Reliability of the Actigraph GT3X+ Accelerometer in Adults under Free-Living Conditions

Background

Reliability of the Actigraph GT3X+ accelerometer has not been determined under normal wear time criteria in a large sample of subjects and accelerometer units. The aim of this study was to assess contralateral hip difference and inter-instrument reliability of the Actigraph GT3X+ monitor in adults under long-term free-living conditions.

Methods

Eighty-seven adult subjects (28 men; mean (standard deviation) age 31.3 (12.2) years; body mass index 23.7 (3.1) kg/m²) concurrently wore two GT3X+ accelerometers (174 units in total) attached to contralateral hips for 21 days. Reliability was assessed using Bland-Altman plots, mixed model regression analyses and absolute measures of agreement for different lengths of data accumulation (single-day-, 7-day- and 21-day periods).

Results

There were no significant differences between contralateral hips (effect size ≤0.042; p ≥.213). Inter-instrument reliability increased with increased length of data-accumulation. For a 7-day measurement period (n = 232 weeks), limits of agreement were ±68 cpm (vertical axis) and ±81.3 cpm (vector magnitude) for overall physical activity (PA) level, ±51 min for sedentary time, ±18.2 min for light PA, ±6.3 min for moderate PA, ±3.5 min for vigorous PA, and ±6.7 min for moderate-to-vigorous PA.

Conclusions

The Actigraph GT3X+ accelerometer is a reliable tool for measuring PA in adults under free-living conditions using normal data-reduction criteria. Contralateral hip differences are very small. We suggest accelerometers be attached to the right hip and data to be accumulated over several days of measurement.     

Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data

Background  

Using DNA microarrays, we have developed two novel models for tumor classification and target gene prediction. First, gene expression profiles are summarized by optimally selected Self-Organizing Maps (SOMs), followed by tumor sample classification by Fuzzy C-means clustering. Then, the prediction of marker genes is accomplished by either manual feature selection (visualizing the weighted/mean SOM component plane) or automatic feature selection (by pair-wise Fisher's linear discriminant).     

Biochemistry on a Leash: The Roles of Tether Length and Geometry in Signal Integration Proteins

We use statistical mechanics and simple ideas from polymer physics to develop a quantitative model of proteins whose activity is controlled by flexibly tethered ligands and receptors. We predict how the properties of tethers influence the function of these proteins and demonstrate how their tether length dependence can be exploited to construct proteins whose integration of multiple signals can be tuned. One case study to which we apply these ideas is that of the Wiskott-Aldrich Syndrome Proteins as activators of actin polymerization. More generally, tethered ligands competing with those free in solution are common phenomena in biology, making this an important specific example of a widespread biological idea.     

The mathematics of tanning

Background  

The pigment melanin is produced by specialized cells, called melanocytes. In healthy skin, melanocytes are sparsely spread among the other cell types in the basal layer of the epidermis. Sun tanning results from an UV-induced increase in the release of melanin to neighbouring keratinocytes, the major cell type component of the epidermis as well as redistribution of melanin among these cells. Here we provide a mathematical conceptualization of our current knowledge of the tanning response, in terms of a dynamic model. The resolution level of the model is tuned to available data, and its primary focus is to describe the tanning response following UV exposure.     

Masking repeats while clustering ESTs

A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. Unlike traditional methods, repeats are inferred directly from the EST data, we do not rely on any external library of known repeats. This makes the method especially suitable for analysing the ESTs from organisms without good repeat libraries. We demonstrate that the result is very similar to performing standard repeat masking before clustering.     

The effects of exogenous histamine in isolated rat hearts

The role of histamine in cardiac physiology and pathophysiology is not clarified, but is dependent on species. The effects of exogenous histamine in Langendorff-perfused rat hearts were investigated. 1 mM, 100, 10, 1 and 0.1 M of histamine (n=7 each) as 15 min infusions were employed in a dose-response study, and compared to control perfused hearts (n=7). In another experimental series, 100 M histamine (n=15) was added during reperfusion after 25 min global ischemia, and compared to control ischemia-reperfusion (n=15). The maximal response to histamine in the dose-response study (100 M) was an increase of left ventricular developed pressure to 126±8% of initial value (mean±SEM, p<0.04), and increase of coronary flow to 152+6% (p<0.02) after 5 min infusion. 100 M histamine did not significantly influence heart rate or rhythm. The lowest concentration (0.1 M) did not have effects cardiac performance. Reperfusion with histamine for 2 min after ischemia reduced left ventricular developed pressure to 68±10% of initial value versus 116+17% in ischemic controls (p<0.05), and increased left ventricular end-diastolic pressure to 24±8 mmHg compared to 6±2 mmHg in controls (p<0.04). Left ventricular pressures were similar in hearts reperfused with histamine and in ischemic controls for the rest of the observation. Coronary flow increased during reperfusion in hearts given histamine. Histamine had a dose-dependent positive inotropic and vasodilatory effect in isolated rat hearts. Exogenous histamine had only minor effects on post-ischemic cardiac function.     

Species,sets, and the derivative nature of Philosophy

Concepts and methods originating in one discipline can distort the structure of another when they are applied to the latter. I exemplify this mostly with reference to systematic biology, especially problems which have arisen in relation to the nature of species. Thus the received views of classes, individuals (which term I suggest be replaced by units to avoid misunderstandings), and sets are all inapplicable, but each can be suitably modified. The concept of fuzzy set was developed to deal with species and I defend its applicability. Taxa at all levels are real and participate in biological processes. Analysis of cause and pattern provides the deep structure in which metabiology is grounded; violation of this principle has led to diverse errors in biology.     

The prognostic impact of TGF-β1, fascin, NF-κB and PKC-ζ expression in soft tissue sarcomas

Aims

Transforming growth factor-β (TGF-β), fascin, nuclear factor-kappa B (NF-κB) p105, protein-kinase C-zeta (PKC-ζ), partioning-defective protein-6 (Par-6), E-cadherin and vimentin are tumor promoting molecules through mechanisms involved in cell dedifferentiation. In soft tissue sarcomas, their expression profile is poorly defined and their significance is uncertain. We aimed to investigate the prognostic impact of TGF-β1, NF-κB p105, PKC-ζ, Par-6α, E-cadherin and vimentin in non-gastrointestinal stromal tumor soft tissue sarcomas (non-GIST STSs).

Patients and Methods

Tumor samples and clinical data from 249 patients with non-GIST STS were obtained, and tissue microarrays (TMAs) were constructed for each specimen. Immunohistochemistry (IHC) was used to evaluate marker expression in tumor cells.

Results

In univariate analysis, the expression levels of TGF-β1 (P = 0.016), fascin (P = 0.006), NF-κB p105 (P = 0.022) and PKC-ζ, (P = 0.042) were significant indicators for disease specific survival (DSS). In the multivariate analysis, high TGF-β1 expression was an independent negative prognostic factor for DSS (HR = 1.6, 95% CI = 1.1–2.4, P = 0.019) in addition to tumor depth, malignancy grade, metastasis at diagnosis, surgery and positive resection margins.

Conclusion

Expression of TGF-β1 was significantly associated with aggressive behavior and shorter DSS in non-GIST STSs.