Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer

Experimental validation of photonic boson sampling

A boson sampling device is a specialized quantum computer that solves a problem that is strongly believed to be computationally hard for classical computers. Recently, a number of small-scale implementations have been reported, all based on multiphoton interference in multimode interferometers. Akin to several quantum simulation and computation tasks, an open problem in the hard-to-simulate regime is to what extent the correctness of the boson sampling outcomes can be certified. Here, we report new boson sampling experiments on larger photonic chips and analyse the data using a recently proposed scalable statistical test. We show that the test successfully validates small experimental data samples against the hypothesis that they are uniformly distributed. In addition, we show how to discriminate data arising from either indistinguishable or distinguishable photons. Our results pave the way towards larger boson sampling experiments whose functioning, despite being non-trivial to simulate, can be certified against alternative hypotheses

Sugarcane mulch C and N dynamics during decomposition under different rates of trash removal

Sugarcane is a worldwide crop that leaves a considerable amount of crop residues (called trash) on the soil surface each year after green cane harvesting. However, the recent industrial valorization of these residues raises the question of how much trash to leave as mulch after harvest. Here, we studied the decomposition of three different trash quantities (4, 8 and 12 Mg ha(-1)) across five experimental sites from a subtropical climate over one year. We quantified the dry matter (DM), carbon (C) and nitrogen (N) contents of the remaining mulch at one-month intervals for one year after trash addition at all sites. The chemical composition of the trash was characterized by proximate analysis at one site. Our results showed that mulch degradation was proportional to the initial amount of trash left on the soil surface, i.e., the degradation rates were similar for the three trash treatments at each site, suggesting no limiting factor to decomposition associated with trash quantity and its contact with the soil. On average, 64% of the trash was degraded after 12 months in all treatments, leading to considerable differences in the mass of C degraded after one year (1.2 +/- 0.1, 2.3 +/- 0.2 and 3.5 +/- 0.3 Mg ha(-1) for the 4, 8 and 12 Mg ha(-1) treatments, respectively). An interaction between trash quantity and site was observed, which translated into more differences in the C degradation rates between sites for the 4 Mg ha(-1) trash treatment. The N content of the remaining mulch was rather stable throughout the year, which indicated the efficient use and recycling of N by the decomposing microflora during trash decomposition. These results will help determine the amount of sugarcane trash that should be left on fields to preserve soil C and soil fertility