Impact of half-wave plate systematics on the measurement of CMB BB-mode polarization

Polarization of the cosmic microwave background (CMB) can help probe the fundamental physics behind cosmic inflation via the measurement of primordial $B$ modes. As this requires exquisite control over instrumental systematics, some next-generation CMB experiments plan to use a rotating half-wave plate (HWP) as polarization modulator. However, the HWP non-idealities, if not properly treated in the analysis, can result in additional systematics. In this paper, we present a simple, semi-analytical end-to-end model to propagate the HWP non-idealities through the macro-steps that make up any CMB experiment (observation of multi-frequency maps, foreground cleaning, and power spectra estimation) and compute the HWP-induced bias on the estimated tensor-to-scalar ratio, $r$. We find that the effective polarization efficiency of the HWP suppresses the polarization signal, leading to an underestimation of $r$. Laboratory measurements of the properties of the HWP can be used to calibrate this effect, but we show how gain calibration of the CMB temperature can also be used to partially mitigate it. On the basis of our findings, we present a set of recommendations for the HWP design that can help maximize the benefits of gain calibration.Comment: 17 pages + appendices and bibliography, 7 figures, 1 table; submitted to JCA

Impact of half-wave plate systematics on the measurement of CMB B-mode polarization

Polarization of the cosmic microwave background (CMB) can help probe the fundamental physics behind cosmic inflation via the measurement of primordial B modes. As this requires exquisite control over instrumental systematics, some next-generation CMB experiments plan to use a rotating half-wave plate (HWP) as polarization modulator. However, the HWP non-idealities, if not properly treated in the analysis, can result in additional systematics. In this paper, we present a simple, semi-analytical end-to-end model to propagate the HWP non-idealities through the macro-steps that make up any CMB experiment (observation of multi-frequency maps, foreground cleaning, and power spectra estimation) and compute the HWP-induced bias on the estimated tensor-to-scalar ratio, r. We find that the effective polarization efficiency of the HWP suppresses the polarization signal, leading to an underestimation of r. Laboratory measurements of the properties of the HWP can be used to calibrate this effect, but we show how gain calibration of the CMB temperature can also be used to partially mitigate it. On the basis of our findings, we present a set of recommendations for the HWP design that can help maximize the benefits of gain calibration

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Prototype design and evaluation of the nine-layer achromatic half-wave plate for the LiteBIRD low frequency telescope

International audienceLiteBIRD is a satellite project to measure the polarization of the CMB with an unprecedented accuracy. LiteBIRD observes all sky for three years at the sun-earth second Lagrange point. The goal of LiteBIRD is to observe the B-mode polarization at large angular scales and to measure the tensor-to-scaler ratio r with an accuracy less than 0.001, exploring the energy scale of the inflation. In order to mitigate the system 1/f noise and systematics, we plan to use continuous rotating half-wave plates (HWPs) as a polarization modulator at each aperture of two telescopes. One of the telescopes, called a low frequency telescope (LFT), covers the frequency range from 34 to 270 GHz, requiring the HWP to have a high modulation efficiency in the wide bandwidth. We employ a Pancharatnam-type achromatic HWP (AHWP) to achieve the broadband coverage. The AHWP consists of nine layer stacked HWPs with the optic axes mutually rotated by the angles optimized for the LFT bandwidth. In this paper, we report our development status of the nine layer AHWP and measurement results on the modulation efficiency and the phase as a function of frequency

Concept design of the LiteBIRD satellite for CMB B-mode polarization

LiteBIRD is a candidate for JAXA's strategic large mission to observe the cosmic microwave background (CMB) polarization over the full sky at large angular scales. It is planned to be launched in the 2020s with an H3 launch vehicle for three years of observations at a Sun-Earth Lagrangian point (L2). The concept design has been studied by researchers from Japan, U.S., Canada and Europe during the ISAS Phase-A1. Large scale measurements of the CMB B-mode polarization are known as the best probe to detect primordial gravitational waves. The goal of LiteBIRD is to measure the tensor-to-scalar ratio (r) with precision of r < 0:001. A 3-year full sky survey will be carried out with a low frequency (34 - 161 GHz) telescope (LFT) and a high frequency (89 - 448 GHz) telescope (HFT), which achieve a sensitivity of 2.5 \u3bcK-arcmin with an angular resolution 30 arcminutes around 100 GHz. The concept design of LiteBIRD system, payload module (PLM), cryo-structure, LFT and verification plan is described in this paper

Concept design of low frequency telescope for CMB B-mode polarization satellite LiteBIRD

LiteBIRD has been selected as JAXA’s strategic large mission in the 2020s, to observe the cosmic microwave background (CMB) B-mode polarization over the full sky at large angular scales. The challenges of LiteBIRD are the wide field-of-view (FoV) and broadband capabilities of millimeter-wave polarization measurements, which are derived from the system requirements. The possible paths of stray light increase with a wider FoV and the far sidelobe knowledge of -56 dB is a challenging optical requirement. A crossed-Dragone configuration was chosen for the low frequency telescope (LFT : 34–161 GHz), one of LiteBIRD’s onboard telescopes. It has a wide field-of-view (18° x 9°) with an aperture of 400 mm in diameter, corresponding to an angular resolution of about 30 arcminutes around 100 GHz. The focal ratio f/3.0 and the crossing angle of the optical axes of 90◦ are chosen after an extensive study of the stray light. The primary and secondary reflectors have rectangular shapes with serrations to reduce the diffraction pattern from the edges of the mirrors. The reflectors and structure are made of aluminum to proportionally contract from warm down to the operating temperature at 5 K. A 1/4 scaled model of the LFT has been developed to validate the wide field-of-view design and to demonstrate the reduced far sidelobes. A polarization modulation unit (PMU), realized with a half-wave plate (HWP) is placed in front of the aperture stop, the entrance pupil of this system. A large focal plane with approximately 1000 AlMn TES detectors and frequency multiplexing SQUID amplifiers is cooled to 100 mK. The lens and sinuous antennas have broadband capability. Performance specifications of the LFT and an outline of the proposed verification plan are presented