The JCMT Gould Belt Survey: radiative heating by OB stars

Radiative feedback can influence subsequent star formation. We quantify the heating from OB stars in the local star-forming regions in the James Clerk Maxwell Telescope (JCMT) Gould Belt Survey. Dust temperatures are calculated from 450/850 μm flux ratios from SCUBA-2 observations at the JCMT assuming a fixed dust opacity spectral index β = 1.8. Mean dust temperatures are calculated for each submillimetre clump along with projected distances from the main OB star in the region. Temperature versus distance is fitted with a simple model of dust heating by the OB star radiation plus the interstellar radiation field and dust cooling through optically thin radiation. Classifying the heating sources by spectral type, O-type stars produce the greatest clump average temperature rises and largest heating extent, with temperatures of over 40 K and significant heating out to at least 2.4 pc. Early-type B stars (B4 and above) produce temperatures of over 20 K and significant heating over 0.4 pc. Late-type B stars show a marginal heating effect within 0.2 pc. For a given projected distance, there is a significant scatter in clump temperatures that is due to local heating by other luminous stars in the region, projection effects, or shadowing effects. Even in these local, ‘low-mass’ star-forming regions, radiative feedback is having an effect on parsec scales, with 24 per cent of the clumps heated to at least 3 K above the 15 K base temperature expected from heating by only the interstellar radiation field, and a mean dust temperature for heated clumps of 24 K

Oxygen Isotope Composition of Almahata Sitta

The name Almahata Sitta is applied collectively to some hundreds of stones that were found in a linear strewn field in the Nubian Desert coincident with the projected Earth-impacting orbit of the Asteroid 2008 TC3. Fragments of the meteorite were collected in December 2008 and March 2009, 2 to 5 months after the asteroid exploded in Earths atmosphere on 7 October 2008

Seasonal Migration and Home Ranges of Female Elk in the Black Hills of South Dakota and Wyoming

Understanding the movement and dispersion patterns of elk (Cervus elaphus) on public lands and the underlying factors that affect each will facilitate elk management and help resolve conflicts between management that benefit elk and other uses of land resources. Consequently, there is a need to identify and examine the movement and dispersion patterns of elk in the Black Hills of South Dakota and Wyoming. Our study quantified seasonal movements, determined home ranges of female elk in two areas of the Black Hills, and examined underlying factors associated with each. Elk in the northern area did not demonstrate seasonal migration patterns. Rather, winter ranges in the northern area were contained mostly within the boundaries of the summer range. Elk in the southern area exhibited a north-south migration pattern that coincided with seasonal patterns of snowfall. These elk migrated to winter range in late November and returned to summer range in late April. Home ranges of elk in the southern area were larger (P \u3c 0.01) than home ranges in the northern area. Landscape characteristics with marginally-significant correlations to elk home range area included road density (P = 0.10), and forage:cover ratio (P = 0.08); density of primary and secondary roads and average slope were significantly correlated with elk home range area (P \u3c 0.01). Managers can use this information to develop strategies that meet population goals and reduce conflicts between management for elk and with other resources

ZOOM Lite: next-generation sequencing data mapping and visualization software

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats. The software is freely available at http://bioinfor.com/zoom/lite/

The JCMT Gould Belt Survey: radiative heating by OB stars

This is the final version. Available from Oxford University Press via the DOI in this recordRadiative feedback can influence subsequent star formation. We quantify the heating from OB stars in the local starforming regions in the JCMT Gould Belt survey. Dust temperatures are calculated from 450/850 µm flux ratios from SCUBA-2 observations at the JCMT assuming a fixed dust opacity spectral index β = 1.8. Mean dust temperatures are calculated for each submillimetre clump along with projected distances from the main OB star in the region. Temperature vs. distance is fit with a simple model of dust heating by the OB star radiation plus the interstellar radiation field and dust cooling through optically thin radiation. Classifying the heating sources by spectral type, O-type stars produce the greatest clump average temperature rises and largest heating extent, with temperatures over 40 K and significant heating out to at least 2.4 pc. Early-type B stars (B4 and above) produce temperatures of over 20 K and significant heating over 0.4 pc. Late-type B stars show a marginal heating effect within 0.2 pc. For a given projected distance, there is a significant scatter in clump temperatures that is due to local heating by other luminous stars in the region, projection effects, or shadowing effects. Even in these local, ‘low-mass’ star-forming regions, radiative feedback is having an effect on parsec scales, with 24% of the clumps heated to at least 3 K above the 15 K base temperature expected from heating by only the interstellar radiation field, and a mean dust temperature for heated clumps of 24 K.Science and Technology Facilities Council (STFC

BFAST: An Alignment Tool for Large Scale Genome Resequencing

BACKGROUND:The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY:We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS:We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net)

Cremation and Grief:Are Ways of Commemorating the Dead Related to Adjustment Over Time?

Funeral services are known to serve multiple functions for bereaved persons. There is also a common, intuitively reasonable assumption of positive associations between engaging in funeral activities and adjustment to bereavement. We examined whether restricting ceremonial cremation arrangements to a minimum has a negative association with grief over time. Bereaved persons in the United Kingdom completed questionnaires 2 to 5 months postloss and again a year later (N = 233 with complete data; dropout = 11.4%). Neither type nor elaborateness of the cremation service, nor satisfaction with arrangements (typically high), emerged as significantly related to grief; no major subgroup differences (e.g., according to income level) were found. Results suggested that it does not matter to grief whether a more minimalistic or elaborate funeral ceremony was observed. We concluded that the funeral industry represented in this investigation is offering bereaved people the range of choices regarding cremation arrangements to meet their needs. Limits to generalizability are discussed

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data in which the reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data, and the hints can be used for more computationally-demanding work. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references known to the server. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients, one of them running in a web browser, in order to demonstrate that gigabytes of raw sequencing reads of unknown origin could be identified without the need to transfer a very large volume of data, and on modestly powered computing devices. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data is available at http://bit.ly/1aURxkc

The JCMT Gould Belt Survey: Evidence for radiative heating in Serpens MWC 297 and its influence on local star formation

We present SCUBA-2 450micron and 850micron observations of the Serpens MWC 297 region, part of the JCMT Gould Belt Survey of nearby star-forming regions. Simulations suggest that radiative feedback influences the star-formation process and we investigate observational evidence for this by constructing temperature maps. Maps are derived from the ratio of SCUBA-2 fluxes and a two component model of the JCMT beam for a fixed dust opacity spectral index of beta = 1.8. Within 40 of the B1.5Ve Herbig star MWC 297, the submillimetre fluxes are contaminated by free-free emission with a spectral index of 1.03+-0.02, consistent with an ultra-compact HII region and polar winds/jets. Contamination accounts for 73+-5 per cent and 82+-4 per cent of peak flux at 450micron and 850micron respectively. The residual thermal disk of the star is almost undetectable at these wavelengths. Young Stellar Objects are confirmed where SCUBA-2 850micron clumps identified by the fellwalker algorithm coincide with Spitzer Gould Belt Survey detections. We identify 23 objects and use Tbol to classify nine YSOs with masses 0.09 to 5.1 Msun. We find two Class 0, one Class 0/I, three Class I and three Class II sources. The mean temperature is 15+-2K for the nine YSOs and 32+-4K for the 14 starless clumps. We observe a starless clump with an abnormally high mean temperature of 46+-2K and conclude that it is radiatively heated by the star MWC 297. Jeans stability provides evidence that radiative heating by the star MWC 297 may be suppressing clump collapse.Comment: 24 pages, 13 figures, 7 table