sectional controlled study. SETTING: University of Ilorin Teaching Hospital, Ilorin, Nigeria. SUBJECTS: One hundred children affected with sickle cell disease (SCD children) consituted the study sample, while the controls comprised of 75 children with bronchial asthma (asthmatics) and 75 with some acute medical illness (AMI). RESULTS: Sickle cell disease (SCD) children (sicklers) were significantly more likely to report social impairment such as restriction in their play and domestic activities, feeling inferior to others, having bad luck, fear of under-achievement in life and fear of potential early death than the control groups. On the Rutter Scale A2, the SCD children were more likely than the controls to report neurotic symptoms but less likely than controls to bully other children. SCD children (30%) were more likely to be identified as probable cases with psychological problems than asthmatics (25%) and AMI children (20%). These differences were, however, not statistically significant. CONCLUSION: This study further substantiates earlier findings of the link between chronic childhood illnesses such as SCD and psychosocial morbidity. The authors, therefore, recommend that comprehensive and affordable psychosocial care should be provided for children suffering from these conditions.

Adolescent↗
PubMed2003

Storm effects on regional beach water quality along the southern California shoreline.

Two regional studies conducted during dry weather demonstrated that the Southern California Bight (SCB) shoreline has good water quality, except near areas that drain land-based runoff. Here, we repeat those regional studies 36 h after a rainstorm to assess the influence of runoff under high flow conditions. Two hundred and fifty-four shoreline sites between Santa Barbara, California and Ensenada, Mexico were sampled using a stratified-random sampling design with four strata: sandy beaches, rocky shoreline, shoreline adjacent to urban runoff outlets that flow intermittently, and shoreline adjacent to outlets that flow year-round. Each site was sampled for total coliforms, fecal coliforms (or E. coli), and enterococci. Sixty percent of the shoreline failed water quality standards after the storm compared to only 6% during dry weather. Failure of water quality standards increased to more than 90% for shoreline areas adjacent to urban runoff outlets. During dry weather, most water quality failures occurred for only one of the three bacterial indicators and concentrations were barely above State of California standards; following the storm, most failures were for multiple indicators and exceeded State of California standards by a large margin. The condition of the shoreline in Mexico and the United States was similar following rainfall, which was not the case during dry weather.

Bathing Beaches↗
PubMed1998

Stability of finite difference deconvolution I: theoretical analysis.

Analysis of the stability of finite difference deconvolution (FDD) shows that it is dependent on the characteristics of the unit impulse response function and the sampling schedule of the input response function, and that stability properties are improved when the cumulative amount function is directly estimated rather than the rate function. The estimated input rate for an intravenous (iv) unit impulse response function and the release rate for an oral solution unit impulse response function are unstable for any sampling schedule of the input response function. However, for an iv unit impulse response function, the estimated cumulative amount absorbed is stable for any sampling schedule of the response function. For an oral unit impulse response function, the estimated cumulative amount released is unstable for all the sampling points of the input response function located before the time of the maximum of the oral unit impulse response function, but it can be made stable if an appropriately designed sampling schedule of the input response function is used. In addition, the theoretical basis for choosing a sampling schedule to overcome the instability of FDD has been established.

Algorithms↗
PubMedDate not supplied

Patient accrual and interim statistical analysis in long-term randomized clinical trials: the French chronic lymphocytic leukemia CLL 80 protocol as a case study.

The CLL 80 clinical trial of treatment for chronic lymphocytic leukemia was designed using a three-stage prognostic classification. Within each stage patients received one of two treatments allocated by randomization, two adjacent stages having a common treatment. The fixed-sample design required 850 patients entered over a period of 8.5 years. Active patient recruitment led to 741 patients being randomized in four years. The first interim analysis, carried out at this point, showed a treatment difference in one stage which was statistically significant (p = 0.001) and justified an early termination of the protocol. This paper discusses practical aspects of patient accrual and interim analysis in this study.

Antineoplastic Combined Chemotherapy Protocols↗
PubMedDate not supplied

A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness.

OBJECTIVES: Our purpose is to highlight some of the past and potential future uses of microarray in nutrition research, while also commenting on some aspects of the design conduct and analysis of microarray data that will leave to improved data quality. METHODS: In this review article we outline some of the aspects of microarray experimentation that must be considered before and during these experiments. These topics include: identification of the experiment's objective (hypothesis), the experimental design, sample size, statistical analysis, data verification, data handling, and experimental interpretation. RESULTS: In order to illustrate the principles we outline in this article we use the methods to layout the design of a microarray experiment to study one aspect of the observation that a diet high in soy is associated with lower rates of breast cancer. CONCLUSIONS: Microarrays are a very powerful tool for studying virtually every nutrition-related disease and trait and can provide valuable insights that are not obtainable with other techniques. However, unless nutrition researchers conduct their studies with scientific hard-mindedness, the studies will be of lower power at least if not completely misleading.

Animals↗
PubMed1997

Polymerase chain reaction determination of RhC, Rhc, and RhE blood types: an evaluation of accuracy and clinical utility.

OBJECTIVE: Polymerase chain reaction amplification of a portion of the RhC/c/E/e gene could lead to a rapid, accurate determination of fetal RhC/c/E status. The purpose of this study was to evaluate the accuracy of this technique by testing for the first time a large number of deoxyribonucleic acid samples derived from individuals whose RhC/c/E status was established by standard serologic methods. We also evaluated the potential clinical utility of polymerase chain reaction to ascertain fetal antigen status. STUDY DESIGN: Samples were obtained from Centre d'Etude du Polymorphisme Humain families used for studies of genetic variation (n = 655). Deoxyribonucleic acid was extracted by standard techniques. With few modifications, published primers and reaction conditions were used. Samples were digested with restriction enzymes yielding characteristic electrophoresis patterns for RhC/c/E. Clinical utility was assessed by review of all patients evaluated for erythrocyte sensitization. RESULTS: RhC-positive (n = 479), RhC-negative (n = 176), Rhc-positive (n = 524), Rhc-negative (n = 131), RhE-positive (n = 131) and RhE-negative (n = 524) samples were evaluated. The sensitivity of RhC/ c and E typing by polymerase chain reaction was 98.3%, 98.1%, and 96.9%, respectively. The specificity of polymerase chain reaction for identifying the RhC/c/E antigens was 91.5%, 94.7%, and 99.2%, respectively. CONCLUSIONS: Although it would appear that use of polymerase chain reaction to establish RhC/c/E type could aid in evaluation of RhC/c/E sensitization, we are concerned about the instances of antigen-positive individuals characterized as antigen negative. Further study is necessary to determine if this reflects a polymorphism, mutation, a data coding error, or a combination. The Centre d'Etude du Polymorphisme Humain database is known to contain such errors at a rate that may surpass the error rate of our testing. A second molecular technique could be used to achieve better accuracy in the ascertainment of Rh C/c/E type. On the basis of a review of our patient population, molecular deoxyribonucleic acid techniques now available could aid the management of erythrocyte sensitization in pregnancy in > 96% of cases.

Blood Grouping and Crossmatching↗
PubMed1998

Enzyme immunoassay method for total urinary follicle-stimulating hormone (FSH) beta subunit and its application for measurement of total urinary FSH.

OBJECTIVE: To develop and validate an enzyme-linked immunosorbent assay (ELISA) for total urinary follicle-stimulating hormone (FSH) that can be used to evaluate frozen-thawed urine samples. DESIGN: A method was developed for dissociating urinary FSH into subunits by boiling. An ELISA for the free beta subunit of FSH was used to measure total FSH in urine samples collected from male and female volunteers. The urinary FSH values were compared with serum FSH concentrations in paired samples. SETTING: A clinical research laboratory. PATIENT(S): Serum and urine samples from normal male and female volunteers and from men with infertility were used to develop and validate an assay for total urinary FSH. INTERVENTION(S): None. RESULT(S): Urinary FSH concentrations in frozen-thawed urine were highly correlated to matched serum FSH concentrations. CONCLUSION(S): A microtiter plate ELISA for FSH beta subunit provides an economical method for evaluating FSH secretion in men and women. This method has practical applications for population-based epidemiologic studies in which urine samples are collected in the field and stored frozen before analysis.

Adult↗
PubMed2000

Very young gay and bisexual men are at risk for HIV infection: the San Francisco Bay Area Young Men's Survey II.

OBJECTIVES: To compare HIV seroprevalence and sexual risk behavior among very young gay and bisexual men (aged 15-17 years) and their older counterparts (aged 18-22 years). To examine drug-use patterns and correlates of sexual risk behavior in both of these age groups. DESIGN AND METHODS: An interviewer-administered cross-sectional survey of 719 gay and bisexual males between 15 and 22 years old was conducted through a venue-based sampling design. Blood specimens were collected and tested for HIV antibodies, hepatitis B, and syphilis. Interviews assessed sexual and drug-use behavior as well as psychosocial variables believed to be related to sexual risk-taking, including self-acceptance of gay or bisexual identity, perceptions of peer norms concerning safer sex, and perceptions of the ability to practice safer sex (safer sex self-efficacy). RESULTS: Of the 719 participants, 100 (16.2%) were aged between 15 and 17 years. HIV seroprevalence was somewhat lower among those aged 15 to 17 years (2.0%) compared with those aged 18 to 22 years (6.8%). Overall, the prevalence of hepatitis-B core antibody was significantly lower in the younger age group (5.0%) than in the older group (14.1%). The men aged 15 to 17 years used alcohol, ecstasy, and heroin less frequently than those aged 18 to 22 years. The age groups did not differ in the proportion of men who reported any unprotected anal intercourse in the previous 6 months (31.2%). In both age groups, use of amphetamines, ecstasy, and amyl nitrate was associated with unprotected anal intercourse. Self-acceptance of gay or bisexual identity was related to less sexual risk for those aged 15 to 17 years. In both age groups, greater safer sex self-efficacy was linked to less HIV sexual risk-taking. In the younger group, perceptions of peer norms that support safer sex were related to less risk behavior. CONCLUSIONS: Very young gay and bisexual men engage in unprotected anal sex at rates comparable with those for their somewhat older counterparts, raising serious concern over their risk of acquiring HIV infection. To prevent seroconversions, interventions must target those <18 years of age, and prevention programs should address the use of certain drugs in relation to sex and sexual risk-taking. To be most effective, programs should develop innovative communication strategies to take into account lack of self-acceptance of gay or bisexual identity and low self-efficacy for practicing safer sex.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗
PubMed1992

Gender and race differences in the correlation between body mass and education in the 1971-1975 NHANES I.

STUDY OBJECTIVE: Differences in the correlation between body mass index and education across four gender and race groups were investigated while simultaneously accounting for occupation, income, marital status, and age. DESIGN: The study used analysis of covariance techniques to calculate average body mass and confidence intervals within education categories while simultaneously adjusting for the covariates: age, square of age, family income, marital status, and occupation. SETTING: Data were drawn from the US National Health and Nutrition Examination Survey (NHANES I), 1971-1975. NHANES I is a national probability sample designed to gather information on the non-institutionalised US civilians, ages 1-74 years. SUBJECTS: Samples of 8211 white women, 1673 black women, 6188 white men, and 1023 black men were drawn from the NHANES I, 1971-1975. MAIN RESULTS: Data in the female samples indicate a strictly inverse relation between body mass and years of schooling among white women and an inverted "U" association among black women, achieving a maximum around 8 to 11 years of schooling. In the male samples data indicate inverted "U" relations among both black and white men, reaching maxima between 12 and 15 years of schooling. The sides of the "U" curve are much steeper for black than for white men. CONCLUSIONS: The four gender/race categories display four different body mass index and education associations. These four associations are only slightly altered by simultaneously adjusting for two additional measures of socioeconomic status: occupation and income.

Age Factors↗
PubMed2006

Initial studies for the phytostabilization of a mine tailing from the Cartagena-La Union Mining District (SE Spain).

Mine tailings are one of the main environmental problems in post-mining landscapes and their removal is often complicated due to their high heavy metal content and dimensions. In this sense, using plant species for in situ stabilization may be an interesting and low cost option. Moreover, there are some plant species that have adapted to these conditions and are usually present at these contaminated sites. In this study, a mine tailing located in South-East Spain was investigated in order to establish lines for further phytostabilization research. A plot sampling design was carried out in order to characterize the soil properties. In addition, two plant species that have naturally colonized some parts of the tailing, Hyparrhenia hirta and Zygophyllum fabago, were sampled, including the analyses of their respective rhizospheric soils. The results of plot soil samples showed pH values from ultra acid to slightly alkaline. The electrical conductivity values were around 4dSm(-1) in plots with vegetation and 8dS m(-1) in the plot without vegetation. Total metal concentrations were high (4000 mg kg(-1) for Pb, 9000-15000 mg kg(-1) for Zn). DTPA- and water-extractable Zn were 5% and 3% of the total, respectively. H. hirta accumulated around 150 mg kg(-1) Pb in both shoots and roots. Zn concentration was 750 mg kg(-1) in Z. fabago shoots. DTPA-extractable Zn and Cu were positively correlated to plant uptake.

Biodegradation, Environmental↗