Time correlations and 1/f behavior in backscattering radar reflectivity measurements from cirrus cloud ice fluctuations

The state of the atmosphere is governed by the classical laws of fluid motion and exhibits correlations in various spatial and temporal scales. These correlations are crucial to understand the short and long term trends in climate. Cirrus clouds are important ingredients of the atmospheric boundary layer. To improve future parameterization of cirrus clouds in climate models, it is important to understand the cloud properties and how they change within the cloud. We study correlations in the fluctuations of radar signals obtained at isodepths of winter and fall cirrus clouds. In particular we focus on three quantities: (i) the backscattering cross-section, (ii) the Doppler velocity and (iii) the Doppler spectral width. They correspond to the physical coefficients used in Navier Stokes equations to describe flows, i.e. bulk modulus, viscosity, and thermal conductivity. In all cases we find that power-law time correlations exist with a crossover between regimes at about 3 to 5 min. We also find that different type of correlations, including 1/f behavior, characterize the top and the bottom layers and the bulk of the clouds. The underlying mechanisms for such correlations are suggested to originate in ice nucleation and crystal growth processes.Comment: 33 pages, 9 figures; to appear in the Journal of Geophysical Research - Atmosphere

GiardiaDB and TrichDB : integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

© 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids Research 37 (2009): D526-D530, doi:10.1093/nar/gkn631.GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.Federal funds from the National Institute of Allergy and Infectious Diseases; Department of Health and Human Services, National Institutes of Health (HHSN266200400037C). Funding for open access charge: National Institutes of Health (HHSN266200400037C)

EuPathDB: the eukaryotic pathogen database

ABSTRACT EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNAseq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010

TriTrypDB: a functional genomic resource for the Trypanosomatidae

TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ‘User Comments’ may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate