MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes

We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated regions (DMRs) from individual tumor methylome samples, without genomic variation information or prior knowledge from other datasets. In simulations with mixed bisulfite reads from cancer and normal cell lines, MethylPurify correctly inferred tumor purity and identified over 96% of the DMRs. From patient data, MethylPurify gave satisfactory DMR calls from tumor methylome samples alone, and revealed potential missed DMRs by tumor to normal comparison due to tumor heterogeneity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0419-x) contains supplementary material, which is available to authorized users

Higgs boson production in photon-photon collision at ILC: a comparative study in different little Higgs models

We study the process \gamma\gamma->h->bb_bar at ILC as a probe of different little Higgs models, including the simplest little Higgs model (SLH), the littlest Higgs model (LH), and two types of littlest Higgs models with T-parity (LHT-I, LHT-II). Compared with the Standard Model (SM) prediction, the production rate is found to be sizably altered in these little Higgs models and, more interestingly, different models give different predictions. We find that the production rate can be possibly enhanced only in the LHT-II for some part of the parameter space, while in all other cases the rate is suppressed. The suppression can be 10% in the LH and as much as 60% in both the SLH and the LHT-I/LHT-II. The severe suppression in the SLH happens for a large \tan\beta and a small m_h, in which the new decay mode h->\eta\eta (\eta is a light pseudo-scalar) is dominant; while for the LHT-I/LHT-II the large suppression occurs when f and m_h are both small so that the new decay mode h->A_H A_H is dominant. Therefore, the precision measurement of such a production process at the ILC will allow for a test of these models and even distinguish between different scenarios.Comment: Version in JHEP (h-g-g & h-gamma-gamma expressions added

Integrative analysis of genomic sequencing data reveals higher prevalence of LRP1B mutations in lung adenocarcinoma patients with COPD

AbstractBoth chronic Obstruction Pulmonary Disease (COPD) and lung cancer are leading causes of death globally. Although COPD and lung cancer coexist frequently, it is unknown whether lung cancer patients with COPD harbor distinct genomic characteristics compared to those without COPD. In this study, we retrospectively analyzed genomic sequencing data from 272 patients with lung adenocarcinoma (LUAD) and compared the genetic alterations in LUAD patients with and without COPD. Integrative analysis of whole-genome and exome sequencing data revealed that COPD and non-COPD groups showed high concordance in mutational burden and spectra. Notably, we also found that EGFR mutations were more prevalent in LUAD patients without COPD, whereas mutated LRP1B was more frequently observed in LUAD patients with COPD. In addition, multi-variable analysis with logistic regression demonstrated that mutation of LRP1B was a predictive marker for the presence of COPD in the patients with LUAD. Our analysis demonstrated for the first time the high concordance in genomic alterations between the tumors from LUAD patients with and without COPD. We also identified higher prevalence of LRP1B among the LUAD patients with COPD, which might help understand the underlying mechanisms which link COPD and lung cancer.</jats:p

Numerical investigation on stress corrosion cracking behavior of dissimilar weld joints in pressurized water reactor plants

There have been incidents recently where stress corrosion cracking (SCC) observed in the dissimilar metal weld (DMW) joints connecting the reactor pressure vessel (RPV) nozzle with the hot leg pipe. Due to the complex microstructure and mechanical heterogeneity in the weld region, dissimilar metal weld joints are more susceptible to SCC than the bulk steels in the simulated high temperature water environment of pressurized water reactor (PWR). Tensile residual stress (RS), in addition to operating loads, has a great contribution to SCC crack growth. Limited experimental conditions, varied influence factors and diverging experimental data make it difficult to accurately predict the SCC behavior of DMW joints with complex geometry, material configuration, operating loads and crack shape. Based on the film slip/dissolution oxidation model and elastic-plastic finite element method (EPFEM), an approach is developed to quantitatively predict the SCC growth rate of a RPV outlet nozzle DMW joint. Moreover, this approach is expected to be a pre-analytical tool for SCC experiment of DMW joints in PWR primary water environment

Characteristics of electric field strengthening between coal-mineral particles under microwave irradiation

Both thermal and non-thermal effects induced by microwave radiation can produce a series of effects on coal and rock, and microwave induced discharge is one of the phenomena of microwave non-thermal effects. Coal has a porous and ore-rich skeleton structure with strong heterogeneity. Its internal pores and minerals can affect the electric field. The microwave discharge phenomenon and electric field strengthening characteristics between different component particles are quite different. At present, the relevant researches mainly focus on the coal matrix in the coal body, ignoring the influence of the minerals in the coal body and the irregular shape of the minerals themselves. As a result, the discharge mechanism between real mineral particles and the factors affecting its discharge intensity are still unclear. Therefore, the shape of real coal and rock particles scanned by electronic X-ray tomography (XCT) was described by drawing software, and COMSOL Multiphysics software was used by in this work to discuss the electric field strengthening characteristics of real coal and rock particles under a microwave field and the causes. The results show that the propagation mode and polarization characteristics of microwave have a significant effect on the enhancement of the intergranular electric field, and the intensity of the intergranlar electric field is the largest in x propagation and y polarization. Compared with the other five particle combinations, the particle size and spacing have the most obvious effect on the electric field strengthening of the pyrite-pyrite combination, and the best effect of the electric field strengthening of the coal-rock particle combination appears in the case of large particle size and no spacing. The change of the Angle between particles has a certain influence on the effect of electric field strengthening, and the maximum value of electric field strengthening corresponding to each particle shape appears when the Angle is 0°. The electric field strengthening effect of regular ore particles (round, square, pentagon, etc.) is directly related to the roundness coefficient of the particles. The maximum electric field strength between particles occurs when the Angle of particle tip is about 60° and the roundness coefficient is 0.71. However, the electric field intensity of irregular ore particles has no relation with roundness coefficient and fractal dimension, but gradually increases with the increase of curvature. In addition, the degree of graphitization of carbonaceous materials has a great influence on the electric field strengthening effect, and the electric field intensity increases with the increase of graphitization degree

Seismogenic structures and spatiotemporal seismicity patterns of the 2022 Ms6.0 Maerkang earthquake sequence, Sichuan, China

The 2022 Ms6.0 Maerkang earthquake sequence, Sichuan, China, occurred in an unexpected area with historically rare seismicity in the Bayan Har block. Here we relocated the earthquake sequence, inverted for the focal mechanisms of the larger events, and calculated the rupture directivity of the earthquake sequence to reveal the seismogenic structures and mechanisms of this sequence. The high-precision relocations indicate that the seismogenic structures consist of several clusters that are generally parallel to the nearby NW-trending Songgang fault, and relatively small-scale conjugate faults are also identified. The seismicity migrated from cluster one in the south to cluster two in the north during the sequence. Furthermore, the hypocenters were largely located at 5–10 km depth, thereby highlighting that the seismogenic structures are buried. The vertical fault planes of the seismogenic structures are consistent with the high-dip focal mechanism solutions from seven events. A stress field inversion based on the focal mechanisms indicates that the sequence occurred in a strike-slip environment that was controlled by a NNW–SSE-striking principal compressive stress. The different rupture directivities of the Ms5.8 (southwestward) and Ms6.0 (southeastward) events prove the existence of conjugate faults. The Ms5.8 event induced a coseismic Coulomb stress change of 1.6 MPa where the Ms6.0 event subsequently occurred, thereby highlighting that the Ms5.8 event triggered the Ms6.0 event and produced the spatiotemporal seismicity pattern of the sequence. We therefore conclude that the seismogenic structures of the 2022 Ms6.0 Maerkang earthquake sequence are previously unknown concealed conjugate structures associated with the main Songgang fault. The complex seismogenic structures and their potential to generate large earthquakes warrant the need to better understand the seismogenesis of this area and the seismic risks that may be present

Whole-Brain Mapping of the Inputs and Outputs of the Medial Part of the Olfactory Tubercle

The medial part of the olfactory tubercle (OT) is a brain structure located at the interface of the reward and olfactory system. It is closely related to pheromone-rewards, natural reinforcement, addiction and many other behaviors. However, the structure of the anatomic circuitry of the medial part of the OT is still unclear. In the present study, the medial part of the OT was found to be highly connected with a wide range of brain areas with the help of the pseudorabies virus tracing tool. In order to further investigate the detailed connections for specific neurons, another tracing tool – rabies virus was utilized for D1R-cre and D2R-cre mice. The D1R and D2R neurons in the medial part of the OT were both preferentially innervated by the olfactory areas, especially the piriform cortex, and both had similar direct input patterns. With the help of the adeno-associated virus labeling, it was found that the two subpopulations of neurons primarily innervate with the reward related brain regions, with slightly less axons projecting to the olfactory areas. Thus, the whole-brain input and output circuitry structures for specific types of neurons in the medial part of the OT were systematically investigated, and the results revealed many unique connecting features. This work could provide new insights for further study into the physiological functions of the medial part of the OT

Origin of the Mass Splitting of Elliptic Anisotropy in a Multiphase Transport Model

The mass splitting of elliptic anisotropy ($v_2$) at low transverse momentum is considered as a hallmark of hydrodynamic collective flow. We investigate a multiphase transport (AMPT) model where the $v_2$ is mainly generated by an anisotropic escape mechanism, not of the hydrodynamic flow nature, and where mass splitting is also observed. We demonstrate that the $v_2$ mass splitting in AMPT is small right after hadronization (especially when resonance decays are included); the mass splitting mainly comes from hadronic rescatterings, even though their contribution to the overall charged hadron $v_2$ is small. These findings are qualitatively the same as those from hybrid models that combine hydrodynamics with a hadron cascade. We further show that there is no qualitative difference between heavy ion collisions and small system collisions. Our results indicate that the $v_2$ mass splitting is not a unique signature of hydrodynamic collective flow and thus cannot distinguish whether the elliptic flow is generated mainly from hydrodynamics or the anisotropic parton escape.Comment: 5 pages, 4 figure

Structure Re-determination and Superconductivity Observation of Bulk 1T MoS2

2H MoS2 has been intensively studied because of layer-dependent electronic structures and novel physical properties. Though the metastable 1T MoS2 with the [MoS6] octahedron was observed from the microscopic area, the true crystal structure of 1T phase has not been determined strictly. Moreover, the true physical properties have not been demonstrated from experiments due to the challenge for the preparation of pure 1T MoS2 crystals. Here, we successfully synthesized the 1T MoS2 single crystals and re-determined the crystal structure of 1T MoS2 from single-crystal X-ray diffraction. 1T MoS2 crystalizes in space group P-3m1 with a cell of a = b = 3.190(3) {\AA} and c = 5.945(6) {\AA}. The individual MoS2 layer consists of MoS6 octahedron sharing edge with each other. More surprisingly, the bulk 1T MoS2 crystals undergo a superconducting transition of Tc = 4 K, which is the first observation of superconductivity in pure 1T MoS2 phase