The BINGO project: VII. Cosmological forecasts from 21 cm intensity mapping

Context. The 21 cm line of neutral hydrogen (HI) opens a new avenue in our exploration of the structure and evolution of the Universe. It provides complementary data to the current large-scale structure (LSS) observations with different systematics, and thus it will be used to improve our understanding of the Icold dark matter (ICDM) model. This will ultimately constrain our cosmological models, attack unresolved tensions, and test our cosmological paradigm. Among several radio cosmological surveys designed to measure this line, BINGO is a single-dish telescope mainly designed to detect baryon acoustic oscillations (BAOs) at low redshifts (0.127 < z < 0.449). Aims. Our goal is to assess the fiducial BINGO setup and its capabilities of constraining the cosmological parameters, and to analyze the effect of different instrument configurations. Methods. We used the 21 cm angular power spectra to extract cosmological information about the HI signal and the Fisher matrix formalism to study BINGO's projected constraining power. Results. We used the Phase 1 fiducial configuration of the BINGO telescope to perform our cosmological forecasts. In addition, we investigated the impact of several instrumental setups, taking into account some instrumental systematics, and different cosmological models. Combining BINGO with Planck temperature and polarization data, the projected constraint improves from a 13% and 25% precision measurement at the 68% confidence level with Planck only to 1% and 3% for the Hubble constant and the dark energy (DE) equation of state (EoS), respectively, within the wCDM model. Assuming a Chevallier- Polarski- Linder (CPL) parameterization, the EoS parameters have standard deviations given by w0 = 0.30 and wa = 1.2, which are improvements on the order of 30% with respect to Planck alone. We also compared BINGO's fiducial forecast with future SKA measurements and found that, although it will not provide competitive constraints on the DE EoS, significant information about HI distribution can be acquired. We can access information about the HI density and bias, obtaining 8.5% and 6% precision, respectively, assuming they vary with redshift at three independent bins. BINGO can also help constrain alternative models, such as interacting dark energy and modified gravity models, improving the cosmological constraints significantly. Conclusions. The fiducial BINGO configuration will be able to extract significant cosmological information from the HI distribution and provide constraints competitive with current and future cosmological surveys. It will also help in understanding the HI physics and systematic effects

The BINGO project: IV. Simulations for mission performance assessment and preliminary component separation steps

Aims. The large-scale distribution of neutral hydrogen (HI) in the Universe is luminous through its 21 cm emission. The goal of the Baryon Acoustic Oscillations from Integrated Neutral Gas Observations (BINGO) radio telescope is to detect baryon acoustic oscillations at radio frequencies through 21 cm intensity mapping (IM). The telescope will span the redshift range 0.127<z<0.449 with an instantaneous field-of-view of 14.75 - 6.0. Methods. In this work we investigate different constructive and operational scenarios of the instrument by generating sky maps as they would be produced by the instrument. In doing this we use a set of end-to-end IM mission simulations. The maps will additionally be used to evaluate the efficiency of a component separation method (GNILC). Results. We have simulated the kind of data that would be produced in a single-dish IM experiment such as BINGO. According to the results obtained, we have optimized the focal plane design of the telescope. In addition, the application of the GNILC method on simulated data shows that it is feasible to extract the cosmological signal across a wide range of multipoles and redshifts. The results are comparable with the standard principal component analysis method

The BINGO Project: III. Optical design and optimization of the focal plane

Context. The Baryon Acoustic Oscillations from Integrated Neutral Gas Observations (BINGO) telescope was designed to measure the fluctuations of the 21 cm radiation arising from the hyperfine transition of neutral hydrogen. It is also aimed at measuring the baryon acoustic oscillations (BAO) from such fluctuations, thereby serving as a pathfinder to future, deeper intensity mapping surveys. The requirements for the Phase 1 of the projects consider a large reflector system (two 40 m-class dishes in a crossed-Dragone configuration) illuminating a focal plane with 28 horns to measure the sky, with two circular polarizations in a drift scan mode to produce measurements of the radiation in intensity (I) as well as the circular (V) polarization. Aims. In this paper, we present the optical design for the instrument. We describe the optical arrangement of the horns in the focal plane to produce a homogeneous and well-sampled map after the end of Phase 1, as well as the intensity and polarization properties of the beams. Our analysis provides an optimal model for the location of the horns in the focal plane, producing a homogeneous and Nyquist-sampled map after the nominal survey time. Methods. We used the GRASP package to model the focal plane arrangement and performed several optimization tasks to arrive at the current configuration, including an estimation of the sidelobes corresponding to the diffraction patterns of the two mirrors. The final model for the focal plane was defined through a combination of neural network and other direct optimization methods. Results. We arrived at an optimal configuration for the optical system that includes the focal plane positioning and the beam behavior of the instrument. We present an estimate of the expected sidelobes both for intensity and polarization, as well as the effect of band averaging on the final sidelobes, as well as an estimation of the cross-polarization leakage for the final configuration. Conclusions. We conclude that the chosen optical design meets the requirements for the project in terms of polarization purity and area coverage as well as a homogeneity of coverage so that BINGO can perform a successful BAO experiment. We further conclude that the requirements on the placement and rms error on the mirrors are also achievable so that a successful experiment can be conducted

The BINGO project: II. Instrument description

Context. The measurement of diffuse 21-cm radiation from the hyperfine transition of neutral hydrogen (Hi signal) in different redshifts is an important tool for modern cosmology. However, detecting this faint signal with non-cryogenic receivers in single-dish telescopes is a challenging task. The BINGO (Baryon Acoustic Oscillations from Integrated Neutral Gas Observations) radio telescope is an instrument designed to detect baryonic acoustic oscillations (BAOs) in the cosmological Hi signal, in the redshift interval 0:127 ≤ z ≤ 0:449. Aims. This paper describes the BINGO radio telescope, including the current status of the optics, receiver, observational strategy, calibration, and the site. Methods. BINGO has been carefully designed to minimize systematics, being a transit instrument with no moving dishes and 28 horns operating in the frequency range 980 ≤ v ≤ 1260 MHz. Comprehensive laboratory tests were conducted for many of the BINGO subsystems and the prototypes of the receiver chain, horn, polarizer, magic tees, and transitions have been successfully tested between 2018-2020. The survey was designed to cover ∼13% of the sky, with the primary mirror pointing at declination δ = -15°. The telescope will see an instantaneous declination strip of 14:75. Results. The results of the prototype tests closely meet those obtained during the modeling process, suggesting BINGO will perform according to our expectations. After one year of observations with a 60% duty cycle and 28 horns, BINGO should achieve an expected sensitivity of 102μK per 9.33MHz frequency channel, one polarization, and be able to measure the Hi power spectrum in a competitive time frame

The BINGO project: I. Baryon acoustic oscillations from integrated neutral gas observations

Context. Observations of the redshifted 21-cm line of neutral hydrogen (HI) are a new and powerful window of observation that offers us the possibility to map the spatial distribution of cosmic HI and learn about cosmology. Baryon Acoustic Oscillations from Integrated Neutral Gas Observations (BINGO) is a new unique radio telescope designed to be one of the first to probe baryon acoustic oscillations (BAO) at radio frequencies. Aims. BINGO has two science goals: cosmology and astrophysics. Cosmology is the main science goal and the driver for BINGO's design and strategy. The key of BINGO is to detect the low redshift BAO to put strong constraints on the dark sector models and test the ICDM (cold dark matter) model. Given the versatility of the BINGO telescope, a secondary goal is astrophysics, where BINGO can help discover and study fast radio bursts (FRB) and other transients, as well as study Galactic and extragalactic science. In this paper, we introduce the latest progress of the BINGO project, its science goals, describing the scientific potential of the project for each goal and the new developments obtained by the collaboration. Methods. BINGO is a single dish transit telescope that will measure the BAO at low-z by making a 3D map of the HI distribution through the technique of intensity mapping over a large area of the sky. In order to achieve the project's goals, a science strategy and a specific pipeline for cleaning and analyzing the produced maps and mock maps was developed by the BINGO team, which we generally summarize here. Results. We introduce the BINGO project and its science goals and give a general summary of recent developments in construction, science potential, and pipeline development obtained by the BINGO Collaboration in the past few years. We show that BINGO will be able to obtain competitive constraints for the dark sector. It also has the potential to discover several FRBs in the southern hemisphere. The capacity of BINGO in obtaining information from 21-cm is also tested in the pipeline introduced here. Following these developments, the construction and observational strategies of BINGO have been defined. Conclusions. There is still no measurement of the BAO in radio, and studying cosmology in this new window of observations is one of the most promising advances in the field. The BINGO project is a radio telescope that has the goal to be one of the first to perform this measurement and it is currently being built in the northeast of Brazil. This paper is the first of a series of papers that describe in detail each part of the development of the BINGO project

Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed

Background: Single nucleotide polymorphisms (SNPs) are an important class of genetic marker for target gene mapping. As of yet, there is no rapid and effective method to identify SNPs linked with agronomic traits in rapeseed and other crop species. Methodology/Principal Findings: We demonstrate a novel method for identifying SNP markers in rapeseed by deep sequencing a representative library and performing bulk segregant analysis. With this method, SNPs associated with rapeseed pod shatter-resistance were discovered. Firstly, a reduced representation of the rapeseed genome was used. Genomic fragments ranging from 450–550 bp were prepared from the susceptible bulk (ten F2 plants with the silique shattering resistance index, SSRI,0.10) and the resistance bulk (ten F2 plants with SSRI.0.90), and also Solexa sequencingproduced 90 bp reads. Approximately 50 million of these sequence reads were assembled into contigs to a depth of 20-fold coverage. Secondly, 60,396 ‘simple SNPs ’ were identified, and the statistical significance was evaluated using Fisher’s exact test. There were 70 associated SNPs whose –log10p value over 16 were selected to be further analyzed. The distribution of these SNPs appeared a tight cluster, which consisted of 14 associated SNPs within a 396 kb region on chromosome A09. Our evidence indicates that this region contains a major quantitative trait locus (QTL). Finally, two associated SNPs from this region were mapped on a major QTL region

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

<p>Abstract</p> <p>Background</p> <p>To enhance capabilities for genomic analyses in rainbow trout, such as genomic selection, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be identified. Expressed Sequence Tags (ESTs) have been used for single nucleotide polymorphism (SNP) discovery in salmonids. In those strategies, the salmonid semi-tetraploid genomes often led to assemblies of paralogous sequences and therefore resulted in a high rate of false positive SNP identification. Sequencing genomic DNA using primers identified from ESTs proved to be an effective but time consuming methodology of SNP identification in rainbow trout, therefore not suitable for high throughput SNP discovery. In this study, we employed a high-throughput strategy that used pyrosequencing technology to generate data from a reduced representation library constructed with genomic DNA pooled from 96 unrelated rainbow trout that represent the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock population.</p> <p>Results</p> <p>The reduced representation library consisted of 440 bp fragments resulting from complete digestion with the restriction enzyme <it>Hae</it>III; sequencing produced 2,000,000 reads providing an average 6 fold coverage of the estimated 150,000 unique genomic restriction fragments (300,000 fragment ends). Three independent data analyses identified 22,022 to 47,128 putative SNPs on 13,140 to 24,627 independent contigs. A set of 384 putative SNPs, randomly selected from the sets produced by the three analyses were genotyped on individual fish to determine the validation rate of putative SNPs among analyses, distinguish apparent SNPs that actually represent paralogous loci in the tetraploid genome, examine Mendelian segregation, and place the validated SNPs on the rainbow trout linkage map. Approximately 48% (183) of the putative SNPs were validated; 167 markers were successfully incorporated into the rainbow trout linkage map. In addition, 2% of the sequences from the validated markers were associated with rainbow trout transcripts.</p> <p>Conclusion</p> <p>The use of reduced representation libraries and pyrosequencing technology proved to be an effective strategy for the discovery of a high number of putative SNPs in rainbow trout; however, modifications to the technique to decrease the false discovery rate resulting from the evolutionary recent genome duplication would be desirable.</p

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

<p>Abstract</p> <p>Background</p> <p>High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera.</p> <p>Results</p> <p>We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of <it>Eucalyptus </it>from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for <it>E. grandis</it>. A systematic assessment of <it>in silico </it>SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous <it>in silico </it>constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species.</p> <p>SNP reliability was high across nine <it>Eucalyptus </it>species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased.</p> <p>Conclusions</p> <p>This study indicates that the GGGT performs well both within and across species of <it>Eucalyptus </it>notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across multiple <it>Eucalyptus </it>species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in <it>Eucalyptus</it>.</p