Slope, grain size, and roughness controls on dry sediment transport and storage on steep hillslopes

Existing hillslope sediment transport models developed for low-relief, soil-mantled landscapes are poorly suited to explain the coupling between steep rocky hillslopes and headwater channels. Here we address this knowledge gap using a series of field and numerical experiments to inform a particle-based model of sediment transport by dry ravel—a mechanism of granular transport characteristic of steep hillslopes. We find that particle travel distance increases as a function of the ratio of particle diameter to fine-scale (1 m) topographic variability associated with rocky landscapes. Applying a 2-D dry-ravel-routing model to lidar-derived surface topography, we show how spatial patterns of local and nonlocal transport control connectivity between hillslopes and steep headwater channels that generate debris flows through failure of ravel-filled channels following wildfire. Our results corroborate field observations of a patchy transition from soil-mantled to bedrock landscapes and suggest that there is a dynamic interplay between sediment storage, roughness, grain sorting, and transport even on hillslopes that well exceed the angle of repose

Standardized and reproducible methodology for the comprehensive and systematic assessment of surgical resection margins during breast-conserving surgery for invasive breast cancer

<p>Abstract</p> <p>Background</p> <p>The primary goal of breast-conserving surgery (BCS) is to completely excise the tumor and achieve "adequate" or "negative" surgical resection margins while maintaining an acceptable level of postoperative cosmetic outcome. Nevertheless, precise determination of the adequacy of BCS has long been debated. In this regard, the aim of the current paper was to describe a standardized and reproducible methodology for comprehensive and systematic assessment of surgical resection margins during BCS.</p> <p>Methods</p> <p>Retrospective analysis of 204 BCS procedures performed for invasive breast cancer from August 2003 to June 2007, in which patients underwent a standard BCS resection and systematic sampling of nine standardized re-resection margins (superior, superior-medial, superior-lateral, medial, lateral, inferior, inferior-medial, inferior-lateral, and deep-posterior). Multiple variables (including patient, tumor, specimen, and follow-up variables) were evaluated.</p> <p>Results</p> <p>6.4% (13/204) of patients had positive BCS specimen margins (defined as tumor at inked edge of BCS specimen) and 4.4% (9/204) of patients had close margins (defined as tumor within 1 mm or less of inked edge but not at inked edge of BCS specimen). 11.8% (24/204) of patients had at least one re-resection margin containing additional disease, independent of the status of the BCS specimen margins. 7.1% (13/182) of patients with negative BCS specimen margins (defined as no tumor cells seen within 1 mm or less of inked edge of BCS specimen) had at least one re-resection margin containing additional disease. Thus, 54.2% (13/24) of patients with additional disease in a re-resection margin would not have been recognized by a standard BCS procedure alone (P < 0.001). The nine standardized resection margins represented only 26.8% of the volume of the BCS specimen and 32.6% of the surface area of the BCS specimen.</p> <p>Conclusion</p> <p>Our methodology accurately assesses the adequacy of surgical resection margins for determination of which individuals may need further resection to the affected breast in order to minimize the potential risk of local recurrence while attempting to limit the volume of additional breast tissue excised, as well as to determine which individuals are not realistically amendable to BCS and instead need a completion mastectomy to successfully remove multifocal disease.</p

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

Sediment flux driven channel geometry adjustment of bedrock and mixed gravel‐bedrock rivers

International audienceSediment supply (Qs) is often overlooked in modelling studies of landscape evolution, despite sediment playing a key role in the physical processes that drive erosion and sedimentation in river channels. Here, we show the direct impact of the supply of coarse‐grained, hard, sediment on the geometry of bedrock channels from the Rangitikei river, New Zealand. Channels receiving a coarse bedload sediment supply are systematically (up to an order of magnitude) wider than channels with no bedload sediment input for a given discharge. We also present physical model experiments of a bedrock river channel with a fixed water discharge (1.5 l/min) under different Qs (between 0 and 20 g/l) that allow the quantification of the role of sediment in setting the width and slope of channels and the distribution of shear stress within channels. The addition of bedload sediment increases the width, slope, and width‐to‐depth ratio of the channels, and increasing sediment loads promote emerging complexity in channel morphology and shear stress distributions. Channels with low Qs are characterised by simple in‐channel morphologies with a uniform distribution of shear stress within the channel while channels with high Qs are characterised by dynamic channels with multiple active threads and a non‐uniform distribution of shear stress. We compare bedrock channel geometries from the Rangitikei and the experiments to alluvial channels and demonstrate that the behaviour is similar, with a transition from single thread and uniform channels to multiple threads occurring when bedload sediment is present. In the experimental bedrock channels, this threshold Qs is when the input sediment supply exceeds the transport capacity of the channel. Caution is required when using the channel geometry to reconstruct past environmental conditions or to invert for tectonic uplift rates, because multiple configurations of channel geometry can exist for a given discharge, solely due to input Qs