PACRR: A Position-Aware Neural IR Model for Relevance Matching

In order to adopt deep learning for information retrieval, models are needed that can capture all relevant information required to assess the relevance of a document to a given user query. While previous works have successfully captured unigram term matches, how to fully employ position-dependent information such as proximity and term dependencies has been insufficiently explored. In this work, we propose a novel neural IR model named PACRR aiming at better modeling position-dependent interactions between a query and a document. Extensive experiments on six years' TREC Web Track data confirm that the proposed model yields better results under multiple benchmarks.Comment: To appear in EMNLP201

Development of a phage cocktail to prevent Proteus mirabilis biofilm formation in urinary catheters

Proteus mirabilis is an enterobacterium that causes catheter-associated urinary tract infections (CAUTIs) due to its ability to form crystalline biofilms on the surfaces. These CAUTIs are very difficult to treat, since the biofilm structures are extremely tolerant to high concentrations of antibiotics. Bacteririophages (phages) have been used widely to control and prevent a diversity of bacterial species, however a limited number of phages for P. mirabilis have been isolated and studied. Here we report the isolation of two novel virulent phages, the myovirus vB_PmiM_5460 and the podovirus vB_PmiP_5461 able to target respectively 57% and 100% of all Proteus strains tested in this study. Both phages have been characterized thoroughly and sequencing data revealed no traces of genes associated with lysogeny. To further evaluate the phages ability to prevent catheter colonization by Proteus, phages adherence to silicon surfaces was assessed. Both phages were able to adhere, but the extent of adhesion was found to be phage dependent. Further tests in phagecoated catheters using a dynamic biofilm model simulating CAUTIs, have shown a 90% significant reduction of P. mirabilis biofilm formation up to 168 h of catheterization. These results highlight the potential usefulness of the two isolated phages for the prevention of surface colonization by this bacterium

Genomic characterization of the Staphylococcus epidermidis-specific bacteriophage SEP1 and evaluation of its lytic activity against bacterial under different metabolic states

Staphylococcus epidermidis is one of the most frequent causative agents of nosocomial infections, predominantly in patients with indwelling medical devices. This microrganism may form biofilms which are microbial structures very tolerant to the host immune defenses and to antibiotherapy. Therefore, studies are needed in order to develop effective methods for biofilm control. Currently, bacteriophages (phages) are seen as an important tool to combat pathogenic organisms. These bacteria-specific viruses are generally very efficient antibacterial agents and possess many advantages over antibiotics. The present study concerns the search for virulent phages with broad host range for S. epidermidis biofilm therapy. Using wastewater treatment plant raw effluents, a novel phage was isolated and characterized. This virus was named phiIBB-SEP1 and TEM micrographs suggested that it belonged to the Twortlikevirus genus. Phage phiIBB-SEP1 is able to infect 41 S. epidermidis clinical isolates used in this study, and contrarily to other polyvalent viruses of the Twortlikevirus genus, phiIBB-SEP1 is highly specific for S. epidermidis strains. The genome of this phage was fully sequenced and presents the typical structure of a member of the Twortlikevirus. However, when compared to other staphylococcal members of this genus, it showed DNA sequence identities no greater than 58.2%, suggesting that phiIBB-SEP1 is a new species within this subfamily. Efficacy studies results showed that phage phiIBB-SEP1 is able to cause a 6 Log CFU per ml reduction of the cell titre in less than 2h for some of the clinical strains in exponential phase; and, in less than 4h for stationary phase cells (using a multiplicity of infection of 1). This phage has also the capacity of reducing, by up to 2 Log CFU per ml, 24h scraped biofilm cells, and in some strains it was observed 50% cell reduction. Besides CFU counting, this cell reduction was confirmed by flow cytometry counting. Additionally, live/death flow cytometry staining allowed the observation that this phage kills biofilms bacteria in different metabolic states. These are promising results, since phage phiIBB-SEP1 presents a broad host strain range and the ability to control S. epidermidis bacteria in different metabolic states. Keywords: bacteriophage, Twortlikevirus, S. epidermidis, staphylococci, biofilm

A tool for implementing privacy in Nano

© 2020 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.We present a work in progress strategy for implementing privacy in Nano at the consensus level, that can be of independent interest. Nano is a cryptocurrency that uses an Open Representative Voting (ORV) as a consensus mechanism, a variant of Delegated Proof of Stake. Each transaction on the network is voted on by representatives, and each vote has a weight equal to the percentage of their total delegated balance. Every account can delegate their stake to any other account (including itself) and change it anytime it wants. The goal of this paper is to achieve a way for the consensus algorithm to function without knowing the individual balances of each account. The tool is composed of three different schemes. The first is a weighted threshold secret sharing scheme based on the Chinese Remainder Theorem for polynomial rings [1] and it's used to generate, in a distributed way, a secret that will be a private key of an additive ElGamal cryptosystem over elliptic curves (EC-EG) [2], which is additive homomorphic. The second scheme is the polynomials commitment scheme presented in [3] and is used to make the previous scheme verifiable, i.e., without the need of a trusted dealer. Finally, the third scheme is used to decrypt a ciphertext of the EC-EG cryptosystem without reconstructing the private key and, because of that, can be used multiple times.IEEEinfo:eu-repo/semantics/submittedVersio

Enhancing Humoral Responses Against HIV Envelope Trimers via Nanoparticle Delivery with Stabilized Synthetic Liposomes

An HIV vaccine capable of eliciting durable neutralizing antibody responses continues to be an important unmet need. Multivalent nanoparticles displaying a high density of envelope trimers may be promising immunogen forms to elicit strong and durable humoral responses to HIV, but critical particle design criteria remain to be fully defined. To this end, we developed strategies to covalently anchor a stabilized gp140 trimer, BG505 MD39, on the surfaces of synthetic liposomes to study the effects of trimer density and vesicle stability on vaccine-elicited humoral responses in mice. CryoEM imaging revealed homogeneously distributed and oriented MD39 on the surface of liposomes irrespective of particle size, lipid composition, and conjugation strategy. Immunization with covalent MD39-coupled liposomes led to increased germinal center and antigen-specific T follicular helper cell responses and significantly higher avidity serum MD39-specific IgG responses compared to immunization with soluble MD39 trimers. A priming immunization with liposomal-MD39 was important for elicitation of high avidity antibody responses, regardless of whether booster immunizations were administered with either soluble or particulate trimers. The stability of trimer anchoring to liposomes was critical for these effects, as germinal center and output antibody responses were further increased by liposome compositions incorporating sphingomyelin that exhibited high in vitro stability in the presence of serum. Together these data highlight key liposome design features for optimizing humoral immunity to lipid nanoparticle immunogens.National Institute of Allergy and Infectious Diseases (U.S.) (Award UM1AI100663)National Institutes of Health (U.S.) (Award P01-AI104715)National Institutes of Health (U.S.) (Award P01-AI048240)National Cancer Institute (U.S.) (Grant P30-CA14051

Species composition and bycatches of a new crustacean trawl in Chile

The species composition and bycatches of a new trawl for crustaceans (Heterocarpus reedi, Cervimunida johni and Pleuroncodes monodon) was studied in central Chile between 2007 and 2009. The spatial and temporal variations of the catch composition were analyzed using univariate and multivariate comparison techniques. In 289 trawl hauls, 72 taxa were recorded, with target species accounting for most of the catch, while the bycatch consisted mainly of Merluccius gayi, Hippoglossina macrops, Coelorinchus aconcagua, Epigonus crassicaudus and Platymera gaudichaudii. 14 species of elasmobranchs were identified, and at least one of these species was present in 50% of the hauls made. The classification and ordination methods showed the existence of three groups, each one associated with a target species, with no significant spatial and temporal effects. The information obtained in this study represents the basis for setting targets in order to reduce the bycatch captured by this trawl. The focused strategy on the most recurring and sensitive species for these fisheries is also discussed. (C) 2011 Elsevier B.V. All rights reserved