Adding Network Coding Capabilities to the WSNet Simulator

This technical report presents the implementation of a Network Coding module in WSNet - a Wireless Sensor Network simulator. This implementation provides a generic programming interface to allow an easy specialization of different coding strategies: random, source/destination-oriented, intra/inter-flow, etc

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

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Connecting real world with virtual space

NTU Co-Space, an implementation of a virtual world replica of NTU with realistic 3D models of the entire campus, allows users to explore NTU through their own virtual avatar. Through this player avatar, users are able to travel to different parts of the campus, interact with intelligent NPCs as well as other players. Implemented as a web version that works on Windows and Mac OS, this ties NTU Co-Space to laptops and desktops which lack mobility and ease of usage. The iPad version of NTU Co-Space brings about a mobility and ease of usage that comes with a tablet. It gives a whole new dimension to the way users interact with NTU Co-Space. First, the NTU Co-Space virtual world environment is implemented on the iPad. Building models are imported from the web version and the NTU virtual world recreated. Basic functions enabling the use of an avatar to explore the world are implemented. Secondly the characteristics that are unique to the iPad such mobility and size are considered. These characteristics are then exploited using features built into the device such as gyroscope, magnetic heading and GPS. This is to fully utilize and explore NTU Co-Space being on an iPad. A number of implementations completed during this project are unique to the iPad version of NTU Co-Space. User feedback was lastly gathered to assess which functionalities are useful and which are future features users would like to see on the iPad version of the device. The aim of this project is to utilize the iPad’s unique characteristics to provide new ways users can explore and use NTU Co-Space.Bachelor of Engineering (Computer Engineering

Utilizing SECONDO moving objects database technology to simulate MRT usage in Singapore

In these days, there are different kinds of databases such as relational databases and temporal databases. Each type of databases is specially implemented to suit the needs of a system. For example, a grocery shop does not require moving objects database to store its transaction of the sales. Thus, a relational database is more suitable. Retrieving of trains that will keep track of coordinates, movements and directions from one place to another are not possible in a relational database model and therefore, moving objects database is required to support these tasks. Moving objects database provides a way to store information where location and time are important for the users. The objective of this project is to demonstrate how to make use of SECONDO, a moving objects database platform to simulate the MRT system in Singapore. In order to use SECONDO, it is necessary to understand some of the key features of the system such as data types and operators. Furthermore, a database design has been drafted out in order to visualise the key elements for the implementation. The implementation will be incorporated with the data from the MRT system. Queries will then be performed to show the results. On top of that, a comparison was made upon the query with and without the aid of an optimizer, a feature provided by SECONDO. The results have shown higher efficiency and better performance as the query time has been improved with the use of an optimizer. It is recommended to setup using a Linux environment as compared to Windows environment due to incompatibly and installation issues. Furthermore, using indexing to do querying in large amount of data may prove to be more efficient.Bachelor of Engineering (Computer Science

A New Transitive Signature Scheme

We present a novel design for stateless transitive signature ( TSTS ) for undirected graph to authenticate dynamically growing graph data. Our construction is built on the widely studied ZSSZSS signature technology [19] with bilinear mapping, and using general cryptographic hash functions (e.g., SHASHA -512 and MD6MD6 ). Compared with the existing stateless TSTS schemes for undirected graph in the literature, our scheme is more efficient. The scheme is also proven transitively unforgeable against adaptive chosen-message attack under the M2SDHM2SDH assumption in the random oracle model

A New Transitive Signature Scheme

We present a novel design for stateless transitive signature ( TSTS ) for undirected graph to authenticate dynamically growing graph data. Our construction is built on the widely studied ZSSZSS signature technology [19] with bilinear mapping, and using general cryptographic hash functions (e.g., SHASHA -512 and MD6MD6 ). Compared with the existing stateless TSTS schemes for undirected graph in the literature, our scheme is more efficient. The scheme is also proven transitively unforgeable against adaptive chosen-message attack under the M2SDHM2SDH assumption in the random oracle model

Does addition of aromatherapy and music help to reduce pain and anxiety during shockwave lithotripsy compared to standard analgesia alone? A randomised controlled trial

PURPOSE: To assess the effect of aromatherapy with lavender oil alone, and in combination with music, on pain and anxiety during extracorporeal shockwave lithotripsy for kidney stones. METHODS: This was a single-centre prospective, randomised controlled trial. The subjects were block randomised into 3 study groups, Group 1: Control; Group 2: Aromatherapy only; Group 3: Aromatherapy and music. All subjects were given patient-controlled intravenous alfentanil as standard analgesia. The primary outcome measures were pain and anxiety scores using visual analogue scale (VAS) and State-Trait Anxiety Inventory. RESULTS: Ninety patients were recruited and randomised prospectively into Group 1 (n = 30), Group 2 (n = 30), and Group 3 (n = 30). For pain outcome, both Group 2 and Group 3 showed a trend towards lower mean VAS pain scores of 2.73 in both groups compared to the control with a mean VAS score of 3.50, but it was not statistically significant (p = 0.272). There was no significant difference in anxiety scores between groups post-treatment. CONCLUSIONS: Our study was unable to show a significant improvement in pain relief and anxiety when aromatherapy with lavender oil was added to standard analgesia alone during shockwave lithotripsy. There was also no difference when aromatherapy was combined with music