Developmental and tissue-specific expression of NITRs

Novel immune-type receptors (NITRs) are encoded by large multi-gene families and share structural and signaling similarities to mammalian natural killer receptors (NKRs). NITRs have been identified in multiple bony fish species, including zebrafish, and may be restricted to this large taxonomic group. Thirty-nine NITR genes that can be classified into 14 families are encoded on zebrafish chromosomes 7 and 14. Herein, we demonstrate the expression of multiple NITR genes in the zebrafish ovary and during embryogenesis. All 14 families of zebrafish NITRs are expressed in hematopoietic kidney, spleen and intestine as are immunoglobulin and T cell antigen receptors. Furthermore, all 14 families of NITRs are shown to be expressed in the lymphocyte lineage, but not in the myeloid lineage, consistent with the hypothesis that NITRs function as NKRs. Sequence analyses of NITR amplicons identify known alleles and reveal additional alleles within the nitr1, nitr2, nitr3, and nitr5 families, reflecting the recent evolution of this gene family

Structural Integrity Program for INTEC Calcined Solids Storage Facilities

This report documents the activities of the structural integrity program at the Idaho Nuclear Technology and Engineering Center relevant to the high-level waste Calcined Solids Storage Facilities and associated equipment, as required by DOE M 435.1-1, “Radioactive Waste Management Manual.” Based on the evaluation documented in this report, the Calcined Solids Storage Facilities are not leaking and are structurally sound for continued service. Recommendations are provided for continued monitoring of the Calcined Solids Storage Facilities

Meeting Report: Knowledge and Gaps in Developing Microbial Criteria for Inland Recreational Waters

The U.S. Environmental Protection Agency (EPA) has committed to issuing in 2012 new or revised criteria designed to protect the health of those who use surface waters for recreation. For this purpose, the U.S. EPA has been conducting epidemiologic studies to establish relationships between microbial measures of water quality and adverse health outcomes among swimmers. New methods for testing water quality that would provide same-day results will likely be elements of the new criteria. Although the epidemiologic studies upon which the criteria will be based were conducted at Great Lakes and marine beaches, the new water quality criteria may be extended to inland waters (IWs). Similarities and important differences between coastal waters (CWs) and IWs that should be considered when developing criteria for IWs were the focus of an expert workshop. Here, we summarize the state of knowledge and research needed to base IWs microbial criteria on sound science. Two key differences between CWs and IWs are the sources of indicator bacteria, which may modify the relationship between indicator microbes and health risk, and the relationship between indicators and pathogens, which also may vary within IWs. Monitoring using rapid molecular methods will require the standardization and simplification of analytical methods, as well as greater clarity about their interpretation. Research needs for the short term and longer term are described

Learning-based Calibration of Flux Crosstalk in Transmon Qubit Arrays

Superconducting quantum processors comprising flux-tunable data and coupler qubits are a promising platform for quantum computation. However, magnetic flux crosstalk between the flux-control lines and the constituent qubits impedes precision control of qubit frequencies, presenting a challenge to scaling this platform. In order to implement high-fidelity digital and analog quantum operations, one must characterize the flux crosstalk and compensate for it. In this work, we introduce a learning-based calibration protocol and demonstrate its experimental performance by calibrating an array of 16 flux-tunable transmon qubits. To demonstrate the extensibility of our protocol, we simulate the crosstalk matrix learning procedure for larger arrays of transmon qubits. We observe an empirically linear scaling with system size, while maintaining a median qubit frequency error below $300$ kHz

Evolution of 1/f1/f Flux Noise in Superconducting Qubits with Weak Magnetic Fields

The microscopic origin of $1/f$ magnetic flux noise in superconducting circuits has remained an open question for several decades despite extensive experimental and theoretical investigation. Recent progress in superconducting devices for quantum information has highlighted the need to mitigate sources of qubit decoherence, driving a renewed interest in understanding the underlying noise mechanism(s). Though a consensus has emerged attributing flux noise to surface spins, their identity and interaction mechanisms remain unclear, prompting further study. Here we apply weak in-plane magnetic fields to a capacitively-shunted flux qubit (where the Zeeman splitting of surface spins lies below the device temperature) and study the flux-noise-limited qubit dephasing, revealing previously unexplored trends that may shed light on the dynamics behind the emergent $1/f$ noise. Notably, we observe an enhancement (suppression) of the spin-echo (Ramsey) pure dephasing time in fields up to $B=100~\text{G}$. With direct noise spectroscopy, we further observe a transition from a $1/f$ to approximately Lorentzian frequency dependence below 10 Hz and a reduction of the noise above 1 MHz with increasing magnetic field. We suggest that these trends are qualitatively consistent with an increase of spin cluster sizes with magnetic field. These results should help to inform a complete microscopic theory of $1/f$ flux noise in superconducting circuits

High-Fidelity, Frequency-Flexible Two-Qubit Fluxonium Gates with a Transmon Coupler

We propose and demonstrate an architecture for fluxonium-fluxonium two-qubit gates mediated by transmon couplers (FTF, for fluxonium-transmon-fluxonium). Relative to architectures that exclusively rely on a direct coupling between fluxonium qubits, FTF enables stronger couplings for gates using non-computational states while simultaneously suppressing the static controlled-phase entangling rate ($ZZ$) down to kHz levels, all without requiring strict parameter matching. Here we implement FTF with a flux-tunable transmon coupler and demonstrate a microwave-activated controlled-Z (CZ) gate whose operation frequency can be tuned over a 2 GHz range, adding frequency allocation freedom for FTF's in larger systems. Across this range, state-of-the-art CZ gate fidelities were observed over many bias points and reproduced across the two devices characterized in this work. After optimizing both the operation frequency and the gate duration, we achieved peak CZ fidelities in the 99.85-99.9\% range. Finally, we implemented model-free reinforcement learning of the pulse parameters to boost the mean gate fidelity up to $99.922\pm0.009\%$, averaged over roughly an hour between scheduled training runs. Beyond the microwave-activated CZ gate we present here, FTF can be applied to a variety of other fluxonium gate schemes to improve gate fidelities and passively reduce unwanted $ZZ$ interactions.Comment: 23 pages, 16 figure

Demonstration of tunable three-body interactions between superconducting qubits

Nonpairwise multi-qubit interactions present a useful resource for quantum information processors. Their implementation would facilitate more efficient quantum simulations of molecules and combinatorial optimization problems, and they could simplify error suppression and error correction schemes. Here we present a superconducting circuit architecture in which a coupling module mediates 2-local and 3-local interactions between three flux qubits by design. The system Hamiltonian is estimated via multi-qubit pulse sequences that implement Ramsey-type interferometry between all neighboring excitation manifolds in the system. The 3-local interaction is coherently tunable over several MHz via the coupler flux biases and can be turned off, which is important for applications in quantum annealing, analog quantum simulation, and gate-model quantum computation.Comment: 14 pages, 11 figure

Super Resolution Microscopy Reveals that Caveolin-1 Is Required for Spatial Organization of CRFB1 and Subsequent Antiviral Signaling in Zebrafish

10.1371/journal.pone.0068759PLoS ONE87-POLN

Bayesian inference of evolutionary histories under time-dependent substitution rates

Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.status: publishe

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15–18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution