Two algorithms for LCS Consecutive Suffix Alignment

AbstractThe problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B.Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS (Longest Common Subsequence) metric, where the LCS metric measures the subsequence of maximal length common to A and B. The first solution is an O(nL) time and space algorithm for constant alphabets, where the size of the compared strings is O(n) and L⩽n denotes the size of the LCS of A and B.The second solution is an O(nL+nlog|Σ|) time and O(n) space algorithm for general alphabets, where Σ denotes the alphabet of the compared strings

Nagaoka ferromagnetism observed in a quantum dot plaquette

Engineered, highly-controllable quantum systems hold promise as simulators of emergent physics beyond the capabilities of classical computers. An important problem in many-body physics is itinerant magnetism, which originates purely from long-range interactions of free electrons and whose existence in real systems has been subject to debate for decades. Here we use a quantum simulator consisting of a four-site square plaquette of quantum dots to demonstrate Nagaoka ferromagnetism. This form of itinerant magnetism has been rigorously studied theoretically but has remained unattainable in experiment. We load the plaquette with three electrons and demonstrate the predicted emergence of spontaneous ferromagnetic correlations through pairwise measurements of spin. We find the ferromagnetic ground state is remarkably robust to engineered disorder in the on-site potentials and can induce a transition to the low-spin state by changing the plaquette topology to an open chain. This demonstration of Nagaoka ferromagnetism highlights that quantum simulators can be used to study physical phenomena that have not yet been observed in any system before. The work also constitutes an important step towards large-scale quantum dot simulators of correlated electron systems.Comment: This version: main (8 pages, 6 figures) + supplementary (15 pages, 8 figures

Compressing the Input for CNNs with the First-Order Scattering Transform

International audienceWe study the first-order scattering transform as a candidate for reducing the signal processed by a convolutional neural network (CNN). We study this transformation and show theoretical and empirical evidence that in the case of natural images and sufficiently small translation invariance, this transform preserves most of the signal information needed for classification while substantially reducing the spatial resolution and total signal size. We show that cascading a CNN with this representation performs on par with ImageNet classification models commonly used in downstream tasks such as the ResNet-50. We subsequently apply our trained hybrid ImageNet model as a base model on a detection system, which has typically larger image inputs. On Pascal VOC and COCO detection tasks we deliver substantial improvements in the inference speed and training memory consumption compared to models trained directly on the input image

The metastasis-associated protein S100A4 promotes the inflammatory response of mononuclear cells via the TLR4 signalling pathway in rheumatoid arthritis

Objectives. S100A4 has been implicated in cancer and several inflammatory diseases, including RA. The aim of the present study was to determine whether S100A4 can stimulate proinflammatory cytokine production in mononuclear cells. Methods. Peripheral blood mononuclear cells (PBMCs) isolated from patients with RA were stimulated with S100A4, S100A8, S100A9 and S100A12. The production of IL-1β, IL-6 and TNF-α was measured by ELISA. Receptor for advanced glycation end products (RAGEs) and Toll-like receptor 4 (TLR4) signalling were examined. For signalling pathway blocking studies, inhibitors of myeloid differentiation primary response gene 88 (MyD88), nuclear factor kappa B (NF-κB) and the mitogen activated protein (MAP) kinases p38, extracellular signal-regulated kinase 1/2 (ERK1/2) and Jun N-terminal kinase (JNK) were used. MAP kinase activation was evaluated by western blotting. Results. Stimulation of PBMCs with S100A4 significantly up-regulated IL-1β, IL-6 and TNF-α production compared with unstimulated cells (P < 0.001). Importantly, the production of these cytokines was markedly enhanced in response to S100A4 compared with S100A8 and S100A12; however, it was less pronounced compared with S100A9. Furthermore, enhanced production of proinflammatory cytokines in S100A4-stimulated PMBCs was at least partly mediated via TLR4, but not RAGEs, and by activation of the transcription factor NF-κB and the MAP kinases p38 and ERK1/2. Conclusion. This is the first study to demonstrate that S100A4 can induce an inflammatory response mediated by TLR4 and by the activation of NF-κB and the kinases p38 and ERK1/2 in mononuclear cells from patients with RA. Therefore S100A4 may be a potential therapeutic target for immune-mediated disease

Ring formation and hydration effects in electron attachment to misonidazole

This research was funded by CZECH SCIENCE FOUNDATION grant number 19-01159S; Czech Ministry of Education Youth and Sports via OP RDE Grant no. CZ.02.2.69/0.0/16_027/0008355; S.D. acknowledges funding from the FWF, Vienna (P30332).We study the reactivity of misonidazole with low-energy electrons in a water environment combining experiment and theoretical modelling. The environment is modelled by sequential hydration of misonidazole clusters in vacuum. The well-defined experimental conditions enable computational modeling of the observed reactions. While the NO- 2 dissociative electron attachment channel is suppressed, as also observed previously for other molecules, the OH- channel remains open. Such behavior is enabled by the high hydration energy of OH- and ring formation in the neutral radical co-fragment. These observations help to understand the mechanism of bio-reductive drug action. Electron-induced formation of covalent bonds is then important not only for biological processes but may find applications also in technology.publishersversionpublishe

Biochar and biochar with N-fertilizer affect soil N2O emission in Haplic Luvisol

The benefits of biochar application are well described in tropical soils, however there is a dearth of information on its effects in agricultural temperate soils. An interesting and little explored interaction may occur in an intensive agriculture setting; biochar addition may modify the effect of commonplace N-fertilization.We conducted a field experiment to study the effects of biochar application at the rate of 0, 10 and 20 t ha−1 (B0, B10 and B20) in combination with 0, 40 and 80 kg N ha−1 of N-fertilizer (N0, N40, N80).We followed nitrous oxide (N2O) emissions, analysed a series of soil physicochemical properties and measured barley yield in a Haplic Luvisol in Central Europe. Seasonal cumulative N2O emissions from B10N0 and B20N0 treatments decreased by 27 and 25% respectively, when compared to B0N0. Cumulative N2O emissions from N40 and N80 combined with B10 and B20 were also lower by 21, 19 and 25, 32%, respectively compared to controls B0N40 and B0N80. Average pH was significantly increased by biochar addition. Increased soil pH and reduces NO−3 content seen in biochar treatments could be the two possible mechanisms responsible for reduced N2O emissions. There was a statistically significant increase of soil water content in B20N0 treatment compared to B0N0 control, possibly as a result of larger surface area and the presence of microspores having altered pore size distribution and water-holding capacity of the soil. Application of biochar at the rate of 10 t ha−1 had a positive effect on spring barley grain yield

The metastasis promoting protein S100A4 is increased in idiopathic inflammatory myopathies

Objectives. The S100A4 protein is known as a metastasis promoting factor; however, its involvement in non-malignant diseases such as RA and psoriasis has been recently described. The aim of this study was to investigate the expression and possible role of S100A4 in idiopathic inflammatory myopathies. Methods. S100A4 protein expression was detected by immunohistochemistry in muscle tissue from control individuals (n = 11) and patients with PM and DM (n = 8/6). IF staining was used to co-localize S100A4 with selected cells. Cytokine expression and protein synthesis in S100A4-treated cells were analysed by RT-PCR and ELISA. Results. S100A4 protein was significantly up-regulated in muscle tissue of patients with inflammatory myopathies compared with control individuals and was associated particularly with the presence of mononuclear infiltrates. Only few regenerating muscle fibres in PM/DM expressed S100A4. Then we analysed the effect of S100A4 on human myocytes and peripheral blood mononuclear cells (PBMCs). Although S100A4 did not affect myocytes, stimulation of PBMCs with S100A4 significantly induced the expression and synthesis of TNF-α, IL-1β and IL-6, but not of IFN-α. We showed that S100A4 is not directly involved in perforin/granzyme B-induced apoptosis and that it does not modulate the expression of Bax and Bcl2 mRNA in myocytes and PBMCs. Conclusion. Increased expression of S100A4 in inflamed muscle tissue highlights its potential role in the pathogenesis of inflammatory myopathies. S100A4 may act as a cytokine-like factor indirectly promoting muscle fibre damage by stimulating mononuclear cells to increase the synthesis of pro-inflammatory cytokine

Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (&gt;2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome