Acoustic measurements of boundary layer flux profiles over a sandy rippled bed under regular waves

The study of boundary layer sediment transport processes requires contemporaneous measurements of the bedforms, the flow and the sediment movement. Obtaining these three parameters, at the required temporal-spatial resolutions, has been traditionally difficult, especially within a few centimetres of the bed. To circumvent some of the deployment of an acoustic backscatter system, ABS, an acoustic ripple profiler, ARP, and an acoustic Doppler velocity profiler, ADVP, to measure sediment entrainment processes above a rippled bed under regular waves. High resolution acoustic observations of the suspend sediment concentration, flow and bedforms have been collected. Here we report on some of the initial results obtained from this study

Field deployment and evaluation of a prototype autonomous two dimensional acoustic backscatter instrument: The Bedform And Suspended Sediment Imager (BASSI)

The processes of sediment entrainment, transport and deposition over bedforms are highly dynamic and temporally and spatially variable. However, most measurements of these processes tend to be collected in a vertical line at one spatial location above the bed; one dimensional in the vertical, 1D-V. Such measurements capture the temporal signature, and, to a lesser degree, the spatial variability when bedforms migrate, and they have contributed greatly to our understanding of sediment transport processes. It is generally acknowledged, however, that such 1D-V systems provide a limited description of the spatially three dimensional processes occurring at the turbulent and intra-wave time scales. It would undoubtedly facilitate the interpretation of fundamental sediment processes above bedforms if other spatial dimensions could be simultaneously interrogated. To this end a multi-frequency acoustic array has been developed to measure suspended sediments and bedforms over a horizontal transect of the bed in the vertical, providing two dimensional observations in the vertical and horizontal, 2D-HV. This new acoustic instrument, the BASSI; Bedform And Suspended Sediment Imager, has been deployed in the River Dee tidal estuary in the UK. The design of the BASSI and results from the deployment are presented and its performance assessed against more conventional instrumentation. Measurements and images of 2D-HV suspended sediments and bedforms are provided to illustrate the capability and future use of the BASSI for the investigation of sediment transport processes

A geometric proof of the Kochen-Specker no-go theorem

We give a short geometric proof of the Kochen-Specker no-go theorem for non-contextual hidden variables models. Note added to this version: I understand from Jan-Aake Larsson that the construction we give here actually contains the original Kochen-Specker construction as well as many others (Bell, Conway and Kochen, Schuette, perhaps also Peres).Comment: This paper appeared some years ago, before the author was aware of quant-ph. It is relevant to recent developments concerning Kochen-Specker theorem

Evidence for prereg posters as a platform for preregistration.

Prereg posters are conference posters that present planned scientific projects. We provide preliminary evidence for their value in receiving constructive feedback, promoting open science, and supporting early career researchers

Evidence for prereg posters as a platform for preregistration

Prereg posters are conference posters that present planned scientific projects. We provide preliminary evidence for their value in receiving constructive feedback, promoting open science and supporting early-career researchers

On the study of boundary layer sediment transport processes using new developmental acoustic techniques

This study aims at presenting a set of novel acoustic flow and sediment measuring tools used in a complementary way for the investigation of fine-scale flow and sediment transport processes above a rippled sand bed under waves. Measurements were conducted in the 100m long wave channel at UPC-LIM with surface gravity waves generating migrating ripples on a mobile sand bed. The set of acoustic instrumentation consisted of an Acoustic 3D Ripple Profiler (3D-ARP), a novel Bedform And Suspended Sediment Imager (BASSI) and three Acoustic Concentration and Velocity Profilers (ACVP). Here we assess the ACVP’s and the BASSI.Postprint (published version

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/

Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids

A broad scientific community is involved in investigations aimed at delineating the mechanisms of formation and cellular processing of oxidatively generated damage to nucleic acids. Perhaps as a consequence of this breadth of research expertise, there are nomenclature problems for several of the oxidized bases including 8-oxo-7,8-dihydroguanine (8-oxoGua), a ubiquitous marker of almost every type of oxidative stress in cells. Efforts to standardize the nomenclature and abbreviations of the main DNA degradation products that arise from oxidative pathways are reported. Information is also provided on the main oxidative radicals, non-radical oxygen species, one-electron agents and enzymes involved in DNA degradation pathways as well in their targets and reactivity. A brief classification of oxidatively generated damage to DNA that may involve single modifications, tandem base modifications, intrastrand and interstrand cross-links together with DNA-protein cross-links and base adducts arising from the addition of lipid peroxides breakdown products is also included

Developments in acoustics for studying wave-driven boundary layer flow and sediment dynamics over rippled sand-beds

The processes of sediment entrainment, transport, and deposition over bedforms are highly dynamic and temporally and spatially variable. Obtaining measurements to understand these processes has led to ongoing developments in instrumentation for studying near-bed sediment dynamics, with the outputs applied to the development and assessment of sediment transport modelling. In the present study results are reported from three acoustic systems deployed to make observations of bedforms, bedload, suspended concentration and horizontal and vertical velocity components. To evaluate the instruments a series of near-bed boundary layer measurements were collected in a large scale flume facility over a rippled bed of medium sand under regular waves. The observations were conducted as part of Joint Research Activities within the EU funded Hydralab project. The suite of acoustic instruments consisted of a Bedform And Suspended Sediment Imager, BASSI, a three dimensional acoustic ripple profiler, 3D-ARP, and three Acoustic Concentration and Velocity Profilers, ACVP's. Here results are reported from the deployment of the instruments, to illustrate the ongoing developments in acoustics and the expanding capability of the application of acoustics to the study of near-bed flow and sediment dynamics