Mutation frequency of non-ESBL phenotype SENTRY (Asia-Pacific) isolates of Klebsiella pneumoniae conversion to an ESBL positive phenotype

Extended spectrum β-lactamases or ESBLs, which are derived from non-ESBL precursors by point mutation of β-lactamase genes (bla), are spreading rapidly all over the world and have caused considerable problems in the treatment of infections caused by bacteria which harbour them. The mechanism of this resistance is not fully understood and a better understanding of these mechanisms might significantly impact on choosing proper diagnostic and treatment strategies. Previous work on SHV β-lactamase gene, blaSHV, has shown that only Klebsiella pneumoniae strains which contain plasmid-borne blaSHV are able to mutate to phenotypically ESBL-positive strains and there was also evidence of an increase in blaSHV copy number. Therefore, it was hypothesised that although specific point mutation is essential for acquisition of ESBL activity, it is not yet enough, and blaSHV copy number amplification is also essential for an ESBL-positive phenotype, with homologous recombination being the likely mechanism of blaSHV copy number expansion. In this study, we investigated the mutation rate of non-ESBL expressing K. pneumoniae isolates to an ESBL-positive status by using the MSS-maximum likelihood method. Our data showed that blaSHV mutation rate of a non-ESBL expressing isolate is lower than the mutation rate of the other single base changes on the chromosome, even with a plasmid-borne blaSHV gene. On the other hand, mutation rate from a low MIC ESBL-positive (≤ 8 µg/mL for cefotaxime) to high MIC ESBL-positive (≥16 µg/mL for cefotaxime) is very high. This is because only gene copy number increase is needed which is probably mediated by homologous recombination that typically takes place at a much higher frequencies than point mutations. Using a subinhibitory concentration of novobiocin, as a homologous recombination inhibitor, revealed that this is the case.

Bearing-only SLAM : a vision-based navigation system for autonomous robots

To navigate successfully in a previously unexplored environment, a mobile robot must be able to estimate the spatial relationships of the objects of interest accurately. A Simultaneous Localization and Mapping (SLAM) sys- tem employs its sensors to build incrementally a map of its surroundings and to localize itself in the map simultaneously. The aim of this research project is to develop a SLAM system suitable for self propelled household lawnmowers. The proposed bearing-only SLAM system requires only an omnidirec- tional camera and some inexpensive landmarks. The main advantage of an omnidirectional camera is the panoramic view of all the landmarks in the scene. Placing landmarks in a lawn field to define the working domain is much easier and more flexible than installing the perimeter wire required by existing autonomous lawnmowers. The common approach of existing bearing-only SLAM methods relies on a motion model for predicting the robot’s pose and a sensor model for updating the pose. In the motion model, the error on the estimates of object positions is cumulated due mainly to the wheel slippage. Quantifying accu- rately the uncertainty of object positions is a fundamental requirement. In bearing-only SLAM, the Probability Density Function (PDF) of landmark position should be uniform along the observed bearing. Existing methods that approximate the PDF with a Gaussian estimation do not satisfy this uniformity requirement. This thesis introduces both geometric and proba- bilistic methods to address the above problems. The main novel contribu- tions of this thesis are: 1. A bearing-only SLAM method not requiring odometry. The proposed method relies solely on the sensor model (landmark bearings only) without relying on the motion model (odometry). The uncertainty of the estimated landmark positions depends on the vision error only, instead of the combination of both odometry and vision errors. 2. The transformation of the spatial uncertainty of objects. This thesis introduces a novel method for translating the spatial un- certainty of objects estimated from a moving frame attached to the robot into the global frame attached to the static landmarks in the environment. 3. The characterization of an improved PDF for representing landmark position in bearing-only SLAM. The proposed PDF is expressed in polar coordinates, and the marginal probability on range is constrained to be uniform. Compared to the PDF estimated from a mixture of Gaussians, the PDF developed here has far fewer parameters and can be easily adopted in a probabilistic framework, such as a particle filtering system. The main advantages of our proposed bearing-only SLAM system are its lower production cost and flexibility of use. The proposed system can be adopted in other domestic robots as well, such as vacuum cleaners or robotic toys when terrain is essentially 2D.

Toward a fuzzy domain ontology extraction method for adaptive e-learning

With the widespread applications of electronic learning (e-Learning) technologies to education at all levels, increasing number of online educational resources and messages are generated from the corresponding e-Learning environments. Nevertheless, it is quite difficult, if not totally impossible, for instructors to read through and analyze the online messages to predict the progress of their students on the fly. The main contribution of this paper is the illustration of a novel concept map generation mechanism which is underpinned by a fuzzy domain ontology extraction algorithm. The proposed mechanism can automatically construct concept maps based on the messages posted to online discussion forums. By browsing the concept maps, instructors can quickly identify the progress of their students and adjust the pedagogical sequence on the fly. Our initial experimental results reveal that the accuracy and the quality of the automatically generated concept maps are promising. Our research work opens the door to the development and application of intelligent software tools to enhance e-Learning.

Mining Negative Relevance Feedback for Information Filtering

It is a big challenge to clearly identify the boundary between positive and negative streams. Several attempts have used negative feedback to solve this challenge; however, there are two issues for using negative relevance feedback to improve the effectiveness of information filtering. The first one is how to select constructive negative samples in order to reduce the space of negative documents. The second issue is how to decide noisy extracted features that should be updated based on the selected negative samples. This paper proposes a pattern mining based approach to select some offenders from the negative documents, where an offender can be used to reduce the side effects of noisy features. It also classifies extracted features (i.e., terms) into three categories: positive specific terms, general terms, and negative specific terms. In this way, multiple revising strategies can be used to update extracted features. An iterative learning algorithm is also proposed to implement this approach on RCV1, and substantial experiments show that the proposed approach achieves encouraging performance.

An effective model of using negative relevance feedback for information filtering

Over the years, people have often held the hypothesis that negative feedback should be very useful for largely improving the performance of information filtering systems; however, we have not obtained very effective models to support this hypothesis. This paper, proposes an effective model that use negative relevance feedback based on a pattern mining approach to improve extracted features. This study focuses on two main issues of using negative relevance feedback: the selection of constructive negative examples to reduce the space of negative examples; and the revision of existing features based on the selected negative examples. The former selects some offender documents, where offender documents are negative documents that are most likely to be classified in the positive group. The later groups the extracted features into three groups: the positive specific category, general category and negative specific category to easily update the weight. An iterative algorithm is also proposed to implement this approach on RCV1 data collections, and substantial experiments show that the proposed approach achieves encouraging performance.

Tag based collaborative filtering for recommender systems

Collaborative tagging can help users organize, share and retrieve information in an easy and quick way. For the collaborative tagging information implies user’s important personal preference information, it can be used to recommend personalized items to users. This paper proposes a novel tag-based collaborative filtering approach for recommending personalized items to users of online communities that are equipped with tagging facilities. Based on the distinctive three dimensional relationships among users, tags and items, a new similarity measure method is proposed to generate the neighborhood of users with similar tagging behavior instead of similar implicit ratings. The promising experiment result shows that by using the tagging information the proposed approach outperforms the standard user and item based collaborative filtering approaches.

Collaborative Filtering Recommender Systems based on Popular Tags

The social tags in web 2.0 are becoming another important information source to profile users' interests and preferences for making personalized recommendations. However, the uncontrolled vocabulary causes a lot of problems to profile users accurately, such as ambiguity, synonyms, misspelling, low information sharing etc. To solve these problems, this paper proposes to use popular tags to represent the actual topics of tags, the content of items, and also the topic interests of users. A novel user profiling approach is proposed in this paper that first identifies popular tags, then represents users’ original tags using the popular tags, finally generates users’ topic interests based on the popular tags. A collaborative filtering based recommender system has been developed that builds the user profile using the proposed approach. The user profile generated using the proposed approach can represent user interests more accurately and the information sharing among users in the profile is also increased. Consequently the neighborhood of a user, which plays a crucial role in collaborative filtering based recommenders, can be much more accurately determined. The experimental results based on real world data obtained from Amazon.com show that the proposed approach outperforms other approaches.

Collaborative filtering recommender systems using tag information

Recommender Systems is one of the effective tools to deal with information overload issue. Similar with the explicit rating and other implicit rating behaviours such as purchase behaviour, click streams, and browsing history etc., the tagging information implies user’s important personal interests and preferences information, which can be used to recommend personalized items to users. This paper is to explore how to utilize tagging information to do personalized recommendations. Based on the distinctive three dimensional relationships among users, tags and items, a new user profiling and similarity measure method is proposed. The experiments suggest that the proposed approach is better than the traditional collaborative filtering recommender systems using only rating data.