Non-specific filtering of beta-distributed data.

BackgroundNon-specific feature selection is a dimension reduction procedure performed prior to cluster analysis of high dimensional molecular data. Not all measured features are expected to show biological variation, so only the most varying are selected for analysis. In DNA methylation studies, DNA methylation is measured as a proportion, bounded between 0 and 1, with variance a function of the mean. Filtering on standard deviation biases the selection of probes to those with mean values near 0.5. We explore the effect this has on clustering, and develop alternate filter methods that utilize a variance stabilizing transformation for Beta distributed data and do not share this bias.ResultsWe compared results for 11 different non-specific filters on eight Infinium HumanMethylation data sets, selected to span a variety of biological conditions. We found that for data sets having a small fraction of samples showing abnormal methylation of a subset of normally unmethylated CpGs, a characteristic of the CpG island methylator phenotype in cancer, a novel filter statistic that utilized a variance-stabilizing transformation for Beta distributed data outperformed the common filter of using standard deviation of the DNA methylation proportion, or its log-transformed M-value, in its ability to detect the cancer subtype in a cluster analysis. However, the standard deviation filter always performed among the best for distinguishing subgroups of normal tissue. The novel filter and standard deviation filter tended to favour features in different genome contexts; for the same data set, the novel filter always selected more features from CpG island promoters and the standard deviation filter always selected more features from non-CpG island intergenic regions. Interestingly, despite selecting largely non-overlapping sets of features, the two filters did find sample subsets that overlapped for some real data sets.ConclusionsWe found two different filter statistics that tended to prioritize features with different characteristics, each performed well for identifying clusters of cancer and non-cancer tissue, and identifying a cancer CpG island hypermethylation phenotype. Since cluster analysis is for discovery, we would suggest trying both filters on any new data sets, evaluating the overlap of features selected and clusters discovered

Validating a Device for Whiplash Motion Simulation in a Porcine Model

Whiplash injury is a common outcome following minor automobile collisions. One theorizedmechanism for whiplash injury is that the rapid head and neck motions induced by a collision caninjure nerve cells in the dorsal root ganglia through pressure gradients developed in the spinalcanal and surrounding tissues. This injury mechanism has previously been studied in humancadaver and porcine models. However, the whiplash motion simulation methods in the latterstudies lacked the control necessary to explore the independent effects of head rotation andretraction on the measured spinal pressures. This project aimed to address the limitations ofprevious porcine whiplash studies by developing and validating a new whiplash motion simulationdevice to enable further study of this injury mechanism. The new proposed device consists of twoservomotors which can be programmed to precisely actuate a headplate through mechanicallinkages. For the current study, an inert surrogate model was used for preliminary testing of thedevice using a whiplash motion profile from previous porcine studies. The time scale of the motionprofile was adjusted to incrementally increase severity. The positional accuracy and repeatabilityof the device was assessed through marker tracking of the headplate and logging of the motorencoder positions. Angular rates and linear accelerations of the plate were also measured. Testingdemonstrated the strengths of the proposed device in accurately and repeatably replicatingprogrammed motion profiles. Some design modifications can potentially enable simulatingwhiplash motion severities commensurate with previous porcine whiplash studies. With futuretesting using this device, our understanding of the pressure-induced whiplash injury mechanismcan be improved, which can inform effective treatments and preventative measures for whiplashinjury

How Ligand Geometry Affects the Reactivity of Co(II) Cyclam Complexes

Cobalt complexes are extensively studied as bioinspired models for non-heme oxygenases as they facilitate both the stabilization and characterization of metal-oxygen intermediates. As an analog to the well-known Co(cyclam) complex Co{N4} (cyclam=1,4,8,11-tetraazacyclotetradecane), the CoII complex Co{i-N4} with the isomeric isocyclam ligand (isocyclam=1,4,7,11-tetraazacyclotetradecane) was synthesized and characterized. Despite the identical N4 donor set of both complexes, Co{i-N4} enables the 2e−/2H+ reduction of O2 with a lower overpotential (ηeff of 385 mV vs. 540 mV for Co{N4}), albeit with a diminished turnover frequency. Characterization of the intermediates formed upon O2 activation of Co{i-N4} reveals a structurally identified stable μ-peroxo CoIII dimer as the main product. A superoxo CoIII species is also formed as a minor product, as indicated by EPR spectroscopy. In further reactivity studies, the electrophilicity of these in situ generated Co−O2 species was demonstrated by the oxidation of the O−H bond of TEMPO−H (2,2,6,6-tetramethylpiperidin-1-ol) via a H atom abstraction process. Unlike the known Co(cyclam), Co{i-N4} can be employed in oxygen atom transfer reactions oxidizing triphenylphosphine to the corresponding phosphine oxide highlighting the impact of geometrical modifications of the ligand while preserving the ring size and donor atom set on the reactivity of biomimetic oxygen activating complexes.Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)Fraunhofer Internal ProgramsPeer Reviewe

Modeling measurement error in tumor characterization studies

<p>Abstract</p> <p>Background</p> <p>Etiologic studies of cancer increasingly use molecular features such as gene expression, DNA methylation and sequence mutation to subclassify the cancer type. In large population-based studies, the tumor tissues available for study are archival specimens that provide variable amounts of amplifiable DNA for molecular analysis. As molecular features measured from small amounts of tumor DNA are inherently noisy, we propose a novel approach to improve statistical efficiency when comparing groups of samples. We illustrate the phenomenon using the MethyLight technology, applying our proposed analysis to compare <it>MLH1 </it>DNA methylation levels in males and females studied in the Colon Cancer Family Registry.</p> <p>Results</p> <p>We introduce two methods for computing empirical weights to model heteroscedasticity that is caused by sampling variable quantities of DNA for molecular analysis. In a simulation study, we show that using these weights in a linear regression model is more powerful for identifying differentially methylated loci than standard regression analysis. The increase in power depends on the underlying relationship between variation in outcome measure and input DNA quantity in the study samples.</p> <p>Conclusions</p> <p>Tumor characteristics measured from small amounts of tumor DNA are inherently noisy. We propose a statistical analysis that accounts for the measurement error due to sampling variation of the molecular feature and show how it can improve the power to detect differential characteristics between patient groups.</p

On stability of linear time-varying second-order differential equations

We derive sufficient conditions for stability and asymptotic stability of second order, scalar differential equations with differentiable coefficients

The role of regulatory T cells in antigen-induced arthritis: aggravation of arthritis after depletion and amelioration after transfer of CD4(+)CD25(+ )T cells

It is now generally accepted that CD4(+)CD25(+ )T(reg )cells play a major role in the prevention of autoimmunity and pathological immune responses. Their involvement in the pathogenesis of chronic arthritis is controversial, however, and so we examined their role in experimental antigen-induced arthritis in mice. Depletion of CD25-expressing cells in immunized animals before arthritis induction led to increased cellular and humoral immune responses to the inducing antigen (methylated bovine serum albumin; mBSA) and autoantigens, and to an exacerbation of arthritis, as indicated by clinical (knee joint swelling) and histological scores. Transfer of CD4(+)CD25(+ )cells into immunized mice at the time of induction of antigen-induced arthritis decreased the severity of disease but was not able to cure established arthritis. No significant changes in mBSA-specific immune responses were detected. In vivo migration studies showed a preferential accumulation of CD4(+)CD25(+ )cells in the inflamed joint as compared with CD4(+)CD25(- )cells. These data imply a significant role for CD4(+)CD25(+ )T(reg )cells in the control of chronic arthritis. However, transferred T(reg )cells appear to be unable to counteract established acute or chronic inflammation. This is of considerable importance for the timing of T(reg )cell transfer in potential therapeutic applications

Sustained Calcium(II)-Release to Impart Bioactivity in Hybrid Glass Scaffolds for Bone Tissue Engineering

In this study, we integrated different calcium sources into sol-gel hybrid glass scaffolds with the aim of producing implants with long-lasting calcium release while maintaining mechanical strength of the implant. Calcium(II)-release was used to introduce bioactivity to the material and eventually support implant integration into a bone tissue defect. Tetraethyl orthosilicate (TEOS) derived silica sols were cross-linked with an ethoxysilylated 4-armed macromer, pentaerythritol ethoxylate and processed into macroporous scaffolds with defined pore structure by indirect rapid prototyping. Triethyl phosphate (TEP) was shown to function as silica sol solvent. In a first approach, we investigated the integration of 1 to 10% CaCl2 in order to test the hypothesis that small CaCl2 amounts can be physically entrapped and slowly released from hybrid glass scaffolds. With 5 and 10% CaCl2 we observed an extensive burst release, whereas slightly improved release profiles were found for lower Calcium(II) contents. In contrast, introduction of melt-derived bioactive 45S5 glass microparticles (BG-MP) into the hybrid glass scaffolds as another Calcium(II) source led to an approximately linear release of Calcium(II) in Tris(hydroxymethyl)aminomethane (TRIS) buffer over 12 weeks. pH increase caused by BG-MP could be controlled by their amount integrated into the scaffolds. Compression strength remained unchanged compared to scaffolds without BG-MP. In cell culture medium as well as in simulated body fluid, we observed a rapid formation of a carbonated hydroxyapatite layer on BG-MP containing scaffolds. However, this mineral layer consumed the released Calcium(II) ions and prevented an additional increase in Calcium(II) concentration in the cell culture medium. Cell culture studies on the different scaffolds with osteoblast-like SaOS-2 cells as well as bone marrow derived mesenchymal stem cells (hMSC) did not show any advantages concerning osteogenic differentiation due to the integration of BG-MP into the scaffolds. Nonetheless, via the formation of a hydroxyapatite layer and the ability to control the pH increase, we speculate that implant integration in vivo and bone regeneration may benefit from this concept