Assessing the Performance of the Haplotype Block Model of Linkage Disequilibrium

Several recent studies have suggested that linkage disequilibrium (LD) in the human genome has a fundamentally “blocklike” structure. However, thus far there has been little formal assessment of how well the haplotype block model captures the underlying structure of LD. Here we propose quantitative criteria for assessing how blocklike LD is and apply these criteria to both real and simulated data. Analyses of several large data sets indicate that real data show a partial fit to the haplotype block model; some regions conform quite well, whereas others do not. Some improvement could be obtained by genotyping higher marker densities but not by increasing the number of samples. Nonetheless, although the real data are only moderately blocklike, our simulations indicate that, under a model of uniform recombination, the structure of LD would actually fit the block model much less well. Simulations of a model in which much of the recombination occurs in narrow hotspots provide a much better fit to the observed patterns of LD, suggesting that there is extensive fine-scale variation in recombination rates across the human genome

Object detection and rangefinding with quantum states using simple detection

In a noisy environment with weak single levels, quantum illumination can outperform classical illumination in determining the presence and range of a target object even in the limit of sub-optimal measurements based on non-simultaneous, phase-insensitive coincidence counts. Motivated by realistic experimental protocols, we present a theoretical framework for analysing coincident multi-shot data with simple detectors. This approach allows for the often-overlooked non-coincidence data to be included, as well as providing a calibration-free threshold for inferring the presence and range of an object, enabling a fair comparison between different detection regimes. Our results quantify the advantage of quantum over classical illumination when performing target discrimination in a noisy thermal environment, including estimating the number of shots required to detect a target with a given confidence level

Measuring the cosmological 21-cm dipole with 21-cm global experiments

A measurement of the 21-cm global signal would be a revealing probe of the Dark Ages, the era of first star formation, and the Epoch of Reionization. It has remained elusive owing to bright galactic and extra-galactic foreground contaminants, coupled with instrumental noise, ionospheric effects, and beam chromaticity. The simultaneous detection of a consistent 21-cm dipole signal alongside the 21-cm global signal would provide confidence in a claimed detection. We use simulated data to investigate the possibility of using drift-scan dipole antenna experiments to achieve a detection of both monopole and dipole. We find that at least two antennae located at different latitudes are required to localise the dipole. In the absence of foregrounds, a total integration time of $\sim 10^4$ hours is required to detect the dipole. With contamination by simple foregrounds, we find that the integration time required increases to $\sim 10^5$ hours. We show that the extraction of the 21-cm dipole from more realistic foregrounds requires a more sophisticated foreground modelling approach. Finally, we motivate a global network of dipole antennae that could reasonably detect the dipole in $\sim 10^3$ hours of integration time.Comment: 12 pages, 15 figure

Coherence in a cold atom photon transistor

Recent experiments have realized an all-optical photon transistor using a cold atomic gas. This approach relies on electromagnetically induced transparency (EIT) in conjunction with the strong interaction among atoms excited to high-lying Rydberg states. The transistor is gated via a so-called Rydberg spinwave, in which a single Rydberg excitation is coherently shared by the whole ensemble. In its absence the incoming photon passes through the atomic ensemble by virtue of EIT while in its presence the photon is scattered rendering the atomic gas opaque. An important current challenge is to preserve the coherence of the Rydberg spinwave during the operation of the transistor, which would enable for example its coherent optical read-out and its further processing in quantum circuits. With a combined field theoretical and quantum jump approach and by employing a simple model description we investigate systematically and comprehensively how the coherence of the Rydberg spinwave is affected by photon scattering. With large-scale numerical calculations we show how coherence becomes increasingly protected with growing interatomic interaction strength. For the strongly interacting limit we derive analytical expressions for the spinwave fidelity as a function of the optical depth and bandwidth of the incoming photon

Demonstration of quantum-enhanced rangefinding robust against classical jamming

In this paper we demonstrate operation of a quantum-enhanced lidar based on a continuously pumped photon pair source combined with simple detection in regimes with over 5 orders of magnitude separation between signal and background levels and target reflectivity down to -52 dB. We characterise the performance of our detector using a log-likelihood analysis framework, and crucially demonstrate the robustness of our system to fast and slow classical jamming, introducing a new protocol to implement dynamic background tracking to eliminate the impact of slow background changes whilst maintaining immunity to high frequency fluctuations. Finally, we extend this system to the regime of rangefinding in the presence of classical jamming to locate a target with an 11 cm spatial resolution limited only by the detector jitter. These results demonstrate the advantage of exploiting quantum correlations for lidar applications, providing a clear route to implementation of this system in real-world scenarios

Sub-kilohertz excitation lasers for quantum information processing with Rydberg atoms

Quantum information processing using atomic qubits requires narrow linewidth lasers with long-term stability for high fidelity coherent manipulation of Rydberg states. In this paper, we report on the construction and characterization of three continuous-wave (CW) narrow linewidth lasers stabilized simultaneously to an ultra- high finesse Fabry-Perot cavity made of ultra-low expansion (ULE) glass, with a tunable offset-lock frequency. One laser operates at 852 nm while the two locked lasers at 1018 nm are frequency doubled to 509 nm for excitation of 133Cs atoms to Rydberg states. The optical beatnote at 509 nm is measured to be 260(5) Hz. We present measurements of the offset between the atomic and cavity resonant frequencies using electromagnetically induced transparency (EIT) for high-resolution spectroscopy on a cold atom cloud. The long-term stability is determined from repeated spectra over a period of 20 days yielding a linear frequency drift of ∼ 1 Hz/s

Theoretical comparison of quantum and classical illumination for simple detection-based LIDAR

Use of non-classical light in a quantum illumination scheme provides an advantage over classical illumination when used for LIDAR with a simple and realistic detection scheme based on Geiger-mode single photon detectors. Here we provide an analysis that accounts for the additional information gained when detectors do not fire that is typically neglected and show an improvement in performance of quantum illumination. Moreover, we provide a theoretical framework quantifying performance of both quantum and classical illumination for simple target detection, showing parameters for which a quantum advantage exists. Knowledge of the regimes that demonstrate a quantum advantage will inform where possible practical quantum LIDAR utilising non-classical light could be realised

A practical compact source of heralded single photons for a simple detection LIDAR

Optical quantum technologies such as quantum sensing, quantum cryptography and quantum computation all utilize properties of non-classical light, such as precise photon-number and entangled photon-pair states, to surpass technologies based on the classical light. A common route for obtaining heralded single photons is spontaneous four-wave mixing in optical fibers, allowing for a well-defined spatial mode, for high efficiency integration into optical fiber networks. These fibers are typically pumped using large, commercial, pulsed lasers requiring high-power (~10 W) pump lasers and are limited to ~MHz repetition rate. Here we propose a cost- efficient, compact and mobile alternative. Photon pairs at 660 nm and 960 nm will be created using four-wave mixing in commercial birefringent optical fiber, pumped using transform limited picosecond pulses with GHz repetition rates derived from a 785 nm CW laser diode using cavity-enhanced optical frequency comb generation. The pulses are predicted to have average power of 275 mW, a peak power of >40 W, and predicted photon yield of >2000 pairs detected per second. This design will be later utilized to implement a quantum illumination scheme based on a coincidence count between idler and signal photons -- instead of joint measurement between signal and idler. This will allow for quantum advantage over classic LIDAR without the requirement for maintaining an interferometric stability in free space

Using Population Mixtures to Optimize the Utility of Genomic Databases: Linkage Disequilibrium and Association Study Design in India

When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis – such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65949/1/j.1469-1809.2008.00457.x.pd

Gastric Helicobacter infection induces iron deficiency in the INS-GAS mouse

There is increasing evidence from clinical and population studies for a role of H. pylori infection in the aetiology of iron deficiency. Rodent models of Helicobacter infection are helpful for investigating any causal links and mechanisms of iron deficiency in the host. The aim of this study was to investigate the effects of gastric Helicobacter infection on iron deficiency and host iron metabolism/transport gene expression in hypergastrinemic INS-GAS mice. INS-GAS mice were infected with Helicobacter felis for 3, 6 and 9 months. At post mortem, blood was taken for assessment of iron status and gastric mucosa for pathology, immunohistology and analysis of gene expression. Chronic Helicobacter infection of INS- GAS mice resulted in decreased serum iron, transferrin saturation and hypoferritinemia and increased Total iron binding capacity (TIBC). Decreased serum iron concentrations were associated with a concomitant reduction in the number of parietal cells, strengthening the association between hypochlorhydria and gastric Helicobacter-induced iron deficiency. Infection with H. felis for nine months was associated with decreased gastric expression of iron metabolism regulators hepcidin, Bmp4 and Bmp6 but increased expression of Ferroportin 1, the iron efflux protein, iron absorption genes such as Divalent metal transporter 1, Transferrin receptor 1 and also Lcn2 a siderophore-binding protein. The INS-GAS mouse is therefore a useful model for studying Helicobacter-induced iron deficiency. Furthermore, the marked changes in expression of gastric iron transporters following Helicobacter infection may be relevant to the more rapid development of carcinogenesis in the Helicobacter infected INS-GAS model