Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Role of the N*(1535) in eta ' production

We study the near-threshold eta ' production mechanism in nucleon-nucleon and pi N collisions under the assumption that subthreshold resonance N*(1535) is predominant. In an effective Lagrangian approach that gives a reasonable description to the pN -> pN eta and pi(-) p -> n eta reactions, we find that the excitation of N*(1535) resonance from the t- channel p exchange makes the dominate contribution to the pN -> pN eta ' process, and a value of 6.5 for the ratio of s(pp -> pp eta ') to sigma (pp -> pp eta ') is predicted. A strongcoupling strength ofN*(1535) to eta ' N (g(eta ' NN*)(2)/4 pi = 1.1) is extracted from a combined analysis to pp -> pp eta ' and pi N -> N eta ', and the possible implication to the intrinsic component of N*(1535) is explored.CAS KJCX3-SYW-N2 KJCX2-SW-N16 Science Foundation of China 10435080 10575123 1071017

Baryon magnetic moment and beta decay ratio in colored quark cluster model

Baryon magnetic moments of p, n, Sigma(+), Sigma(-), Xi(0), Xi(-) and the beta decay ratios (G(A)/G(V)) of n -> p, Sigma(-) -> n and Xi(0) -> Sigma(+) are calculated in a colored quark cluster model. With SU(3) breaking, the model gives a good fit to the experimental values of those baryon magnetic moments and the beta decay ratios. Our results show that the orbital motion has a significant contribution to the spin and magnetic moments of those baryons and the strange component. in nucleon is small

Strangeness production process pp -> nK(+)Sigma(+) within resonance model

We explore production mechanism and final state interaction in the pp -> nK(+)Sigma(+) channel based on the inconsistent experimental data published respectively by COSY-11 and COSY-ANKE. The scattering parameter a > 0 for n Sigma(+) interaction is favoured by large near-threshold cross section within a nonrelativistic parametrization investigation, and a strong n Sigma(+) interaction comparable to pp interaction is also indicated. Based on this analysis we calculate the contribution from resonance Delta*(1920) through pi(+) exchange within resonance model, and the numerical result suggests a rather small near-threshold total cross section, which is consistent with the COSY-ANKE data. With an additional sub-threshold resonance Delta*(1620), the model gives a much better description to the rather large near-threshold total cross section published by COSY-11SupportedbytheKnowledgeInnovationProjectofChineseAcademyofSciencesunderGrantNosKJCX3-SYW-N2and KJCX2-SW-N16,andtheNationalNaturalScienceFoundationofChinaunderGrantNos10435080,10575123,and10710172

BRST invariant theory of a generalized 1+1 Dimensional nonlinear sigma model with topological term

We give a generalized Lagrangian density of 1 + 1 Dimensional O( 3) nonlinear sigma model with subsidiary constraints, different Lagrange multiplier fields and topological term, find a lost intrinsic constraint condition, convert the subsidiary constraints into inner constraints in the nonlinear sigma model, give the example of not introducing the lost constraint. N = 0, by comparing the example with the case of introducing the lost constraint, we obtain that when not introducing the lost constraint, one has to obtain a lot of various non-intrinsic constraints. We further deduce the gauge generator, give general BRST transformation of the model under the general conditions. It is discovered that there exists a gauge parameter beta originating from the freedom degree of BRST transformation in a general O( 3) nonlinear sigma model, and we gain the general commutation relations of ghost field

General SU(2)(L) x SU(2)(R) x U(1)(EM) sigma model with external sources, dynamical breaking and spontaneous vacuum symmetry breaking

We give a general SU(2)(L) x SU(2)(R) x U(1)(EM) sigma model with external sources, dynamical breaking and spontaneous vacuum symmetry breaking, and present the general formulation of the model. It is found that sigma and pi(0) without electric charges have electromagnetic interaction effects coming front the internal structures. A general Lorentz transformation relative to external sources J(gauge) - (J(A mu) J(A mu)(kappa)) derived, using the general Lorentz transformation and the four-dimensional current of nuclear matter of the ground si ate with J(gauge) = 0, we give the four-dimensional general relations between the different currents of nuclear matter systems with J(gauge) not equal 0 and those with J(gauge) = 0. The relation of the density's coupling with external magnetic field is derived, which conforms well to dense nuclear matter in a strong magnetic field. We show different condensed effects in strong interaction about fermions and antifermions, and give the concrete scalar and pseudoscalar condensed expressions of sigma(0) and pi(0) bosons. About different dynamical breaking and spontaneous vacuum symmetry breaking, the concrete expressions of different mass spectra are obtained in field theory. This paper acquires the running spontaneous vacuum breaking value sigma'(0), and obtains the spontaneous vacuum breaking in tenus of the running sigma'(0), which make nucleon, sigma, and pi particles gain effective masses. We achieve both the effect of external sources and nonvanishing value of the condensed scalar and pseudoscalar paticles. It is deduced that the masses of nucleons, sigma and pi generally depend on different external sources

Isospin effect of nucleon-nucleon cross section on the isoscaling parameter alpha

对两对重离子中心碰撞系统40C+40Ca 和60Ca+40Ca以及112Sn+112Sn和124Sn+124Sn反应中就同位素标度参数α对于核子-核子碰撞截面的同位旋效应进行了研究.计算结果表明α对同位旋相关核子-核子碰撞截面σmedNNKey Program of the National Natural Science Foundation of China 10435080 National Natural Science Foundation of China 10447006 10575075 Main Direction Program of Knowledge Innovation of the Chinese Academy of Siciences KJCX2-SW-N0

Isospin effect in the nuclear reaction induced by neutron-halo nuclei

We study the average property of the isospin effect of reaction induced by halo-neutron nuclei He-8 and He-10 in the intermediate energy heavy ion collisions using the isospin-dependent quantum molecular dynamics model (IQMD). This study is based on the extended neutron density distribution for the halo-neutron nuclei, which includes the average property of the isospin effect-of reaction mechanism and loose inner structure. The extended neutron density distribution brings an important isospin. effect into the average property of reaction mechanism because the interaction potential and nucleon-nucleon(N-N) cross section in IQMD model depend sensitively on the density distribution of colliding system. In order to see clearly the average properties of reaction mechanism induced by halo-neutron nuclei we also compare the results for the neutron-halo colliding systems with those for the corresponding stable colliding systems under the same incident channel condition. We found that the extended density distribution for the neutron-halo projectile brings an important isospin effect to the reaction mechanism, which leads to the decrease of nuclear stopping R, yet induces obvious increase of the neutron-proton ratio of nucleon emissions and isospin fractionation ratio for all beam energies studied in this work, compared to the corresponding stable colliding system. In this case, nuclear stopping, the neutron-proton ratio of nucleon emissions and isospin fractionation ratio induced by halo-neutron nuclei can be used as possible probes for studying the average property of the isospin effect of reaction mechanism and extracting the information of symmetry potential and in-medium N-N cross section by the neutron-halo nuclei in heavy ion collisions

Deconfinement phase Transition including perturbative QCD corrections in (proto)neutron star matter

Deconfinement phase transition and neutrino trapping in (proto)neutron star matter are investigated in a chiral hadronic model (also referred to as the FST model) for the hadronic phase (HP) and in the color-flavor-locked (CFL) quark model for the deconfined quark phase. We include a perturbative QCD correction parameter alpha(s) in the CFL quark matter equation of states. It is shown that the CFL quark core with K-0 condensation forms in neutron star matter with the large value of alpha(s). If the small value of alpha(s) is taken, hyperons suppress the CFL quark phase and the HP is dominant in the high-density region of (proto)neutron star matter. Neutrino trapping makes the fraction of the CFL quark matter decrease compared with those without neutrino trapping. Moreover, increasing the QCD correction parameter alpha(s) or decreasing the bag constant B and the strange quark mass m(s) can make the fraction of the CFL quark matter increase, simultaneously, the fraction of neutrino in protoneutron star matter increases, too. The maximum masses and the corresponding radii of (proto)neutron stars are not sensitive to the QCD correction parameter alpha(s).Th e p r o j e c t s u p p o r t e d b y Na t i o n a l Na t u r a l S c i e n c e F o u n d a t i o n o f Ch i n a u n d e r Gr a n t No s ． 1 0 5 7 5 0 0 5 ， 1 0 4 3 5 0 8 0 ，1 0 4 2 5 5 2 1 ， 1 0 1 3 5 0 3 0 ， a n d 1 0 5 7 5 1 2 3 ， t h e Ke y Gr a n t Pr o j e c t o f t h e Mi n i s t r y o f Ed u c a t i o n u n d e r Gr a n t No ． 3 0 5 0 0 1 ， a nd t h e CAS Kn o wl e d g e I n n o v a t i o n P r o j e c t u nd e r Gr an t No．KJ c x2 一 s w- N0

Medium effect of nucleon-nucleon cross section on the isoscaling parameter alpha

The medium effect of in-medium nucleon-nucleon cross section sigma(med)(NN) (alpha(m)) on the isoscaling parameter a is investigated for two couples of central nuclear reactions Ca-40 + Ca-48 and Ca-60 + Ca-48; Sn-112 + Sn-112 and Sn-124 + Sn-124 at beam energy region from 40 to 60 MeV/nucleon with isospin dependent quantum molecular dynamics. It is found that there is the obvious medium effect of sigma(med)(NN) (alpha(m)) on the isoscaling parameters alpha. The mechanism for the medium effect of sigma(med)(NN) (alpha(m)) on a is investigated