Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data

We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/

The dominant role of the solvent-water interface in water droplet templating of polymers

We investigate the formation of microstructured polymer networks known as Breath Figure templated structures created by the presence of water vapour over evaporating polymer solutions. We use a highly controlled experimental approach to examine this dynamic and non-equilibrium process to uniquely compare pure solvent systems with polymer solutions and demonstrate using a combination of optical microscopy, focused ion-beam milling and SEM analysis that the porous polymer microstructure is completely controlled by the interfacial forces that exist between the water droplet and the solvent until a final drying dilation of the imprints. Water droplet contact angles are the same in the presence or absence of polymer and are independent of size for droplets above 5 μm. The polymer acts a spectator that serves to trap water droplets present at the air interface, and to transfer their shape into the polymer film. For the smallest pores, however, there are unexpected variations in the contact angle with pore size that are consistent with a possible contribution from line tension at these smaller dimensions. © The Royal Society of Chemistry.

Kelvin-Helmholtz-like instabilities in turbulent flows over complex surfaces

Riblets are small surface protrusions aligned with the flow direction, which confer an anisotropic roughness to the surface [6]. We have recently reported that the transitional-roughness effect in riblets, which limits their performance, is due to a Kelvin–Helmholtz-like instability of the overlying mean flow [7]. According to our DNSs, the instability sets on as the Reynolds number based on the roughness size of the riblets increases, and coherent, elongated spanwise vortices begin to develop immediately above the riblet tips, causing the degradation of the drag-reduction effect. This is a very novel concept, since prior studies had proposed that the degradation was due to the interaction of riblets with the flow as independent units, either to the lodging of quasi-streamwise vortices in the surface grooves [2] or to the shedding of secondary streamwise vorticity at the riblet peaks [9]. We have proposed an approximate inviscid analysis for the instability, in which the presence of riblets is modelled through an average boundary condition for an overlying, spanwise-independent mean flow. This simplification lacks the accuracy of an exact analysis [4], but in turn applies to riblet surfaces in general. Our analysis succeeds in predicting the riblet size for the onset of the instability, while qualitatively reproducing the wavelengths and shapes of the spanwise structures observed in the DNSs. The analysis also connects the observations with the Kelvin–Helmholtz instability of mixing layers. The fundamental riblet length scale for the onset of the instability is a ‘penetration length,’ which reflects how easily the perturbation flow moves through the riblet grooves. This result is in excellent agreement with the available experimental evidence, and has enabled the identification of the key geometric parameters to delay the breakdown. Although the appearance of elongated spanwise vortices was unexpected in the case of riblets, similar phenomena had already been observed over other rough [3], porous [1] and permeable [11] surfaces, as well as over plant [5,14] and urban [12] canopies, both in the transitional and in the fully-rough regimes. However, the theoretical analyses that support the connection of these observations with the Kelvin–Helmholtz instability are somewhat scarce [7, 11, 13]. It has been recently proposed that Kelvin–Helmholtz-like instabilities are a dominant feature common to “obstructed” shear flows [8]. It is interesting that the instability does not require an inflection point to develop, as is often claimed in the literature. The Kelvin-Helmholtz rollers are rather triggered by the apparent wall-normal-transpiration ability of the flow at the plane immediately above the obstructing elements [7,11]. Although both conditions are generally complementary, if wall-normal transpiration is not present the spanwise vortices may not develop, even if an inflection point exists within the roughness [10]. REFERENCES [1] Breugem, W. P., Boersma, B. J. & Uittenbogaard, R. E. 2006 J. Fluid Mech. 562, 35–72. [2] Choi, H., Moin, P. & Kim, J. 1993 J. Fluid Mech. 255, 503–539. [3] Coceal, O., Dobre, A., Thomas, T. G. & Belcher, S. E. 2007 J. Fluid Mech. 589, 375–409. [4] Ehrenstein, U. 2009 Phys. Fluids 8, 3194–3196. [5] Finnigan, J. 2000 Ann. Rev. Fluid Mech. 32, 519–571. [6] Garcia-Mayoral, R. & Jimenez, J. 2011 Phil. Trans. R. Soc. A 369, 1412–1427. [7] Garcia-Mayoral, R. & Jimenez, J. 2011 J. Fluid Mech. doi: 10.1017/jfm.2011.114. [8] Ghisalberti, M. 2009 J. Fluid Mech. 641, 51–61. [9] Goldstein, D. B. & Tuan, T. C. 1998 J. Fluid Mech. 363, 115–151. [10] Hahn, S., Je, J. & Choi, H. 2002 J. Fluid Mech. 450, 259–285. [11] Jimenez, J., Uhlman, M., Pinelli, A. & G., K. 2001 J. Fluid Mech. 442, 89–117. [12] Letzel, M. O., Krane, M. & Raasch, S. 2008 Atmos. Environ. 42, 8770–8784. [13] Py, C., de Langre, E. & Moulia, B. 2006 J. Fluid Mech. 568, 425–449. [14] Raupach, M. R., Finnigan, J. & Brunet, Y. 1996 Boundary-Layer Meteorol. 78, 351–382.

Investigation of the Young's modulus and thermal expansion of amorphous titania-doped tantala films

The current generation of advanced gravitational wave detectors utilize titania-doped tantala/silica multilayer stacks for their mirror coatings. The properties of the low-refractive-index silica are well known; however, in the absence of detailed direct measurements, the material parameters of Young's modulus and coefficient of thermal expansion (CTE) of the high refractive index material, titania-doped tantala, have been assumed to be equal to values measured for pure tantala coatings. In order to ascertain the true values necessary for thermal noise calculations, we have undertaken measurements of Young's modulus and CTE through the use of nanoindentation and thermal-bending measurements. The measurements were designed to assess the effects of titania doping concentration and post-deposition heat-treatment on the measured values in order to evaluate the possibility of optimizing material parameters to further improve thermal noise in the detector. Young's modulus measurements on pure tantala and 25% and 55% titania-doped tantala show a wide range of values, from 132 to 177 GPa, dependent on both titania concentration and heat-treatment. Measurements of CTE give values of (3.9 +/- 0.1) x 10^-6 K^-1 and (4.9 +/- 0.3) x 10^-6 K^-1 for 25% and 55% titania-doped tantala, respectively, without dependence on post-deposition heat-treatment.

The photon scanning tunneling microscope and its applications

A simple photon scanning tunneling microscope (PSTM) is described. Its lateral resolution (similar to 10nm with a maximal scanning range of 10 mu m x 10 mu m ) is much better than that of a conventional optical microscope. Its principle, the fiber optic tip fabrication and PSTM images of different samples such as mica, HDPE and LiNbO3 are presented.

L_n-PIR的粘弹行为及其对分子链结构、分子量和分子量分布的依赖性

本论文应用应力应变和动态力学方法，系统地表征了L_n-PIR的粘弹行为及其对聚合物链结构、分子量和分子量分布的依赖性，建立了有关力学量与分子量和分子量之间的相互作用规律的数学模式。结果表明，聚合物的粘弹力学量可以用有效分子量的概念来描述：P=K{(M-bar)_ηexp[(M-bar)_w/(M-bar)_n-1]}~(-α) <1>不同类型的分子量的K_D值是不同的，其K_D大小顺序为：(M-bar)_n > (M-bar)_w > (M-bar)_k > (M-bar)_z。弹性物理量对分子量分布的依赖性较粘性物理量为小。分子量和分子量分布对屈服行为的影响，可以归结为分子链缠结行为的作用。L_n-PIR的屈服强度与链缠结点数(m-1)之间的关系满足如下指数方程λ_yσ_y=5.99*10~5(m-1)~(0.47)，达因·厘米~(-2) <2>聚合物的屈服活化能与解链缠结活化能等值等效，均是为使分子链开始解缠结，克服缠结间链段的分子间作用力所做的功，是链缠结分子量的函数。对L_n-PIR，ΔEy与Me之间的关系为 ΔEy=-148.0+40.0 logMe，千焦/摩尔 <3>在M-bar=Mc时，ΔEy达最大值，为其流动活化能。L_n-PIR的屈服破坏能等效于解分子链缠结能，是为使缠结点解脱，克服缠结点的单体单元之间的范德华力所做的功。ΔEd是缠结点数(m-1)的函数ΔEd.=1.38*10~4(m-1)，焦耳·摩尔~(-1) <4>单个链缠结点对ΔEd的贡献是相同的，约为0.143er，相当于相互缠结的两分子链段的链节单元之间的距离接近于范德华平衡半径re=2.84A的分子间作用力。另由于L_n-PIR聚合物本体内存在的紧密的分子链缠结结构，导致非牛顿效应，其流变行为和应力松弛行为偏离牛顿线性流动规律。L_n-PIR的本体粘度与分子量和分子量分布的关系为η_0~(100)=8.91*10~(-19) (M-bar)_η~(4.25)exp[-0.30*4.25((M-bar)_w/(M-bar)_n-1)]，达因·厘米~(-2)·秒 <5>正应力系数与分子量和分子量分布之关系为ξ_0~(100)=1.43*10~(-32) (M-bar)_η~(6.86)exp[-1.10((M-bar)_w/(M-bar)_n-1)]，达因·厘米~(-2)·秒<6>由于分子链的热运动状况不同，回复柔量对分子链结构和分子结构的依赖性是随温度而变化的。L_n-PIR在25 ℃和100 ℃时，回复柔量与分子量和分子量分布的关系为25 ℃: Je-o=0.158(M-bar)_η~(-0.75)exp[+0.298((M-bar)_w/(M-bar)_n-1)]，达因~(-1)·厘米~2 <7> 100 ℃: Je-o=1.32*10~6(M-bar)_η~(-1.81)exp[0.704((M-bar)_w/(M-bar)_n-1)]达因~(-1)·厘米~2 <8>最大松弛时间与(M-bar)_η、MWD之关系为Jm=1.19*10~(-6)(M-bar)_η~(1.72)exp[-0.282((M-bar)_w/(M-bar)_n-1)]，秒<9> Rouse松弛时间与(M-bar)_η、MWD之关系为Jr=1.79*10~(-14)(M-bar)_η~(3.46)exp[-0.567((M-bar)_w/(M-bar)_n-1)]，秒 <10>。

The photon scanning tunneling microscope and its applications

A simple photon scanning tunneling microscope (PSTM) is described. Its lateral resolution (similar to 10nm with a maximal scanning range of 10 mu m x 10 mu m ) is much better than that of a conventional optical microscope. Its principle, the fiber optic tip fabrication and PSTM images of different samples such as mica, HDPE and LiNbO3 are presented.

System size dependence of associated yields in hadron-triggered jets STAR Collaboration

We present results on the system size dependence of high transverse momentum di-hadron correlations at root s(NN) = 200 GeV as measured by STAR at RHIC. Measurements in d + Au, Cu + Cu and Au + Au collisions reveal similar jet-like near-side correlation yields (correlations at small angular separation Delta phi similar to 0, Delta eta similar to 0) for all systems and centralities. Previous measurements have shown Chat the away-side (Delta phi similar to pi) yield is suppressed in heavy-ion collisions. We present measurements of the away-side Suppression as a function of transverse momentum and centrality in Cu + Cu and Au + Au collisions. The suppression is found to be similar in Cu + Cu and An + An collisions at a similar number of participants. The results are compared to theoretical calculations based on the patron quenching model and the modified fragmentation model. The observed differences between data and theory indicate that the correlated yields presented here will further constrain dynamic energy loss models and provide information about the dynamic density profile in heavy-ion collisions. (C) 2009 Elsevier B.V. All rights reserved.

Measurement of the Bottom Quark Contribution to Nonphotonic Electron Production in p plus p Collisions at root s=200 GeV

The contribution of B meson decays to nonphotonic electrons, which are mainly produced by the semileptonic decays of heavy-flavor mesons, in p + p collisions at root s = 200 GeV has been measured using azimuthal correlations between nonphotonic electrons and hadrons. The extracted B decay contribution is approximately 50% at a transverse momentum of p(T) >= 5 GeV/c. These measurements constrain the nuclear modification factor for electrons from B and D meson decays. The result indicates that B meson production in heavy ion collisions is also suppressed at high p(T).

Higher Moments of Net Proton Multiplicity Distributions at RHIC

200 GeV corresponding to baryon chemical potentials (mu(B)) between 200 and 20 MeV. Our measurements of the products kappa sigma(2) and S sigma, which can be related to theoretical calculations sensitive to baryon number susceptibilities and long-range correlations, are constant as functions of collision centrality. We compare these products with results from lattice QCD and various models without a critical point and study the root s(NN) dependence of kappa sigma(2). From the measurements at the three beam energies, we find no evidence for a critical point in the QCD phase diagram for mu(B) below 200 MeV.