Evolutionary Conservation of the PA-X Open Reading Frame in Segment 3 of Influenza A Virus

PA-X is a fusion protein of influenza A virus encoded in part from a +1 frameshifted X open reading frame (X-ORF) in segment 3. We show that the X-ORFs of diverse influenza A viruses can be divided into two groups that differ in selection pressure and likely function, reflected in the presence of an internal stop codon and a change in synonymous diversity. Notably, truncated forms of PA-X evolved convergently in swine and dogs, suggesting a strong species-specific effect

WISE/NEOWISE Observations of Comet 103P/Hartley 2

We report results based on mid-infrared photometry of comet 103P/Hartley 2 taken during 2010 May 4-13 (when the comet was at a heliocentric distance of 2.3 AU, and an observer distance of 2.0 AU) by the Wide-field Infrared Survey Explorer. Photometry of the coma at 22 μm and data from the University of Hawaii 2.2 m telescope obtained on 2010 May 22 provide constraints on the dust particle size distribution, d log n/d log m, yielding power-law slope values of alpha = –0.97 ± 0.10, steeper than that found for the inbound particle fluence during the Stardust encounter of comet 81P/Wild 2. The extracted nucleus signal at 12 μm is consistent with a body of average spherical radius of 0.6 ± 0.2 km (one standard deviation), assuming a beaming parameter of 1.2. The 4.6 μm band signal in excess of dust and nucleus reflected and thermal contributions may be attributed to carbon monoxide or carbon dioxide emission lines and provides limits and estimates of species production. Derived carbon dioxide coma production rates are 3.5(± 0.9) × 10^(24) molecules per second. Analyses of the trail signal present in the stacked image with an effective exposure time of 158.4 s yields optical-depth values near 9 × 10^(–10) at a delta mean anomaly of 0.2 deg trailing the comet nucleus, in both 12 and 22 μm bands. A minimum chi-squared analysis of the dust trail position yields a beta-parameter value of 1.0 × 10^(–4), consistent with a derived mean trail-grain diameter of 1.1/ρ cm for grains of ρ g cm^(–3) density. This leads to a total detected trail mass of at least 4 × 10^(10) ρ kg

Rapid cryogenic characterisation of 1024 integrated silicon quantum dots

Quantum computers are nearing the thousand qubit mark, with the current focus on scaling to improve computational performance. As quantum processors grow in complexity, new challenges arise such as the management of device variability and the interface with supporting electronics. Spin qubits in silicon quantum dots are poised to address these challenges with their proven control fidelities and potential for compatibility with large-scale integration. Here, we demonstrate the integration of 1024 silicon quantum dots with on-chip digital and analogue electronics, all operating below 1 K. A high-frequency analogue multiplexer provides fast access to all devices with minimal electrical connections, enabling characteristic data across the quantum dot array to be acquired in just 5 minutes. We achieve this by leveraging radio-frequency reflectometry with state-of-the-art signal integrity, reaching a minimum integration time of 160 ps. Key quantum dot parameters are extracted by fast automated machine learning routines to assess quantum dot yield and understand the impact of device design. We find correlations between quantum dot parameters and room temperature transistor behaviour that may be used as a proxy for in-line process monitoring. Our results show how rapid large-scale studies of silicon quantum devices can be performed at lower temperatures and measurement rates orders of magnitude faster than current probing techniques, and form a platform for the future on-chip addressing of large scale qubit arrays.Comment: Main text: 14 pages, 8 figures, 1 table Supplementary: 8 pages, 6 figure

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.

MotivationMultiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.ResultsWe performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.Availability and implementationDatasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.Supplementary informationSupplementary data are available at Bioinformatics online

Centaurs and Scattered Disk Objects in the Thermal Infrared: Analysis of WISE/NEOWISE Observations

The Wide-field Infrared Survey Explorer (WISE) observed 52 Centaurs and scattered disk objects (SDOs) in the thermal infrared, including 15 new discoveries. We present analyses of these observations to estimate sizes and mean optical albedos. We find mean albedos of 0.08 ± 0.04 for the entire data set. Thermal fits yield average beaming parameters of 0.9 ± 0.2 that are similar for both SDO and Centaur sub-classes. Biased cumulative size distributions yield size-frequency distribution power law indices of ~–1.7 ± 0.3. The data also reveal a relation between albedo and color at the 3σ level. No significant relation between diameter and albedos is found