BLAST: improvements for better sequence analysis

Basic local alignment search tool (BLAST) is a sequence similarity search program. The National Center for Biotechnology Information (NCBI) maintains a BLAST server with a home page at . We report here on recent enhancements to the results produced by the BLAST server at the NCBI. These include features to highlight mismatches between similar sequences, show where the query was masked for low-complexity sequence, and integrate information about the database sequences from the NCBI Entrez system into the BLAST display. Changes to how the database sequences are fetched have also improved the speed of the report generator

Charge Collection Physics in Semiconductor Detectors

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

Effects of Acceptance and Commitment Therapy on Impulsive Decision Making

This study examined the transdiagnostic effect of acceptance and commitment therapy (ACT) on impulsive decision making in a community sample. Forty adults were randomized to eight individual sessions of ACT or an inactive control. Participants completed pre-, mid-, and post-assessments for psychological symptoms, overall behavior change, valued living, delay discounting, psychological flexibility, and distress tolerance. Data were analyzed with multilevel modeling of growth curves. Significant interaction effects of time and condition were observed for psychological flexibility, distress tolerance, psychological symptoms, and the obstruction subscale of valued living. No significant interaction effect was found for two delay discounting tasks nor the progress subscale of valued living. The ACT condition had a significantly larger reduction of problem behavior at post-assessment. The results support use of ACT as a transdiagnostic treatment for impulsive behaviors. The lack of change in delay discounting contrasts previous research

The Building Blocks of Interoperability. A Multisite Analysis of Patient Demographic Attributes Available for Matching.

BackgroundPatient matching is a key barrier to achieving interoperability. Patient demographic elements must be consistently collected over time and region to be valuable elements for patient matching.ObjectivesWe sought to determine what patient demographic attributes are collected at multiple institutions in the United States and see how their availability changes over time and across clinical sites.MethodsWe compiled a list of 36 demographic elements that stakeholders previously identified as essential patient demographic attributes that should be collected for the purpose of linking patient records. We studied a convenience sample of 9 health care systems from geographically distinct sites around the country. We identified changes in the availability of individual patient demographic attributes over time and across clinical sites.ResultsSeveral attributes were consistently available over the study period (2005-2014) including last name (99.96%), first name (99.95%), date of birth (98.82%), gender/sex (99.73%), postal code (94.71%), and full street address (94.65%). Other attributes changed significantly from 2005-2014: Social security number (SSN) availability declined from 83.3% to 50.44% (p<0.0001). Email address availability increased from 8.94% up to 54% availability (p<0.0001). Work phone number increased from 20.61% to 52.33% (p<0.0001).ConclusionsOverall, first name, last name, date of birth, gender/sex and address were widely collected across institutional sites and over time. Availability of emerging attributes such as email and phone numbers are increasing while SSN use is declining. Understanding the relative availability of patient attributes can inform strategies for optimal matching in healthcare

BLAST+: architecture and applications

BACKGROUND: Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. RESULTS: We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. CONCLUSION: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications

The Herschel Virgo Cluster Survey: II. Truncated dust disks in HI-deficient spirals

By combining Herschel-SPIRE observations obtained as part of the Herschel Virgo Cluster Survey with 21 cm HI data from the literature, we investigate the role of the cluster environment on the dust content of Virgo spiral galaxies.We show for the first time that the extent of the dust disk is significantly reduced in HI-deficient galaxies, following remarkably well the observed 'truncation' of the HI disk. The ratio of the submillimetre-to- optical diameter correlates with the HI-deficiency, suggesting that the cluster environment is able to strip dust as well as gas. These results provide important insights not only into the evolution of cluster galaxies but also into the metal enrichment of the intra-cluster medium.Comment: Letter accepted for publication in A&A (Herschel special issue

Database indexing for production MegaBLAST searches

Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar

The Herschel Virgo Cluster Survey: VII. Dust in cluster dwarf elliptical galaxies

We use the Science Demonstration Phase data of the Herschel Virgo Cluster Survey to search for dust emission of early-type dwarf galaxies in the central regions of the Virgo Cluster as an alternative way of identifying the interstellar medium.We present the first possible far-infrared detection of cluster early-type dwarf galaxies: VCC781 and VCC951 are detected at the 10 sigma level in the SPIRE 250 micron image. Both detected galaxies have dust masses of the order of 10^5 Msun and average dust temperatures ~20K. The detection rate (less than 1%) is quite high compared to the 1.7% detection rate for Hi emission, considering that dwarfs in the central regions are more Hi deficient. We conclude that the removal of interstellar dust from dwarf galaxies resulting from ram pressure stripping, harassment, or tidal effects must be as efficient as the removal of interstellar gas.Comment: Letter accepted for publication in A&A (Herschel special issue

The Herschel Virgo Cluster Survey. IX. Dust-to-gas mass ratio and metallicity gradients in four Virgo spiral galaxies

Using Herschel data from the Open Time Key Project the Herschel Virgo Cluster Survey (HeViCS), we investigated the relationship between the metallicity gradients expressed by metal abundances in the gas phase as traced by the chemical composition of HII regions, and in the solid phase, as traced by the dust-to-gas mass ratio. We derived the radial gradient of the dust-to-gas mass ratio for all galaxies observed by HeViCS whose metallicity gradients are available in the literature. They are all late type Sbc galaxies, namely NGC4254, NGC4303, NGC4321, and NGC4501. We examined different dependencies on metallicity of the CO-to-H$_2$ conversion factor (\xco), used to transform the $^{12}$CO observations into the amount of molecular hydrogen. We found that in these galaxies the dust-to-gas mass ratio radial profile is extremely sensitive to choice of the \xco\ value, since the molecular gas is the dominant component in the inner parts. We found that for three galaxies of our sample, namely NGC4254, NGC4321, and NGC4501, the slopes of the oxygen and of the dust-to-gas radial gradients agree up to $\sim$0.6-0.7R$_{25}$ using \xco\ values in the range 1/3-1/2 Galactic \xco. For NGC4303 a lower value of \xco$\sim0.1\times$ 10$^{20}$ is necessary. We suggest that such low \xco\ values might be due to a metallicity dependence of \xco (from close to linear for NGC4254, NGC4321, and NGC4501 to superlinear for NGC4303), especially in the radial regions R$_G<$0.6-0.7R$_{25}$ where the molecular gas dominates. On the other hand, the outer regions, where the atomic gas component is dominant, are less affected by the choice of \xco, and thus we cannot put constraints on its value.Comment: 13 pages, 8 figures, A&A accepte

Training of Instrumentalists and Development of New Technologies on SOFIA

This white paper is submitted to the Astronomy and Astrophysics 2010 Decadal Survey (Astro2010)1 Committee on the State of the Profession to emphasize the potential of the Stratospheric Observatory for Infrared Astronomy (SOFIA) to contribute to the training of instrumentalists and observers, and to related technology developments. This potential goes beyond the primary mission of SOFIA, which is to carry out unique, high priority astronomical research. SOFIA is a Boeing 747SP aircraft with a 2.5 meter telescope. It will enable astronomical observations anywhere, any time, and at most wavelengths between 0.3 microns and 1.6 mm not accessible from ground-based observatories. These attributes, accruing from the mobility and flight altitude of SOFIA, guarantee a wealth of scientific return. Its instrument teams (nine in the first generation) and guest investigators will do suborbital astronomy in a shirt-sleeve environment. The project will invest $10M per year in science instrument development over a lifetime of 20 years. This, frequent flight opportunities, and operation that enables rapid changes of science instruments and hands-on in-flight access to the instruments, assure a unique and extensive potential - both for training young instrumentalists and for encouraging and deploying nascent technologies. Novel instruments covering optical, infrared, and submillimeter bands can be developed for and tested on SOFIA by their developers (including apprentices) for their own observations and for those of guest observers, to validate technologies and maximize observational effectiveness.Comment: 10 pages, no figures, White Paper for Astro 2010 Survey Committee on State of the Professio