Bridging mechanisms of through-thickness reinforcement in dynamic mode Iⅈ delamination

Z-pin through-thickness reinforcement is used to improve the impact resistance of composite structures; however, the effect of loading rate on Z-pin behaviour is not well understood. The dyna mic response of Z-pins in mode I and II delamination of quasi-isotropic IM7/8552 laminates was characterized experimentally in this work. Z-pinned samples were loaded at both quasi-static and dynamic rates, up to a separation velocity of 12 m/s. The efficiency of Z-pins in mode I delamination decreased with loading rate, which was mainly due to the change in the pin misalignment, the failure surface morphology and to inertia. The Z-pins failed at small displacements in the mode II loading experiments, resulting in much lower energy dissipation in comparison with the mode I case. The total energy dissipation decreased with increasing loading rate, while enhanced interfacial friction due to failed pins may be largely responsible for the higher energy dissipation in quasi-static experiments

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size

Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences

BACKGROUND: CTX-M-producing Escherichia coli strains are regarded as major global pathogens. METHODOLOGY/PRINCIPAL FINDINGS: The nucleotide sequence of three plasmids (pEC_B24: 73801-bp; pEC_L8: 118525-bp and pEC_L46: 144871-bp) from Escherichia coli isolates obtained from patients with urinary tract infections and one plasmid (pEC_Bactec: 92970-bp) from an Escherichia coli strain isolated from the joint of a horse with arthritis were determined. Plasmid pEC_Bactec belongs to the IncI1 group and carries two resistance genes: bla(TEM-1) and bla(CTX-M-15). It shares more than 90% homology with a previously published bla(CTX-M)-plasmid from E. coli of human origin. Plasmid pEC_B24 belongs to the IncFII group whereas plasmids pEC_L8 and pEC_L46 represent a fusion of two replicons of type FII and FIA. On the pEC_B24 backbone, two resistance genes, bla(TEM-1) and bla(CTX-M-15), were found. Six resistance genes, bla(TEM-1), bla(CTX-M-15), bla(OXA-1), aac6'-lb-cr, tetA and catB4, were detected on the pEC_L8 backbone. The same antimicrobial drug resistance genes, with the exception of tetA, were also identified on the pEC_L46 backbone. Genome analysis of all 4 plasmids studied provides evidence of a seemingly frequent transposition event of the bla(CTX-M-15)-ISEcp1 element. This element seems to have a preferred insertion site at the tnpA gene of a bla(TEM)-carrying Tn3-like transposon, the latter itself being inserted by a transposition event. The IS26-composite transposon, which contains the bla(OXA-1), aac6'-lb-cr and catB4 genes, was inserted into plasmids pEC_L8 and pEC_L46 by homologous recombination rather than a transposition event. Results obtained for pEC_L46 indicated that IS26 also plays an important role in structural rearrangements of the plasmid backbone and seems to facilitate the mobilisation of fragments from other plasmids. CONCLUSIONS: Collectively, these data suggests that IS26 together with ISEcp1 could play a critical role in the evolution of diverse multiresistant plasmids found in clinical Enterobacteriaceae

BEYONDPLANCK

We describe the correction procedure for Analog-to-Digital Converter (ADC) differential non-linearities (DNL) adopted in the Bayesian end-to-end BEYONDPLANCK analysis framework. This method is nearly identical to that developed for the official Planck Low Frequency Instrument (LFI) Data Processing Center (DPC) analysis, and relies on the binned rms noise profile of each detector data stream. However, rather than building the correction profile directly from the raw rms profile, we first fit a Gaussian to each significant ADC-induced rms decrement, and then derive the corresponding correction model from this smooth model. The main advantage of this approach is that only samples which are significantly affected by ADC DNLs are corrected, as opposed to the DPC approach in which the correction is applied to all samples, filtering out signals not associated with ADC DNLs. The new corrections are only applied to data for which there is a clear detection of the non-linearities, and for which they perform at least comparably with the DPC corrections. Out of a total of 88 LFI data streams (sky and reference load for each of the 44 detectors) we apply the new minimal ADC corrections in 25 cases, and maintain the DPC corrections in 8 cases. All these corrections are applied to 44 or 70 GHz channels, while, as in previous analyses, none of the 30 GHz ADCs show significant evidence of non-linearity. By comparing the BEYONDPLANCK and DPC ADC correction methods, we estimate that the residual ADC uncertainty is about two orders of magnitude below the total noise of both the 44 and 70 GHz channels, and their impact on current cosmological parameter estimation is small. However, we also show that non-idealities in the ADC corrections can generate sharp stripes in the final frequency maps, and these could be important for future joint analyses with the Planck High Frequency Instrument (HFI), Wilkinson Microwave Anisotropy Probe (WMAP), or other datasets. We therefore conclude that, although the existing corrections are adequate for LFI-based cosmological parameter analysis, further work on LFI ADC corrections is still warranted

BEYONDPLANCK

We discuss the treatment of bandpass and beam leakage corrections in the Bayesian BEYONDPLANCK cosmic microwave background (CMB) analysis pipeline as applied to the Planck LFI measurements. As a preparatory step, we first applied three corrections to the nominal LFI bandpass profiles, including the removal of a known systematic effect in the ground measuring equipment at 61 GHz, along with a smoothing of standing wave ripples and edge regularization. The main net impact of these modifications is an overall shift in the 70 GHz bandpass of +0.6 GHz. We argue that any analysis of LFI data products, either from Planck or BEYONDPLANCK, should use these new bandpasses. In addition, we fit a single free bandpass parameter for each radiometer of the form δiâ =â δ0+δi, where δ0 represents an absolute frequency shift per frequency band and δi is a relative shift per detector. The absolute correction is only fitted at 30 GHz, with a full Ï 2-based likelihood, resulting in a correction of δ30â =â 0.24±0.03â GHz. The relative corrections were fitted using a spurious map approach that is fundamentally similar to the method pioneered by the WMAP team, but excluding the introduction of many additional degrees of freedom. All the bandpass parameters were sampled using a standard Metropolis sampler within the main BEYONDPLANCK Gibbs chain and the bandpass uncertainties were thus propagated to all other data products in the analysis. In summary, we find that our bandpass model significantly reduces leakage effects. For beam leakage corrections, we adopted the official Planck LFI beam estimates without any additional degrees of freedom and we only marginalized over the underlying sky model. We note that this is the first time that leakage from beam mismatch has been included for Planck LFI maps

BEYONDPLANCK

We present posterior sample-based cosmic microwave background (CMB) constraints from Planck LFI and WMAP observations as derived through global end-to-end Bayesian processing within the BeyondPlanck framework. We first used these samples to study correlations between CMB, foreground, and instrumental parameters. We identified a particularly strong degeneracy between CMB temperature fluctuations and free-free emission on intermediate angular scales (400 ≤ ∫ ≤ 600), mitigated through model reduction, masking, and resampling. We compared our posterior-based CMB results with previous Planck products and found a generally good agreement, however, with notably higher noise due to our exclusion of Planck HFI data.We found a best-fit CMB dipole amplitude of 3362:7 ± 1:4 μK, which is in excellent agreement with previous Planck results. The quoted dipole uncertainty is derived directly from the sampled posterior distribution and does not involve any ad hoc contributions for Planck instrumental systematic effects. Similarly, we find a temperature quadrupole amplitude of φTT 2 = 229 ± 97 μK2, which is in good agreement with previous results in terms of the amplitude, but the uncertainty is one order of magnitude greater than the naive diagonal Fisher uncertainty. Concurrently, we find less evidence of a possible alignment between the quadrupole and octopole than previously reported, due to a much larger scatter in the individual quadrupole coeffcients that is caused both by marginalizing over a more complete set of systematic effects – as well as by requiring a more conservative analysis mask to mitigate the free-free degeneracy. For higher multipoles, we find that the angular temperature power spectrum is generally in good agreement with both Planck and WMAP. At the same time, we note that this is the first time that the sample-based, asymptotically exact Blackwell-Rao estimator has been successfully established for multipoles up to ∫ ≤ 600. It now accounts for the majority of the cosmologically important information. Overall, this analysis demonstrates the unique capabilities of the Bayesian approach with respect to end-to-end systematic uncertainty propagation and we believe it can and should play an important role in the analysis of future CMB experiments. Cosmological parameter constraints are presented in a companion paper

BeyondPlanck VIII. Efficient Sidelobe Convolution and Correction through Spin Harmonics

We introduce a new formulation of the Conviqt convolution algorithm in terms of spin harmonics, and apply this to the problem of sidelobe correction for BeyondPlanck, the first end-to-end Bayesian Gibbs sampling framework for CMB analysis. We compare our implementation to the previous Planck LevelS implementation, and find good agreement between the two codes in terms of accuracy, but with a speed-up reaching a factor of 3--10, depending on the frequency bandlimits, $l_{\textrm{max}}$ and $m_{\textrm{max}}$. The new algorithm is significantly simpler to implement and maintain, since all low-level calculations are handled through an external spherical harmonic transform library. We find that our mean sidelobe estimates for Planck LFI agree well with previous efforts. Additionally, we present novel sidelobe rms maps that quantify the uncertainty in the sidelobe corrections due to variations in the sky model.Comment: 9 pages, 8 figures. Part of the BeyondPlanck paper suit

BEYONDPLANCK

We present a Gibbs sampling solution to the mapmaking problem for cosmic microwave background (CMB) measurements that builds on existing destriping methodology. Gibbs sampling breaks the computationally heavy destriping problem into two separate steps: noise filtering and map binning. Considered as two separate steps, both are computationally much cheaper than solving the combined problem. This provides a huge performance benefit as compared to traditional methods and it allows us, for the first time, to bring the destriping baseline length to a single sample. Here, we applied the Gibbs procedure to simulated Planck 30 GHz data. We find that gaps in the time-ordered data are handled efficiently by filling them in with simulated noise as part of the Gibbs process. The Gibbs procedure yields a chain of map samples, from which we are able to compute the posterior mean as a best-estimate map. The variation in the chain provides information on the correlated residual noise, without the need to construct a full noise covariance matrix. However, if only a single maximum-likelihood frequency map estimate is required, we find that traditional conjugate gradient solvers converge much faster than a Gibbs sampler in terms of the total number of iterations. The conceptual advantages of the Gibbs sampling approach lies in statistically well-defined error propagation and systematic error correction. This methodology thus forms the conceptual basis for the mapmaking algorithm employed in the BEYONDPLANCK framework, which implements the first end-to-end Bayesian analysis pipeline for CMB observations

BEYONDPLANCK

We describe the computational infrastructure for end-to-end Bayesian cosmic microwave background (CMB) analysis implemented by the BeyondPlanck Collaboration. The code is called Commander3. It provides a statistically consistent framework for global analysis of CMB and microwave observations and may be useful for a wide range of legacy, current, and future experiments. The paper has three main goals. Firstly, we provide a high-level overview of the existing code base, aiming to guide readers who wish to extend and adapt the code according to their own needs or re-implement it from scratch in a different programming language. Secondly, we discuss some critical computational challenges that arise within any global CMB analysis framework, for instance in-memory compression of time-ordered data, fast Fourier transform optimization, and parallelization and load-balancing. Thirdly, we quantify the CPU and RAM requirements for the current BEYONDPLANCK analysis, finding that a total of 1.5 TB of RAM is required for efficient analysis and that the total cost of a full Gibbs sample for LFI is 170 CPU-hrs, including both low-level processing and high-level component separation, which is well within the capabilities of current low-cost computing facilities. The existing code base is made publicly available under a GNU General Public Library (GPL) license