Towards practical use of Bloom Filter based IP lookup in operational network

International audienceBloom Filter is a widely used data structure in computer science. It enables memory efficient and fast set membership queries. Bloom filter-based solutions have been proposed in the past decade for lookup in forwarding tables of backbone routers [2]. However, the main shortcomings of using Bloom Filters for lookup lie in the absence of support for deletion operations that are needed to update the forwarding tables. Counting Bloom Filter supporting deletion has therefore to be used, increasing significantly the memory requirement. Moreover, Counting Bloom Filter suffers from both false positive and false negative. In this paper, we propose to solve the issue with deletion of Bloom Filters by using a Withdrawal To annOuncement (WTO) mapping that replaces withdrawal with announcements, transforming deletions into additions or record changes. Experimental evaluation show that the proposed techniques improve largely the performance of Bloom Filter used for forwarding lookup and open way for the use of Bloom Filters in real operational settings

Inferring structural variant cancer cell fraction

Abstract: We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone’s performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Chairman's Communist Party of China member status and targeted poverty alleviation: Evidence from China.

Based on the data of Chinese listed private companies from 2016 to 2020, this paper investigates the influence of the Chairman's member status of Communist Party of China (CPC) on targeted poverty alleviation. The research results demonstrate that the Chairman's CPC member status of private companies significantly increases the companies' willingness and the amounts of investment in poverty alleviation. The construction of the CPC organization can strengthen the role of the chairman's Communist Party of China member status in promoting targeted poverty alleviation. The conclusions are still valid through robustness tests, such as substituting dependent variables, adjusting the sample range, and PSM-paired samples. In addition, the Impact Threshold for a Confounding Variable is used to deal with endogenous problems

Based on DNA Strand Displacement and Functionalized Magnetic Nanoparticles: A Promising Strategy for Enzyme Immobilization

The efforts to enhance the stability of enzymes and improve their activity have generated considerable interest because of their wide applications in bioenergy conversion, proteomics research, and bioassays. This study reports a promising strategy for enzyme immobilization based on toehold-mediated DNA strand displacement on functionalized magnetic nanoparticles for the first time. The strategy provided a convenient approach to achieve sequential displacement and immobilization of different enzymes, using alkaline phosphatase (ALP), horseradish peroxidase (HRP), and trypsin as different model enzymes. Taking trypsin as an example, the enzyme immobilization procedure by DNA strand displacement exhibited high reversibility and reproducibility, which could retrieve more than 87% of the enzymatic activity after consecutive hybridization and dehybridization cycles. The thermal stability of the immobilized trypsin was significantly enhanced up to 3.1- and 2.3-fold greater than free enzyme after 45 min incubation at 60 and 70 °C, respectively, and the immobilized enzyme preserved promising enzymatic activity of more than 87% after 10 cycles. Notably, the immobilized enzyme exhibited excellent long-term incubation stability and storage stability as compared with free enzyme and showed up to 11-fold higher stability than free enzyme toward different solvents. Significantly improved digestion efficiency of myoglobin, glycated hemoglobin, and cytochrome C was achieved with this immobilized enzyme within 10 min, and the obtained sequence coverages were 1.5-, 1.3-, and 1.6-fold higher than conventional in-solution digestion for 12 h. Thus, the developed strategy exhibited a promising alternative platform with high magnetic responsiveness and significantly enhanced properties for the immobilization of important enzymes and their broad applications

Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health

Abstract Background Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study. Results The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references. Conclusions In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health

Study on the Creep-Sliding Mechanism of the Giant Xiongba Ancient Landslide Based on the SBAS-InSAR Method, Tibetan Plateau, China

The geohazards associated with strongly deformed and reactivated large-scale ancient landslide are analyzed through a study of the Xiongba ancient landslide. The SBAS-InSAR method, combined with remote sensing interpretation, was used to obtain the Xiongba ancient landslide surface deformation characteristics, on the western bank of the Jinsha River, during the period from October 2017 to June 2020. Two large strong deformation zones were discovered in this study, H1 and H2, which were located at the front edge of the Xiongba landslide. The maximum cumulative deformation in the H1 deformation zone was approximately 204 mm, and the deformation in the H2 deformation zone was approximately 302 mm. Influenced by the Jinsha River erosion, the Baige landslide-dammed lake-dam breakage-debris (LDLDB) flow/flood hazard chains, which occurred 75 km upstream reaches in October and November 2018, and the erosion of the foot of the Xiongba ancient landslide foot resulted in notably enhanced deformation. The creep rate in the H1 deformation zone was 14~16 times that before the Baige landslide hazard chains occurred, and the hazard chains caused sliding in the H2 zone. The Xiongba ancient landslide is undergoing retrogressive reactivation. The Xiongba ancient landslide is currently experiencing continuously creep-sliding, and the deformation rate in some areas is accelerating, which may induce a large-scale reactivation of the Xiongba ancient landslide and an LDLDB hazard chain

The neuropathological mechanism of EV-A71 infection attributes to inflammatory pryoptosis and viral replication via activating the hsa_circ_0045431/ hsa_miR_584/NLRP3 regulatory axis

Neuropathological damage has been considered to be the main cause of death from EV-A71 infection, but the underlying mechanism has not been elucidated. Pyroptosis, a new form of inflammatory programmed cell death, has been verified to be involved in the pathogenesis of various viruses. circRNAs are a novel type of endogenous noncoding RNA gaining research interest in recent years, especially their special roles in the process of virus infection. Thus, in this study, we combined EV-A71, pyroptosis and circRNA to find a breakthrough in the pathogenesis of EV-A71 infection. Firstly, whether EV-A71 infection leaded to pyroptosis formation was examined by a series detection of cell death, cell viability, LDH release, caspase 1 activity, the expression levels of pyroptosis-related molecules and the concentrations of IL-1β and IL-18. Secondly, high-throughput sequencing of circRNAs was carried out to excavate the circRNA-miRNA-mRNA regulatory axis which might be associated with pyroptosis formation. Finally, the gain- and loss-of-functional experiments were further conducted to identify their functions. Our results showed that EV-A71 infection caused pyroptosis formation in SH-SY5Y cells. The circRNA sequencing analyzed the differentially expressed circRNAs and their possible functions. It was found that the hsa_circ_0045431/hsa_miR_584/NLRP3 regulatory axis might be involved in pyroptosis formation during EV-A71 infection. Then, hsa_circ_0045431 sponged hsa_miR_584 and hsa_miR_584 directly targeted NLRP3 were validated by IF, dual-luciferase, qRT-PCR and WB assays. Functional experiments were performed to further uncover that the up-regulation of hsa_circ_0045431 and NLRP3 promoted the inflammatory pyroptosis and viral replication, while the up-regulation of hsa_miR_584 suppressed the inflammatory pyroptosis and viral replication, and vice versa. Collectively, our study demystified that EV-A71 infection induced pyroptosis formation by activating hsa_circ_0045431/hsa_miR_584/NLRP3 regulatory axis, which could further effect viral replication. These findings provided novel insights into the pathogenesis of EV-A71 infection, and meanwhile revealed that the hsa_circ_0045431/ hsa_miR_584/NLRP3 regulatory axis can serve as a potential biological therapeutic target for EV-A71 infection

Physics Informed Neural Networks (PINN) for Low Snr Magnetic Resonance Electrical Properties Tomography (MREPT)

Electrical properties (EPs) of tissues facilitate early detection of cancerous tissues. Magnetic resonance electrical properties tomography (MREPT) is a technique to non-invasively probe the EPs of tissues from MRI measurements. Most MREPT methods rely on numerical differentiation (ND) to solve partial differential Equations (PDEs) to reconstruct the EPs. However, they are not practical for clinical data because ND is noise sensitive and the MRI measurements for MREPT are noisy in nature. Recently, Physics informed neural networks (PINNs) have been introduced to solve PDEs by substituting ND with automatic differentiation (AD). To the best of our knowledge, it has not been applied to MREPT due to the challenges in using PINN on MREPT as (i) a PINN requires part of ground-truth EPs as collocation points to optimize the network’s AD, (ii) the noisy input data disrupts the optimization of PINNs despite the noise-filtering nature of NNs and additional denoising processes. In this work, we propose a PINN-MREPT model based on a canonical analytic MREPT model. A reference padding layer with known EPs was added to surround the region of interest for providing additive collocation points. Moreover, an optimizable diffusion coefficient was embedded in the analytic MREPT model used in the PINN-MREPT. The noise robustness of the proposed PINN-MREPT for single-sample reconstruction was tested by using numerical phantoms of human brain with extra tumor-like tissues at different noise levels. The results of numerical experiments show that PINN-MREPT outperforms two typical numerical MREPT methods in terms of reconstruction accuracy, sensitivity to the extra tissues, and the correlations of line profiles in the regions of interest. The advantage of the PINN-MREPT is shown by the results of an experiment on phantom measurement, too. Moreover, it is found that the diffusion term plays an important role to achieve a noise-robust PINN-MREPT. This is an important step moving forward to a clinical application of MREPT