The Panchromatic Hubble Andromeda Treasury: Triangulum Extended Region (PHATTER). V. The Structure of M33 in Resolved Stellar Populations

We present a detailed analysis of the the structure of the Local Group flocculent spiral galaxy M33, as measured using the Panchromatic Hubble Andromeda Treasury Triangulum Extended Region (PHATTER) survey. Leveraging the multiwavelength coverage of PHATTER, we find that the oldest populations are dominated by a smooth exponential disk with two distinct spiral arms and a classical central bar $-$ completely distinct from what is seen in broadband optical imaging, and the first-ever confirmation of a bar in M33. We estimate a bar extent of $\sim$1 kpc. The two spiral arms are asymmetric in orientation and strength, and likely represent the innermost impact of the recent tidal interaction responsible for M33's warp at larger scales. The flocculent multi-armed morphology for which M33 is known is only visible in the young upper main sequence population, which closely tracks the morphology of the ISM. We investigate the stability of M33's disk, finding $Q{\sim}1$ over the majority of the disk. We fit multiple components to the old stellar density distribution and find that, when considering recent stellar kinematics, M33's bulk structure favors the inclusion of an accreted halo component, modeled as a broken power-law. The best-fit halo model has an outer power-law index of $-$3 and accurately describes observational evidence of M33's stellar halo from both resolved stellar spectroscopy in the disk and its stellar populations at large radius. Integrating this profile yields a total halo stellar mass of ${\sim}5{\times}10^8\ M_{\odot}$, giving a total stellar halo mass fraction of 16%, most of which resides in the innermost 2.5 kpc.Comment: 31 pages, 17 figures, 5 tables, Accepted for publication in Ap

The Panchromatic Hubble Andromeda Treasury: Triangulum Extended Region (PHATTER) I. Ultraviolet to Infrared Photometry of 22 Million Stars in M33

We present panchromatic resolved stellar photometry for 22 million stars in the Local Group dwarf spiral Triangulum (M33), derived from Hubble Space Telescope (HST) observations with the Advanced Camera for Surveys (ACS) in the optical (F475W, F814W), and the Wide Field Camera 3 (WFC3) in the near ultraviolet (F275W, F336W) and near-infrared (F110W, F160W) bands. The large, contiguous survey area covers $\sim$14 square kpc and extends to 3.5 kpc (14 arcmin, or 1.5-2 scale lengths) from the center of M33. The PHATTER observing strategy and photometry technique closely mimic those of the Panchromatic Hubble Andromeda Treasury (PHAT), but with updated photometry techniques that take full advantage of all overlapping pointings (aligned to within $<$5-10 milliarcseconds) and improved treatment of spatially-varying point spread functions. The photometry reaches a completeness-limited depth of F475W$\sim$28.5 in the lowest surface density regions observed in M33 and F475W$\sim$26.5 in the most crowded regions found near the center of M33. We find the young populations trace several relatively tight arms, while the old populations show a clear, looser two-armed structure. We present extensive analysis of the data quality including artificial star tests to quantify completeness, photometric uncertainties, and flux biases. This stellar catalog is the largest ever produced for M33, and is publicly available for download by the community.Comment: 38 pages, 6 tables, 25 figures, accepted for publication in ApJ

FastBLAST: Homology Relationships for Millions of Proteins

BackgroundAll-versus-all BLAST, which searches for homologous pairs of sequences in a database of proteins, is used to identify potential orthologs, to find new protein families, and to provide rapid access to these homology relationships. As DNA sequencing accelerates and data sets grow, all-versus-all BLAST has become computationally demanding.Methodology/principal findingsWe present FastBLAST, a heuristic replacement for all-versus-all BLAST that relies on alignments of proteins to known families, obtained from tools such as PSI-BLAST and HMMer. FastBLAST avoids most of the work of all-versus-all BLAST by taking advantage of these alignments and by clustering similar sequences. FastBLAST runs in two stages: the first stage identifies additional families and aligns them, and the second stage quickly identifies the homologs of a query sequence, based on the alignments of the families, before generating pairwise alignments. On 6.53 million proteins from the non-redundant Genbank database ("NR"), FastBLAST identifies new families 25 times faster than all-versus-all BLAST. Once the first stage is completed, FastBLAST identifies homologs for the average query in less than 5 seconds (8.6 times faster than BLAST) and gives nearly identical results. For hits above 70 bits, FastBLAST identifies 98% of the top 3,250 hits per query.Conclusions/significanceFastBLAST enables research groups that do not have supercomputers to analyze large protein sequence data sets. FastBLAST is open source software and is available at http://microbesonline.org/fastblast

Viscerotropic disease: case definition and guidelines for collection, analysis, and presentation of immunization safety data

Viscerotropic disease (VTD) is defined as acute multiple organ system dysfunction that occurs following vaccination. The severity of VTD ranges from relatively mild multisystem disease to severe multiple organ system failure and death. The term VTD was first used shortly after the initial published reports in 2001 of febrile multiple organ system failure following yellow fever (YF) vaccination. To date, VTD has been reported only in association with YF vaccine and has been thus referred to as YF vaccine-associated viscerotropic disease (YEL-AVD)

The Consensus Coding Sequence (Ccds) Project: Identifying a Common Protein-Coding Gene Set for the Human and Mouse Genomes

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.National Human Genome Research Institute (U.S.) (Grant number 1U54HG004555-01)Wellcome Trust (London, England) (Grant number WT062023)Wellcome Trust (London, England) (Grant number WT077198

Standards recommendations for the Earth BioGenome Project

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met

Granger Causality Analysis of Steady-State Electroencephalographic Signals during Propofol-Induced Anaesthesia

Changes in conscious level have been associated with changes in dynamical integration and segregation among distributed brain regions. Recent theoretical developments emphasize changes in directed functional (i.e., causal) connectivity as reflected in quantities such as ‘integrated information’ and ‘causal density’. Here we develop and illustrate a rigorous methodology for assessing causal connectivity from electroencephalographic (EEG) signals using Granger causality (GC). Our method addresses the challenges of non-stationarity and bias by dividing data into short segments and applying permutation analysis. We apply the method to EEG data obtained from subjects undergoing propofol-induced anaesthesia, with signals source-localized to the anterior and posterior cingulate cortices. We found significant increases in bidirectional GC in most subjects during loss-of-consciousness, especially in the beta and gamma frequency ranges. Corroborating a previous analysis we also found increases in synchrony in these ranges; importantly, the Granger causality analysis showed higher inter-subject consistency than the synchrony analysis. Finally, we validate our method using simulated data generated from a model for which GC values can be analytically derived. In summary, our findings advance the methodology of Granger causality analysis of EEG data and carry implications for integrated information and causal density theories of consciousness

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another