Morphological evolution of creek networks in 10 restored coastal wetlands in the UK

Coastal wetlands provide crucial ecosystem services including flood protection and carbon storage, but are being lost rapidly worldwide to the combined effects of sea-level rise, erosion and coastal urbanisation. Managed Realignment (MR) aims to mitigate for these losses by restoring reclaimed land to tidal influence. Data of creek evolution is critical to assess the performance of design strategies and improve design and implementation practices. This data descriptor provides a dataset of the horizontal morphological evolution of creek systems from various initial conditions in 10 MR schemes across the UK. Using a semi-automated workflow, morphological creek parameters were extracted from 52 lidar datasets at 1 m horizontal resolution spanning 2 to 20 years post-breach. This constitutes the most comprehensive systematic monitoring of MR creek morphology to date. The dataset will assist future MR design and provide baseline morphological information for ecological and biogeochemical surveying

BARDEX II: Nearshore sediment resuspension and bed morphology

Sediment resuspension in the region outside the surf zone is known to contribute to the morphological response of barrier beaches to wave forcing, such as onshore bar migration processes. However, few measurements in this region exist, limiting our ability to quantify its contribution. These processes are complicated by the presence of bedforms in the nearshore, which alter the sand transport processes while modifying bed roughness in a complex feedback mechanism. The Hydralab IV funded BARDEX II experiments, which took place in the Delta Flume in 2012, were used to provide measurements of these processes in the nearshore of a sandy barrier beach (D50 = 0.42mm) under a range of wave conditions (Hs = 0.3 - 0.8 m; Tp = 4 – 2 s) and water levels, through deployment of a suite of acoustic instruments measuring flow velocity, near-bed turbulence, sediment resuspension profiles and bed morphology in cross-section and plan view. Initial findings indicate that sediment suspension in the nearshore appears to be controlled by a combination of near-bed turbulent bursting processes which results in near-instantaneous low concentration suspensions restricted to the bottom boundary layer, and vortex shedding from bedforms which results in higher concentration suspensions which are larger in scale than vertical eddy sizes, and perpetuate outside of the bottom boundary layer

Observations of a tidal intrusion front in a tidal channel

A visible front indicated by a surface colour change, and sometimes associated with foam or debris lines, was observed in a tidal channel during neap tide. This is an example of a tidal intrusion front occurring in the absence of sudden topographical changes or reversing flows, typically reported to be associated with such fronts. Detailed Acoustic Doppler Current Profiler and conductivity/temperature/depth measurements were taken on repeated transects both with fronts apparent and with fronts absent. The results indicated that the front occurred as a result of stratification, which was sustained by the buoyancy flux and the weak tide-induced mixing during neap ebb tide. The stronger tide-induced mixing during spring tide restrained stratification, leading to the absence of a front. The mechanism of the frontogenesis was the density gradient between the stratified water formed during neap ebb tide, and the more mixed seawater during neap flood tide; thus, the water on the landward (southwestern) side of the front was stratified, and that on the seaward side (northeastern) of the front was vertically well mixed. Gradient Richardson number estimates suggest that the flow between the stratified and mixed water was near the threshold 0.25 for shear instability. Meanwhile, the density gradient would provide an initial baroclinic contribution to velocity convergence, which is indicated by the accumulation of buoyant matter such as foam, grass, and debris into a sharply defined line along the surface. The front migrates with the flood current, with a local maximum towards the eastern side of the channel, leading to an asymmetrical shape with the eastern side of the front driven further into the Tiaozhoumen tidal channel

Sediment dispersal from a typical Mediterranean flood: the Tête River, Gulf of Lions

This paper describes an integrated study of a typical Mediterranean flood event in the Gulf of Lions. A flood with a 5-year return interval occurred in the Têt River basin and adjacent inner-shelf in the Gulf of Lions, northwest Mediterranean, during April 2004. Data were collected during this flood as part of event-response investigations of the EU-funded Eurostrataform (European Margin Strata Formation) project. Southeasterly storm winds led to a flood which directly modified the inner-shelf hydrodynamics. Sediment delivery to the coastal zone during this flood represented more than half of the mean annual discharge of the Têt River to the Gulf of Lions. This river transported a large amount of sand in suspension, representing 25% of the total suspended load, and as bedload representing 8% of the total load, during this event. Sand introduced in the nearshore was transported northwards during the peak storm and nourished a small delta. Fine sediments were separated from coarse sediments at the river mouth, and were advected southwards and seawards by the counter-clockwise general circulation. Fine-grained sediments were transported via a hypopycnal plume along the coast towards the southern tip of the Gulf of Lions and the Cap Creus canyon. The along-shore currents, which intensified from north to south of the Gulf of Lions, particularly between the Cap Creus promontory and the Cap Creus canyon, favoured the transfer of fine-grained sediments from the continental shelf of the Gulf of Lions towards the continental slope. Our results show that floods with a few-year return interval in small coastal rivers can play a significant role in the transport of sediments on microtidal continental margins and their export from the shelf through canyons

Whole-genome sequencing reveals host factors underlying critical COVID-19

Altres ajuts: Department of Health and Social Care (DHSC); Illumina; LifeArc; Medical Research Council (MRC); UKRI; Sepsis Research (the Fiona Elizabeth Agnew Trust); the Intensive Care Society, Wellcome Trust Senior Research Fellowship (223164/Z/21/Z); BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070, BBS/E/D/30002275); UKRI grants (MC_PC_20004, MC_PC_19025, MC_PC_1905, MRNO2995X/1); UK Research and Innovation (MC_PC_20029); the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z); the Edinburgh Clinical Academic Track (ECAT) programme; the National Institute for Health Research, the Wellcome Trust; the MRC; Cancer Research UK; the DHSC; NHS England; the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health (CTSA award number UL1TR001878); the Perelman School of Medicine at the University of Pennsylvania; National Institute on Aging (NIA U01AG009740); the National Institute on Aging (RC2 AG036495, RC4 AG039029); the Common Fund of the Office of the Director of the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA; NIMH; NINDS.Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care or hospitalization after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

DUNE Offline Computing Conceptual Design Report

This document describes Offline Software and Computing for the Deep Underground Neutrino Experiment (DUNE) experiment, in particular, the conceptual design of the offline computing needed to accomplish its physics goals. Our emphasis in this document is the development of the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes. In this effort, we concentrate on developing the tools and systems thatfacilitate the development and deployment of advanced algorithms. Rather than prescribing particular algorithms, our goal is to provide resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves and to provide computing that achieves the physics goals of the DUNE experiment

DUNE Offline Computing Conceptual Design Report

International audienceThis document describes Offline Software and Computing for the Deep Underground Neutrino Experiment (DUNE) experiment, in particular, the conceptual design of the offline computing needed to accomplish its physics goals. Our emphasis in this document is the development of the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes. In this effort, we concentrate on developing the tools and systems thatfacilitate the development and deployment of advanced algorithms. Rather than prescribing particular algorithms, our goal is to provide resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves and to provide computing that achieves the physics goals of the DUNE experiment

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6 $\times$ 6 $\times$ 6 m$^3$ liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019–2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6x6x6m3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties

The DUNE Far Detector Vertical Drift Technology, Technical Design Report

International audienceDUNE is an international experiment dedicated to addressing some of the questions at the forefront of particle physics and astrophysics, including the mystifying preponderance of matter over antimatter in the early universe. The dual-site experiment will employ an intense neutrino beam focused on a near and a far detector as it aims to determine the neutrino mass hierarchy and to make high-precision measurements of the PMNS matrix parameters, including the CP-violating phase. It will also stand ready to observe supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector implements liquid argon time-projection chamber (LArTPC) technology, and combines the many tens-of-kiloton fiducial mass necessary for rare event searches with the sub-centimeter spatial resolution required to image those events with high precision. The addition of a photon detection system enhances physics capabilities for all DUNE physics drivers and opens prospects for further physics explorations. Given its size, the far detector will be implemented as a set of modules, with LArTPC designs that differ from one another as newer technologies arise. In the vertical drift LArTPC design, a horizontal cathode bisects the detector, creating two stacked drift volumes in which ionization charges drift towards anodes at either the top or bottom. The anodes are composed of perforated PCB layers with conductive strips, enabling reconstruction in 3D. Light-trap-style photon detection modules are placed both on the cryostat's side walls and on the central cathode where they are optically powered. This Technical Design Report describes in detail the technical implementations of each subsystem of this LArTPC that, together with the other far detector modules and the near detector, will enable DUNE to achieve its physics goals

Separation of track- and shower-like energy deposits in ProtoDUNE-SP using a convolutional neural network

International audienceLiquid argon time projection chamber detector technology provides high spatial and calorimetric resolutions on the charged particles traversing liquid argon. As a result, the technology has been used in a number of recent neutrino experiments, and is the technology of choice for the Deep Underground Neutrino Experiment (DUNE). In order to perform high precision measurements of neutrinos in the detector, final state particles need to be effectively identified, and their energy accurately reconstructed. This article proposes an algorithm based on a convolutional neural network to perform the classification of energy deposits and reconstructed particles as track-like or arising from electromagnetic cascades. Results from testing the algorithm on experimental data from ProtoDUNE-SP, a prototype of the DUNE far detector, are presented. The network identifies track- and shower-like particles, as well as Michel electrons, with high efficiency. The performance of the algorithm is consistent between experimental data and simulation