PathGPS: discover shared genetic architecture using GWAS summary data.

The increasing availability and scale of biobanks and "omic" datasets bring new horizons for understanding biological mechanisms. PathGPS is an exploratory data analysis tool to discover genetic architectures using Genome Wide Association Studies (GWAS) summary data. PathGPS is based on a linear structural equation model where traits are regulated by both genetic and environmental pathways. PathGPS decouples the genetic and environmental components by contrasting the GWAS associations of "signal" genes with those of "noise" genes. From the estimated genetic component, PathGPS then extracts genetic pathways via principal component and factor analysis, leveraging the low-rank and sparse properties. In addition, we provide a bootstrap aggregating ("bagging") algorithm to improve stability under data perturbation and hyperparameter tuning. When applied to a metabolomics dataset and the UK Biobank, PathGPS confirms several known gene-trait clusters and suggests multiple new hypotheses for future investigations.

Causal inference for heritable phenotypic risk factors using heterogeneous genetic instruments.

Over a decade of genome-wide association studies (GWAS) have led to the finding of extreme polygenicity of complex traits. The phenomenon that "all genes affect every complex trait" complicates Mendelian Randomization (MR) studies, where natural genetic variations are used as instruments to infer the causal effect of heritable risk factors. We reexamine the assumptions of existing MR methods and show how they need to be clarified to allow for pervasive horizontal pleiotropy and heterogeneous effect sizes. We propose a comprehensive framework GRAPPLE to analyze the causal effect of target risk factors with heterogeneous genetic instruments and identify possible pleiotropic patterns from data. By using GWAS summary statistics, GRAPPLE can efficiently use both strong and weak genetic instruments, detect the existence of multiple pleiotropic pathways, determine the causal direction and perform multivariable MR to adjust for confounding risk factors. With GRAPPLE, we analyze the effect of blood lipids, body mass index, and systolic blood pressure on 25 disease outcomes, gaining new information on their causal relationships and potential pleiotropic pathways involved.

Polarizer-free measurement of the full Stokes vector using a fiber-coupled superconducting nanowire single photon detector with a polarization extinction ratio of ∼2.

The characterization and manipulation of polarization state at single photon level are of great importance in research fields such as quantum information processing and quantum key distribution, where photons are normally delivered using single mode optical fibers. To date, the demonstrated polarimetry measurement techniques based on a superconducting nanowire single photon detector (SNSPD) require the SNSPD to be either highly sensitive or highly insensitive to the photon's polarization state, therefore placing an unavoidable challenge on the SNSPD's design and fabrication processes. In this article, we present the development of an alternative polarimetry measurement technique, of which the stringent requirement on the SNSPD's polarization sensitivity is removed. We validate the proposed technique by a rigorous theoretical analysis and comparisons of the experimental results obtained using a fiber-coupled SNSPD with a polarization extinction ratio of ∼2 to that obtained using other well-established known methods. Based on the full Stokes data measured by the proposed technique, we also demonstrate that at the single photon level (∼ -100 dBm), the polarization state of the photon delivered to the superconducting nanowire facet plane can be controlled at will using a further developed algorithm. Note that other than the fiber-coupled SNSPD, the only component involved is a quarter-wave plate (no external polarizer is necessary), which when aligned well has a paid insertion loss less than 0.5 dB.

Image distortion by ambiguous multiple-photon detections in a superconducting nanowire single-photon imager and the correction method.

Scaling up superconducting nanowire single-photon detectors (SNSPDs) into a large array for imaging applications is the current pursuit. Although various readout architectures have been proposed, they cannot resolve multiple-photon detections (MPDs) currently, which limits the operation of the SNSPD arrays at high photon flux. In this study, we focused on the readout ambiguity of a superconducting nanowire single-photon imager applying time-of-flight multiplexing readout. The results showed that image distortion depended on both the incident photon flux and the imaging object. By extracting multiple-photon detections on idle pixels, which were virtual because of the incorrect mapping from the ambiguous readout, a correction method was proposed. An improvement factor of 1.3~9.3 at a photon flux of µ = 5 photon/pulse was obtained, which indicated that joint development of the pixel design and restoration algorithm could compensate for the readout ambiguity and increase the dynamic range.

Molecular evolution of the hemoglobin gene family across vertebrates.

Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, ß-globin genes of jawed vertebrates encode tetrameric ((α2ß2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the ß-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.

Probabilistic Energy-to-Amplitude Mapping in a Tapered Superconducting Nanowire Single-Photon Detector.

A spectrum-resolved photon detector is crucial for cutting-edge quantum optics, astronomical observation, and spectroscopic sensing. However, such an ability is rarely obtained because a direct linear conversion from weak single-photon energy to a readable electrical signal above the noise level without causing an avalanche is challenging. Here, we overcame these difficulties by building a probabilistic energy-to-amplitude mapping in a tapered superconducting nanowire single-photon detector and combining a computational reconstruction to obtain equivalent spectral resolving capacity. Distinguished dependence of pulse amplitude distributions on varied input spectra has been observed experimentally. As the energy-to-amplitude mapping is probabilistic, statistical measurements are required. By collecting around a few hundred photons, we have demonstrated wavelength perception over a wide spectral range from 600 to 1700 nm with a resolution of 100 nm. These findings represent a new approach to designing spectrum-sensitive SNSPDs for low-light spectroscopic applications.

Bimetal Substitution Enabled Energetic Polyanion Cathode for Sodium-Ion Batteries.

The practical application of Na-superionic conductor structured materials is hindered by limited energy density and structure damage upon activating the third Na+. We propose a bimetal substitution strategy with cheaper Fe and Ni elements for costive vanadium in the polyanion to improve both ionic and electronic conductivities, and a single two-phase reaction during Na+ intercalation/deintercalation and much reduced Na+ diffusion barrier are uncovered by ex-situ X-ray diffraction and density functional theory calculations. Thus, the obtained cathode, Na3Fe0.8VNi0.2(PO4)3, shows excellent electrochemical performances including high specific capacity (102.2 mAh g-1 at 0.1C), excellent rate capability (79.3 mAh g-1 at 20C), cycling stability (84.6% of capacity retention over 1400 cycles at 20C), low-temperature performance (89.7 mAh g-1 at 2C and -10 °C), and structure stability in an extended voltage window for the third Na+ utilization. A competitive energy density of ≈287 Wh kg-1 for full batteries based on cathode and anode materials is also confirmed.

Mendelian randomisation with coarsened exposures.

A key assumption in Mendelian randomisation is that the relationship between the genetic instruments and the outcome is fully mediated by the exposure, known as the exclusion restriction assumption. However, in epidemiological studies, the exposure is often a coarsened approximation to some latent continuous trait. For example, latent liability to schizophrenia can be thought of as underlying the binary diagnosis measure. Genetically driven variation in the outcome can exist within categories of the exposure measurement, thus violating this assumption. We propose a framework to clarify this violation, deriving a simple expression for the resulting bias and showing that it may inflate or deflate effect estimates but will not reverse their sign. We then characterise a set of assumptions and a straight-forward method for estimating the effect of SD increases in the latent exposure. Our method relies on a sensitivity parameter which can be interpreted as the genetic variance of the latent exposure. We show that this method can be applied in both the one-sample and two-sample settings. We conclude by demonstrating our method in an applied example and reanalysing two papers which are likely to suffer from this type of bias, allowing meaningful interpretation of their effect sizes.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes.

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

Fast and accurate measurement of the polarization-dependent detection efficiency of superconducting nanowire single photon detectors.

Superconducting nanowire single photon detectors (SNSPDs) have been extensively investigated due to their superior characteristics, including high system detection efficiency, low dark count rate and short recovery time. The polarization sensitivity introduced by the meandering-type superconductor nanowires is an intrinsic property of SNSPD, which is normally measured by sweeping hundreds of points on the Poincaré sphere to overcome the unknown birefringent problem of the SNSPD's delivery fiber. In this paper, we propose an alternative method to characterize the optical absorptance of SNSPDs, without sweeping hundreds of points on the Poincaré sphere. It is shown theoretically that measurements on the system detection efficiencies (SDEs) subject to cases of four specific photon polarization states are sufficient to reveal the two eigen-absorptances of the SNSPD. We validate the proposed method by comparing the measured detection spectra with the spectra attained from sweeping points on the Poincaré sphere and the simulated absorption spectra.

64-Pixel Mo80Si20 superconducting nanowire single-photon imager with a saturated internal quantum efficiency at 1.5 µm.

A superconducting nanowire single-photon imager (SNSPI) uses a time-multiplexing method to reduce the readout complexity. However, due to the serial connection, the nanowire should be uniform so that a common bias can set all segments of the nanowire to their maximum detection efficiency, which becomes more challenging as the scalability (i.e., the length of the nanowire) increases. Here, we have developed a 64-pixel SNSPI based on amorphous Mo80Si20 film, which yielded a uniform nanowire and slow transmission line. Adjacent detectors were separated by delay lines, giving an imaging field of 270 µm × 240 µm. Benefiting from the high kinetic inductance of Mo80Si20 films, the delay line gave a phase velocity as low as 4.6 µm/ps. The positions of all pixels can be read out with a negligible electrical cross talk of 0.02% by using cryogenic amplifiers. The timing jitter was 100.8 ps. Saturated internal quantum efficiency was observed at a wavelength of 1550 nm. These results demonstrate that amorphous film is a promising material for achieving SNSPIs with large scalability and high efficiency.

Profile-likelihood Bayesian model averaging for two-sample summary data Mendelian randomization in the presence of horizontal pleiotropy.

Two-sample summary data Mendelian randomization is a popular method for assessing causality in epidemiology, by using genetic variants as instrumental variables. If genes exert pleiotropic effects on the outcome not entirely through the exposure of interest, this can lead to heterogeneous and (potentially) biased estimates of causal effect. We investigate the use of Bayesian model averaging to preferentially search the space of models with the highest posterior likelihood. We develop a Metropolis-Hasting algorithm to perform the search using the recently developed MR-RAPS as the basis for defining a posterior distribution that efficiently accounts for pleiotropic and weak instrument bias. We demonstrate how our general modeling approach can be extended from a standard one-component causal model to a two-component model, which allows a large proportion of SNPs to violate the InSIDE assumption. We use Monte Carlo simulations to illustrate our methods and compare it to several related approaches. We finish by applying our approach to investigate the causal role of cholesterol on the development age-related macular degeneration.

Selective inference for effect modification via the lasso.

Effect modification occurs when the effect of the treatment on an outcome varies according to the level of other covariates and often has important implications in decision-making. When there are tens or hundreds of covariates, it becomes necessary to use the observed data to select a simpler model for effect modification and then make valid statistical inference. We propose a two-stage procedure to solve this problem. First, we use Robinson's transformation to decouple the nuisance parameters from the treatment effect of interest and use machine learning algorithms to estimate the nuisance parameters. Next, after plugging in the estimates of the nuisance parameters, we use the lasso to choose a low-complexity model for effect modification. Compared to a full model consisting of all the covariates, the selected model is much more interpretable. Compared to the univariate subgroup analyses, the selected model greatly reduces the number of false discoveries. We show that the conditional selective inference for the selected model is asymptotically valid given the rate assumptions in classical semiparametric regression. Extensive simulation studies are conducted to verify the asymptotic results and an epidemiological application is used to demonstrate the method.

Single-Detector Spectrometer Using a Superconducting Nanowire.

Designing a spectrometer without the need for wavelength multiplexing optics can effectively reduce the complexity and physical footprint. On the basis of the computational spectroscopic strategy and combining a broadband-responsive dynamic detector, we successfully demonstrate an optics-free single-detector spectrometer that maps the tunable quantum efficiency of a superconducting nanowire into a matrix to build a solvable mathematical equation. Such a spectrometer can realize a broadband spectral responsivity ranging from 660 to 1900 nm. The spectral resolution at the telecom is sub-10 nm, exceeding the energy resolving capacity of existing infrared single-photon detectors. Meanwhile, benefiting from the optics-free setup, precise time-of-flight measurements can be simultaneously achieved. We have demonstrated a spectral LiDAR with eight spectral channels. This spectrometer scheme paves the way for applying superconducting nanowire detectors in multifunctional spectroscopy and represents a conceptual advancement for on-chip spectroscopy and spectral imaging.

Molecular Evolution of clock Genes in Vertebrates.

Circadian rhythms not only influence the overall daily routine of organisms but also directly affect life activities to varying degrees. Circadian locomotor output cycle kaput (Clock), the most critical gene in the circadian rhythm feedback system, plays an important role in the regulation of biological rhythms. Here, we aimed to elucidate the evolutionary history of the clock gene family in a taxonomically diverse set of vertebrates, providing novel insights into the evolution of the clock gene family based on 102 vertebrate genomes. Using genome-wide analysis, we extracted 264 clock sequences. In lobe-finned fishes and some basal non-teleost ray-finned fishes, only two clock isotypes were found (clock1 and clock2). However, the majority of teleosts possess three clock genes (two clock1 genes and one clock2 gene) owing to extra whole-genome duplication. The following syntenic analysis confirmed that clock1a, clock1b, and clock2 are conserved in teleost species. Interestingly, we discovered that osteoglossomorph fishes possess two clock2 genes. Moreover, protein sequence comparisons indicate that CLOCK protein changes among vertebrates were concentrated at the N-terminal and poly Q regions. We also performed a dN/dS analysis, and the results suggest that clock1 and clock2 may show distinct fates for duplicated genes between the lobe-finned and ray-finned fish clades. Collectively, these results provide a genome-wide insight into clock gene evolution in vertebrates.

A Superconducting Binary Encoder with Multigate Nanowire Cryotrons.

Many classic and quantum devices need to operate at cryogenic temperatures, demanding advanced cryogenic digital electronics for processing the input and output signals on a chip to extend their scalability and performance. Here, we report a superconducting binary encoder with ultralow power dissipation and ultracompact size. We introduce a multigate superconducting nanowire cryotron (nTron) that functions as an 8-input OR gate within a footprint of approximately 0.5 µm2. Four cryotrons compose a 4-bit encoder that has a bias margin of 18.9%, an operation speed greater than 250 MHz, an average switching jitter of 75 ps, and a power dissipation of less than 1 µW. We apply this encoder to read out a superconducting-nanowire single-photon detector array whose pixel location is digitized into a 4-bit binary address. The small size of the nanowire combined with the low power dissipation makes nTrons promising for future monolithic integration.

Noise-tolerant single-photon imaging with a superconducting nanowire camera.

The quality of an image is limited to the signal-to-noise ratio of the output from sensors. As the background noise increases much more than the signal, which can be caused by either a huge attenuation of light pulses after a long-haul transmission or a blinding attack with a strong flood illumination, an imaging system stops working properly. Here we built a superconducting single-photon infrared camera of negligible dark counts and 60 ps timing resolution. Combining with an adaptive 3D slicing algorithm that gives each pixel an optimal temporal window to distinguish clustered signal photons from a uniformly distributed background, we successfully reconstructed 3D single-photon images at both a low signal level (∼1 average photon per pixel) and extremely high noise background (background-to-signal ratio = 200 within a period of 50 ns before denoising). Among all detection events, we were able to remove 99.45% of the noise photons while keeping the signal photon loss at 0.74%. This Letter is a direct outcome of quantum-inspired imaging that asks for a co-development of sensors and computational methods. We envision that the proposed methods can increase the working distance of a long-haul imaging system or defend it from blinding attacks.

Planar double-slot antenna integrated into a Nb5N6 microbolometer THz detector.

In this Letter, we propose and demonstrate a new type of planar double-slot antenna for a Nb5N6 microbolometer terahertz (THz) detector. The calculated results show that the planar antenna possessed high coupling efficiency, and the THz signals were obviously focused on the antenna center place. The new planar antenna was integrated with Nb5N6 microbolometer THz detectors using micro-fabrication technology. The measured results showed that the maximum optical voltage responsivity (Ro) of the detectors reached up to 113 V/W at 0.643 THz, and the corresponding noise equivalent power was 44pW/√Hz. In addition, the performance of double-slot antennas applied into array detectors in a tunable Fabry-Perot cavity was investigated. The measured results of the Nb5N6 THz detector remained almost unchanged when the distance between the chip substrate and the copper plate was altered. This indicated that this planar double-slot antenna, which possessed the advantages of high coupling efficiency and easy integration, has great application prospects in a THz detector.

Falsification Tests for Instrumental Variable Designs With an Application to Tendency to Operate.

BACKGROUND: Instrumental variable (IV) methods are becoming an increasingly important tool in health services research as they can provide consistent estimates of causal effects in the presence of unobserved confounding. However, investigators must provide justifications that the IV is independent with any unmeasured confounder and its effect on the outcome occurs only through receipt of the exposure. These assumptions, while plausible in some contexts, cannot be verified from the data. METHODS: Falsification tests can be applied to provide evidence for the key IV assumptions. A falsification test cannot prove the assumptions hold, but can provide decisive evidence when the assumption fails. We provide a general overview of falsification tests for IV designs. We highlight a falsification test that utilizes a subpopulation of the data where an overwhelming proportion of units are treated or untreated. If the IV assumptions hold, we should find the intention-to-treat effect is zero within these subpopulations. RESULTS: We demonstrate the usage of falsification tests for IV designs using an IV known as tendency to operate from health services research. We show that the falsification test provides no evidence against the IV assumptions in this application.

Demonstration of a superconducting nanowire single photon detector with an ultrahigh polarization extinction ratio over 400.

Polarization sensitive photo-detectors are the key to the implementation of the polarimetric imaging systems, which are proved to have superior performance than their traditional counterparts based on intensity discriminations. In this article, we report the demonstration of a superconducting nanowire single photon detector (SNSPD) of which the response is ultra-sensitive to the polarization state of the incident photons. Measurements carried out on a fabricated SNSPD show that a device efficiency of ~48% can be achieved at 1550 nm for the case of parallel polarization, which is ~420 times larger than that for the case of perpendicular polarization. While the reported polarization ultra-sensitive technique is demonstrated on a single-pixel SNSPD, it is also fully compatible with the multi-pixel SNSPD array platforms that emerged recently.