Genetic characteristics and integration specificity of Salmonella enterica temperate phages

IntroductionTemperate phages can engage in the horizontal transfer of functional genes to their bacterial hosts. Thus, their genetic material becomes an intimate part of bacterial genomes and plays essential roles in bacterial mutation and evolution. Specifically, temperate phages can naturally transmit genes by integrating their genomes into the bacterial host genomes via integrases. Our previous study showed that Salmonella enterica contains the largest number of temperate phages among all publicly available bacterial species. S. enterica is an important pathogen that can cause serious systemic infections and even fatalities.MethodsInitially, we extracted all S. enterica temperate phages from the extensively developed temperate phage database established in our previous study. Subsequently, we conducted an in-depth analysis of the genetic characteristics and integration specificity exhibited by these S. enterica temperate phages.ResultsHere we identified 8,777 S. enterica temperate phages, all of which have integrases in their genomes. We found 491 non-redundant S. enterica temperate phage integrases (integrase entries). S. enterica temperate phage integrases were classified into three types: intA, intS, and phiRv2. Correlation analysis showed that the sequence lengths of S. enterica integrase and core regions of attB and attP were strongly correlated. Further phylogenetic analysis and taxonomic classification indicated that both the S. enterica temperate phage genomes and the integrase gene sequences were of high diversities.DiscussionOur work provides insight into the essential integration specificity and genetic diversity of S. enterica temperate phages. This study paves the way for a better understanding of the interactions between phages and S. enterica. By analyzing a large number of S. enterica temperate phages and their integrases, we provide valuable insights into the genetic diversity and prevalence of these elements. This knowledge has important implications for developing targeted therapeutic interventions, such as phage therapy, to combat S. enterica infections. By harnessing the lytic capabilities of temperate phages, they can be engineered or utilized in phage cocktails to specifically target and eradicate S. enterica strains, offering an alternative or complementary approach to traditional antibiotic treatments. Our study has implications for public health and holds potential significance in combating clinical infections caused by S. enterica

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

One-against-all weighted dynamic time warping for language-independent and speaker-dependent speech recognition in adverse conditions.

Considering personal privacy and difficulty of obtaining training material for many seldom used English words and (often non-English) names, language-independent (LI) with lightweight speaker-dependent (SD) automatic speech recognition (ASR) is a promising option to solve the problem. The dynamic time warping (DTW) algorithm is the state-of-the-art algorithm for small foot-print SD ASR applications with limited storage space and small vocabulary, such as voice dialing on mobile devices, menu-driven recognition, and voice control on vehicles and robotics. Even though we have successfully developed two fast and accurate DTW variations for clean speech data, speech recognition for adverse conditions is still a big challenge. In order to improve recognition accuracy in noisy environment and bad recording conditions such as too high or low volume, we introduce a novel one-against-all weighted DTW (OAWDTW). This method defines a one-against-all index (OAI) for each time frame of training data and applies the OAIs to the core DTW process. Given two speech signals, OAWDTW tunes their final alignment score by using OAI in the DTW process. Our method achieves better accuracies than DTW and merge-weighted DTW (MWDTW), as 6.97% relative reduction of error rate (RRER) compared with DTW and 15.91% RRER compared with MWDTW are observed in our extensive experiments on one representative SD dataset of four speakers' recordings. To the best of our knowledge, OAWDTW approach is the first weighted DTW specially designed for speech data in adverse conditions

Accuracy (%) by using original DTW on different (non)normalized dimensional MFCC.

<p>In the first column, numbers represent dimensions, ‘Norm’ means normalized MFCC, and ‘NonNorm’ means unnormalized MFCC.</p

DTW accuracy (DTW Acc) and OAWDTW accuracy (OAWDTWAcc)(%) comparison, and OAWDTW relative reduction of error rate (OAWDTW RRER) (%) based on DTW.

<p>DTW accuracy (DTW Acc) and OAWDTW accuracy (OAWDTWAcc)(%) comparison, and OAWDTW relative reduction of error rate (OAWDTW RRER) (%) based on DTW.</p

Algorithm 1: Dynamic Time Warping.

<p>Algorithm 1: Dynamic Time Warping.</p