Reproductive performance of pandemic influenza A virus infected sow herds before and after implementation of a vaccine against the influenza A (H1N1)pdm09 virus

Background: Reproductive failure in sow herds due to infection with influenza A viruses has been described in the literature, but only a few studies have focused on the pathogenesis and the clinical signs of the infection. Case reports indicate an association between infections with influenza A viruses and reduced reproductive performance, although it has been difficult to experimentally reproduce the clinical outcome of poor reproductive performance. The aim of the present longitudinal field study was to compare the reproductive performance parameters before and after the implementation of vaccination against the influenza A (H1N1)pdm09 virus in sow herds infected with pandemic influenza A virus. Therefore, farm-specific data of 137 sow herds in Germany, including 60,153 sows, as well as the clinical presentation of the infection were surveyed via questionnaire. Furthermore, average performance parameters (return to oestrus rate, abortion rate, stillbirth rate, number of piglets born alive per litter, preweaning mortality rate and number of piglets weaned per sow per year) were recorded for 6 months before vaccination and 6 months after completion of primary vaccination. Results: In 79.8% of the farms, the clinical presentation of the infection was characterised by a reduced reproductive performance. These findings were confirmed by analysis of the performance parameters, which revealed a significant decline in the return to oestrus rate (p < 0.001), abortion rate (p < 0.001) and preweaning mortality rate (p = 0.023) and a significant increase of the number in piglets born alive (p = 0.001) and piglets weaned per sow per year (p < 0.001) after immunisation. The stillbirth rate did not change significantly. Conclusion: The present study represents the first attempt to demonstrate the association of influenza A virus infection, vaccination and the alteration in reproductive performance parameters, investigating a large number of cases. The results show that by vaccinating against the influenza A (H1N1)pdm09 virus, an improvement in reproductive performance can be achieved in sow herds infected with pandemic influenza A virus. Additionally, the large number of herds that were affected by poor reproductive performance after infection with the aforementioned virus confirms the assumption of an association between pandemic influenza A virus and reproductive losses

Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes of RNAs that are characterized by structural similarities, and typically consist of multiple RNA families. Recent advances in high-throughput transcriptomics and comparative genomics have produced very large sets of putative noncoding RNAs and regulatory RNA signals. For many of them, evidence for stabilizing selection acting on their secondary structures has been derived, and at least approximate models of their structures have been computed. The overwhelming majority of these hypothetical RNAs cannot be assigned to established families or classes. We present here a structure-based clustering approach that is capable of extracting putative RNA classes from genome-wide surveys for structured RNAs. The LocARNA (local alignment of RNA) tool implements a novel variant of the Sankoff algorithm that is sufficiently fast to deal with several thousand candidate sequences. The method is also robust against false positive predictions, i.e., a contamination of the input data with unstructured or nonconserved sequences. We have successfully tested the LocARNA-based clustering approach on the sequences of the RFAM-seed alignments. Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005) Noncoding RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2): i77–i78). In addition to recovering, e.g., tRNAs as a structure-based class, the method identifies several RNA families, including microRNA and snoRNA candidates, and suggests several novel classes of ncRNAs for which to date no representative has been experimentally characterized

The impact of dynamic pressure bumps on the observational properties of protoplanetary disks

Over the last years, large (sub-)millimetre surveys of protoplanetary disks have well constrained the demographics of disks, such as their millimetre luminosities, spectral indices, and disk radii. Additionally, several high-resolution observations have revealed an abundance of substructures in the disks dust continuum. The most prominent are ring like structures, likely due to pressure bumps trapping dust particles. The origins and characteristics of these bumps, nevertheless, need to be further investigated. The purpose of this work is to study how dynamic pressure bumps affect observational properties of protoplanetary disks. We further aim to differentiate between the planetary- versus zonal flow-origin of pressure bumps. We perform one-dimensional gas and dust evolution simulations, setting up models with varying pressure bump features. We subsequently run radiative transfer calculations to obtain synthetic images and the different quantities of observations. We find that the outermost pressure bump determines the disks dust size across different millimetre wavelengths. Our modelled dust traps need to form early (< 0.1 Myr), fast (on viscous timescales), and must be long lived (> Myr) to obtain the observed high millimetre luminosities and low spectral indices of disks. While the planetary bump models can reproduce these observables irrespectively of the opacity prescription, the highest opacities are needed for the zonal flow bump model to be in line with observations. Our findings favour the planetary- over the zonal flow-origin of pressure bumps and support the idea that planet formation already occurs in early class 0-1 stages of circumstellar disks. The determination of the disks effective size through its outermost pressure bump also delivers a possible answer to why disks in recent low-resolution surveys appear to have the same sizes across different millimetre wavelengths.Comment: 22 pages, 15 figures. To be published in Astronomy & Astrophysic

Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2

The effective reproductive number; R; e; is a key indicator of the growth of an epidemic. Since the start of the SARS-CoV-2 pandemic, many methods and online dashboards have sprung up to monitor this number through time. However, these methods are not always thoroughly tested, correctly placed in time, or are overly confident during high incidence periods. Here, we present a method for timely estimation of; R; e; , applied to COVID-19 epidemic data from 170 countries. We thoroughly evaluate the method on simulated data, and present an intuitive web interface for interactive data exploration. We show that, in early 2020, in the majority of countries the estimated; R; e; dropped below 1 only after the introduction of major non-pharmaceutical interventions. For Europe the implementation of non-pharmaceutical interventions was broadly associated with reductions in the estimated; R; e; . Globally though, relaxing non-pharmaceutical interventions had more varied effects on subsequent; R; e; estimates. Our framework is useful to inform governments and the general public on the status of epidemics in their country, and is used as the official source of; R; e; estimates for SARS-CoV-2 in Switzerland. It further allows detailed comparison between countries and in relation to covariates such as implemented public health policies, mobility, behaviour, or weather data

A quantum algorithm for solving open system dynamics on quantum computers using noise

In this paper we present a quantum algorithm that uses noise as a resource. The goal of our quantum algorithm is the calculation of operator averages of an open quantum system evolving in time. Selected low-noise system qubits and noisy bath qubits represent the system and the bath of the open quantum system. All incoherent qubit noise can be mapped to bath spectral functions. The form of the spectral functions can be tuned digitally, allowing for the time evolution of a wide range of open-system models at finite temperature. We study the feasibility of this approach with a focus on the solution of the spin-boson model and assume intrinsic qubit noise that is dominated by damping and dephasing. We find that classes of open quantum systems exist where our algorithm performs very well, even with gate errors as high as 1%. In general the presented algorithm performs best if the system-bath interactions can be decomposed into native gates.Comment: 19 pages, 8 figures in total: 10 pages main text with 7 figure

Observation of a Fragmented, Strongly Interacting Fermi Gas

We study the emergence of a fragmented state in a strongly interacting Fermi gas subject to a tunable disorder. We investigate its properties using a combination of high-resolution in situ imaging and conductance measurements. The fragmented state exhibits saturated density modulations, a strongly reduced density percolation threshold, lower than the average density, and a resistance equal to that of a noninteracting Fermi gas in the same potential landscape. The transport measurements further indicate that this state is connected to the superfluid state as disorder is reduced. We propose that the fragmented state consists of unpercolated islands of bound pairs, whose binding energy is enhanced by the disorder