Probabilistic optimization for conceptual rainfall-runoff models: a comparison of the shuffled complex evolution and simulated annealing algorithms

Automatic optimization algorithms are used routinely to calibrate conceptual rainfall-runoff (CRR) models. The goal of calibration is to estimate a feasible and unique (global) set of parameter estimates that best fit the observed runoff data. Most if not all optimization algorithms have difficulty in locating the global optimum because of response surfaces that contain multiple local optima with regions of attraction of differing size, discontinuities, and long ridges and valleys. Extensive research has been undertaken to develop efficient and robust global optimization algorithms over the last 10 years. This study compares the performance of two probabilistic global optimization methods: the shuffled complex evolution algorithm SCE-UA, and the three-phase simulated annealing algorithm SA-SX. Both algorithms are used to calibrate two parameter sets of a modified version of Boughtoh's [1984] SFB model using data from two Australian catchments that have low and high runoff yields. For the reduced, well-identified parameter set the algorithms have a similar efficiency for the low-yielding catchment, but SCE-UA is almost twice as robust. Although the robustness of the algorithms is similar for the high-yielding catchment, SCE-UA is six times more efficient than SA-SX. When fitting the full parameter set the performance of SA-SX deteriorated markedly for both catchments. These results indicated that SCE-UA's use of multiple complexes and shuffling provided a more effective search of the parameter space than SA-SX's single simplex with stochastic step acceptance criterion, especially when the level of parameterization is increased. Examination of the response surface for the low-yielding catchment revealed some reasons why SCE-UA outperformed SA-SX and why probabilistic optimization algorithms can experience difficulty in locating the global optimum.Mark Thyer and George Kuczera, Bryson C. Bate

Silicon uptake by a pasture grass experiencing simulated grazing is greatest under elevated precipitation

Background Grasses are hyper-accumulators of silicon (Si) and often up-regulate Si following herbivory. Positive correlations exist between Si and plant water content, yet the extent to which Si uptake responses can be mediated by changes in soil water availability has rarely been studied and never, to our knowledge, under field conditions. We used field-based rain-exclusion shelters to investigate how simulated grazing (shoot clipping) and altered rainfall patterns (drought and elevated precipitation, representing 50% and 150% of ambient precipitation levels, respectively) affected initial patterns of root- and shoot-Si uptake in a native Australian grass (Microlaena stipoides) in Si-supplemented and untreated soils. Results Si supplementation increased soil water retention under ambient and elevated precipitation but not under drought, although this had little effect on Si uptake and growth (tiller numbers or root biomass) of M. stipoides. Changes in rainfall patterns and clipping had strong individual effects on plant growth and Si uptake and storage, whereby clipping increased Si uptake by M. stipoides under all rainfall treatments but to the greatest extent under elevated precipitation. Moreover, above-ground–below-ground Si distribution only changed following elevated precipitation by decreasing the ratio of root:shoot Si concentrations. Conclusions Results highlight the importance of soil water availability for Si uptake and suggest a role for both active and passive Si transport mechanisms. Such manipulative field studies may provide a more realistic insight into how grasses initially respond to herbivory in terms of Si-based defence under different environmental conditions

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

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

A Power-Efficient Access Point Operation for Infrastructure Basic Service Set in IEEE 802.11 MAC Protocol

<p/> <p>Infrastructure-based wireless LAN technology has been widely used in today's personal communication environment. Power efficiency and battery management have been the center of attention in the design of handheld devices with wireless LAN capability. In this paper, a hybrid protocol named improved PCF operation is proposed, which intelligently chooses the access point- (AP-) assisted DCF (distributed coordinator function) and enhanced PCF (point coordinator function) transmission mechanism of IEEE 802.11 protocol in an infrastructure-based wireless LAN environment. Received signal strength indicator (RSSI) is used to determine the tradeoff between direct mobile-to-mobile transmission and transmission routed by AP. Based on the estimation, mobile stations can efficiently communicate directly instead of being routed through AP if they are in the vicinity of each other. Furthermore, a smart AP protocol is proposed as extension to the improved PCF operation by utilizing the historical end-to-end delay information to decide the waking up time of mobile stations. Simulation results show that using the proposed protocol, energy consumption of mobile devices can be reduced at the cost of slightly longer end-to-end packet delay compared to traditional IEEE 802.11 PCF protocol. However, in a non-time-critical environment, this option can significantly prolong the operation time of mobile devices.</p