The behaviour of random forest permutation-based variable importance measures under predictor correlation

<p>Abstract</p> <p>Background</p> <p>Random forests (RF) have been increasingly used in applications such as genome-wide association and microarray studies where predictor correlation is frequently observed. Recent works on permutation-based variable importance measures (VIMs) used in RF have come to apparently contradictory conclusions. We present an extended simulation study to synthesize results.</p> <p>Results</p> <p>In the case when both predictor correlation was present and predictors were associated with the outcome (H_A), the unconditional RF VIM attributed a higher share of importance to correlated predictors, while under the null hypothesis that no predictors are associated with the outcome (H₀) the unconditional RF VIM was unbiased. Conditional VIMs showed a decrease in VIM values for correlated predictors versus the unconditional VIMs under H_Aand was unbiased under H₀. Scaled VIMs were clearly biased under H_Aand H₀.</p> <p>Conclusions</p> <p>Unconditional unscaled VIMs are a computationally tractable choice for large datasets and are unbiased under the null hypothesis. Whether the observed increased VIMs for correlated predictors may be considered a "bias" - because they do not directly reflect the coefficients in the generating model - or if it is a beneficial attribute of these VIMs is dependent on the application. For example, in genetic association studies, where correlation between markers may help to localize the functionally relevant variant, the increased importance of correlated predictors may be an advantage. On the other hand, we show examples where this increased importance may result in spurious signals.</p

Polymorphisms of the NADPH Oxidase p22phox Gene in a Caucasian Population with Intracranial Aneurysms

Background: Vascular remodeling generated by reactive oxygen species contributes to aneurysm formation. The NADPH oxidase system is a major source of superoxide anion not only in phagocytes, but also in endothelial and vascular smooth muscle cells. Polymorphisms of p22phox, an essential component of the NADPH oxidase system, are found to be associated with atherosclerosis, while a recent study found a significant association between the 214C>T polymorphism and the occurrence of ischemic cerebrovascular disease. We conducted a case-control study to investigate the relationship of five polymorphisms of the p22phox gene and the occurrence of cerebral aneurysms. Methods: The study population consisted of 113 patients with intracranial aneurysms and 53 control subjects. The 214C>T polymorphism was investigated by restriction fragment length polymorphism analysis, while polymorphisms 381T>C, 480G>A, 521C>T, and *24A>G were analyzed by direct sequencing of exon 6 and adjacent intronic sequences. Results: The analysis of a primary study sample comprising 35 cases and 28 controls failed to show a significant association between any of the five polymorphisms and the occurrence of intracranial aneurysms using both allele frequencies and genotypes (all nominal p > 0.05). Although there was a deviation from Hardy-Weinberg equilibrium in cases at the 521C>T locus (nominal p T, 521C>T, and *24A>G); haplotype frequencies in cases and controls were not significantly different. Conclusion: Although polymorphisms of the p22phox gene located in the coding region and the 3′-untranslated region were reported to be associated with atherosclerosis and cerebrovascular disease, our data provide evidence that there is no association between these polymorphisms and the occurrence of cerebral aneurysms in Caucasians.Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich

Optical Hall conductivity of systems with gapped spectral nodes

We calculate the optical Hall conductivity within the Kubo formalism for systems with gapped spectral nodes, where the latter have a power-law dispersion with exponent n. The optical conductivity is proportional to n and there is a characteristic logarithmic singularity as the frequency approaches the gap energy. The optical Hall conductivity is almost unaffected by thermal fluctuations and disorder for n=1, whereas disorder has a stronger effect on transport properties if n=2

The first three-dimensional visualization of a thrombus in transit trapped between the leads of a permanent dual-chamber pacemaker: a case report

<p>Abstract</p> <p>Introduction</p> <p>Two-dimensional echocardiography is a useful tool in diagnosing cardiac masses. However, the three-dimensional offline reconstruction technique of transesophageal echocardiography might be superior to two-dimensional transesophageal echocardiography in providing additional information of structural details.</p> <p>Case presentation</p> <p>We report the case of a 76-year-old Caucasian man with a permanent dual-chamber pacemaker and a worm-like right-heart thrombus in transit. Two-dimensional transthoracic echocardiography and two-dimensional transesophageal echocardiography showed that it was debatable as to whether "the worm" was originating from the leads. Offline three-dimensional transesophageal echocardiography reconstruction technique proved superior in identifying the cardiac mass as a thrombus trapped between the leads of the pacemaker. The thrombus was successfully dissolved by systemic heparin therapy.</p> <p>Conclusions</p> <p>The three-dimensional transesophageal echocardiography is useful and effective in patients with implanted pacemakers or defibrillators when other closely competing imaging modalities are contraindicated, such as magnetic resonance imaging. In patients with pacemakers and trapped thrombus in transit for whom surgical therapy might be a high risk, medical therapy seems to offer a safer and convincing alternative. Whether the management of right-heart thrombi has to be modified due to the presence of pacemaker leads is controversial.</p

Hard x-ray characterization of a HEFT single-reflection prototype

We have measured the hard X-ray reflectivity and imaging performance from depth graded W/Si multilayer coated mirror segments mounted in a single reflection cylindrical prototype for the hard X-ray telescopes to be flown on the High Energy Focusing Telescope (HEFT) balloon mission. Data have been obtained in the energy range from 18 - 170 keV at the European Synchrotron Radiation Facility and at the Danish Space Research Institute at 8 keV. The modeling of the reflectivity data demonstrate that the multilayer structure can be well described by the intended power law distribution of the bilayer thicknesses optimized for the telescope performance and we find that all the data is consistent with an interfacial width of 4.5 Å. We have also demonstrated that the required 5% uniformity of the coatings is obtained over the mirror surface and we have shown that it is feasible to use similar W/Si coatings for much higher energies than the nominal energy range of HEFT leading the way for designing Gamma-ray telescopes for future astronomical applications. Finally we have demonstrate 35 arcsecond Half Power Diameter imaging performance of the one bounce prototype throughout the energy range of the HEFT telescopes

CD69 is a TGF-β/1α,25-dihydroxyvitamin D3 target gene in monocytes

CD69 is a transmembrane lectin that can be expressed on most hematopoietic cells. In monocytes, it has been functionally linked to the 5-lipoxygenase pathway in which the leukotrienes, a class of highly potent inflammatory mediators, are produced. However, regarding CD69 gene expression and its regulatory mechanisms in monocytes, only scarce data are available. Here, we report that CD69 mRNA expression, analogous to that of 5-lipoxygenase, is induced by the physiologic stimuli transforming growth factor-β (TGF-β) and 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) in monocytic cells. Comparison with T- and B-cell lines showed that the effect was specific for monocytes. CD69 expression levels were increased in a concentration-dependent manner, and kinetic analysis revealed a rapid onset of mRNA expression, indicating that CD69 is a primary TGF-β/1α,25(OH)2D3 target gene. PCR analysis of different regions of the CD69 mRNA revealed that de novo transcription was initiated and proximal and distal parts were induced concomitantly. In common with 5-lipoxygenase, no activation of 0.7 kb or ~2.3 kb promoter fragments by TGF-β and 1α,25(OH)2D3 could be observed in transient reporter assays for CD69. Analysis of mRNA stability using a transcription inhibitor and a 3′UTR reporter construct showed that TGF-β and 1α,25(OH)2D3 do not influence CD69 mRNA stability. Functional knockdown of Smad3 clearly demonstrated that upregulation of CD69 mRNA, in contrast to 5-LO, depends on Smad3. Comparative studies with different inhibitors for mitogen activated protein kinases (MAPKs) revealed that MAPK signalling is involved in CD69 gene regulation, whereas 5-lipoxygenase gene expression was only partly affected. Mechanistically, we found evidence that CD69 gene upregulation depends on TAK1-mediated p38 activation. In summary, our data indicate that CD69 gene expression, conforming with 5-lipoxygenase, is regulated monocyte-specifically by the physiologic stimuli TGF-β and 1α,25(OH)2D3 on mRNA level, although different mechanisms account for the upregulation of each gene

Improving compliance to colorectal cancer screening using blood and stool based tests in patients refusing screening colonoscopy in Germany

Background Despite strong recommendations for colorectal cancer (CRC) screening, participation rates are low. Understanding factors that affect screening choices is essential to developing future screening strategies. Therefore, this study assessed patient willingness to use non-invasive stool or blood based screening tests after refusing colonoscopy. Methods Participants were recruited during regular consultations. Demographic, health, psychological and socioeconomic factors were recorded. All subjects were advised to undergo screening by colonoscopy. Subjects who refused colonoscopy were offered a choice of non-invasive tests. Subjects who selected stool testing received a collection kit and instructions; subjects who selected plasma testing had a blood draw during the office visit. Stool samples were tested with the Hb/Hp Complex Elisa test, and blood samples were tested with the Epi proColon® 2.0 test. Patients who were positive for either were advised to have a diagnostic colonoscopy. Results 63 of 172 subjects were compliant to screening colonoscopy (37%). 106 of the 109 subjects who refused colonoscopy accepted an alternative non-invasive method (97%). 90 selected the Septin9 blood test (83%), 16 selected a stool test (15%) and 3 refused any test (3%). Reasons for blood test preference included convenience of an office draw, overall convenience and less time consuming procedure. Conclusions 97% of subjects refusing colonoscopy accepted a non-invasive screening test of which 83% chose the Septin9 blood test. The observation that participation can be increased by offering non-invasive tests, and that a blood test is the preferred option should be validated in a prospective trial in the screening setting