GRB 060313: A New Paradigm for Short-Hard Bursts?

We report the simultaneous observations of the prompt emission in the gamma-ray and hard X-ray bands by the Swift-BAT and the KONUS-Wind instruments of the short-hard burst, GRB 060313. The observations reveal multiple peaks in both the gamma-ray and hard X-ray bands suggesting a highly variable outflow from the central explosion. We also describe the early-time observations of the X-ray and UV/Optical afterglows by the Swift XRT and UVOT instruments. The combination of the X-ray and UV/Optical observations provide the most comprehensive lightcurves to date of a short-hard burst at such an early epoch. The afterglows exhibit complex structure with different decay indices and flaring. This behavior can be explained by the combination of a structured jet, radiative loss of energy, and decreasing microphysics parameters occurring in a circum-burst medium with densities varying by a factor of approximately two on a length scale of 10^17 cm. These density variations are normally associated with the environment of a massive star and inhomogeneities in its windy medium. However, the mean density of the observed medium (n approximately 10^−4 cm^3) is much less than that expected for a massive star. Although the collapse of a massive star as the origin of GRB 060313 is unlikely, the merger of a compact binary also poses problems for explaining the behavior of this burst. Two possible suggestions for explaining this scenario are: some short bursts may arise from a mechanism that does not invoke the conventional compact binary model, or soft late-time central engine activity is producing UV/optical but no X-ray flaring.Comment: 28 pages, 6 figures. Accepted for publication in ApJ. Clarifications made and typos correcte

Stroke in children with posterior fossa brain malformations, hemangiomas, arterial anomalies, coarctation of the aorta and cardiac defects, and eye abnormalities (PHACE) syndrome: a systematic review of the literature.

Background and purposePHACE is an acronym for posterior fossa brain malformations, hemangiomas, arterial anomalies, coarctation of the aorta and cardiac defects, and eye abnormalities. Several case reports of arterial ischemic stroke (AIS) in individuals with PHACE have been published, but risk factors for AIS in PHACE have not been clearly defined. The objective of this article is to review all cases of stroke in PHACE in children and describe clinical characteristics that may be associated with an increased risk of AIS.MethodsA literature and registry search was conducted to identify patients with PHACE who had experienced AIS. Data were analyzed to determine age of onset, presenting signs and symptoms, and clinical features among this cohort compared with PHACE without AIS.ResultsTwenty-two individuals with PHACE and AIS were identified. Imaging of the arteries of the head and neck was reported in 20 of 22. Narrowing or nonvisualization of at least 1 great cerebral vessel was present in 19 of 20 and of those, 15 had ≥ 2 vessels involved. Aortic arch anomalies were reported in 13 of 22 individuals.ConclusionsAplasia, hypoplasia, or occlusion of a major cerebral artery appears to be a significant risk factor for AIS in children with PHACE, especially when >1 vessel is involved or if there is coarctation of the aorta

Stratospheric CH4 and CO2 profiles derived from SCIAMACHY solar occultation measurements

Stratospheric profiles of methane (CH$_{4}$) and carbon dioxide (CO$_{2}$) have been derived from solar occultation measurements of the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY). The retrieval is performed using a method called onion peeling DOAS (ONPD), which combines an onion peeling approach with a weighting function DOAS (differential optical absorption spectroscopy) fit in the spectral region between 1559 and 1671 nm. By use of updated pointing information and optimisation of the data selection as well as of the retrieval approach, the altitude range for reasonable CH$_{4}$ could be broadened from 20 to 40 km to about 17 to 45 km. Furthermore, the quality of the derived CO$_{2}$ has been assessed such that now the first stratospheric profiles (17–45 km) of CO$_{2}$ from SCIAMACHY are available. Comparisons with independent data sets yield an estimated accuracy of the new SCIAMACHY stratospheric profiles of about 5–10% for CH$_{4}$ and 2–3% for CO$_{2}$. The accuracy of the products is currently mainly restricted by the appearance of unexpected vertical oscillations in the derived profiles which need further investigation. Using the improved ONPD retrieval, CH$_{4}$ and CO$_{2}$ stratospheric data sets covering the whole SCIAMACHY time series (August 2002–April 2012) and the latitudinal range between about 50 and 70° N have been derived. Based on these time series, CH$_{4}$ and CO$_{2}$ 2 trends have been estimated. CH$_{4}$ trends above about 20 km are not significantly different from zero and the trend at 17 km is about 3 ppbvyear$^{-1}$. The derived CO$_{2}$ trends show a general decrease with altitude with values of about 1.9 ppmvyear$^{-1}$ at 21 km and about 1.3 ppmvyear$^{-1}$ at 39 km. These results are in reasonable agreement with total column trends for these gases. This shows that the new SCIAMACHY data sets can provide valuable information about the stratosphere

Swift Observations of the highly X-ray variable Narrow Line Seyfert 1 galaxy RX J0148.3-2758

We report on Swift observations of the Narrow-Line Seyfert 1 galaxy (NLS1) RX J0148.3--2758. It was observed for 41.6 ks in 2005 May and for 15.8 ks in 2005 December. On short as well as on long timescales RX J0148.3--2758 is a highly variable source. It doubles its X-ray flux within 18-25 ks. The observation of 2005 December 09, which had a flux 4 times lower than during the 2005 May observations, shows a significant hardening of the X-ray hardness ratio compared with the 2005-May and 2005-December 20/21 observations. A detailed analysis of the X-ray spectra shows that we actually observe two spectral changes in RX J0148.3-2758: First a decrease of the soft X-ray component between 2005 May and December 09, which is most likely due to an increase of the intrinsic absorber column, and second a decrease of the hard X-ray flux in the December 20/21 observations. The soft X-ray spectral slope $\alpha_{\rm X, soft}$=2.58$^{+0.15}_{-0.12}$ during the high state in 2005 May agrees well with that measured by ROSAT (\axs=2.54\plm0.82). In contrast to the strong X-ray variability, the analysis of the Swift UVOT photometry from December 2005 of RX J0148.3--2758 shows no significant variability in any of the 6 UVOT filters. From the simultaneous X-ray and UV observations in 2005 December we measured the X-ray loudness alpha-ox varies between alpha-ox=1.5 and 1.8. Our Swift observations of RX J0148.3-2758 demonstrate the great potential the multi-wavelength observatory Swift has for AGN science. (shortened)Comment: 19 pages; accepted for publication the Astronomical Journa

Using genetic variants to evaluate the causal effect of cholesterol lowering on head and neck cancer risk:a Mendelian randomization study

Head and neck squamous cell carcinoma (HNSCC), which includes cancers of the oral cavity and oropharynx, is a cause of substantial global morbidity and mortality. Strategies to reduce disease burden include discovery of novel therapies and repurposing of existing drugs. Statins are commonly prescribed for lowering circulating cholesterol by inhibiting HMG-CoA reductase (HMGCR). Results from some observational studies suggest that statin use may reduce HNSCC risk. We appraised the relationship of genetically-proxied cholesterol-lowering drug targets and other circulating lipid traits with oral (OC) and oropharyngeal (OPC) cancer risk using two-sample Mendelian randomization (MR). For the primary analysis, germline genetic variants in HMGCR, NPC1L1, CETP, PCSK9 and LDLR were used to proxy the effect of low-density lipoprotein cholesterol (LDL-C) lowering therapies. In secondary analyses, variants were used to proxy circulating levels of other lipid traits in a genome-wide association study (GWAS) meta-analysis of 188,578 individuals. Both primary and secondary analyses aimed to estimate the downstream causal effect of cholesterol lowering therapies on OC and OPC risk. The second sample for MR was taken from a GWAS of 6,034 OC and OPC cases and 6,585 controls (GAME-ON). Analyses were replicated in UK Biobank, using 839 OC and OPC cases and 372,016 controls and the results of the GAME-ON and UK Biobank analyses combined in a fixed-effects meta-analysis. We found limited evidence of a causal effect of genetically-proxied LDL-C lowering using HMGCR, NPC1L1, CETP or other circulating lipid traits on either OC or OPC risk. Genetically-proxied PCSK9 inhibition equivalent to a 1 mmol/L (38.7 mg/dL) reduction in LDL-C was associated with an increased risk of OC and OPC combined (OR 1.8 95%CI 1.2, 2.8, p = 9.31 x10-05), with good concordance between GAME-ON and UK Biobank (I2 = 22%). Effects for PCSK9 appeared stronger in relation to OPC (OR 2.6 95%CI 1.4, 4.9) than OC (OR 1.4 95%CI 0.8, 2.4). LDLR variants, resulting in genetically-proxied reduction in LDL-C equivalent to a 1 mmol/L (38.7 mg/dL), reduced the risk of OC and OPC combined (OR 0.7, 95%CI 0.5, 1.0, p = 0.006). A series of pleiotropy-robust and outlier detection methods showed that pleiotropy did not bias our findings. We found limited evidence for a role of cholesterol-lowering in OC and OPC risk, suggesting previous observational results may have been confounded. There was some evidence that genetically-proxied inhibition of PCSK9 increased risk, while lipid-lowering variants in LDLR, reduced risk of combined OC and OPC. This result suggests that the mechanisms of action of PCSK9 on OC and OPC risk may be independent of its cholesterol lowering effects; however, this was not supported uniformly across all sensitivity analyses and further replication of this finding is required

GRB 050117: Simultaneous Gamma-ray and X-ray Observations with the Swift Satellite

The Swift Gamma-Ray Burst Explorer performed its first autonomous, X-ray follow-up to a newly detected GRB on 2005 January 17, within 193 seconds of the burst trigger by the Swift Burst Alert Telescope. While the burst was still in progress, the X-ray Telescope obtained a position and an image for an un-catalogued X-ray source; simultaneous with the gamma-ray observation. The XRT observed flux during the prompt emission was 1.1 x 10^{-8} ergs cm^{-2} s^{-1} in the 0.5-10 keV energy band. The emission in the X-ray band decreased by three orders of magnitude within 700 seconds, following the prompt emission. This is found to be consistent with the gamma-ray decay when extrapolated into the XRT energy band. During the following 6.3 hours, the XRT observed the afterglow in an automated sequence for an additional 947 seconds, until the burst became fully obscured by the Earth limb. A faint, extremely slowly decaying afterglow, alpha=-0.21$, was detected. Finally, a break in the lightcurve occurred and the flux decayed with alpha<-1.2$. The X-ray position triggered many follow-up observations: no optical afterglow could be confirmed, although a candidate was identified 3 arcsecs from the XRT position.Comment: 27 pages, 6 figures. Accepted for publication in Ap

Investigating the effect of sexual behaviour on oropharyngeal cancer risk:a methodological assessment of Mendelian randomization

BACKGROUND: Human papilloma virus infection is known to influence oropharyngeal cancer (OPC) risk, likely via sexual transmission. However, sexual behaviour has been correlated with other risk factors including smoking and alcohol, meaning independent effects are difficult to establish. We aimed to evaluate the causal effect of sexual behaviour on the risk of OPC using Mendelian randomization (MR). METHODS: Genetic variants robustly associated with age at first sex (AFS) and the number of sexual partners (NSP) were used to perform both univariable and multivariable MR analyses with summary data on 2641 OPC cases and 6585 controls, obtained from the largest available genome-wide association studies (GWAS). Given the potential for genetic pleiotropy, we performed a number of sensitivity analyses: (i) MR methods to account for horizontal pleiotropy, (ii) MR of sexual behaviours on positive (cervical cancer and seropositivity for Chlamydia trachomatis) and negative control outcomes (lung and oral cancer), (iii) Causal Analysis Using Summary Effect estimates (CAUSE), to account for correlated and uncorrelated horizontal pleiotropic effects, (iv) multivariable MR analysis to account for the effects of smoking, alcohol, risk tolerance and educational attainment. RESULTS: In univariable MR, we found evidence supportive of an effect of both later AFS (IVW OR = 0.4, 95%CI (0.3, 0.7), per standard deviation (SD), p = < 0.001) and increasing NSP (IVW OR = 2.2, 95%CI (1.3, 3.8) per SD, p = < 0.001) on OPC risk. These effects were largely robust to sensitivity analyses accounting for horizontal pleiotropy. However, negative control analysis suggested potential violation of the core MR assumptions and subsequent CAUSE analysis implicated pleiotropy of the genetic instruments used to proxy sexual behaviours. Finally, there was some attenuation of the univariable MR results in the multivariable models (AFS IVW OR = 0.7, 95%CI (0.4, 1.2), p = 0.21; NSP IVW OR = 0.9, 95%CI (0.5 1.7), p = 0.76). CONCLUSIONS: Despite using genetic variants strongly related sexual behaviour traits in large-scale GWAS, we found evidence for correlated pleiotropy. This emphasizes a need for multivariable approaches and the triangulation of evidence when performing MR of complex behavioural traits. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12916-022-02233-3

Very Early Optical Afterglows of Gamma-Ray Bursts: Evidence for Relative Paucity of Detection

Very early observations with the Swift satellite of gamma-ray burst (GRB) afterglows reveal that the optical component is not detected in a large number of cases. This is in contrast to the bright optical flashes previously discovered in some GRBs (e.g. GRB 990123 and GRB 021211). Comparisons of the X-ray afterglow flux to the optical afterglow flux and prompt gamma-ray fluence is used to quantify the seemingly deficient optical, and in some cases X-ray, light at these early epochs. This comparison reveals that some of these bursts appear to have higher than normal gamma-ray efficiencies. We discuss possible mechanisms and their feasibility for explaining the apparent lack of early optical emission. The mechanisms considered include: foreground extinction, circumburst absorption, Ly-alpha blanketing and absorption due to high redshift, low density environments, rapid temporal decay, and intrinsic weakness of the reverse shock. Of these, foreground extinction, circumburst absorption, and high redshift provide the best explanations for most of the non-detections in our sample. There is tentative evidence of suppression of the strong reverse shock emission. This could be because of a Poynting-flux-dominated flow or a pure non-relativistic hydrodynamical reverse shock.Comment: 22 pages, 5 figures. Accepted for publication in Ap

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead