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Mining detailed opinions buried in the vast amount of review text data is an important, yet quite challenging task with widespread applications in multiple domains. Latent Aspect Rating Analysis (LARA) refers to the task of inferring both opinion ratings on topical aspects (e.g., location, service of a hotel) and the relative weights reviewers have placed on each aspect based on review content and the associated overall ratings. A major limitation of previous work on LARA is the assumption of pre-specified aspects by keywords. However, the aspect information is not always available, and it may be difficult to pre-define appropriate aspects without a good knowledge about what aspects are actually commented on in the reviews.In this paper, we propose a unified generative model for LARA, which does not need pre-specified aspect keywords and simultaneously mines 1) latent topical aspects, 2) ratings on each identified aspect, and 3) weights placed on different aspects by a reviewer. Experiment results on two different review data sets demonstrate that the proposed model can effectively perform the Latent Aspect Rating Analysis task without the supervision of aspect keywords. Because of its generality, the proposed model can be applied to explore all kinds of opinionated text data containing overall sentiment judgments and support a wide range of interesting application tasks, such as aspect-based opinion summarization, personalized entity ranking and recommendation, and reviewer behavior analysis.

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Motivation: Medical Subject Headings (MeSH) indexing, which is to assign a set of MeSH main headings to citations, is crucial for many important tasks in biomedical text mining and information retrieval. Large-scale MeSH indexing has two challenging aspects: the citation side and MeSH side. For the citation side, all existing methods, including Medical Text Indexer (MTI) by National Library of Medicine and the state-of-the-art method, MeSHLabeler, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well.Methods: We propose DeepMeSH that incorporates deep semantic information for large-scale MeSH indexing. It addresses the two challenges in both citation and MeSH sides. The citation side challenge is solved by a new deep semantic representation, D2V-TFIDF, which concatenates both sparse and dense semantic representations. The MeSH side challenge is solved by using the ‘learning to rank’ framework of MeSHLabeler, which integrates various types of evidence generated from the new semantic representation.Results: DeepMeSH achieved a Micro F-measure of 0.6323, 2% higher than 0.6218 of MeSHLabeler and 12% higher than 0.5637 of MTI, for BioASQ3 challenge data with 6000 citations.Availability and Implementation: The software is available upon request.Contact: zhusf@fudan.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.

Personalized search systems tailor search results to the current user intent using historic search interactions. This relies on being able to find pertinent information in that user's search history, which can be challenging for unseen queries and for new search scenarios. Building richer models of users' current and historic search tasks can help improve the likelihood of finding relevant content and enhance the relevance and coverage of personalization methods. The task-based approach can be applied to the current user's search history, or as we focus on here, all users' search histories as so-called "groupization" (a variant of personalization whereby other users' profiles can be used to personalize the search experience). We describe a method whereby we mine historic search-engine logs to find other users performing similar tasks to the current user and leverage their on-task behavior to identify Web pages to promote in the current ranking. We investigate the effectiveness of this approach versus query-based matching and finding related historic activity from the current user (i.e., group versus individual). As part of our studies we also explore the use of the on-task behavior of particular user cohorts, such as people who are expert in the topic currently being searched, rather than all other users. Our approach yields promising gains in retrieval performance, and has direct implications for improving personalization in search systems.

The mcr-1 gene was detected in 5.11% (58/1136) of Escherichia coli isolates of chicken origin from 13 provinces in China. A novel mcr-1 variant, named mcr-1.3, encoding an Ile-to-Val functional variant of MCR-1 was identified in a sequence type 155 (ST155) strain. An mcr-1.3-containing IncI2 plasmid, pHeN867 (60,757 bp), was identified. The transfer of pHeN867 led to a 32-fold increase in the MIC of colistin in the recipient, exhibiting an effect on colistin resistance that was similar to that of mcr-1. KEYWORDS E. coli, colistin resistance, mcr-1.3, plasmid P olymyxins (polymyxin B and colistin) are a last-resort treatment for infections caused by multidrug-resistant (MDR) Gram-negative bacteria (1). In veterinary use, colistin is administered with food in pig and poultry farming to prevent infections caused by pathogens (2). The mcr-1 gene, which confers plasmid-mediated colistin resistance to Enterobacteriaceae, was identified in an IncI2 plasmid from Escherichia coli and Klebsiella pneumoniae in China in 2016 (3). The mcr-1 gene found in E. coli (4), K. pneumoniae (5), and Salmonella spp. (6) has been proven to disseminate ubiquitously. The transmission of mcr-1-mediated colistin resistance between animals and human has been a threat to human health. It has also been demonstrated that the mcr-1 gene can coexist with bla CTX-M (5), bla NDM (7), and other resistance genes (4), which threatens a return of untreatable infections worldwide. Previous reports described the unique mcr-1 gene sequence compared with that of the originally published sequence (3), which indicates that mcr-1 is relatively conserved. Recently, a point mutation of A¡T at position 8 in mcr-1 was identified in K. pneumoniae (8). To investigate the epidemiology of mcr-1 and its variant, E. coli isolates collected from chickens nationwide in China were assessed.In total, 1,136 nonduplicate E. coli isolates were collected between 2010 and 2015 from sick chickens in 20 provinces and municipalities in China. All of these isolates were preliminarily screened on Mueller-Hinton agar medium with 2 g/ml colistin. Because the cooccurrence of mcr-1 with bla CTX-M may accelerate the transmission of resistance to colistin and cephalosporins, the mcr-1 (3) and bla CTX-M (9) genes were detected by PCR amplification of the isolates with resistance to colistin. The corresponding primers used to amplify the whole mcr-1 gene and parts of the ISApl1 element are listed in Table S1 in the supplemental material. For all of the positive PCR products of mcr-1, Sanger sequencing was performed (Tsingke Biological Technology, Chengdu, China) by using a DNA analyzer (Applied Biosystems, Life Technologies, Carlsbad, CA). We found a total of 58 (5.11%) mcr-1-positive isolates, including one isolate harboring the mcr-1 gene with mutations not found in the originally published gene sequence (3). MICs of colistin

The aim of the present study was to investigate the antibiotic resistance profiles and the molecular epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates from two production swine operations in Sichuan Province, China, between August 2002 and February 2007. The prevalence of ESBL-producing E. coli increased dramatically from 2.2% to 10.7% during this period. This increase appeared mostly related to dissemination of CTX-M-type ESBLs among E. coli isolates. Of 212 E. coli isolates studied, 14 harbored ESBL genes. Among them, 13 harbored bla(CTX-M-15/22) and one harbored bla(SHV-2). To our knowledge, this is the first study to identify bla(CTX-M-22) from production animals. One isolate in 2002 harbored bla(SHV-2), indicating that ESBL genes have been present in farm animals in China since at least 2002. Molecular characterization and pulsed-field gel electrophoresis of the ESBL-producing isolates suggested that different mechanisms may be involved in the dissemination of the CTX-M genes and revealed that additional resistance determinants for non-beta-lactam antibiotics were carried by plasmids encoding certain ESBL genes. Results of this study provide an example of how ESBL genes, particularly those of CTX-M lineages, are rapidly spreading among E. coli isolates from commercial pig farms in Sichuan province of China.

Arcanobacterium pyogenes is commonly isolated from ruminant animals as an opportunistic pathogen that co-infects with other bacteria, normally causing surface or internal abscesses. Twenty-eight strains of A. pyogenes isolated from forest musk deer suppurative samples were identified by their 16S rRNA gene sequences, and confirmed by amplification of the pyolysinencoding gene (plo) in all isolates. The MICs of 14 commonly used antibiotics were determined by an agar dilution method. Class 1 and 2 intI genes were amplified to determine whether integrons were present in the A. pyogenes genome. Class 1 gene cassettes were detected by specific primers and analysed by sequencing. All of the strains were susceptible to most fluoroquinolone antibiotics; however, high resistance rates were observed for b-lactams and trimethoprim. A total of 18 of the isolates (64.3 %) were positive for the class 1 intI gene, and 16 (57.1 %) contained class 1 gene cassettes with the aacC, aadA1, aadA2, blaP1 and dfr2a genes. Most were present in the multi-resistant isolates, indicating a general concordance between the presence of gene cassettes and antibiotic resistance, and that the integrons have played an important role in the dissemination of antimicrobial resistance in this species. INTRODUCTIONForest musk deer (Moschus berezovskii) are solitary ruminants encountered mainly in South-West China. The musk secreted by the deer is a traditional and precious Chinese medicine, and is also used in the manufacture of perfumes. As a result of the decreasing population size, all forest musk deer species were categorized as first-class key species of wildlife protected by Chinese legislation in 2002 (Chen et al., 2007;Guha et al., 2007;Guan et al., 2009). Artificial breeding of forest musk deer started in the 1950s, and diseases were the most significant restriction factor preventing a population increase (Lu et al., 2009). In Miyaluo Farm (Sichuan Province, China), every eight to ten forest musk deer are fed in one fold of about 200 m 2 due to the timid and leaping character of these animals, which means that they easily hurt themselves. Dyspepsia, pneumonia, metritis, urinary stones and abscesses are common diseases of forest musk deer here, and abscesses in particular have cause hundreds of deaths. Antibiotics have been used here for over 15 years, but due to the previous negligent management where drug abuse was prevalent and the dose was always on the high side, resistance has developed, meaning that many of the drugs have become useless against some of the pathogenic infections.Arcanobacterium pyogenes is considered an important opportunistic pathogen of the upper respiratory tract and in puerperal uterine infections of cattle, sheep, swine, birds, humans and many other species (Nattermann & Horsch, 1977;Queen et al., 1994;Narayanan et al., 1998;Silva et al., 2008). It was recently reclassified from the genus Actinomyces on the basis of the rRNA gene sequence (Pascual Ramos et al., 1997). The organisms enter the blood stream and interact...