River planform, soil stratigraphy and the temporal and palaeoenvironmental significance of terraced valley fill deposits in upland Scotland, with specific reference to Glen Feshie, south-west Cairngorms

River terraces form prominent features of the valley floor morphology of many upland valleys in Scotland. Little is known, however, about valley floor landform development in many of these valleys. Previous studies have generally explained the terraces as the outwash products of meltwaters from the most recent cold periods. Detailed investigation of a major valley in the Scottish Highlands challenges, for at least one site, this well established concept and proposes the occurrence of at least three phases of Holocene terrace development.The correlation of terrace surfaces has traditionally been based upon the construction of height-range diagrams. An alternative approach to terrace correlation and dating is developed in this study using data from Glen Feshie, south-west Cairngorms. Terrace fragments are numerically classified and objectively grouped using quantitative soil-stratigraphic data. Principal Components Analysis and a hierarchical clustering technique numerically define five soil-stratigraphic units and place these on a relative time scale. Various methods of absolute dating control permit association of these units with five phases of terrace development. These are placed at 13,000, 10,000, 3,600, 1,000, 80, radiocarbon years BP.Comparison of palaeochannel networks preserved on the terrace surfaces suggests that these phases of terrace development have been associated with changes in channel pattern morphology. A unified approach to analysis of channel pattern morphology is developed and from this a new technique for palaeohydrological interpretation of gravel-bed streams. A segment density index is developed which allows total sinuosity to be predicted from just a part of the braided channel network. Application of these techniques to the Glen Feshie terraces demonstrates a trend for an overall decrease in discharge from the oldest terrace surfaces to the present day.Assessment of these landform changes within the context of known environmental fluctuations in the Cairngorms suggests that the early-mid Holocene was a period of relative landscape stability while the late Holocene was characterised by increasing instability. These changes may have been associated with the changes in river behaviour. However, spatial variation in the depth of the fill/bedrock interface may produce a discontinuous river response to changing environmental conditions

Fractal Properties of the Distribution of Earthquake Hypocenters

We investigate a recent suggestion that the spatial distribution of earthquake hypocenters makes a fractal set with a structure and fractal dimensionality close to those of the backbone of critical percolation clusters, by analyzing four different sets of data for the hypocenter distributions and calculating the dynamical properties of the geometrical distribution such as the spectral dimension $d_s$. We find that the value of $d_s$ is consistent with that of the backbone, thus supporting further the identification of the hypocenter distribution as having the structure of the percolation backbone.Comment: 11 pages, LaTeX, HLRZ 68/9

Southern Ocean Sector Centennial Climate Variability and Recent Decadal Trends

Evidence is presented for the notion that some contribution to the recent decadal trends observed in the Southern Hemisphere, including the lack of a strong Southern Ocean surface warming, may have originated from longer-term internal centennial variability originating in the Southern Ocean. The existence of such centennial variability is supported by the instrumental sea surface temperatures (SSTs), a multimillennial reconstruction of Tasmanian summer temperatures from tree rings, and a millennial control integration of the Kiel Climate Model (KCM). The model variability was previously shown to be linked to changes in Weddell Sea deep convection. During phases of deep convection the surface Southern Ocean warms, the abyssal Southern Ocean cools, Antarctic sea ice extent retreats, and the low-level atmospheric circulation over the Southern Ocean weakens. After the halt of deep convection the surface Southern Ocean cools, the abyssal Southern Ocean warms, Antarctic sea ice expands, and the low-level atmospheric circulation over the Southern Ocean intensifies, consistent with what has been observed during the recent decades. A strong sensitivity of the time scale to model formulation is noted. In the KCM, the centennial variability is associated with global-average surface air temperature (SAT) changes of the order of a few tenths of a degree per century. The model results thus suggest that internal centennial variability originating in the Southern Ocean should be considered in addition to other internal variability and external forcing when discussing the climate of the twentieth century and projecting that of the twenty-first century

Analysis of reach-scale elevation distribution in braided rivers: Definition of a new morphologic indicator and estimation of mean quantities

This work has been carried out within the SMART Joint Doctorate (Science forthe MAnagement of Rivers and theirTidal systems) funded with the support of the Erasmus Mundus programme of the European Union. Data of the Rees River were derived as part of UKNatural Environment Research Council grant (NE/G005427/1) awarded to PI Brasington, along with further support from the NERC Geophysical Equipmen tFacility (Loan 892) and Leverhulme Trust IAF2014-03

Environmental controls, morphodynamic processes, and ecogeomorphic interactions of barchan to parabolic dune transformations

The transformation of barchans into parabolic dunes has been observed in various dune systems around the world. Precise details of how environmental controls influence the dune transformation and stabilisation mechanism, however, remain poorly understood. A ‘horns-anchoring’ mechanism and a ‘nebkhas-initiation’ mechanism have previously been proposed and selected environmental controls on the transformation have been explored by some modelling efforts, but the morphodynamic processes and eco-geomorphic interactions involved are unclear and comparison between different dune systems is challenging. This study extends a cellular automaton model, informed by empirical data from fieldwork and remote sensing, to fully explore how vegetation characteristics, boundary conditions, and wind regime influence the transformation process and the resulting dune morphologies. A ‘dynamic growth function’ is introduced for clump-like perennials to differentiate between growing and non-growing seasons and to simulate the development of young plants into mature plants over multiple years. Modelling results show that environmental parameters interact with each other in a complex manner to impact the transformation process. The study finds a fundamental power-law relation between a non-dimensional parameter group, so-called the ‘dune stabilising index’ (S⁎), and the normalised migration distance of the transforming dune, which can be used to reconstruct paleo-environmental conditions and monitor the impacts of changes in climate or land-use on a dune system. Four basic eco-geomorphic interaction zones are identified which bear different functionality in the barchan to parabolic dune transformation. The roles of different environmental controls in changing the eco-geomorphic interaction zones, transforming processes, and resulting dune morphologies are also clarified

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment