Magnetic resonance imaging based determination of body compartments with the versatile, interactive sparse sampling (VISS) method

To investigate the inhomogeneity of radiofrequency fields at higher field strengths that can interfere with established volumetric methods, in particular for the determination of visceral (VAT) and subcutaneous adipose tissue (SCAT). A versatile, interactive sparse sampling (VISS) method is proposed to determine VAT, SCAT, and also total body volume (TBV).

Good agreement between capillary and venous sampling for lectin pathway proteins

Background: The lectin pathway of complement activation, in particular mannose-binding lectin (MBL), has been extensively investigated over recent years. So far, studies were exclusively based on venous samples. The aim of this study was to investigate whether measurements of lectin pathway proteins obtained by capillary sampling are in agreement with venous samples. Methods: Prospective study including 31 infants that were admitted with suspected early-onset sepsis. Lectin pathway proteins were measured in simultaneously obtained capillary and venous samples. Bland–Altman plots of logarithmized results were constructed, and the mean capillary to venous ratios (ratiocap/ven) were calculated with their 95% confidence intervals (CI). Results: The agreement between capillary and venous sampling was very high for MBL (mean ratiocap/ven, 1.01; 95% CI, 0.85–1.19). Similarly, high agreement was observed for H-ficolin (mean ratiocap/ven, 1.02; 95% CI, 0.72–1.44), MASP-2 (1.04; 0.59–1.84), MASP-3 (0.96; 0.71–1.28), and MAp44 (1.01; 0.82–1.25), while the agreement was moderate for M-ficolin (mean ratiocap/ven, 0.78; 95% CI, 0.27–2.28). Conclusions: The results of this study show an excellent agreement between capillary and venous samples for most lectin pathway proteins. Except for M-ficolin, small volume capillary samples can thus be used when assessing lectin pathway proteins in neonates and young children.

Post-mortem tissue sampling using computed tomography guidance

PURPOSE: Currently, in forensic medicine cross-sectional imaging gains recognition and a wide use as a non-invasive examination approach. Today, computed tomography (CT) or magnetic resonance imaging that are available for patients are unable to provide tissue information on the cellular level in a non-invasive manner and also diatom detection, DNA, bacteriological, chemical toxicological and other specific tissue analyses are impossible using radiology. We hypothesised that post-mortem minimally invasive tissue sampling using needle biopsies under CT guidance might significantly enhance the potential of virtual autopsy. The purpose of this study was to test the use of a clinically approved biopsy needle for minimally invasive post-mortem sampling of tissue specimens under CT guidance. MATERIAL AND METHODS: ACN III biopsy core needles 14 gauge x 160 mm with automatic pistol device were used on three bodies dedicated to research from the local anatomical institute. Tissue probes from the brain, heart, lung, liver, spleen, kidney and muscle tissue were obtained under CT fluoroscopy. RESULTS: CT fluoroscopy enabled accurate placement of the needle within the organs and tissues. The needles allowed for sampling of tissue probes with a mean width of 1.7 mm (range 1.2-2 mm) and the maximal length of 20 mm at all locations. The obtained tissue specimens were of sufficient size and adequate quality for histological analysis. CONCLUSION: Our results indicate that, similar to the clinical experience but in many more organs, the tissue specimens obtained using the clinically approved biopsy needle are of a sufficient size and adequate quality for a histological examination. We suggest that post-mortem biopsy using the ACN III needle under CT guidance may become a reliable method for targeted sampling of tissue probes of the body.

GEOSTATISTICAL INFERENCE UNDER PREFERENTIAL SAMPLING

Geostatistics involves the fitting of spatially continuous models to spatially discrete data (Chil`es and Delfiner, 1999). Preferential sampling arises when the process that determines the data-locations and the process being modelled are stochastically dependent. Conventional geostatistical methods assume, if only implicitly, that sampling is non-preferential. However, these methods are often used in situations where sampling is likely to be preferential. For example, in mineral exploration samples may be concentrated in areas thought likely to yield high-grade ore. We give a general expression for the likelihood function of preferentially sampled geostatistical data and describe how this can be evaluated approximately using Monte Carlo methods. We present a model for preferential sampling, and demonstrate through simulated examples that ignoring preferential sampling can lead to seriously misleading inferences. We describe an application of the model to a set of bio-monitoring data from Galicia, northern Spain, in which making allowance for preferential sampling materially changes the inferences.

Analyzing Bivariate Survival Data with Interval Sampling and Application to Cancer Epidemiology

In medical follow-up studies, ordered bivariate survival data are frequently encountered when bivariate failure events are used as the outcomes to identify the progression of a disease. In cancer studies interest could be focused on bivariate failure times, for example, time from birth to cancer onset and time from cancer onset to death. This paper considers a sampling scheme where the first failure event (cancer onset) is identified within a calendar time interval, the time of the initiating event (birth) can be retrospectively confirmed, and the occurrence of the second event (death) is observed sub ject to right censoring. To analyze this type of bivariate failure time data, it is important to recognize the presence of bias arising due to interval sampling. In this paper, nonparametric and semiparametric methods are developed to analyze the bivariate survival data with interval sampling under stationary and semi-stationary conditions. Numerical studies demonstrate the proposed estimating approaches perform well with practical sample sizes in different simulated models. We apply the proposed methods to SEER ovarian cancer registry data for illustration of the methods and theory.

Methods and representativeness of a European survey in children and adolescents: the KIDSCREEN study

BACKGROUND: The objective of the present study was to compare three different sampling and questionnaire administration methods used in the international KIDSCREEN study in terms of participation, response rates, and external validity. METHODS: Children and adolescents aged 8-18 years were surveyed in 13 European countries using either telephone sampling and mail administration, random sampling of school listings followed by classroom or mail administration, or multistage random sampling of communities and households with self-administration of the survey materials at home. Cooperation, completion, and response rates were compared across countries and survey methods. Data on non-respondents was collected in 8 countries. The population fraction (PF, respondents in each sex-age, or educational level category, divided by the population in the same category from Eurostat census data) and population fraction ratio (PFR, ratio of PF) and their corresponding 95% confidence intervals were used to analyze differences by country between the KIDSCREEN samples and a reference Eurostat population. RESULTS: Response rates by country ranged from 18.9% to 91.2%. Response rates were highest in the school-based surveys (69.0%-91.2%). Sample proportions by age and gender were similar to the reference Eurostat population in most countries, although boys and adolescents were slightly underrepresented (PFR <1). Parents in lower educational categories were less likely to participate (PFR <1 in 5 countries). Parents in higher educational categories were overrepresented when the school and household sampling strategies were used (PFR = 1.78-2.97). CONCLUSION: School-based sampling achieved the highest overall response rates but also produced slightly more biased samples than the other methods. The results suggest that the samples were sufficiently representative to provide reference population values for the KIDSCREEN instrument.

Similarities in the Subgingival Microbiota Assessed by a Curet Sampling Method at Sites With Chronic Periodontitis

Background: The goal of this study was to determine whether site-specific differences in the subgingival microbiota could be detected by the checkerboard method in subjects with periodontitis. Methods: Subjects with at least six periodontal pockets with a probing depth (PD) between 5 and 7 mm were enrolled in the study. Subgingival plaque samples were collected with sterile curets by a single-stroke procedure at six selected periodontal sites from 161 subjects (966 subgingival sites). Subgingival bacterial samples were assayed with the checkerboard DNA-DNA hybridization method identifying 37 species. Results: Probing depths of 5, 6, and 7 mm were found at 50% (n = 483), 34% (n = 328), and 16% (n = 155) of sites, respectively. Statistical analysis failed to demonstrate differences in the sum of bacterial counts by tooth type (P = 0.18) or specific location of the sample (P = 0.78). With the exceptions of Campylobacter gracilis (P <0.001) and Actinomyces naeslundii (P <0.001), analysis by general linear model multivariate regression failed to identify subject or sample location factors as explanatory to microbiologic results. A trend of difference in bacterial load by tooth type was found for Prevotella nigrescens (P <0.01). At a cutoff level of >/=1.0 x 10(5), Porphyromonas gingivalis and Tannerella forsythia (previously T. forsythensis) were present at 48.0% to 56.3% and 46.0% to 51.2% of sampled sites, respectively. Conclusions: Given the similarities in the clinical evidence of periodontitis, the presence and levels of 37 species commonly studied in periodontitis are similar, with no differences between molar, premolar, and incisor/cuspid subgingival sites. This may facilitate microbiologic sampling strategies in subjects during periodontal therapy.

A comparison of ground cover and frequency estimation methods for post-harvest soil monitoring

The amount and type of ground cover is an important characteristic to measure when collecting soil disturbance monitoring data after a timber harvest. Estimates of ground cover and bare soil can be used for tracking changes in invasive species, plant growth and regeneration, woody debris loadings, and the risk of surface water runoff and soil erosion. A new method of assessing ground cover and soil disturbance was recently published by the U.S. Forest Service, the Forest Soil Disturbance Monitoring Protocol (FSDMP). This protocol uses the frequency of cover types in small circular (15cm) plots to compare ground surface in pre- and post-harvest condition. While both frequency and percent cover are common methods of describing vegetation, frequency has rarely been used to measure ground surface cover. In this study, three methods for assessing ground cover percent (step-point, 15cm dia. circular and 1x5m visual plot estimates) were compared to the FSDMP frequency method. Results show that the FSDMP method provides significantly higher estimates of ground surface condition for most soil cover types, except coarse wood. The three cover methods had similar estimates for most cover values. The FSDMP method also produced the highest value when bare soil estimates were used to model erosion risk. In a person-hour analysis, estimating ground cover percent in 15cm dia. plots required the least sampling time, and provided standard errors similar to the other cover estimates even at low sampling intensities (n=18). If ground cover estimates are desired in soil monitoring, then a small plot size (15cm dia. circle), or a step-point method can provide a more accurate estimate in less time than the current FSDMP method.

What do case-control studies estimate? Survey of methods and assumptions in published case-control research

To evaluate strategies used to select cases and controls and how reported odds ratios are interpreted, the authors examined 150 case-control studies published in leading general medicine, epidemiology, and clinical specialist journals from 2001 to 2007. Most of the studies (125/150; 83%) were based on incident cases; among these, the source population was mostly dynamic (102/125; 82%). A minority (23/125; 18%) sampled from a fixed cohort. Among studies with incident cases, 105 (84%) could interpret the odds ratio as a rate ratio. Fifty-seven (46% of 125) required the source population to be stable for such interpretation, while the remaining 48 (38% of 125) did not need any assumptions because of matching on time or concurrent sampling. Another 17 (14% of 125) studies with incident cases could interpret the odds ratio as a risk ratio, with 16 of them requiring the rare disease assumption for this interpretation. The rare disease assumption was discussed in 4 studies but was not relevant to any of them. No investigators mentioned the need for a stable population. The authors conclude that in current case-control research, a stable exposure distribution is much more frequently needed to interpret odds ratios than the rare disease assumption. At present, investigators conducting case-control studies rarely discuss what their odds ratios estimate.

Long-Range Pollution Transport: Trans-Atlantic Mechanisms and Lagrangian Modeling Methods

Over the past several decades, it has become apparent that anthropogenic activities have resulted in the large-scale enhancement of the levels of many trace gases throughout the troposphere. More recently, attention has been given to the transport pathway taken by these emissions as they are dispersed throughout the atmosphere. The transport pathway determines the physical characteristics of emissions plumes and therefore plays an important role in the chemical transformations that can occur downwind of source regions. For example, the production of ozone (O3) is strongly dependent upon the transport its precursors undergo. O3 can initially be formed within air masses while still over polluted source regions. These polluted air masses can experience continued O3 production or O3 destruction downwind, depending on the air mass's chemical and transport characteristics. At present, however, there are a number of uncertainties in the relationships between transport and O3 production in the North Atlantic lower free troposphere. The first phase of the study presented here used measurements made at the Pico Mountain observatory and model simulations to determine transport pathways for US emissions to the observatory. The Pico Mountain observatory was established in the summer of 2001 in order to address the need to understand the relationships between transport and O3 production. Measurements from the observatory were analyzed in conjunction with model simulations from the Lagrangian particle dispersion model (LPDM), FLEX-PART, in order to determine the transport pathway for events observed at the Pico Mountain observatory during July 2003. A total of 16 events were observed, 4 of which were analyzed in detail. The transport time for these 16 events varied from 4.5 to 7 days, while the transport altitudes over the ocean ranged from 2-8 km, but were typically less than 3 km. In three of the case studies, eastward advection and transport in a weak warm conveyor belt (WCB) airflow was responsible for the export of North American emissions into the FT, while transport in the FT was governed by easterly winds driven by the Azores/Bermuda High (ABH) and transient northerly lows. In the fourth case study, North American emissions were lofted to 6-8 km in a WCB before being entrained in the same cyclone's dry airstream and transported down to the observatory. The results of this study show that the lower marine FT may provide an important transport environment where O3 production may continue, in contrast to transport in the marine boundary layer, where O3 destruction is believed to dominate. The second phase of the study presented here focused on improving the analysis methods that are available with LPDMs. While LPDMs are popular and useful for the analysis of atmospheric trace gas measurements, identifying the transport pathway of emissions from their source to a receptor (the Pico Mountain observatory in our case) using the standard gridded model output, particularly during complex meteorological scenarios can be difficult can be difficult or impossible. The transport study in phase 1 was limited to only 1 month out of more than 3 years of available data and included only 4 case studies out of the 16 events specifically due to this confounding factor. The second phase of this study addressed this difficulty by presenting a method to clearly and easily identify the pathway taken by only those emissions that arrive at a receptor at a particular time, by combining the standard gridded output from forward (i.e., concentrations) and backward (i.e., residence time) LPDM simulations, greatly simplifying similar analyses. The ability of the method to successfully determine the source-to-receptor pathway, restoring this Lagrangian information that is lost when the data are gridded, is proven by comparing the pathway determined from this method with the particle trajectories from both the forward and backward models. A sample analysis is also presented, demonstrating that this method is more accurate and easier to use than existing methods using standard LPDM products. Finally, we discuss potential future work that would be possible by combining the backward LPDM simulation with gridded data from other sources (e.g., chemical transport models) to obtain a Lagrangian sampling of the air that will eventually arrive at a receptor.

Comparison of two non-bronchoscopic methods for evaluating inflammation in patients with acute hypoxaemic respiratory failure

INTRODUCTION: The simple bedside method for sampling undiluted distal pulmonary edema fluid through a normal suction catheter (s-Cath) has been experimentally and clinically validated. However, there are no data comparing non-bronchoscopic bronchoalveolar lavage (mini-BAL) and s-Cath for assessing lung inflammation in acute hypoxaemic respiratory failure. We designed a prospective study in two groups of patients, those with acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) and those with acute cardiogenic lung edema (ACLE), designed to investigate the clinical feasibility of these techniques and to evaluate inflammation in both groups using undiluted sampling obtained by s-Cath. To test the interchangeability of the two methods in the same patient for studying the inflammation response, we further compared mini-BAL and s-Cath for agreement of protein concentration and percentage of polymorphonuclear cells (PMNs). METHODS: Mini-BAL and s-Cath sampling was assessed in 30 mechanically ventilated patients, 21 with ALI/ARDS and 9 with ACLE. To analyse agreement between the two sampling techniques, we considered only simultaneously collected mini-BAL and s-Cath paired samples. The protein concentration and polymorphonuclear cell (PMN) count comparisons were performed using undiluted sampling. Bland-Altman plots were used for assessing the mean bias and the limits of agreement between the two sampling techniques; comparison between groups was performed by using the non-parametric Mann-Whitney-U test; continuous variables were compared by using the Student t-test, Wilcoxon signed rank test, analysis of variance or Student-Newman-Keuls test; and categorical variables were compared by using chi-square analysis or Fisher exact test. RESULTS: Using protein content and PMN percentage as parameters, we identified substantial variations between the two sampling techniques. When the protein concentration in the lung was high, the s-Cath was a more sensitive method; by contrast, as inflammation increased, both methods provided similar estimates of neutrophil percentages in the lung. The patients with ACLE showed an increased PMN count, suggesting that hydrostatic lung edema can be associated with a concomitant inflammatory process. CONCLUSIONS: There are significant differences between the s-Cath and mini-BAL sampling techniques, indicating that these procedures cannot be used interchangeably for studying the lung inflammatory response in patients with acute hypoxaemic lung injury.

The role of psychological stress in inflammatory bowel disease: quality assessment of methods of 18 prospective studies and suggestions for future research

BACKGROUND: Enquiries among patients on the one hand and experimental and observational studies on the other suggest an influence of stress on inflammatory bowel diseases (IBD). However, since this influence remains hypothetical, further research is essential. We aimed to devise recommendations for future investigations in IBD by means of scrutinizing previously applied methodology. METHODS: We critically reviewed prospective clinical studies on the effect of psychological stress on IBD. Eligible studies were searched by means of the PubMed electronic library and through checking the bibliographies of located sources. RESULTS: We identified 20 publications resulting from 18 different studies. Sample sizes ranged between 10 and 155 participants. Study designs in terms of patient assessment, control variables, and applied psychometric instruments varied substantially across studies. Methodological strengths and weaknesses were irregularly dispersed. Thirteen studies reported significant relationships between stress and adverse outcomes. CONCLUSIONS: Study designs, including accuracy of outcome assessment and repeated sampling of outcomes (i.e. symptoms, clinical, and endoscopic), depended upon conditions like sample size, participants' compliance, and available resources. Meeting additional criteria of sound methodology, like taking into account covariates of the disease and its course, is strongly recommended to possibly improve study designs in future IBD research.

Age modeling of young non-varved lake sediments: methods and limits. Examples from two lakes in Central Chile

High-resolution and highly precise age models for recent lake sediments (last 100–150 years) are essential for quantitative paleoclimate research. These are particularly important for sedimentological and geochemical proxies, where transfer functions cannot be established and calibration must be based upon the relation of sedimentary records to instrumental data. High-precision dating for the calibration period is most critical as it determines directly the quality of the calibration statistics. Here, as an example, we compare radionuclide age models obtained on two high-elevation glacial lakes in the Central Chilean Andes (Laguna Negra: 33°38′S/70°08′W, 2,680 m a.s.l. and Laguna El Ocho: 34°02′S/70°19′W, 3,250 m a.s.l.). We show the different numerical models that produce accurate age-depth chronologies based on 210Pb profiles, and we explain how to obtain reduced age-error bars at the bottom part of the profiles, i.e., typically around the end of the 19th century. In order to constrain the age models, we propose a method with five steps: (i) sampling at irregularly-spaced intervals for 226Ra, 210Pb and 137Cs depending on the stratigraphy and microfacies, (ii) a systematic comparison of numerical models for the calculation of 210Pb-based age models: constant flux constant sedimentation (CFCS), constant initial concentration (CIC), constant rate of supply (CRS) and sediment isotope tomography (SIT), (iii) numerical constraining of the CRS and SIT models with the 137Cs chronomarker of AD 1964 and, (iv) step-wise cross-validation with independent diagnostic environmental stratigraphic markers of known age (e.g., volcanic ash layer, historical flood and earthquakes). In both examples, we also use airborne pollutants such as spheroidal carbonaceous particles (reflecting the history of fossil fuel emissions), excess atmospheric Cu deposition (reflecting the production history of a large local Cu mine), and turbidites related to historical earthquakes. Our results show that the SIT model constrained with the 137Cs AD 1964 peak performs best over the entire chronological profile (last 100–150 years) and yields the smallest standard deviations for the sediment ages. Such precision is critical for the calibration statistics, and ultimately, for the quality of the quantitative paleoclimate reconstruction. The systematic comparison of CRS and SIT models also helps to validate the robustness of the chronologies in different sections of the profile. Although surprisingly poorly known and under-explored in paleolimnological research, the SIT model has a great potential in paleoclimatological reconstructions based on lake sediments

A connection between two nonparametric tests for perfect ranking in balanced ranked set sampling

In this note, we show that an extension of a test for perfect ranking in a balanced ranked set sample given by Li and Balakrishnan (2008) to the multi-cycle case turns out to be equivalent to the test statistic proposed by Frey et al. (2007). This provides an alternative interpretation and motivation for their test statistic.