In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
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Question: Motivation: Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture. Results: We demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. Availability and implementation: metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix Contact: sofia.morfopoulou.10@ucl.ac.uk Supplementary information: Supplementary data are available at Bionformatics online.

Answer: Bayesian mixture analysis for metagenomic community profiling


Question: showing signs of disease in southern China during the period from 2013-2015. The nucleotide and amino acid sequences from the isolated field strains were compared to 42 published references. Nucleotide homologies ranged from 63.1-99.9% and amino acid homologies ranging from 60.2-100%. At least seven IBV genotypes were co-circulating in commercial chicken farms in southern China. The IBV isolates were genetically diverse and underwent continuing evolution. The QX-type, TW I-type, and 4/91-type were the most common genotypes during the three-year observation period and accounted for 88.8% of the isolated strains. Notably, the prevalence of the TW I-type strains has been increasing in recent years and has become the most common genotype in China. The emergence of variant IBV strains can be attributed to recombination. Serologic analysis and antigenic 3D cartography of 4 reference and 14 field isolated strains indicated the surveyed IBVs had diverse serology types and that the serotype of the isolated QX-type and TW I-type strains was distinct from the vaccines strains. Therefore, long-term continuing surveillance is necessary for IBV prevention and control. Avian infectious bronchitis (IB) is an acute and highly contagious disease caused by the avian infectious bronchitis virus (IBV). IB causes substantial economic losses throughout the poultry industry worldwide. IBV affects chickens of all ages causing upper respiratory disease, nephritic syndromes, and decreased egg production 1 . IBV has been circulating in China since 1982. The epidemiology of IBV in China is complicated due to the large geographical area, and multiple IBV genotypes and serotypes are known to coexist 2 . Our previous epidemiology monitoring during 2004 to 2012, found at least seven genotypes of IBV circulating. In that study, the QX-like IBV genotype that causes nephritis had become predominant in China 3-6 . Although IBV vaccines are widely used and most commercial chickens have been vaccinated, there are still frequent outbreaks of IB that cause clinical disease and production problems 7-9 . For example, widespread use of vaccines derived from Massachusetts (Mass) serotypes such as H120 and H52 did not prevent frequent outbreaks of IB in chicken flocks 10, 11 . IBV belongs to the genus Gammacoronavirus, family Coronaviridae, and order Nidovirales. Its genome is linear, non-segmented, positive-sense, single-stranded RNA that is approximately 27.6 kilobases (kb) in length. As with other coronaviruses, the IBV S1 glycoprotein contains virus neutralizing epitopes and serotype-specific sequences 12, 13 . The S1 protein is involved in infectivity and plays an important role in attachment to the host cell, as well as induction of neutralizing antibodies 14 . Given the importance of the S1 protein virus/host interactions, IBV genetic analysis and research of IBV has been primarily based on the S1 gene 15 . Variation in the S1 protein is the basis for genotype and serotype classification, defines antigen characteristics, contributes to emergence of IBV variants, and poor vaccine protection 13, 16 . S1 variability is due in part to the lack of proofreading by the RNA-dependent RNA polymerase (RDRP) that introduces mutations into the viral genome during replication. Variation is also introduced by the specific template switching mechanism used by coronaviruses, which frequently leads to genetic recombination 17, 18 . At least 30 serotypes of IBV have been identified worldwide. Vaccine cross-protection between serotypes is minimal 19 . Therefore, phylogenetic and genetic analyses have become tools for monitoring the molecular evolution of IBV and provide a fast and accurate method for genotype classification. In some studies, the genotype analyses have been used to predict IBV serotype and used to inform vaccine selection 20 . In this study, long-term surveillance was conducted with the aim of identifying IBV strains isolated from commercial chicken farms in south China. During 2013-2015, IBV strains were isolated from flocks with clinical outbreaks. Genetic, phylogenetic, and recombination analyses were performed to study the genetic diversity of the S1 gene in field isolated IBV strains. Cross-neutralization tests and antigenic cartography were performed to determine the serological and antigenic relationship between a part of the isolated and vaccine strains.

Answer: Epidemiology and characterization of avian infectious bronchitis virus strains circulating in southern China during the period from 2013-2015 OPEN


Question: Poyang Lake is situated within the East Asian Flyway, a migratory corridor for waterfowl that also encompasses Guangdong Province, China, the epicenter of highly pathogenic avian influenza (HPAI) H5N1. The lake is the largest freshwater body in China and a significant congregation site for waterfowl; however, surrounding rice fields and poultry grazing have created an overlap with wild waterbirds, a situation conducive to avian influenza transmission. Reports of HPAI H5N1 in healthy wild ducks at Poyang Lake have raised concerns about the potential of resilient freeranging birds to disseminate the virus. Yet the role wild ducks play in connecting regions of HPAI H5N1 outbreak in Asia is hindered by a lack of information about their migratory ecology. During 2007-08 we marked wild ducks at Poyang Lake with satellite transmitters to examine the location and timing of spring migration and identify any spatiotemporal relationship with HPAI H5N1 outbreaks. Species included the Eurasian wigeon (Anas penelope), northern pintail (Anas acuta), K

Answer:
Migration of Waterfowl in the East Asian Flyway and Spatial Relationship to HPAI H5N1 Outbreaks HHS Public Access