Abstract
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project ...(https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.
We demonstrate that distinguishable gamma-ray burst (GRB) pulses exhibit similar behaviors as evidenced by correlations among the observable pulse properties of duration, peak luminosity, fluence, ...spectral hardness, energy-dependent lag, and asymmetry. Long and Short burst pulses exhibit these behaviors, suggesting that a similar process is responsible for producing all GRB pulses. That these properties correlate in the observer's frame indicates that intrinsic correlations are strong enough to not be diluted into insignificance by the dispersion in distances and redshift. We show how all correlated pulse characteristics can be explained by hard-to-soft pulse evolution, and we demonstrate that 'intensity tracking' pulses not having these properties are not single pulses; they instead appear to be composed of two or more overlapping hard-to-soft pulses. In order to better understand pulse characteristics, we recognize that hard-to-soft evolution provides a more accurate definition of a pulse than its intensity variation. This realization, coupled with the observation that pulses begin near-simultaneously across a wide range of energies, leads us to conclude that the observed pulse emission represents the energy decay resulting from an initial injection, and that one simple and as yet unspecified physical mechanism is likely to be responsible for all GRB pulses regardless of the environment in which they form and, if GRBs originate from different progenitors, then of the progenitors that supply them with energy.
Abstract We propose that gamma-ray burst (GRB) pulses are produced when highly relativistic jets sweep across an observer’s line of sight. We hypothesize that axisymmetric jet profiles, coupled with ...special relativistic effects, produce the time-reversed properties of GRB pulses. Curvature resulting from rapid jet expansion is responsible for much of the observed pulse asymmetry and hard-to-soft evolution. The relative obliqueness with which the jet crosses the line of sight explains the known GRB pulse morphological types. We explore two scenarios: one in which a rigid/semirigid jet moves laterally and another in which a ballistic jet sprays material from a laterally moving nozzle. The ballistic jet model is favored based upon its consistency with standard emission mechanisms.
We present a systematic spectral analysis of 350 bright gamma-ray bursts (GRBs) observed with the Burst and Transient Source Experiment (BATSE; 630 keV-2 MeV) with high temporal and spectral ...resolution. Our sample was selected from the complete set of 2704 BATSE GRBs based on their energy fluence or peak photon flux values to assure good statistics and included 17 short GRBs. To obtain well-constrained spectral parameters, several photon models were used to fit each spectrum. We compared spectral parameters resulting from the fits using different models, and the spectral parameters that best represent each spectrum were statistically determined, taking into account the parameterization differences among the models. A thorough analysis was performed on 350 time-integrated and 8459 time-resolved burst spectra, and the effects of integration times in determining the spectral parameters were explored. Using the results, we studied correlations among spectral parameters and their evolution pattern within each burst. The resulting spectral catalog is the most comprehensive study of spectral properties of GRB prompt emission to date and is available electronically from the High-Energy Astrophysics Science Archive Research Center (HEASARC). The catalog provides reliable constraints on particle acceleration and emission mechanisms in GRBs.
A study of a set of well-isolated pulses in long and intermediate gamma-ray burst (GRB) light curves indicates that simple pulse models having smooth and monotonic pulse rise and decay regions are ...inadequate. Examining the residuals of fits of pulses to such models suggests the following patterns of departure from smooth pulses: three separate wavelike peaks found in the residuals of each pulse (the precursor peak, the central peak, and the decay peak) combine with the underlying Norris et al. pulse model to produce five distinct regions in the temporal evolution of each pulse. The Precursor Shelf occurs prior to or concurrent with the exponential Rapid Rise. The pulse reaches maximum intensity at the Peak Plateau, then undergoes a Rapid Decay. The decay gradually slows into an Extended Tail. Despite these distinct temporal segments, the pulses studied are almost universally characterized by hard-to-soft spectral evolution, arguing that the new pulse features reflect a single evolution, rather than being artifacts of pulse overlap. The fluctuations can give a single pulse the appearance of having up to three distinct localized peaks, leading to ambiguities in pulse-fitting if an incorrect pulse model is used. The approach demonstrates that complex GRBs may be composed of fewer pulses than indicated by the number of peaks. The large degree of similar spectro-temporal behavior within GRB pulses indicates that a single process is responsible for producing pulses spanning a tremendous range of durations, luminosities, and spectral hardnesses, and the correlated characteristics of the wavelike peaks are related to the pulse asymmetry, suggesting kinematic origins that seem supportive of relativistic shocks.
The heat stress response is associated with several beneficial adaptations that promote cell health and survival. Specifically, in vitro and animal investigations suggest that repeated exposures to a ...mild heat stress (~40°C) elicit positive mitochondrial adaptations in skeletal muscle comparable to those observed with exercise. To assess whether such adaptations translate to human skeletal muscle, we produced local, deep tissue heating of the vastus lateralis via pulsed shortwave diathermy in 20 men and women ( n = 10 men; n = 10 women). Diathermy increased muscle temperature by 3.9°C within 30 min of application. Immediately following a single 2-h heating session, we observed increased phosphorylation of AMP-activated protein kinase and ERK1/2 but not of p38 MAPK or JNK. Following repeated heat exposures (2 h daily for 6 consecutive days), we observed a significant cellular heat stress response, as heat shock protein 70 and 90 increased 45% and 38%, respectively. In addition, peroxisome proliferator-activated receptor gamma, coactivator-1 alpha and mitochondrial electron transport protein complexes I and V expression were increased after heating. These increases were accompanied by augmentation of maximal coupled and uncoupled respiratory capacity, measured via high-resolution respirometry. Our data provide the first evidence that mitochondrial adaptation can be elicited in human skeletal muscle in response to repeated exposures to mild heat stress. NEW & NOTEWORTHY Heat stress has been shown to elicit mitochondrial adaptations in cell culture and animal research. We used pulsed shortwave diathermy to produce deep tissue heating and explore whether beneficial mitochondrial adaptations would translate to human skeletal muscle in vivo. We report, for the first time, positive mitochondrial adaptations in human skeletal muscle following recurrent heat stress. The results of this study have clinical implications for many conditions characterized by diminished skeletal muscle mitochondrial function.
Building on Nakar & Piran's analysis of the Amati relation relating gamma-ray burst peak energies, E sub(p), and isotropic energies, E sub(iso), we test the consistency of a large sample of BATSE ...bursts with the Amati and Ghirlanda (which relate peak energies and actual gamma-ray energies, E sub( gamma )) relations. Each of these relations can be expressed as a ratio of the different energies that is a function of redshift (for both the Amati and Ghirlanda relations) and beaming fraction f sub(B) (for the Ghirlanda relation). The most rigorous test, which allows bursts to be at any redshift, corroborates Nakar & Piran's result--88% of the BATSE bursts are inconsistent with the Amati relation--while only 1.6% of the bursts are inconsistent with the Ghirlanda relation if f sub(B) = 1. Even when we allow for a real dispersion in the Amati relation, we find an inconsistency. Modeling the redshift distribution results in an energy ratio distribution for the Amati relation that is shifted by an order of magnitude relative to the observed distribution; any subpopulation satisfying the Amati relation can comprise at most similar to 18% of our burst sample. A similar analysis of the Ghirlanda relation depends sensitively on the beaming fraction distribution for small values of f sub(B); for reasonable estimates of this distribution about a third of the burst sample is inconsistent with the Ghirlanda relation. Our results indicate that these relations are an artifact of the selection effects of the burst sample in which they were found; these selection effects may favor subpopulations for which these relations are valid.
The BATSE 5B Gamma-Ray Burst Spectral Catalog Goldstein, A; Preece, R D; Mallozzi, R S ...
The Astrophysical journal. Supplement series,
10/2013, Volume:
208, Issue:
2
Journal Article
Peer reviewed
Open access
We present systematic spectral analyses of GRBs detected with the Burst and Transient Source Experiment (BATSE) onboard the Compton Gamma-Ray Observatory (CGRO) during its entire nine years of ...operation. This catalog contains two types of spectra extracted from 2145 GRBs and fitted with five different spectral models resulting in a compendium of over 19000 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 procedures 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 BATSE Science Team, and the data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center (HEASARC).
ABSTRACT Photospheric (thermal) emission is inherent to the gamma-ray burst (GRB) 'fireball' model. We show here that inclusion of this component in the analysis of the GRB prompt emission phase ...naturally explains some of the prompt GRB spectra seen by the Fermi satellite over its entire energy band. The sub-MeV peak is explained as multicolour blackbody emission, and the high-energy tail, extending up to the GeV band, results from roughly similar contributions of synchrotron emission, synchrotron self-Compton and Comptonization of the thermal photons by energetic electrons originating after dissipation of the kinetic energy above the photosphere. We show how this analysis method results in a complete, self-consistent picture of the physical conditions at both emission sites of the thermal and non-thermal radiation. We study the connection between the thermal and non-thermal parts of the spectrum, and show how the values of the free model parameters are deduced from the data. We demonstrate our analysis method on GRB090902B: we deduce a Lorentz factor in the range 920 ≤η≤ 1070, photospheric radius r ph 7.2-8.4 × 1011cm and dissipation radius r γ≥ 3.5-4.1 × 1015cm. By comparison to afterglow data, we deduce that a large fraction straight epsilondasymptotically = 85-95 per cent of the kinetic energy is dissipated, and that a large fraction, equipartition of this energy, is carried by the electrons and the magnetic field. This high value of straight epsilond questions the 'internal shock' scenario as the main energy dissipation mechanism for this GRB.
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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