Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

Sample size estimation: an overview with applications to orthodontic clinical trial designs

Proper sample size estimation is an important part of clinical trial methodology and closely related to the precision and power of the trial's results. Trials with sufficient sample sizes are scientifically and ethically justified and more credible compared with trials with insufficient sizes. Planning clinical trials with inadequate sample sizes might be considered as a waste of time and resources, as well as unethical, since patients might be enrolled in a study in which the expected results will not be trusted and are unlikely to have an impact on clinical practice. Because of the low emphasis of sample size calculation in clinical trials in orthodontics, it is the objective of this article to introduce the orthodontic clinician to the importance and the general principles of sample size calculations for randomized controlled trials to serve as guidance for study designs and as a tool for quality assessment when reviewing published clinical trials in our specialty. Examples of calculations are shown for 2-arm parallel trials applicable to orthodontics. The working examples are analyzed, and the implications of design or inherent complexities in each category are discussed.

MIAWARA-C, a new ground based water vapor radiometer for measurement campaigns

In this paper a new 22 GHz water vapor spectro-radiometer which has been specifically designed for profile measurement campaigns of the middle atmosphere is presented. The instrument is of a compact design and has a simple set up procedure. It can be operated as a standalone instrument as it maintains its own weather station and a calibration scheme that does not rely on other instruments or the use of liquid nitrogen. The optical system of MIAWARA-C combines a choked gaussian horn antenna with a parabolic mirror which reduces the size of the instrument in comparison with currently existing radiometers. For the data acquisition a correlation receiver is used together with a digital cross correlating spectrometer. The complete backend section, including the computer, is located in the same housing as the instrument. The receiver section is temperature stabilized to minimize gain fluctuations. Calibration of the instrument is achieved through a balancing scheme with the sky used as the cold load and the tropospheric properties are determined by performing regular tipping curves. Since MIAWARA-C is used in measurement campaigns it is important to be able to determine the elevation pointing in a simple manner as this is a crucial parameter in the calibration process. Here we present two different methods; scanning the sky and the Sun. Finally, we report on the first spectra and retrieved water vapor profiles acquired during the Lapbiat campaign at the Finnish Meteorological Institute Arctic Research Centre in Sodankylä, Finland. The performance of MIAWARA-C is validated here by comparison of the presented profiles against the equivalent profiles from the Microwave Limb Sounder on the EOS/Aura satellite.

Vapor bubble generation around gold nano-particles and its application to damaging of cells

We investigated vapor bubbles generated upon irradiation of gold nanoparticles with nanosecond laser pulses. Bubble formation was studied both with optical and acoustic means on supported single gold nanoparticles and single nanoparticles in suspension. Formation thresholds determined at different wavelengths indicate a bubble formation efficiency increasing with the irradiation wavelength. Vapor bubble generation in Bac-1 cells containing accumulations of the same particles was also investigated at different wavelengths. Similarly, they showed an increasing cell damage efficiency for longer wavelengths. Vapor bubbles generated by single laser pulses were about half the cell size when inducing acute damage.

Levels and determinants of inflammatory biomarkers in a Swiss population-based sample (CoLaus study)

Objective to assess the levels and determinants of interleukin (IL)-1β, IL-6, tumour necrosis factor (TNF)-α and C-reactive protein (CRP) in a healthy Caucasian population. Methods population sample of 2884 men and 3201 women aged 35 to 75. IL-1β, IL-6 and TNF-α were assessed by a multiplexed particle-based flow cytometric assay and CRP by an immunometric assay. Results Spearman rank correlations between duplicate cytokine measurements (N = 80) ranged between 0.89 and 0.96; intra-class correlation coefficients ranged between 0.94 and 0.97, indicating good reproducibility. Among the 6085 participants, 2289 (37.6%), 451 (7.4%) and 43 (0.7%) had IL-1β, IL-6 and TNF-α levels below detection limits, respectively. Median (interquartile range) for participants with detectable values were 1.17 (0.48–3.90) pg/ml for IL-1β; 1.47 (0.71–3.53) pg/ml for IL-6; 2.89 (1.82–4.53) pg/ml for TNF-α and 1.3 (0.6–2.7) ng/ml for CRP. On multivariate analysis, greater age was the only factor inversely associated with IL-1β levels. Male sex, increased BMI and smoking were associated with greater IL-6 levels, while no relationship was found for age and leisure-time PA. Male sex, greater age, increased BMI and current smoking were associated with greater TNF-α levels, while no relationship was found with leisure-time PA. CRP levels were positively related to age, BMI and smoking, and inversely to male sex and physical activity. Conclusion Population-based levels of several cytokines were established. Increased age and BMI, and to a lesser degree sex and smoking, significantly and differentially impact cytokine levels, while leisure-time physical activity has little effect.

Associations between alcohol consumption and selected cytokines in a Swiss population-based sample (CoLaus study)

To assess the associations between alcohol consumption and cytokine levels (interleukin-1beta - IL-1β; interleukin-6 - IL-6 and tumor necrosis factor-α - TNF-α) in a Caucasian population.

Association between circulating cytokine levels, diabetes and insulin resistance in a population-based sample (CoLaus study)

OBJECTIVE: The associations between inflammation, diabetes and insulin resistance remain controversial. Hence, we assessed the associations between diabetes, insulin resistance (using HOMA-IR) and metabolic syndrome with the inflammatory markers high sensitivity C-reactive protein (hs-CRP), interleukin-1beta (IL-1β), interleukin-6 (IL-6) and tumour necrosis factor-α (TNF-α). DESIGN: CROSS-SECTIONAL STUDY: PARTICIPANTS: 2884 MEN AND 3201 WOMEN AGED 35 TO 75: METHODS: CRP was assessed by immunoassay and cytokines by multiplexed flow cytometric assay. In a subgroup of 532 participants an oral glucose tolerance test was performed to screen for impaired glucose tolerance (IGT). RESULTS: IL-6, TNF-α and hs-CRP were significantly and positively correlated with fasting plasma glucose, insulin and HOMA-IR. Participants with diabetes had higher IL-6, TNF-α and hs-CRP levels than participants without diabetes; this difference persisted for hs-CRP after multivariate adjustment. Participants with metabolic syndrome had increased IL-6, TNF-α and hs-CRP levels; these differences persisted after multivariate adjustment. Participants in the highest quartile of HOMA-IR had increased IL-6, TNF-α and hs-CRP levels; these differences persisted for TNF-α and hs-CRP after multivariate adjustment. No association was found between IL-1β levels and all diabetes and insulin resistance markers studied. Finally, participants with IGT had higher hs-CRP levels than participants with a normal OGTT, but this difference disappeared after controlling for body mass index (BMI). CONCLUSION: subjects with diabetes, metabolic syndrome and increased insulin resistance present with increased levels of IL6, TNF-α and hs-CRP, while no association was found with IL-1β. The increased inflammatory state of subjects with IGT is partially explained by increased BMI. © 2012 Blackwell Publishing Ltd.