What vs how : comparing students' testing and coding skills

The well-known difficulties students exhibit when learning to program are often characterised as either difficulties in understanding the problem to be solved or difficulties in devising and coding a computational solution. It would therefore be helpful to understand which of these gives students the greatest trouble. Unit testing is a mainstay of large-scale software development and maintenance. A unit test suite serves not only for acceptance testing, but is also a form of requirements specification, as exemplified by agile programming methodologies in which the tests are developed before the corresponding program code. In order to better understand students’ conceptual difficulties with programming, we conducted a series of experiments in which students were required to write both unit tests and program code for non-trivial problems. Their code and tests were then assessed separately for correctness and ‘coverage’, respectively. The results allowed us to directly compare students’ abilities to characterise a computational problem, as a unit test suite, and develop a corresponding solution, as executable code. Since understanding a problem is a pre-requisite to solving it, we expected students’ unit testing skills to be a strong predictor of their ability to successfully implement the corresponding program. Instead, however, we found that students’testing abilities lag well behind their coding skills.

Shortfalls in malnutrition coding : a mandate for action

The International Classification of Diseases, Version 10, Australian modification (ICD-10- AM) is commonly used to classify diseases in hospital patients. ICD-10-AM defines malnutrition as “BMI < 18.5 kg/m2 or unintentional weight loss of ≥ 5% with evidence of suboptimal intake resulting in subcutaneous fat loss and/or muscle wasting”. The Australasian Nutrition Care Day Survey (ANCDS) is the most comprehensive survey to evaluate malnutrition prevalence in acute care patients from Australian and New Zealand hospitals1. This study determined if malnourished participants were assigned malnutritionrelated codes as per ICD-10-AM. The ANCDS recruited acute care patients from 56 hospitals. Hospital-based dietitians evaluated participants’ nutritional status using BMI and Subjective Global Assessment (SGA). In keeping with the ICD-10-AM definition, malnutrition was defined as BMI <18.5kg/m2, SGA-B (moderately malnourished) or SGA-C (severely malnourished). After three months, in this prospective cohort study, hospitals’ health information/medical records department provided coding results for malnourished participants. Although malnutrition was prevalent in 32% (n= 993) of the cohort (N= 3122), a significantly small number were coded for malnutrition (n= 162, 16%, p<0.001). In 21 hospitals, none of the malnourished participants were coded. This is the largest study to provide a snapshot of malnutrition-coding in Australian and New Zealand hospitals. Findings highlight gaps in malnutrition documentation and/or subsequent coding, which could potentially result in significant loss of casemix-related revenue for hospitals. Dietitians must lead the way in developing structured processes for malnutrition identification, documentation and coding.

Standard preanalytical coding for biospecimens: Review and implementation of the Sample PREanalytical Code (SPREC)

The first version of the Standard PREanalytical Code (SPREC) was developed in 2009 by the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group to facilitate documentation and communication of the most important preanalytical quality parameters of different types of biospecimens used for research. This same Working Group has now updated the SPREC to version 2.0, presented here, so that it contains more options to allow for recent technological developments. Existing elements have been fine tuned. An interface to the Biospecimen Reporting for Improved Study Quality (BRISQ) has been defined, and informatics solutions for SPREC implementation have been developed. A glossary with SPRECrelated definitions has also been added.

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

Long non coding RNAs (lncRNAs) are dysregulated in Malignant Pleural Mesothelioma (MPM)

Malignant Pleural Mesothelioma (MPM) is an aggressive cancer that is often diagnosed at an advanced stage and is characterized by a long latency period (20-40 years between initial exposure and diagnosis) and prior exposure to asbestos. Currently accurate diagnosis of MPM is difficult due to the lack of sensitive biomarkers and despite minor improvements in treatment, median survival rates do not exceed 12 months. Accumulating evidence suggests that aberrant expression of long non-coding RNAs (lncRNAs) play an important functional role in cancer biology. LncRNAs are a class of recently discovered non-protein coding RNAs >200 nucleotides in length with a role in regulating transcription. Here we used NCode long noncoding microarrays to identify differentially expressed lncRNAs potentially involved in MPM pathogenesis. High priority candidate lncRNAs were selected on the basis of statistical (P<0.05) and biological significance (>3-fold difference). Expression levels of 9 candidate lncRNAs were technically validated using RT-qPCR, and biologically validated in three independent test sets: (1) 57 archived MPM tissues obtained from extrapleural pneumonectomy patients, (2) 15 cryopreserved MPM and 3 benign pleura, and (3) an extended panel of 10 MPM cell lines. RT-qPCR analysis demonstrated consistent up-regulation of these lncRNAs in independent datasets. ROC curve analysis showed that two candidates were able to separate benign pleura and MPM with high sensitivity and specificity, and were associated with nodal metastases and survival following induction chemotherapy. These results suggest that lncRNAs have potential to serve as biomarkers in MPM.

Identification of a long non-coding RNA gene, GHSROS (growth hormone secretagogue receptor opposite strand), which stimulates cell migration in non-small cell lung cancer cell lines

The molecular mechanisms involved in non‑small cell lung cancer tumourigenesis are largely unknown; however, recent studies have suggested that long non-coding RNAs (lncRNAs) are likely to play a role. In this study, we used public databases to identify an mRNA-like, candidate long non-coding RNA, GHSROS (GHSR opposite strand), transcribed from the antisense strand of the ghrelin receptor gene, growth hormone secretagogue receptor (GHSR). Quantitative real-time RT-PCR revealed higher expression of GHSROS in lung cancer tissue compared to adjacent, non-tumour lung tissue. In common with many long non-coding RNAs, GHSROS is 5' capped and 3' polyadenylated (mRNA-like), lacks an extensive open reading frame and harbours a transposable element. Engineered overexpression of GHSROS stimulated cell migration in the A549 and NCI-H1299 non-small cell lung cancer cell lines, but suppressed cell migration in the Beas-2B normal lung-derived bronchoepithelial cell line. This suggests that GHSROS function may be dependent on the oncogenic context. The identification of GHSROS, which is expressed in lung cancer and stimulates cell migration in lung cancer cell lines, contributes to the growing number of non-coding RNAs that play a role in the regulation of tumourigenesis and metastatic cancer progression.

Preventing pollution attacks in multi-source network coding

Network coding is a method for achieving channel capacity in networks. The key idea is to allow network routers to linearly mix packets as they traverse the network so that recipients receive linear combinations of packets. Network coded systems are vulnerable to pollution attacks where a single malicious node floods the network with bad packets and prevents the receiver from decoding correctly. Cryptographic defenses to these problems are based on homomorphic signatures and MACs. These proposals, however, cannot handle mixing of packets from multiple sources, which is needed to achieve the full benefits of network coding. In this paper we address integrity of multi-source mixing. We propose a security model for this setting and provide a generic construction.

Malnutrition coding shortfalls in Australian and New Zealand hospitals

Aim The International Classification of Diseases, version 10, Australian modification (ICD-10-AM) is used to classify diseases in hospital patients in Australia and New Zealand. ICD-10-AM defines malnutrition as ‘[body mass index] BMI <18.5 kg/m2 or unintentional weight loss of ≥5% with evidence of suboptimal intake resulting in subcutaneous fat loss and/or muscle wasting’. The Australasian Nutrition Care Day Survey (ANCDS) is the most comprehensive survey to evaluate malnutrition prevalence in acute care patients from Australian and New Zealand hospitals. This study determined if malnourished participants were assigned malnutrition-related codes according to ICD-10-AM. Methods The ANCDS recruited acute care patients from 56 hospitals. Hospital-based dietitians evaluated participants' nutritional status using BMI and Subjective Global Assessment (SGA). In keeping with the ICD-10-AM definition, malnutrition was defined as BMI <18.5 kg/m2, SGA-B (moderately malnourished) or SGA-C (severely malnourished). After 3 months, in this prospective cohort study, staff members from each hospital's health information/medical records department provided coding results for malnourished participants. Results Malnutrition was prevalent in 30% (n = 869) of the cohort (n = 2976) and a significantly small number of malnourished patients were coded for malnutrition (n = 162, 19%, P < 0.001). In 21 hospitals, none of the malnourished participants were coded. Conclusions This is the largest study to provide a snapshot of malnutrition coding in Australian and New Zealand hospitals. Findings highlight gaps in malnutrition documentation and/or subsequent coding, which could potentially result in significant loss of casemix-related revenue for hospitals. Dietitians must lead the way in developing structured processes for malnutrition identification, documentation and coding.

A coding approach to the multicast stream authentication problem

We study the multicast stream authentication problem when an opponent can drop, reorder and introduce data packets into the communication channel. In such a model, packet overhead and computing efficiency are two parameters to be taken into account when designing a multicast stream protocol. In this paper, we propose to use two families of erasure codes to deal with this problem, namely, rateless codes and maximum distance separable codes. Our constructions will have the following advantages. First, our packet overhead will be small. Second, the number of signature verifications to be performed at the receiver is O(1). Third, every receiver will be able to recover all the original data packets emitted by the sender despite losses and injection occurred during the transmission of information.

Improved image set classification via joint sparse approximated nearest subspaces

Existing multi-model approaches for image set classification extract local models by clustering each image set individually only once, with fixed clusters used for matching with other image sets. However, this may result in the two closest clusters to represent different characteristics of an object, due to different undesirable environmental conditions (such as variations in illumination and pose). To address this problem, we propose to constrain the clustering of each query image set by forcing the clusters to have resemblance to the clusters in the gallery image sets. We first define a Frobenius norm distance between subspaces over Grassmann manifolds based on reconstruction error. We then extract local linear subspaces from a gallery image set via sparse representation. For each local linear subspace, we adaptively construct the corresponding closest subspace from the samples of a probe image set by joint sparse representation. We show that by minimising the sparse representation reconstruction error, we approach the nearest point on a Grassmann manifold. Experiments on Honda, ETH-80 and Cambridge-Gesture datasets show that the proposed method consistently outperforms several other recent techniques, such as Affine Hull based Image Set Distance (AHISD), Sparse Approximated Nearest Points (SANP) and Manifold Discriminant Analysis (MDA).

A sparse hybrid map for vision-guided mobile robots

This paper introduces a minimalistic approach to produce a visual hybrid map of a mobile robot’s working environment. The proposed system uses omnidirectional images along with odometry information to build an initial dense posegraph map. Then a two level hybrid map is extracted from the dense graph. The hybrid map consists of global and local levels. The global level contains a sparse topological map extracted from the initial graph using a dual clustering approach. The local level contains a spherical view stored at each node of the global level. The spherical views provide both an appearance signature for the nodes, which the robot uses to localize itself in the environment, and heading information when the robot uses the map for visual navigation. In order to show the usefulness of the map, an experiment was conducted where the map was used for multiple visual navigation tasks inside an office workplace.

Drosophila 3′ UTRs are more complex than protein-coding sequences

The 3′ UTRs of eukaryotic genes participate in a variety of post-transcriptional (and some transcriptional) regulatory interactions. Some of these interactions are well characterised, but an undetermined number remain to be discovered. While some regulatory sequences in 3′ UTRs may be conserved over long evolutionary time scales, others may have only ephemeral functional significance as regulatory profiles respond to changing selective pressures. Here we propose a sensitive segmentation methodology for investigating patterns of composition and conservation in 3′ UTRs based on comparison of closely related species. We describe encodings of pairwise and three-way alignments integrating information about conservation, GC content and transition/transversion ratios and apply the method to three closely related Drosophila species: D. melanogaster, D. simulans and D. yakuba. Incorporating multiple data types greatly increased the number of segment classes identified compared to similar methods based on conservation or GC content alone. We propose that the number of segments and number of types of segment identified by the method can be used as proxies for functional complexity. Our main finding is that the number of segments and segment classes identified in 3′ UTRs is greater than in the same length of protein-coding sequence, suggesting greater functional complexity in 3′ UTRs. There is thus a need for sustained and extensive efforts by bioinformaticians to delineate functional elements in this important genomic fraction. C code, data and results are available upon request.

Technicolouring the fridge : reducing food waste through uses of colour-coding and cameras

Domestic food wastage is a growing problem for the environment and food security. Some causes of domestic food wastes are attributed to a consumer’s behaviours during food purchasing, storage and consumption, such as: excessive food purchases and stockpiling in storage. Recent efforts in human-computer interaction research have examined ways of influencing consumer behaviour. The outcomes have led to a number of interventions that assist users with performing everyday tasks. The Internet Fridge is an example of such an intervention. However, new pioneering technologies frequently confront barriers that restrict their future impact in the market place, which has prompted investigations into the effectiveness of behaviour changing interventions used to encourage more sustainable practices. In this paper, we investigate and compare the effectiveness of two interventions that encourage behaviour change: FridgeCam and the Colour Code Project. We use FridgeCam to examine how improving a consumer’s food supply knowledge can reduce food stockpiling. We use the Colour Code Project to examine how improving consumer awareness of food location can encourage consumption of forgotten foods. We explore opportunities to integrate these interventions into commercially available technologies, such as the Internet Fridge, to: (i) increase the technology’s benefit and value to users, and (ii) promote reduced domestic food wastage. We conclude that interventions improving consumer food supply and location knowledge can promote behaviours that reduce domestic food waste over a longer term. The implications of this research present new opportunities for existing and future technologies to play a key role in reducing domestic food waste.

Fine-mapping the HOXB region detects common variants tagging a rare coding allele : evidence for synthetic association in prostate cancer

The HOXB13 gene has been implicated in prostate cancer (PrCa) susceptibility. We performed a high resolution fine-mapping analysis to comprehensively evaluate the association between common genetic variation across the HOXB genetic locus at 17q21 and PrCa risk. This involved genotyping 700 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of 3195 SNPs in 20,440 PrCa cases and 21,469 controls in The PRACTICAL consortium. We identified a cluster of highly correlated common variants situated within or closely upstream of HOXB13 that were significantly associated with PrCa risk, described by rs117576373 (OR 1.30, P = 2.62×10(-14)). Additional genotyping, conditional regression and haplotype analyses indicated that the newly identified common variants tag a rare, partially correlated coding variant in the HOXB13 gene (G84E, rs138213197), which has been identified recently as a moderate penetrance PrCa susceptibility allele. The potential for GWAS associations detected through common SNPs to be driven by rare causal variants with higher relative risks has long been proposed; however, to our knowledge this is the first experimental evidence for this phenomenon of synthetic association contributing to cancer susceptibility.

Association study of MTHFD1 coding polymorphisms R134K and R653Q with migraine susceptibility

Objective There is evidence that folate metabolism has a role in migraine pathophysiology, particularly in the migraine with aura subtype. In this study we investigate whether two non-synonymous single nucleotide polymorphisms (SNPs), rs1950902 (C401T; R134K) and rs2236225 (G1958A; R653Q), in MTHDF1 are associated with migraine in an Australian case-control population. Background Increased plasma levels of homocysteine (HCy), one of the metabolites produced in the folate pathway, has been found to be a risk factor for migraine. There is also a genetic link, as a common polymorphism (C667T) that reduces the catalytic activity of MTHFR, the enzyme that catalyses the formation of HCy, is associated with an increase in risk of the migraine with aura (MA) subtype. MTHFD1 is a crucial multifunctional enzyme that catalyses three separate reactions of the folate pathway and therefore variants in MTHFD1 may also influence migraine susceptibility. Methods The R134K and R653Q variants in MTHFD1 were genotyped in an Australian cohort of 520 unrelated migraineurs (162 were diagnosed with migraine without aura [MO] and 358 with MA) and 520 matched controls. Data were analysed for association with migraine and for interaction with the MTHFR C667T polymorphism. Results We find no significant differences in genotype or allele frequencies for either SNP between migraineurs and controls, or when either MO or MA cases were compared to controls. In addition these MTHFD1 polymorphisms did not appear to influence the risk of MA conferred by the MTHFR 667T allele. Conclusions We find no evidence for association of the MTHFD1 R134K and R653Q polymorphisms with migraine in our Australian case-control population. However, as folate metabolism appears to be important in migraine, particularly with respect to the aura component, future studies using high throughput methods to expand the number of SNPs in folate-related genes genotyped and investigation of interactions between SNPs may be justified.