SQPR: Stream Query Planning with Reuse

When users submit new queries to a distributed stream processing system (DSPS), a query planner must allocate physical resources, such as CPU cores, memory and network bandwidth, from a set of hosts to queries. Allocation decisions must provide the correct mix of resources required by queries, while achieving an efficient overall allocation to scale in the number of admitted queries. By exploiting overlap between queries and reusing partial results, a query planner can conserve resources but has to carry out more complex planning decisions. In this paper, we describe SQPR, a query planner that targets DSPSs in data centre environments with heterogeneous resources. SQPR models query admission, allocation and reuse as a single constrained optimisation problem and solves an approximate version to achieve scalability. It prevents individual resources from becoming bottlenecks by re-planning past allocation decisions and supports different allocation objectives. As our experimental evaluation in comparison with a state-of-the-art planner shows SQPR makes efficient resource allocation decisions, even with a high utilisation of resources, with acceptable overheads

A self-consistent estimate for linear viscoelastic polycrystals with internal variables inferred from the collocation method

The correspondence principle is customarily used with the Laplace–Carson transform technique to tackle the homogenization of linear viscoelastic heterogeneous media. The main drawback of this method lies in the fact that the whole stress and strain histories have to be considered to compute the mechanical response of the material during a given macroscopic loading. Following a remark of Mandel (1966 Mécanique des Milieux Continus(Paris, France: Gauthier-Villars)), Ricaud and Masson (2009 Int. J. Solids Struct. 46 1599–1606) have shown the equivalence between the collocation method used to invert Laplace–Carson transforms and an internal variables formulation. In this paper, this new method is developed for the case of polycrystalline materials with general anisotropic properties for local and macroscopic behavior. Applications are provided for the case of constitutive relations accounting for glide of dislocations on particular slip systems. It is shown that the method yields accurate results that perfectly match the standard collocation method and reference full-field results obtained with a FFT numerical scheme. The formulation is then extended to the case of time- and strain-dependent viscous properties, leading to the incremental collocation method (ICM) that can be solved efficiently by a step-by-step procedure. Specifically, the introduction of isotropic and kinematic hardening at the slip system scale is considered

The Association between Peptic Ulcer Disease and Gastric Cancer: Results from the Stomach Cancer Pooling (StoP) Project Consortium

Background. Gastric cancer (GC) is the fifth most common type of cancer and the fourth most common cause of cancer-related mortality. Although the risk of GC and peptic ulcer disease (PUD) is known to be increased by H. pylori infection, evidence regarding the direct relationship between PUD and GC across ethnicities is inconclusive. Therefore, we investigated the association between PUD and GC in the Stomach cancer Pooling (StoP) consortium. Methods. History of peptic ulcer disease was collected using a structured questionnaire in 11 studies in the StoP consortium, including 4106 GC cases and 6922 controls. The two-stage individual-participant data meta-analysis approach was adopted to generate a priori. Unconditional logistic regression and Firth’s penalized maximum likelihood estimator were used to calculate study-specific odds ratios (ORs) and 95% confidence intervals (CIs) for the association between gastric ulcer (GU)/duodenal ulcer (DU) and risk of GC. Results. History of GU and DU was thoroughly reported and used in association analysis, respectively, by 487 cases (12.5%) and 276 controls (4.1%), and 253 cases (7.8%) and 318 controls (6.0%). We found that GU was associated with an increased risk of GC (OR = 3.04, 95% CI: 2.07–4.49). No association between DU and GC risk was observed (OR = 1.03, 95% CI: 0.77–1.39). Conclusions. In the pooled analysis of 11 case–control studies in a large consortium (i.e., the Stomach cancer Pooling (StoP) consortium), we found a positive association between GU and risk of GC and no association between DU and GC risk. © 2022 by the authors.This work is supported by Associazione Italiana per la Ricerca sul Cancro (AIRC), Project no. 21378 (Investigator Grant); Fondazione Italiana per la Ricerca sul Cancro (FIRC); Italian League for the Fight Against Cancer (LILT); European Cancer Prevention (ECP) Organization; and UPMC Start-up Grant (to HNL). P Paragomi was supported by a cancer research training grant from NIH (grant # T32CA186873)

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Complete genome characterization of two wild-type measles viruses from Vietnamese infants during the 2014 outbreak

A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool samples collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak

Genome sequences of a novel Vietnamese bat bunyavirus

To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined

A Quality-Centric Data Model for Distributed Stream Management Systems

It is challenging for large-scale stream management systems to return always perfect results when processing data streams originating from distributed sources. Data sources and intermediate processing nodes may fail during the lifetime of a stream query. In addition, individual nodes may become overloaded due to processing demands. In practice, users have to accept incomplete or inaccurate query results because of failure or overload. In this case, stream processing systems would benefit from knowing the impact of imperfect processing on data quality when making decisions about query optimisation and fault recovery. In addition, users would want to know how much the result quality was degraded. In this paper, we propose a quality-centric relational stream data model that can be used together with existing query processing methods over distributed data streams. Besides giving useful feedback about the quality of tuples to users, the model provides the distributed stream management system with information on how to optimise query processing and enhance fault tolerance. We demonstrate how our data model can be applied to an existing distributed stream management system. Our evaluation shows that it enables quality-aware load-shedding, while introducing only a small pertuple overhead

Enhancing Electron Transfer and Stability of Screen-Printed Carbon Electrodes Modified with AgNP-Reduced Graphene Oxide Nanocomposite

This paper presents a reliable solution to enhance the electron transfer and stability of screen-printed carbon electrodes (SPCEs) for the direct detection of pathogenic bacteria. A nanocomposite of silver nanoparticles (AgNPs) and reduced graphene oxide (rGO) was used to modify the SPCEs. Herein, the nanocomposite was synthesized via a hydrothermal method and then characterized by physicochemical methods. The electron transfer rate and electrochemical properties of the AgNP-rGO nanocomposite-modified SPCEs were investigated using cyclic voltammetry (CV) and electrochemical impedance spectroscopy. Measurements were performed for the detection of Salmonella bacteria without any labels. Results showed that the nanocomposite firmly adhered to the surfaces of the SPCEs, led to an increase of approximately 160% in the peak current, and decreased the charge transfer resistance to 0.45 kΩ. Electrochemical stability was found in 30 CV cycles. The modified SPCEs could detect Salmonella bacteria directly at concentrations of 10–105 CFU/mL, with a limit of detection (LoD) of as low as 22 CFU/mL. A possible mechanism was proposed to explain the enhanced electron transfer on the surface and the stability of the AgNP-rGO nanocomposite-modified SPCEs. The biosensor showed high stability, cost-effectiveness, and simplicity for the direct detection of pathogenic bacteria. Graphical Abstract: [Figure not available: see fulltext.