Mosaicism for r(X) and der(X)del(X)(p11.23)dup(X)(p11.21p11.22) provides insight into the possible mechanism of rearrangement

We report a patient with a unique and complex cytogenetic abnormality involving mosaicism for a small ring X and deleted Xp derivative chromosome with tandem duplication at the break point. The patient presented with failure to thrive, muscular hypotonia, and minor facial anatomic anomalies, all concerning for Turner syndrome. Brain MRI revealed mild thinning of the corpus callosum, an apparent decrease in ventricular white matter volume, and an asymmetric myelination pattern. Array comparative genome hybridization analysis revealed mosaicism for the X chromosome, deletion of the short arm of an X chromosome, and a duplication of chromosome region Xp11.21-p11.22. G-banded chromosome and FISH analyses revealed three abnormal cell lines: 46,X,der(X)del(X)(p11.23)dup(X)(p11.21p11.22)/46,X,r(X)(q11.1q13.1)/45,X. The small ring X chromosome was estimated to be 5.2 Mb in size and encompassed the centromere and Xq pericentromeric region. X chromosome inactivation (XCI) studies demonstrated a skewed pattern suggesting that the ring X remained active, likely contributing to the observed clinical features of brain dysmyelination. We hypothesize that a prezygotic asymmetric crossing over within a loop formed during meiosis in an X chromosome with a paracentric inversion resulted in an intermediate dicentric chromosome. An uneven breakage of the dicentric chromosome in the early postzygotic period might have resulted in the formation of one cell line with the X chromosome carrying a terminal deletion and pericentromeric duplication of the short arm and the second cell line with the X chromosome carrying a complete deletion of Xp. The cell line carrying the deletion of Xp could have then stabilized through self-circularization and formation of the ring X chromosome

Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing

PurposeWe applied whole genome sequencing to children diagnosed with neoplasms and found to carry apparently balanced constitutional translocations, to discover novel genic disruptions.MethodsWe applied SV calling programs CREST, Break Dancer, SV-STAT and CGAP-CNV, and developed an annotative filtering strategy to achieve nucleotide resolution at the translocations.ResultsWe identified the breakpoints for t(6;12) (p21.1;q24.31) disrupting HNF1A in a patient diagnosed with hepatic adenomas and Maturity Onset Diabetes of the Young (MODY). Translocation as the disruptive event of HNF1A, a gene known to be involved in MODY3, has not been previously reported. In a subject with Hodgkin’s lymphoma and subsequent low-grade glioma, we identified t(5;18) (q35.1;q21.2), disrupting both SLIT3 and DCC, genes previously implicated in both glioma and lymphoma.ConclusionsThese examples suggest that implementing clinical whole genome sequencing in the diagnostic work-up of patients with novel but apparently balanced translocations may reveal unanticipated disruption of disease-associated genes and aid in prediction of the clinical phenotype

Z=50 shell gap near 100^{100}Sn from intermediate-energy Coulomb excitations in even-mass 106−−112^{106--112}Sn isotopes

Rare isotope beams of neutron-deficient $^{106,108,110}$Sn nuclei from the fragmentation of $^{124}$Xe were employed in an intermediate-energy Coulomb excitation experiment yielding $B(E2, 0^+_1 \to 2^+_1)$ transition strengths. The results indicate that these $B(E2,0^+_1 \to 2^+_1)$ values are much larger than predicted by current state-of-the-art shell model calculations. This discrepancy can be explained if protons from within the Z = 50 shell are contributing to the structure of low-energy excited states in this region. Such contributions imply a breaking of the doubly-magic $^{100}$Sn core in the light Sn isotopes.Comment: 4 pages, 4 figure

Shape and structure of N=Z 64Ge; Electromagnetic transition rates from the application of the Recoil Distance Method to knock-out reaction

Transition rate measurements are reported for the first and the second 2+ states in N=Z 64Ge. The experimental results are in excellent agreement with large-scale Shell Model calculations applying the recently developed GXPF1A interactions. Theoretical analysis suggests that 64Ge is a collective gamma-soft anharmonic vibrator. The measurement was done using the Recoil Distance Method (RDM) and a unique combination of state-of-the-art instruments at the National Superconducting Cyclotron Laboratory (NSCL). States of interest were populated via an intermediate-energy single-neutron knock-out reaction. RDM studies of knock-out and fragmentation reaction products hold the promise of reaching far from stability and providing lifetime information for excited states in a wide range of nuclei

Paper II: Calibration of the Swift ultraviolet/optical telescope

The Ultraviolet/Optical Telescope (UVOT) is one of three instruments onboard the Swift observatory. The photometric calibration has been published, and this paper follows up with details on other aspects of the calibration including a measurement of the point spread function with an assessment of the orbital variation and the effect on photometry. A correction for large scale variations in sensitivity over the field of view is described, as well as a model of the coincidence loss which is used to assess the coincidence correction in extended regions. We have provided a correction for the detector distortion and measured the resulting internal astrometric accuracy of the UVOT, also giving the absolute accuracy with respect to the International Celestial Reference System. We have compiled statistics on the background count rates, and discuss the sources of the background, including instrumental scattered light. In each case we describe any impact on UVOT measurements, whether any correction is applied in the standard pipeline data processing or whether further steps are recommended.Comment: Accepted for publication in MNRAS. 15 pages, 21 figures, 4 table

The First Swift Ultra-Violet/Optical Telescope GRB Afterglow Catalog

We present the first Swift Ultra-Violet/Optical Telescope (UVOT) gamma-ray burst (GRB) afterglow catalog. The catalog contains data from over 64,000 independent UVOT image observations of 229 GRBs first detected by Swift, the High Energy Transient Explorer 2 (HETE2), the INTErnational Gamma-Ray Astrophysics Laboratory (INTEGRAL), and the Interplanetary Network (IPN). The catalog covers GRBs occurring during the period from 2005 Jan 17 to 2007 Jun 16 and includes ~86% of the bursts detected by the Swift Burst Alert Telescope (BAT). The catalog provides detailed burst positional, temporal, and photometric information extracted from each of the UVOT images. Positions for bursts detected at the 3-sigma-level are provided with a nominal accuracy, relative to the USNO-B1 catalog, of ~0.25 arcseconds. Photometry for each burst is given in three UV bands, three optical bands, and a 'white' or open filter. Upper limits for magnitudes are reported for sources detected below 3-sigma. General properties of the burst sample and light curves, including the filter-dependent temporal slopes, are also provided. The majority of the UVOT light curves, for bursts detected at the 3-sigma-level, can be fit by a single power-law, with a median temporal slope (alpha) of 0.96, beginning several hundred seconds after the burst trigger and ending at ~1x10^5 s. The median UVOT v-band (~5500 Angstroms) magnitude at 2000 s for a sample of "well" detected bursts is 18.02. The UVOT flux interpolated to 2000 s after the burst, shows relatively strong correlations with both the prompt Swift BAT fluence, and the Swift X-ray flux at 11 hours after the trigger.Comment: 60 pages, 17 figures, 8 tables, accepted for publication by the Astrophysical Journa

Two-neutron transfer reaction mechanisms in 12^{12}C(6^6He,4^{4}He)14^{14}C using a realistic three-body 6^{6}He model

The reaction mechanisms of the two-neutron transfer reaction $^{12}$C($^6$He,$^4$He) have been studied at 30 MeV at the TRIUMF ISAC-II facility using the SHARC charged-particle detector array. Optical potential parameters have been extracted from the analysis of the elastic scattering angular distribution. The new potential has been applied to the study of the transfer angular distribution to the 2$^+_2$ 8.32 MeV state in $^{14}$C, using a realistic 3-body $^6$He model and advanced shell model calculations for the carbon structure, allowing to calculate the relative contributions of the simultaneous and sequential two-neutron transfer. The reaction model provides a good description of the 30 MeV data set and shows that the simultaneous process is the dominant transfer mechanism. Sensitivity tests of optical potential parameters show that the final results can be considerably affected by the choice of optical potentials. A reanalysis of data measured previously at 18 MeV however, is not as well described by the same reaction model, suggesting that one needs to include higher order effects in the reaction mechanism.Comment: 9 pages, 9 figure

Photometric Calibration of the Swift Ultraviolet/Optical Telescope

We present the photometric calibration of the Swift UltraViolet/Optical Telescope (UVOT) which includes: optimum photometric and background apertures, effective area curves, colour transformations, conversion factors for count rates to flux, and the photometric zero points (which are accurate to better than 4 per cent) for each of the seven UVOT broadband filters. The calibration was performed with observations of standard stars and standard star fields that represent a wide range of spectral star types. The calibration results include the position dependent uniformity, and instrument response over the 1600-8000A operational range. Because the UVOT is a photon counting instrument, we also discuss the effect of coincidence loss on the calibration results. We provide practical guidelines for using the calibration in UVOT data analysis. The results presented here supersede previous calibration results.Comment: Minor improvements after referees report. Accepted for publication in MNRA

A statistical study of gamma-ray burst afterglows measured by the Swift Ultra-violet Optical Telescope

We present the first statistical analysis of 27 UVOT optical/ultra-violet lightcurves of GRB afterglows. We have found, through analysis of the lightcurves in the observer's frame, that a significant fraction rise in the first 500s after the GRB trigger, that all lightcurves decay after 500s, typically as a power-law with a relatively narrow distribution of decay indices, and that the brightest optical afterglows tend to decay the quickest. We find that the rise could either be produced physically by the start of the forward shock, when the jet begins to plough into the external medium, or geometrically where an off-axis observer sees a rising lightcurve as an increasing amount of emission enters the observers line of sight, which occurs as the jet slows. We find that at 99.8% confidence, there is a correlation, in the observed frame, between the apparent magnitude of the lightcurves at 400s and the rate of decay after 500s. However, in the rest frame a Spearman Rank test shows only a weak correlation of low statistical significance between luminosity and decay rate. A correlation should be expected if the afterglows were produced by off-axis jets, suggesting that the jet is viewed from within the half-opening angle theta or within a core of uniform energy density theta_c. We also produced logarithmic luminosity distributions for three rest frame epochs. We find no evidence for bimodality in any of the distributions. Finally, we compare our sample of UVOT lightcurves with the XRT lightcurve canonical model. The range in decay indices seen in UVOT lightcurves at any epoch is most similar to the range in decay of the shallow decay segment of the XRT canonical model. However, in the XRT canonical model there is no indication of the rising behaviour observed in the UVOT lightcurves.Comment: 16 pages, 9 figures, accepted MNRA