| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
- Burgess, J Michael, et al.
(författare)
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Constraints on the Synchrotron Shock Model for the Fermi GRB 090820A Observed by Gamma-Ray Burst Monitor
- 2011
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 741:1
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Tidskriftsartikel (refereegranskat)abstract
- Discerning the radiative dissipation mechanism for prompt emission in gamma-ray bursts (GRBs) requires detailed spectroscopic modeling that straddles the vF(v) peak in the 100 keV-1 MeV range. Historically, empirical fits such as the popular Band function have been employed with considerable success in interpreting the observations. While extrapolations of the Band parameters can provide some physical insight into the emission mechanisms responsible for GRBs, these inferences do not provide a unique way of discerning between models. By fitting physical models directly, this degeneracy can be broken, eliminating the need for empirical functions; our analysis here offers a first step in this direction. One of the oldest, and leading, theoretical ideas for the production of the prompt signal is the synchrotron shock model. Here we explore the applicability of this model to a bright Fermi gamma-ray burst monitor (GBM) burst with a simple temporal structure, GRB 090820A. Our investigation implements, for the first time, thermal and non-thermal synchrotron emissivities in the RMFIT forward-folding spectral analysis software often used in GBM burst studies. We find that these synchrotron emissivities, together with a blackbody shape, provide at least as good a match to the data as the Band GRB spectral fitting function. This success is achieved in both time-integrated and time-resolved spectral fits.
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| 3. |
- Goldstein, Adam, et al.
(författare)
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The Fermi GBM Gamma-Ray Burst Spectral Catalog : The First Two Years
- 2012
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 199:1
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Tidskriftsartikel (refereegranskat)abstract
- We present systematic spectral analyses of gamma-ray bursts (GRBs) detected by the Fermi Gamma-Ray Burst Monitor (GBM) during its first two years of operation. This catalog contains two types of spectra extracted from 487 GRBs, and by fitting four different spectral models, this results in a compendium of over 3800 spectra. The models were selected based on their empirical importance to the spectral shape of many GRBs, and the analysis performed was devised to be as thorough and objective as possible. We describe in detail our procedure and criteria for the analyses, and present the bulk results in the form of parameter distributions. This catalog should be considered an official product from the Fermi GBM Science Team, and the data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center.
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| 4. |
- Paciesas, William S, et al.
(författare)
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The Fermi GBM Gamma-Ray Burst Catalog : The First Two Years
- 2012
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 199:1
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Tidskriftsartikel (refereegranskat)abstract
- The Fermi Gamma-ray Burst Monitor (GBM) is designed to enhance the scientific return from Fermi in studying gamma-ray bursts (GRBs). In its first two years of operation GBM triggered on 491 GRBs. We summarize the criteria used for triggering and quantify the general characteristics of the triggered GRBs, including their locations, durations, peak flux, and fluence. This catalog is an official product of the Fermi GBM science team, and the data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center.
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| 5. |
- von Kienlin, Andreas, et al.
(författare)
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The Second Fermi GBM Gamma-Ray Burst Catalog : The First Four Years
- 2014
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 211:1
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Tidskriftsartikel (refereegranskat)abstract
- This is the second of a series of catalogs of gamma-ray bursts (GRBs) observed with the Fermi Gamma-ray Burst Monitor (GBM). It extends the first two-year catalog by two more years, resulting in an overall list of 953 GBM triggered GRBs. The intention of the GBM GRB catalog is to provide information to the community on the most important observables of the GBM detected GRBs. For each GRB the location and main characteristics of the prompt emission, the duration, peak flux and fluence are derived. The latter two quantities are calculated for the 50-300 keV energy band, where the maximum energy release of GRBs in the instrument reference system is observed and also for a broader energy band from 10-1000 keV, exploiting the full energy range of GBMs low-energy detectors. Furthermore, information is given on the settings and modifications of the triggering criteria and exceptional operational conditions during years three and four in the mission. This second catalog is an official product of the Fermi GBM science team, and the data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center.
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| 6. |
- Buhnerkempe, Michael G., et al.
(författare)
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The Impact of Movements and Animal Density on Continental Scale Cattle Disease Outbreaks in the United States
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 9:3, s. 0091724-
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Tidskriftsartikel (refereegranskat)abstract
- Globalization has increased the potential for the introduction and spread of novel pathogens over large spatial scales necessitating continental-scale disease models to guide emergency preparedness. Livestock disease spread models, such as those for the 2001 foot-and-mouth disease (FMD) epidemic in the United Kingdom, represent some of the best case studies of large-scale disease spread. However, generalization of these models to explore disease outcomes in other systems, such as the United Statess cattle industry, has been hampered by differences in system size and complexity and the absence of suitable livestock movement data. Here, a unique database of US cattle shipments allows estimation of synthetic movement networks that inform a near-continental scale disease model of a potential FMD-like (i.e., rapidly spreading) epidemic in US cattle. The largest epidemics may affect over one-third of the US and 120,000 cattle premises, but cattle movement restrictions from infected counties, as opposed to national movement moratoriums, are found to effectively contain outbreaks. Slow detection or weak compliance may necessitate more severe state-level bans for similar control. Such results highlight the role of large-scale disease models in emergency preparedness, particularly for systems lacking comprehensive movement and outbreak data, and the need to rapidly implement multi-scale contingency plans during a potential US outbreak.
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| 7. |
- Colleen, S, et al.
(författare)
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Urogenitalt trauma.
- 2012
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Ingår i: Urologi 2ed. eds: Damber JE, Peeker R.. - Lund, Sverige : Lund: Studentlitteratur. - 9789144075921
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Guiriec, Sylvain, et al.
(författare)
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Detection of a thermal spectral component in the prompt emission of GRB 100724B
- 2011
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Ingår i: ASTROPHYSICAL JOURNAL LETTERS. - 2041-8205. ; 727:2, s. L33-
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Tidskriftsartikel (refereegranskat)abstract
- Observations of GRB 100724B with the Fermi Gamma-Ray Burst Monitor find that the spectrum is dominated by the typical Band functional form, which is usually taken to represent a non-thermal emission component, but also includes a statistically highly significant thermal spectral contribution. The simultaneous observation of the thermal and non-thermal components allows us to confidently identify the two emission components. The fact that these seem to vary independently favors the idea that the thermal component is of photospheric origin while the dominant non-thermal emission occurs at larger radii. Our results imply either a very high efficiency for the non-thermal process or a very small size of the region at the base of the flow, both quite challenging for the standard fireball model. These problems are resolved if the jet is initially highly magnetized and has a substantial Poynting flux.
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| 9. |
- Guiriec, Sylvain, et al.
(författare)
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Time-resolved Spectroscopy of the Three Brightest and Hardest Short Gamma-ray Bursts Observed with the Fermi Gamma-ray Burst Monitor
- 2010
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 725:1, s. 225-241
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Tidskriftsartikel (refereegranskat)abstract
- From 2008 July to 2009 October, the Gamma-ray Burst Monitor (GBM) on board the Fermi Gamma-ray Space Telescope has detected 320 gamma-ray bursts (GRBs). About 20% of these events are classified as short based on their T90 duration below 2 s. We present here for the first time time-resolved spectroscopy at timescales as short as 2 ms for the three brightest short GRBs observed with GBM. The time-integrated spectra of the events deviate from the Band function, indicating the existence of an additional spectral component, which can be fit by a power law with index ∼-1.5. The time-integrated Epeak values exceed 2 MeV for two of the bursts and are well above the values observed in the brightest long GRBs. Their Epeak values and their low-energy power-law indices (a) confirm that short GRBs are harder than long ones. We find that short GRBs are very similar to long ones, but with light curves contracted in time and with harder spectra stretched toward higher energies. In our time-resolved spectroscopy analysis, we find that the Epeak values range from a few tens of keV up to more than 6MeV. In general, the hardness evolutions during the bursts follow their flux/intensity variations, similar to long bursts. However, we do not always see the Epeak leading the light-curve rises and confirm the zero/short average light-curve spectral lag below 1 MeV, already established for short GRBs. We also find that the time-resolved low-energy power-law indices of the Band function mostly violate the limits imposed by the synchrotron models for both slow and fast electron cooling and may require additional emission processes to explain the data. Finally, we interpreted these observations in the context of the current existing models and emission mechanisms for the prompt emission of GRBs.
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| 10. |
- Lindström, Tom, et al.
(författare)
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A Bayesian Approach for Modeling Cattle Movements in the United States: Scaling up a Partially Observed Network
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on Bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full networks that incorporate the uncertainty of sampled and unobserved contacts.
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