| 1. |
- Bergman, A. S., et al.
(författare)
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280 GHz Focal Plane Unit Design and Characterization for the SPIDER-2 Suborbital Polarimeter
- 2018
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Ingår i: Journal of Low Temperature Physics. - : Springer Science and Business Media LLC. - 0022-2291 .- 1573-7357. ; 193:5-6, s. 1075-1084
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Tidskriftsartikel (refereegranskat)abstract
- We describe the construction and characterization of the 280 GHz bolometric focal plane units (FPUs) to be deployed on the second flight of the balloon-borne SPIDER instrument. These FPUs are vital to SPIDER's primary science goal of detecting or placing an upper limit on the amplitude of the primordial gravitational wave signature in the cosmic microwave background (CMB) by constraining the B-mode contamination in the CMB from Galactic dust emission. Each 280 GHz focal plane contains a 16 x 16 grid of corrugated silicon feedhorns coupled to an array of aluminum-manganese transition-edge sensor (TES) bolometers fabricated on 150 mm diameter substrates. In total, the three 280 GHz FPUs contain 1530 polarization-sensitive bolometers (765 spatial pixels) optimized for the low loading environment in flight and read out by time-division SQUID multiplexing. In this paper, we describe the mechanical, thermal, and magnetic shielding architecture of the focal planes and present cryogenic measurements which characterize yield and the uniformity of several bolometer parameters. The assembled FPUs have high yields, with one array as high as 95% including defects from wiring and readout. We demonstrate high uniformity in device parameters, finding the median saturation power for each TES array to be similar to 3 pW at 300 mK with a less than 6% variation across each array at 1 sigma. These focal planes will be deployed alongside the 95 and 150 GHz telescopes in the SPIDER-2 instrument, slated to fly from McMurdo Station in Antarctica in December 2018.
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| 2. |
- Machiela, Mitchell J., et al.
(författare)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 3. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 4. |
- Gualtieri, R., et al.
(författare)
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SPIDER : CMB Polarimetry from the Edge of Space
- 2018
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Ingår i: Journal of Low Temperature Physics. - : Springer Science and Business Media LLC. - 0022-2291 .- 1573-7357. ; 193:5-6, s. 1112-1121
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Tidskriftsartikel (refereegranskat)abstract
- SPIDER is a balloon-borne instrument designed to map the polarization of the millimeter-wave sky at large angular scales. Spider targets the B-mode signature of primordial gravitational waves in the cosmic microwave background (CMB), with a focus on mapping a large sky area with high fidelity at multiple frequencies. SPIDER's first long-duration balloon (LDB) flight in January 2015 deployed a total of 2400 antenna-coupled transition-edge sensors (TESs) at 90 GHz and 150 GHz. In this work we review the design and in-flight performance of the SPIDER instrument, with a particular focus on the measured performance of the detectors and instrument in a space-like loading and radiation environment. SPIDER's second flight in December 2018 will incorporate payload upgrades and new receivers to map the sky at 285 GHz, providing valuable information for cleaning polarized dust emission from CMB maps.
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| 5. |
- Jacobs, Kevin B, et al.
(författare)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Tidskriftsartikel (refereegranskat)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 6. |
- Nagy, J. M., et al.
(författare)
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A New Limit on CMB Circular Polarization from SPIDER
- 2017
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 844:2
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Tidskriftsartikel (refereegranskat)abstract
- We present a new upper limit on cosmic microwave background (CMB) circular polarization from the 2015 flight of SPIDER, a balloon-borne telescope designed to search for B-mode linear polarization from cosmic inflation. Although the level of circular polarization in the CMB is predicted to be very small, experimental limits provide a valuable test of the underlying models. By exploiting the nonzero circular-to-linear polarization coupling of the half-wave plate polarization modulators, data from SPIDER's 2015 Antarctic flight provide a constraint on Stokes V at 95 and 150 GHz in the range 33 < l < 307. No other limits exist over this full range of angular scales, and SPIDER improves on the previous limit by several orders of magnitude, providing 95% C.L. constraints on l (l + 1)C-l(VV) /(2 pi) ranging from 141 to 255 mu K-2 at 150 GHz for a thermal CMB spectrum. As linear CMB polarization experiments become increasingly sensitive, the techniques described in this paper can be applied to obtain even stronger constraints on circular polarization.
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| 7. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 8. |
- Ade, P. A. R., et al.
(författare)
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A Constraint on Primordial B-modes from the First Flight of the Spider Balloon-borne Telescope
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 927:2
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Tidskriftsartikel (refereegranskat)abstract
- We present the first linear polarization measurements from the 2015 long-duration balloon flight of SPIDER, which is an experiment that is designed to map the polarization of the cosmic microwave background (CMB) on degree angular scales. The results from these measurements include maps and angular power spectra from observations of 4.8% of the sky at 95 and 150 GHz, along with the results of internal consistency tests on these data. While the polarized CMB anisotropy from primordial density perturbations is the dominant signal in this region of sky, Galactic dust emission is also detected with high significance. Galactic synchrotron emission is found to be negligible in the SPIDER bands. We employ two independent foreground-removal techniques to explore the sensitivity of the cosmological result to the assumptions made by each. The primary method uses a dust template derived from Planck data to subtract the Galactic dust signal. A second approach, which constitutes a joint analysis of SPIDER and Planck data in the harmonic domain, assumes a modified-blackbody model for the spectral energy distribution of the dust with no constraint on its spatial morphology. Using a likelihood that jointly samples the template amplitude and r parameter space, we derive 95% upper limits on the primordial tensor-to-scalar ratio from Feldman-Cousins and Bayesian constructions, finding r < 0.11 and r < 0.19, respectively. Roughly half the uncertainty in r derives from noise associated with the template subtraction. New data at 280 GHz from SPIDER´s second flight will complement the Planck polarization maps, providing powerful measurements of the polarized Galactic dust emission.
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| 9. |
- Filippini, J. P., et al.
(författare)
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In-Flight Gain Monitoring of SPIDER's Transition-Edge Sensor Arrays
- 2022
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Ingår i: Journal of Low Temperature Physics. - : Springer Science and Business Media LLC. - 0022-2291 .- 1573-7357. ; 209:3-4, s. 649-657
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Tidskriftsartikel (refereegranskat)abstract
- Experiments deploying large arrays of transition-edge sensors (TESs) often require a robust method to monitor gain variations with minimal loss of observing time. We propose a sensitive and non-intrusive method for monitoring variations in TES responsivity using small square waves applied to the TES bias. We construct an estimator for a TES's small-signal power response from its electrical response that is exact in the limit of strong electrothermal feedback. We discuss the application and validation of this method using flight data from SPIDER, a balloon-borne telescope that observes the polarization of the cosmic microwave background with more than 2000 TESs. This method may prove useful for future balloon- and space-based instruments, where observing time and ground control bandwidth are limited.
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| 10. |
- Gambrel, A. E., et al.
(författare)
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The XFaster Power Spectrum and Likelihood Estimator for the Analysis of Cosmic Microwave Background Maps
- 2021
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 922:2
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Tidskriftsartikel (refereegranskat)abstract
- We present the XFaster analysis package, a fast, iterative angular power spectrum estimator based on a diagonal approximation to the quadratic Fisher matrix estimator. It uses Monte Carlo simulations to compute noise biases and filter transfer functions and is thus a hybrid of both Monte Carlo and quadratic estimator methods. In contrast to conventional pseudo-Cℓ–based methods, the algorithm described here requires a minimal number of simulations and does not require them to be precisely representative of the data to estimate accurate covariance matrices for the bandpowers. The formalism works with polarization-sensitive observations and also data sets with identical, partially overlapping, or independent survey regions. The method was first implemented for the analysis of BOOMERanG data and also used as part of the Planck analysis. Here we describe the full, publicly available analysis package, written in Python, as developed for the analysis of data from the 2015 flight of the Spider instrument. The package includes extensions for self-consistently estimating null spectra and estimating fits for Galactic foreground contributions. We show results from the extensive validation of XFaster using simulations and its application to the Spider data set.
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