Three years of Fermi GBM Earth Occultation Monitoring: Observations of Hard X-ray/Soft Gamma-Ray Sources

The Gamma ray Burst Monitor (GBM) on board Fermi has been providing continuous data to the astronomical community since 2008 August 12. In this paper we present the results of the analysis of the first three years of these continuous data using the Earth occultation technique to monitor a catalog of 209 sources. From this catalog, we detect 99 sources, including 40 low-mass X-ray binary/neutron star systems, 31 high-mass X-ray binary neutron star systems, 12 black hole binaries, 12 active galaxies, 2 other sources, plus the Crab Nebula, and the Sun. Nine of these sources are detected in the 100-300 keV band, including seven black-hole binaries, the active galaxy Cen A, and the Crab. The Crab and Cyg X-1 are also detected in the 300-500 keV band. GBM provides complementary data to other sky-monitors below 100 keV and is the only all-sky monitor above 100 keV. Up-to-date light curves for all of the catalog sources can be found at http://heastro.phys.lsu.edu/gbm/.Comment: 24 pages, 12 figures, accepted for publication in ApJ

RNAcentral : a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org

When a Standard Candle Flickers: Hard X-ray Variations in the Crab Nebula

In the first two years of science operations of the Fermi Gamma-ray Burst Monitor (GBM), August 2008 to August 2010, an approximately 7% (70 mcrab) decline was discovered in the overall Crab nebula flux in the 15 - 50 keV band, measured with the Earth occultation technique. This decline was independently confirmed with four other instruments: the RXTE/PCA, Swift/BAT, INTEGRAL/IBIS, and INTEGRAL/SPI. The pulsed flux measured with RXTE/PCA from 1999-2010 was consistent with the pulsar spin-down, indicating that the observed changes were nebular. From 2001 to 2010, the Crab nebula flux measured with RXTE/PCA was particularly variable, changing by up to approximately3.5% per year in the 15-50 keV band. These variations were confirmed with INTEGRAL/SPI starting in 2003, Swift/BAT starting in 2005, and Fermi GBM starting in 2008. Before 2001 and since 2010, the Crab nebula flux has appeared more stable, varying by less than 2% per year. At higher energies, above 50 keV, the Crab flux appears to be slowly recovering to its 2008 levels. I will present updated light curves in multiple energy bands for the Crab nebula, including recent data from Fermi GBM, Swift/BAT, INTEGRAL, MAXI, and NuSTAR and a 16-year long light curve from RXTE/PCA. We will compare these variations to higher energies as well, e.g. Fermi LAT

When a Standard Candle Flickers

The Crab is the only bright steady source in the X-ray sky. The Crab consists of a pulsar wind nebula, a synchrotron nebula, and a cloud of expanding ejecta. On small scales, the Crab is extremely complex and turbulent. X-ray astronomers have often used the Crab as a standard candle to calibrate instruments, assuming its spectrum and overall flux remains constant over time. Four instruments (Fermi/GBM, RXTE/PCA, Swift/BAT, INTEGRAL/ISGRI) show a approx.5% (50 m Crab) decline in the Crab from 2008-2010. This decline appears to be larger with increasing energy and is not present in the pulsed flux, implying changes in the shock acceleration, electron population or magnetic field in the nebula. The Crab is known to be dynamic on small scales, so it is not too surprising that its total flux varies as well. Caution should be taken when using the Crab for in-orbit calibrations

All-Sky Monitoring of Variable Sources with Fermi GBM

This slide presentation reviews the monitoring of variable sources with the Fermi Gamma Ray Burst Monitor (GBM). It reviews the use of the Earth Occultation technique, the observations of the Crab Nebula with the GBM, and the comparison with other satellite's observations. The instruments on board the four satellites indicate a decline in the Crab from 2008-2010

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

The Gene Ontology in 2010: extensions and refinements

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Oxford University Press. The published article can be found at: http://nar.oxfordjournals.org/