Interpreting complex fluvial channel and barform architecture: Carboniferous Central Pennine Province, northern England

The Bashkirian Lower Brimham Grit of North Yorkshire, England, is a fluvio-deltaic sandstone succession that crops out as a complex series of pinnacles, the three-dimensional arrangement of which allows high-resolution architectural analysis of genetically-related lithofacies assemblages. Combined analysis of sedimentary graphic log profiles, architectural panels and palaeocurrent data have enabled three-dimensional geometrical relationships to be established for a suite of architectural elements so as to develop a comprehensive depositional model. Small-scale observations of facies have been related to larger-scale architectural elements to facilitate interpretation of the palaeoenvironment of deposition to a level of detail that has rarely been attempted previously, thereby allowing interpretation of formative processes. Detailed architectural panels form the basis of a semi-quantitative technique for recording the variety and complexity of the sedimentary lithofacies present, their association within recognizable architectural elements and, thus, the inferred spatio-temporal relationship of neighbouring elements. Fluvial channel-fill elements bounded by erosional surfaces are characterized internally by a hierarchy of sets and cosets with subtly varying compositions, textures and structures. Simple, cross-bedded sets represent in-channel migration of isolated mesoforms (dunes); cosets of both trough and planar-tabular cross-bedded facies represent lateral-accreting and downstream-accreting macroforms (bars) characterized by highly variable, yet predictable, patterns of palaeocurrent indicators. Relationships between sandstone-dominated strata bounded by third-order and fifth-order surfaces, which represent in-channel bar deposits and incised channel bases respectively, chronicle the origin of the preserved succession in response to autocyclic barform development and abandonment, major episodes of incision probably influenced by episodic tectonic subsidence, differential tilting and fluvial incision associated with slip on the nearby North Craven Fault system. Overall, the succession represents the preserved product of an upper-delta plain system that was traversed by a migratory fluvial braid-belt system comprising a poorly-confined network of fluvial channels developed between major sandy barforms that evolved via combined lateral-accretion and downstream-accretion

Improved Nearside-Farside Decomposition of Elastic Scattering Amplitudes

A simple technique is described, that provides improved nearside-farside (NF) decompositions of elastic scattering amplitudes. The technique, involving the resummation of a Legendre partial wave series, reduces the importance of unphysical contributions to NF subamplitudes, which can arise in more conventional NF decompositions. Applications are made to a strong absorption model and to a $^{16}$O + $^{12}$C optical potential at $E_{\text{lab}} = 132$ MeV.Comment: 5 pages, 2 figure

Back-flow ripples in troughs downstream of unit bars: Formation, preservation and value for interpreting flow conditions

Back-flow ripples are bedforms created within the lee-side eddy of a larger bedform with migration directions opposed or oblique to that of the host bedform. In the flume experiments described in this article, back-flow ripples formed in the trough downstream of a unit bar and changed with mean flow velocity; varying from small incipient back-flow ripples at low velocities, to well-formed back-flow ripples with greater velocity, to rapidly migrating transient back-flow ripples formed at the greatest velocities tested. In these experiments back-flow ripples formed at much lower mean back-flow velocities than predicted from previously published descriptions. This lower threshold mean back-flow velocity is attributed to the pattern of velocity variation within the lee-side eddy of the host bedform. The back-flow velocity variations are attributed to vortex shedding from the separation zone, wake flapping and increases in the size of, and turbulent intensity within, the flow separation eddy controlled by the passage of superimposed bedforms approaching the crest of the bar. Short duration high velocity packets, whatever their cause, may form back-flow ripples if they exceed the minimum bed shear stress for ripple generation for long enough or, if much faster, may wash them out. Variation in back-flow ripple cross-lamination has been observed in the rock record and, by comparison with flume observations, the preserved back-flow ripple morphology may be useful for interpreting formative flow and sediment transport dynamics

Dark Matter attempts for CoGeNT and DAMA

Recently, the CoGeNT collaboration presented a positive signal for an annual modulation in their data set. In light of the long standing annual modulation signal in DAMA/LIBRA, we analyze the compatibility of both of these signal within the hypothesis of dark matter (DM) scattering on nuclei, taking into account existing experimental constraints. We consider the cases of elastic and inelastic scattering with either spin-dependent or spin-independent coupling to nucleons. We allow for isospin violating interactions as well as for light mediators. We find that there is some tension between the size of the modulation signal and the time-integrated event excess in CoGeNT, making it difficult to explain both simultaneously. Moreover, within the wide range of DM interaction models considered, we do not find a simultaneous explanation of CoGeNT and DAMA/LIBRA compatible with constraints from other experiments. However, in certain cases part of the data can be made consistent. For example, the modulation signal from CoGeNT becomes consistent with the total rate and with limits from other DM searches at 90% CL (but not with the DAMA/LIBRA signal) if DM scattering is inelastic spin-independent with just the right couplings to protons and neutrons to reduce the scattering rate on xenon. Conversely the DAMA/LIBRA signal (but not CoGeNT) can be explained by spin-dependent inelastic DM scattering.Comment: 20 pages, 9 figure

Macroinvertebrate Diversity in Urban and Rural Ponds: Implications for Freshwater Biodiversity Conservation

Ponds are among the most biodiverse freshwater ecosystems, yet face significant threats from removal, habitat degradation and a lack of legislative protection globally. Information regarding the habitat quality and biodiversity of ponds across a range of land uses is vital for the long term conservation and management of ecological resources. In this study we examine the biodiversity and conservation value of macroinvertebrates from 91 lowland ponds across 3 land use types (35 floodplain meadow, 15 arable and 41 urban ponds). A total of 224 macroinvertebrate taxa were recorded across all ponds, with urban ponds and floodplain ponds supporting a greater richness than arable ponds at the landscape scale. However, at the alpha scale, urban ponds supported lower faunal diversity (mean: 22 taxa) than floodplain (mean: 32 taxa) or arable ponds (mean: 30 taxa). Floodplain ponds were found to support taxonomically distinct communities compared to arable and urban ponds. A total of 13 macroinvertebrate taxa with a national conservation designation were recorded across the study area and 12 ponds (11 floodplain and 1 arable pond) supported assemblages of high or very high conservation value. Pond conservation currently relies on the designation of individual ponds based on very high biodiversity or the presence of taxa with specific conservation designations. However, this site specific approach fails to acknowledge the contribution of ponds to freshwater biodiversity at the landscape scale. Ponds are highly appropriate sites outside of protected areas (urban/arable), with which the general public are already familiar, for local and landscape scale conservation of freshwater habitats

High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall glycans immobilized on nitrocellulose was assessed. Hierarchical clustering of microarray binding profiles from newly produced mAbs, together with the profiles for mAbs with previously defined specificities allowed the rapid assignments of mAb binding to antigen classes. mAb specificities were further investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls in plant materials

Unit bar architecture in a highly‐variable fluvial discharge regime: Examples from the Burdekin River, Australia

Unit bars are relatively large bedforms that develop in rivers over a wide range of climatic regimes. Unit bars formed within the highly-variable discharge Burdekin River in Queensland, Australia, were examined over three field campaigns between 2015 and 2017. These bars had complex internal structures, dominated by co-sets of cross-stratified and planar-stratified sets. The cross-stratified sets tended to down-climb. The development of complex internal structures was primarily a result of three processes: (i) superimposed bedforms reworking the unit bar avalanche face; (ii) variable discharge triggering reactivation surfaces; and (iii) changes in bar growth direction induced by stage change. Internal structures varied along the length and across the width of unit bars. For the former, down-climbing cross-stratified sets tended to pass into single planar cross-stratified deposits at the downstream end of emergent bars; such variation related to changes in fluvial conditions whilst bars were active. A hierarchy of six categories of fluvial unsteadiness is proposed, with these discussed in relation to their effects on unit bar (and dune) internal structure. Across-deposit variation was caused by changes in superimposed bedform and bar character along bar crests; such changes related to the three-dimensionality of the channel and bar geometry when bars were active. Variation in internal structure is likely to be more pronounced in unit bar deposits than in smaller bedform (for example, dune) deposits formed in the same river. This is because smaller bedforms are more easily washed out or modified by changing discharge conditions and their smaller dimensions restrict the variation in flow conditions that occur over their width. In regimes where unit bar deposits are well-preserved, their architectural variability is a potential aid to their identification. This complex architecture also allows greater resolution in interpreting the conditions before and during bar initiation and development

Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications

Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each splicing context remains difficult. Here, we describe Introme, which uses machine learning to integrate predictions from several splice detection tools, additional splicing rules, and gene architecture features to comprehensively evaluate the likelihood of a variant impacting splicing. Through extensive benchmarking across 21,000 splice-altering variants, Introme outperformed all tools (auPRC: 0.98) for the detection of clinically significant splice variants. Introme is available at https://github.com/CCICB/introme .Patricia J. Sullivan, Velimir Gayevskiy, Ryan L. Davis, Marie Wong, Chelsea Mayoh, Amali Mallawaarachchi, Yvonne Hort, Mark J. McCabe, Sarah Beecroft, Matilda R. Jackson, Peer Arts, Andrew Dubowsky, Nigel Laing, Marcel E. Dinger, Hamish S. Scott, Emily Oates, Mark Pinese, and Mark J. Cowle

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix