915 research outputs found
Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods
The National Institute of Standards and Technology (NIST) Standard Reference Materials 2373 is a set of genomic DNA samples prepared from five breast cancer cell lines with certified values for the ratio of the HER2 gene copy number to the copy numbers of reference genes determined by real-time quantitative PCR and digital PCR. Targeted-amplicon, whole-exome, and whole-genome sequencing measurements were used with the reference material to compare the performance of both the laboratory steps and the bioinformatic approaches of the different methods using a range of amplification ratios. Although good reproducibility was observed in each next-generation sequencing method, slightly different HER2 copy numbers associated with platform-specific biases were obtained. This study clearly demonstrates the value of Standard Reference Materials 2373 as reference material and as a calibrator for evaluating assay performance as well as for increasing confidence in reporting HER2 amplification for clinical applications
The discovery of an M4+T8.5 binary system
The original article can be found at: http://www3.interscience.wiley.com Copyright Blackwell Publishing / Royal Astronomical Society. DOI: 10.1111/j.1365-2966.2009.14620.xWe report the discovery of a T8.5 dwarf, which is a companion to the M4 dwarf Wolf 940. [Please see original online abstract for complete version with correct notation]Peer reviewe
Nucleon-Gold Collisions at 200 AGeV Using Tagged d+Au Interactions in PHOBOS
Forward calorimetry in the PHOBOS detector has been used to study charged
hadron production in d+Au, p+Au and n+Au collisions at sqrt(s_nn) = 200 GeV.
The forward proton calorimeter detectors are described and a procedure for
determining collision centrality with these detectors is detailed. The
deposition of energy by deuteron spectator nucleons in the forward calorimeters
is used to identify p+Au and n+Au collisions in the data. A weighted
combination of the yield of p+Au and n+Au is constructed to build a reference
for Au+Au collisions that better matches the isospin composition of the gold
nucleus. The p_T and centrality dependence of the yield of this improved
reference system is found to match that of d+Au. The shape of the charged
particle transverse momentum distribution is observed to extrapolate smoothly
from pbar+p to central d+Au as a function of the charged particle
pseudorapidity density. The asymmetry of positively- and negatively-charged
hadron production in p+Au is compared to that of n+Au. No significant asymmetry
is observed at mid-rapidity. These studies augment recent results from
experiments at the LHC and RHIC facilities to give a more complete description
of particle production in p+A and d+A collisions, essential for the
understanding the medium produced in high energy nucleus-nucleus collisions.Comment: 17 pages, 18 figure
Germline whole exome sequencing and large-scale replication identifies FANCM as a likely high grade serous ovarian cancer susceptibility gene.
We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one HGSOC case. Gene-set enrichment analysis showed enrichment for genes involved in DNA repair (p = 1.8×10-3). Twelve DNA repair genes - APEX1, APLF, ATX, EME1, FANCL, FANCM, MAD2L2, PARP2, PARP3, POLN, RAD54L and SMUG1 - were prioritized for targeted sequencing in up to 3,107 HGSOC cases, 1,491 cases of other epithelial ovarian cancer (EOC) subtypes and 3,368 unaffected controls of European origin. We estimated mutation prevalence for each gene and tested for associations with disease risk. Mutations were identified in both cases and controls in all genes except MAD2L2, where we found no evidence of mutations in controls. In FANCM we observed a higher mutation frequency in HGSOC cases compared to controls (29/3,107 cases, 0.96 percent; 13/3,368 controls, 0.38 percent; P=0.008) with little evidence for association with other subtypes (6/1,491, 0.40 percent; P=0.82). The relative risk of HGSOC associated with deleterious FANCM mutations was estimated to be 2.5 (95% CI 1.3 - 5.0; P=0.006). In summary, whole exome sequencing of EOC cases with large-scale replication in case-control studies has identified FANCM as a likely novel susceptibility gene for HGSOC, with mutations associated with a moderate increase in risk. These data may have clinical implications for risk prediction and prevention approaches for high-grade serous ovarian cancer in the future and a significant impact on reducing disease mortality
Business excellence model: an overarching framework for managing and aligning multiple organisational improvement initiatives
Business Excellence Models (BEMs) are used by organisations to assess and improve their work practices and performance. The authors’ research identified that there are currently 94 national Quality/Business Excellence (BE) Awards used in 83 countries. While the use of BEMs is widespread, it was identified that many organisations wanted guidance in terms of which improvement initiatives to implement to assist them on their BE journey. This paper discusses how the BEM can be used as an overarching framework for managing and/or aligning multiple improvement initiatives within the organisation. A new model is developed showing some of the main improvement initiatives that can be adopted towards achieving BE, which are arranged according to the common enabling criteria of BEMs and levels of BE maturity. This proposed model can be used as a pathway/roadmap to BE. In developing this model, a literature review, a document review and several semi-structured interviews were conducted. Sixteen quality and BE experts were interviewed in New Zealand, Singapore, and Malaysia
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Nightside clouds and disequilibrium chemistry on the hot Jupiter WASP-43b
Hot Jupiters are among the best-studied exoplanets, but it is still poorly understood how their chemical composition and cloud properties vary with longitude. Theoretical models predict that clouds may condense on the nightside and that molecular abundances can be driven out of equilibrium by zonal winds. Here we report a phase-resolved emission spectrum of the hot Jupiter WASP-43b measured from 5 μm to 12 μm with the JWST’s Mid-Infrared Instrument. The spectra reveal a large day–night temperature contrast (with average brightness temperatures of 1,524 ± 35 K and 863 ± 23 K, respectively) and evidence for water absorption at all orbital phases. Comparisons with three-dimensional atmospheric models show that both the phase-curve shape and emission spectra strongly suggest the presence of nightside clouds that become optically thick to thermal emission at pressures greater than ~100 mbar. The dayside is consistent with a cloudless atmosphere above the mid-infrared photosphere. Contrary to expectations from equilibrium chemistry but consistent with disequilibrium kinetics models, methane is not detected on the nightside (2σ upper limit of 1–6 ppm, depending on model assumptions). Our results provide strong evidence that the atmosphere of WASP-43b is shaped by disequilibrium processes and provide new insights into the properties of the planet’s nightside clouds. However, the remaining discrepancies between our observations and our predictive atmospheric models emphasize the importance of further exploring the effects of clouds and disequilibrium chemistry in numerical models.Peer reviewe
Nightside clouds and disequilibrium chemistry on the hot Jupiter WASP-43b
Hot Jupiters are among the best-studied exoplanets, but it is still poorly understood how their chemical composition and cloud properties vary with longitude. Theoretical models predict that clouds may condense on the nightside and that molecular abundances can be driven out of equilibrium by zonal winds. Here we report a phase-resolved emission spectrum of the hot Jupiter WASP-43b measured from 5-12 μm with JWST's Mid-Infrared Instrument (MIRI). The spectra reveal a large day-night temperature contrast (with average brightness temperatures of 1524±35 and 863±23 Kelvin, respectively) and evidence for water absorption at all orbital phases. Comparisons with three-dimensional atmospheric models show that both the phase curve shape and emission spectra strongly suggest the presence of nightside clouds which become optically thick to thermal emission at pressures greater than ~100 mbar. The dayside is consistent with a cloudless atmosphere above the mid-infrared photosphere. Contrary to expectations from equilibrium chemistry but consistent with disequilibrium kinetics models, methane is not detected on the nightside (2σ upper limit of 1-6 parts per million, depending on model assumptions)
Nightside clouds and disequilibrium chemistry on the hot Jupiter WASP-43b
Hot Jupiters are among the best-studied exoplanets, but it is still poorly
understood how their chemical composition and cloud properties vary with
longitude. Theoretical models predict that clouds may condense on the nightside
and that molecular abundances can be driven out of equilibrium by zonal winds.
Here we report a phase-resolved emission spectrum of the hot Jupiter WASP-43b
measured from 5-12 m with JWST's Mid-Infrared Instrument (MIRI). The
spectra reveal a large day-night temperature contrast (with average brightness
temperatures of 152435 and 86323 Kelvin, respectively) and evidence
for water absorption at all orbital phases. Comparisons with three-dimensional
atmospheric models show that both the phase curve shape and emission spectra
strongly suggest the presence of nightside clouds which become optically thick
to thermal emission at pressures greater than ~100 mbar. The dayside is
consistent with a cloudless atmosphere above the mid-infrared photosphere.
Contrary to expectations from equilibrium chemistry but consistent with
disequilibrium kinetics models, methane is not detected on the nightside
(2 upper limit of 1-6 parts per million, depending on model
assumptions).Comment: 61 pages, 13 figures, 4 tables. This preprint has been submitted to
and accepted in principle for publication in Nature Astronomy without
significant change
Photochemically-produced SO in the atmosphere of WASP-39b
Photochemistry is a fundamental process of planetary atmospheres that
regulates the atmospheric composition and stability. However, no unambiguous
photochemical products have been detected in exoplanet atmospheres to date.
Recent observations from the JWST Transiting Exoplanet Early Release Science
Program found a spectral absorption feature at 4.05 m arising from SO
in the atmosphere of WASP-39b. WASP-39b is a 1.27-Jupiter-radii, Saturn-mass
(0.28 M) gas giant exoplanet orbiting a Sun-like star with an equilibrium
temperature of 1100 K. The most plausible way of generating SO in
such an atmosphere is through photochemical processes. Here we show that the
SO distribution computed by a suite of photochemical models robustly
explains the 4.05 m spectral feature identified by JWST transmission
observations with NIRSpec PRISM (2.7) and G395H (4.5). SO
is produced by successive oxidation of sulphur radicals freed when hydrogen
sulphide (HS) is destroyed. The sensitivity of the SO feature to the
enrichment of the atmosphere by heavy elements (metallicity) suggests that it
can be used as a tracer of atmospheric properties, with WASP-39b exhibiting an
inferred metallicity of 10 solar. We further point out that
SO also shows observable features at ultraviolet and thermal infrared
wavelengths not available from the existing observations.Comment: 39 pages, 14 figures, accepted to be published in Natur
Photochemically produced SO2 in the atmosphere of WASP-39b
Photochemistry is a fundamental process of planetary atmospheres that regulates the atmospheric composition and stability1. However, no unambiguous photochemical products have been detected in exoplanet atmospheres so far. Recent observations from the JWST Transiting Exoplanet Community Early Release Science Program2,3 found a spectral absorption feature at 4.05 μm arising from sulfur dioxide (SO2) in the atmosphere of WASP-39b. WASP-39b is a 1.27-Jupiter-radii, Saturn-mass (0.28 MJ) gas giant exoplanet orbiting a Sun-like star with an equilibrium temperature of around 1,100 K (ref. 4). The most plausible way of generating SO2 in such an atmosphere is through photochemical processes5,6. Here we show that the SO2 distribution computed by a suite of photochemical models robustly explains the 4.05-μm spectral feature identified by JWST transmission observations7 with NIRSpec PRISM (2.7σ)8 and G395H (4.5σ)9. SO2 is produced by successive oxidation of sulfur radicals freed when hydrogen sulfide (H2S) is destroyed. The sensitivity of the SO2 feature to the enrichment of the atmosphere by heavy elements (metallicity) suggests that it can be used as a tracer of atmospheric properties, with WASP-39b exhibiting an inferred metallicity of about 10× solar. We further point out that SO2 also shows observable features at ultraviolet and thermal infrared wavelengths not available from the existing observations
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