Summary The Cancer Genome Atlas (TCGA) project has analyzed mRNA expression, miRNA expression, promoter methylation, and DNA copy number in 489 high-grade serous ovarian adenocarcinomas (HGS-OvCa) and the DNA sequences of exons from coding genes in 316 of these tumors. These results show that HGS-OvCa is characterized by TP53 mutations in almost all tumors (96%); low prevalence but statistically recurrent somatic mutations in 9 additional genes including NF1, BRCA1, BRCA2, RB1, and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three miRNA subtypes, four promoter methylation subtypes, a transcriptional signature associated with survival duration and shed new light on the impact on survival of tumors with BRCA1/2 and CCNE1 aberrations. Pathway analyses suggested that homologous recombination is defective in about half of tumors, and that Notch and FOXM1 signaling are involved in serous ovarian cancer pathophysiology.

Summary To characterize somatic alterations in colorectal carcinoma (CRC), we conducted genome-scale analysis of 276 samples, analyzing exome sequence, DNA copy number, promoter methylation, mRNA and microRNA expression. A subset (97) underwent low-depth-of-coverage whole-genome sequencing. 16% of CRC have hypermutation, three quarters of which have the expected high microsatellite instability (MSI), usually with hypermethylation and MLH1 silencing, but one quarter has somatic mismatch repair gene mutations. Excluding hypermutated cancers, colon and rectum cancers have remarkably similar patterns of genomic alteration. Twenty-four genes are significantly mutated. In addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9, and FAM123B/WTX. Recurrent copy number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive CRC and important role for MYC-directed transcriptional activation and repression.

Polarization-division multiplexed (PDM) transmission based on the nonlinear Fourier transform (NFT) is proposed for optical fiber communication. The NFT algorithms are generalized from the scalar nonlinear Schrödinger equation for one polarization to the Manakov system for two polarizations. The transmission performance of the PDM nonlinear frequency-division multiplexing (NFDM) and PDM orthogonal frequency-division multiplexing (OFDM) are determined. It is shown that the transmission performance in terms of Q-factor is approximately the same in PDM-NFDM and single polarization NFDM at twice the data rate and that the polarization-mode dispersion does not seriously degrade system performance. Compared with PDM-OFDM, PDM-NFDM achieves a Q-factor gain of 6.4 dB. The theory can be generalized to multi-mode fibers in the strong coupling regime, paving the way for the application of the NFT to address the nonlinear effects in space-division multiplexing.

The problem of a one-dimensional stationary nonlinear electrostatic wave in a plasma free from interparticle collisions is solved exactly by elementary means. It is demonstrated that, by adding appropriate numbers of particles trapped in the potential-energy troughs, essentially arbitrary traveling wave solutions can be constructed. When one passes to the limit of small-amplitude waves it turns out that the distribution function does not possess an expansion whose first term is linear in the amplitude, as is conventionally assumed. This disparity is associated with the trapped particles. It is possible, however, to salvage the usual linearized theory by admitting singular distribution functions. These, of course, do not exhibit Landau damping, which is associated with the restriction to well-behaved distribution functions.The possible existence of such waves in an actual plasma will depend on factors ignored in this paper, as in most previous works, namely interparticle collisions, and the stability of the solutions against various types of perturbations.