We propose a U(1)×Z2 effective gauge theory for vortices in a px+ipy superfluid in two dimensions. The combined gauge transformation binds U(1) and Z2 defects so that the total transformation remains single-valued and manifestly preserves the the particle-hole symmetry of the action. The Z2 gauge field introduces a complete Chern-Simons term in addition to a partial one associated with the U(1) gauge field. The theory reproduces the known physics of vortex dynamics such as a Magnus force proportional to the superfluid density. More importantly, it predicts a universal Abelian phase, exp(iπ/8), upon the exchange of two vortices. This phase is modified by non-universal corrections due to the partial Chern-Simon term, which are nevertheless screened in a charged superfluid at distances that are larger than the penetration depth.

Extra or missing chromosomes—a phenomenon termed aneuploidy—frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.

[1] The termination shock (TS) is a quasi-perpendicular shock with broad regions on both sides that are populated by high energy ions. These energetic particles play an important role in the formation of the TS structure, which distinguishes it from planetary bow shocks. The pressure of the pickup ions is calculated by solving numerically the Vlasov equation in a time-stationary one-dimensional model shock with the parameters taken from the TS observations. The solution is obtained by backward tracing of the ion trajectories in the shock front. It is found that, in order to maintain the shock stationarity, the upstream density of the pickup ions should be comparable to the density of the solar wind protons.

Extra or missing chromosomes—a phenomenon termed aneuploidy—frequently arises during human meiosis and embryonic mitosis and is the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05x and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.

The physics of a planar chiral p ± ip superconductor is studied for various vortex configurations. The occurrence of vortex quasiparticle bound states is exposed together with their ensuing collective properties, such as subgap bands induced by intervortex tunneling. A general method to diagonalize the Hamiltonian of a superconductor in the presence of a vortex lattice is developed that employs only smooth gauge transformations. It renders the Hamiltonian to be periodic (thus allowing the use of the Bloch theorem) and enables the treatment of systems with vortices of finite radii. The pertinent anomalous charge response c xy is calculated (using the Streda formula) and reveals that it contains a quantized contribution. This is attributed to the response to the nucleation of vortices from which we deduce the system's quantum phase.

Mendel’s Law of Segregation states that the offspring of a diploid, heterozygous parent will inherit either allele with equal probability. While the vast majority of loci adhere to this rule, research in model and non-model organisms has uncovered numerous exceptions whereby “selfish” alleles are disproportionately transmitted to the next generation. Evidence of such “transmission distortion” (TD) in humans remains equivocal in part because scans of human pedigrees have been under-powered to detect small effects. Recently published single-cell sequencing data from individual human sperm (n = 41,189; 969-3,377 cells from each of 25 donors) offer an opportunity to revisit this question with unprecedented statistical power, but require new methods tailored to extremely low-coverage data (~0.01× per cell). To this end, we developed a method, named rhapsodi, that leverages sparse gamete genotype data to phase the diploid genomes of the donor individuals, impute missing gamete genotypes, and discover meiotic recombination breakpoints, benchmarking its performance across a wide range of study designs. After applying rhapsodi to the sperm sequencing data, we then scanned the gametes for evidence of TD. Our results exhibited close concordance with binomial expectations under balanced transmission, in contrast to tenuous signals of TD that were previously reported in pedigree-based studies. Together, our work excludes the existence of even weak TD in this sample, while offering a powerful quantitative framework for testing this and related hypotheses in other cohorts and study systems.

We consider a modified setup for measuring the Aharonov-Casher phase which consists of a Josephson vortex trapped in an annular topological superconducting junction. The junction encloses both electric charge and magnetic flux. We discover a deviation from the Aharonov-Casher prediction whose origin we identify in an additive universal topological phase that remarkably depends only on the parity of the number of vortices enclosed by the junction. We show that this phase is ±2π times the topological spin of the Josephson vortex and is proportional to the Chern number. The presence of this phase can be measured through its effect on the junction's voltage characteristics, thus revealing the topological properties of the Josephson vortex and the superconducting state.

Meiotic recombination is a fundamental source of human genetic diversity and is also critical for ensuring the accuracy of chromosome segregation. Understanding the landscape of meiotic recombination, its variation across individuals, and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring the landscape of recombination either rely on population genetic patterns of linkage disequilibrium (LD)—capturing a time-averaged view—or direct detection of crossovers in gametes or multi-generation pedigrees, limiting the scale and availability of relevant datasets. Here, we introduce an approach for inferring sex-specific landscapes of recombination from retrospective analysis of data from preimplantation genetic testing for aneuploidy (PGT-A) based on low-coverage (<0.05×) whole-genome sequencing of biopsies from in vitro fertilized (IVF) embryos. To overcome the sparsity of these data, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, as well as the frequent occurrence of chromosome loss in embryos, whereby the remaining chromosome is phased by default. Based on extensive simulation, we show that our method retains high accuracy down to coverages as low as 0.02×. Applying this method to low-coverage PGT-A data from 18,967 embryos, we mapped 70,660 recombination events at an average resolution of ~150 kbp, replicating key features of sex-specific recombination maps from the literature. We observed that the total length of the female genetic map is reduced for trisomies compared to disomies, while the genomic distribution of crossovers is also altered in a chromosome-specific manner. Based on haplotype configurations detected in regions surrounding the centromeres, our data additionally indicate that individual chromosomes possess unique propensities for different mechanisms of meiotic error. Together, our results provide a detailed view of the role of aberrant meiotic recombination in the origins of human aneuploidies, as well as a flexible tool for mapping crossovers in low-coverage sequencing data from multiple siblings.