Value-Compressed Sparse Column (VCSC): Sparse Matrix Storage for Redundant Data

Compressed Sparse Column (CSC) and Coordinate (COO) are popular compression formats for sparse matrices. However, both CSC and COO are general purpose and cannot take advantage of any of the properties of the data other than sparsity, such as data redundancy. Highly redundant sparse data is common in many machine learning applications, such as genomics, and is often too large for in-core computation using conventional sparse storage formats. In this paper, we present two extensions to CSC: (1) Value-Compressed Sparse Column (VCSC) and (2) Index- and Value-Compressed Sparse Column (IVCSC). VCSC takes advantage of high redundancy within a column to further compress data up to 3-fold over COO and 2.25-fold over CSC, without significant negative impact to performance characteristics. IVCSC extends VCSC by compressing index arrays through delta encoding and byte-packing, achieving a 10-fold decrease in memory usage over COO and 7.5-fold decrease over CSC. Our benchmarks on simulated and real data show that VCSC and IVCSC can be read in compressed form with little added computational cost. These two novel compression formats offer a broadly useful solution to encoding and reading redundant sparse data

The glueball among the light scalar mesons

In our phenomenological analysis of the spectroscopy of light scalar mesons we do not find compelling evidence for the existence of the low mass \kappa(900) or \sigma(600) states nor for f_0(1370) as single resonance. If the f_0(980) and and f_0(1500) are taken as members of the q qbar nonet there remains a broad object formed by f_0(400-1200) and f_0(1370) which is a glueball candidate gb(1000).Comment: Talk (by W.O.) given at the QCD 02 9th International High-Energy Physics Conference in QuantumChromoDynamics (Montpellier 2-9th July 2002), 4 page

Electromagnetic Compatibility Testing of Implantable Neurostimulators Exposed to Metal Detectors

This paper presents results of electromagnetic compatibility (EMC) testing of three implantable neurostimulators exposed to the magnetic fields emitted from several walk-through and hand-held metal detectors. The motivation behind this testing comes from numerous adverse event reports involving active implantable medical devices (AIMDs) and security systems that have been received by the Food and Drug Administration (FDA). EMC testing was performed using three neurostimulators exposed to the emissions from 12 walk-through metal detectors (WTMDs) and 32 hand-held metal detectors (HHMDs). Emission measurements were performed on all HHMDs and WTMDs and summary data is presented. Results from the EMC testing indicate possible electromagnetic interference (EMI) between one of the neurostimulators and one WTMD and indicate that EMI between the three neurostimulators and HHMDs is unlikely. The results suggest that worst case situations for EMC testing are hard to predict and testing all major medical device modes and setting parameters are necessary to understand and characterize the EMC of AIMDs

Time-Resolved Infrared Spectroscopy Reveals the pH-Independence of the First Electron Transfer Step in the [FeFe] Hydrogenase Catalytic Cycle.

[FeFe] hydrogenases are highly active catalysts for hydrogen conversion. Their active site has two components: a [4Fe-4S] electron relay covalently attached to the H2 binding site and a diiron cluster ligated by CO, CN-, and 2-azapropane-1,3-dithiolate (ADT) ligands. Reduction of the [4Fe-4S] site was proposed to be coupled with protonation of one of its cysteine ligands. Here, we used time-resolved infrared (TRIR) spectroscopy on the [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1) containing a propane-1,3-dithiolate (PDT) ligand instead of the native ADT ligand. The PDT modification does not affect the electron transfer step to [4Fe-4S]H but prevents the enzyme from proceeding further through the catalytic cycle. We show that the rate of the first electron transfer step is independent of the pH, supporting a simple electron transfer rather than a proton-coupled event. These results have important implications for our understanding of the catalytic mechanism of [FeFe] hydrogenases and highlight the utility of TRIR

Acyl Chain-Dependent Effect of Lysophosphatidylcholine on Endothelium-Dependent Vasorelaxation

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Graphs in molecular biology

Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network

Using Remote Sensing to Map the Risk of Human Monkeypox Virus in the Congo Basin

Although the incidence of human monkeypox has greatly increased in Central Africa over the last decade, resources for surveillance remain extremely limited. We conducted a geospatial analysis using existing data to better inform future surveillance efforts. Using active surveillance data collected between 2005 and 2007, we identified locations in Sankuru district, Democratic Republic of Congo (DRC) where there have been one or more cases of human monkeypox. To assess what taxa constitute the main reservoirs of monkeypox, we tested whether human cases were associated with (i) rope squirrels (Funisciurus sp.), which were implicated in monkeypox outbreaks elsewhere in the DRC in the 1980s, or (ii) terrestrial rodents in the genera Cricetomys and Graphiurus, which are believed to be monkeypox reservoirs in West Africa. Results suggest that the best predictors of human monkeypox cases are proximity to dense forests and associated habitat preferred by rope squirrels. The risk of contracting monkeypox is significantly greater near sites predicted to be habitable for squirrels (OR = 1.32; 95% CI 1.08–1.63). We recommend that semi-deciduous rainforests with oil-palm, the rope squirrel’s main food source, be prioritized for monitoring

BioDeepTime : a database of biodiversity time series for modern and fossil assemblages

We thank the Paleosynthesis Project and the Volkswagen Stiftung for funding that supported this project (Az 96 796). M.C.R. acknowledges the German Research Foundation (DFG) for funding through the Cluster of Excellence ‘The Ocean Floor – Earth's Uncharted Interface’ (EXC 2077, grant no. 390741603). E.E.S. acknowledges funding from Leverhulme Trust grant RPG-201170, the Leverhulme Prize and the National Science Research Council grant NE/V011405/1. Q.J.L. and L.N. acknowledge support from the Youth Innovation Promotion Association (2019310) and the Chinese Academy of Sciences (CAS-WX2021SF-0205). A.M.P. acknowledges funding from the Leverhulme Trust through research grant RPG-2019-402. M.D. acknowledges funding from Leverhulme Trust through the Leverhulme Centre for Anthropocene Biodiversity (RC-2018-021) and a research grant (RPG-2019-402), and the European Union (ERC coralINT, 101044975). L. H. L. acknowledges funding from the European Research Council (macroevolution.abc ERC grant no. 724324). K.H.P acknowledges funding from the National Science Foundation Graduate Research Fellowship Program (DGE-2139841). H.H.M.H. acknowledges support from Peter Buck Postdoc Fellowship, Smithsonian Institution. A.T. acknowledges funding from the Slovak Research and Development Agency (APVV 22-0523) and the Slovak Scientific Grant Agency (VEGA 02/0106/23).Motivation We have little understanding of how communities respond to varying magnitudes and rates of environmental perturbations across temporal scales. BioDeepTime harmonizes assemblage time series of presence and abundance data to help facilitate investigations of community dynamics across timescales and the response of communities to natural and anthropogenic stressors. BioDeepTime includes time series of terrestrial and aquatic assemblages of varying spatial and temporal grain and extent from the present-day to millions of years ago. Main Types of Variables Included BioDeepTime currently contains 7,437,847 taxon records from 10,062 assemblage time series, each with a minimum of 10 time steps. Age constraints, sampling method, environment and taxonomic scope are provided for each time series. Spatial Location and Grain The database includes 8752 unique sampling locations from freshwater, marine and terrestrial ecosystems. Spatial grain represented by individual samples varies from quadrats on the order of several cm2 to grid cells of ~100 km2. Time Period and Grain BioDeepTime in aggregate currently spans the last 451?million years, with the 10,062 modern and fossil assemblage time series ranging in extent from years to millions of years. The median extent of modern time series is 18.7?years and for fossil series is 54,872?years. Temporal grain, the time encompassed by individual samples, ranges from days to tens of thousands of years. Major Taxa and Level of Measurement The database contains information on 28,777 unique taxa with 4,769,789 records at the species level and another 271,218 records known to the genus level, including time series of benthic and planktonic foraminifera, coccolithophores, diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates. There are to date 7012 modern and 3050 fossil time series in BioDeepTime. Software Format SQLite, Comma-separated values.Publisher PDFPeer reviewe

Frizzled-3a and Wnt-8b genetically interact during forebrain commissural formation in embryonic zebrafish

The commissural plate forms the rostral surface of the embryonic vertebrate forebrain and provides a cellular substrate for forebrain commissural axons. We have previously reported that the Wnt receptor frizzled-3a (fzd3a) restricts the expression of the chemorepulsive guidance ligand slit2 to a discrete domain of neuroepithelial cells in the commissural plate of embryonic zebrafish. Loss of Fzd3a function perturbed slit2 expression and disrupted the formation of glial bridges which guide the formation of forebrain commissures. We now show that Wnt8b is also necessary for anterior commissural formation as well as for patterning of slit2 expression at the midline. Knock down of Wnt8b produced the same phenotype as loss of Fzd3a which suggested that these genes were acting together to regulate axon guidance. Simultaneous sub-threshold knock down of both Fzd3a and Wnt8b led to a greater than additive increase in the penetrance of the mutant phenotype which indicated that these two genes were indeed interacting. We have shown here that Fzd3a/Wnt8b signaling is essential for normal patterning of the commissural plate and that loss-of-function in either receptor or ligand causes Slit2-dependent defects in glial bridge morphology which indirectly attenuated axon midline crossing in the embryonic vertebrate forebrain. (C) 2013 Elsevier B.V. All rights reserved