Clines in cuticular hydrocarbons in two Drosophila species with independent population histories

We took a comparative approach utilizing clines to investigate the extent to which natural selection may have shaped population divergence in cuticular hydrocarbons (CHCs) that are also under sexual selection in Drosophila. We detected the presence of CHC clines along a latitudinal gradient on the east coast of Australia in two fly species with independent phylogenetic and population histories, suggesting adaptation to shared abiotic factors. For both species, significant associations were detected between clinal variation in CHCs and temperature variation along the gradient, suggesting temperature maxima as a candidate abiotic factor shaping CHC variation among populations. However, rainfall and humidity correlated with CHC variation to differing extents in the two species, suggesting that response to these abiotic factors may vary in a species-specific manner. Our results suggest that natural selection, in addition to sexual selection, plays a significant role in structuring among-population variation in sexually selected traits in Drosophila.

Automatic region-of-interest detection and prioritisation for visually optimised coding of low bit rate videos

The increasing popularity of video consumption from mobile devices requires an effective video coding strategy. To overcome diverse communication networks, video services often need to maintain sustainable quality when the available bandwidth is limited. One of the strategy for a visually-optimised video adaptation is by implementing a region-of-interest (ROI) based scalability, whereby important regions can be encoded at a higher quality while maintaining sufficient quality for the rest of the frame. The result is an improved perceived quality at the same bit rate as normal encoding, which is particularly obvious at the range of lower bit rate. However, because of the difficulties of predicting region-of-interest (ROI) accurately, there is a limited research and development of ROI-based video coding for general videos. In this paper, the phase spectrum quaternion of Fourier Transform (PQFT) method is adopted to determine the ROI. To improve the results of ROI detection, the saliency map from the PQFT is augmented with maps created from high level knowledge of factors that are known to attract human attention. Hence, maps that locate faces and emphasise the centre of the screen are used in combination with the saliency map to determine the ROI. The contribution of this paper lies on the automatic ROI detection technique for coding a low bit rate videos which include the ROI prioritisation technique to give different level of encoding qualities for multiple ROIs, and the evaluation of the proposed automatic ROI detection that is shown to have a close performance to human ROI, based on the eye fixation data.

Quality based frame selection for video face recognition

Quality based frame selection is a crucial task in video face recognition, to both improve the recognition rate and to reduce the computational cost. In this paper we present a framework that uses a variety of cues (face symmetry, sharpness, contrast, closeness of mouth, brightness and openness of the eye) to select the highest quality facial images available in a video sequence for recognition. Normalized feature scores are fused using a neural network and frames with high quality scores are used in a Local Gabor Binary Pattern Histogram Sequence based face recognition system. Experiments on the Honda/UCSD database shows that the proposed method selects the best quality face images in the video sequence, resulting in improved recognition performance.

Tell me what you see : Pre-service teachers' recognition of exemplary digital pedagogy

How do you identify "good" teaching practice in the complexity of a real classroom? How do you know that beginning teachers can recognise effective digital pedagogy when they see it? How can teacher educators see through their students’ eyes? The study in this paper has arisen from our interest in what pre-service teachers “see” when observing effective classroom practice and how this might reveal their own technological, pedagogical and content knowledge. We asked 104 pre-service teachers from Early Years, Primary and Secondary cohorts to watch and comment upon selected exemplary videos of teachers using ICT (information and communication technologies) in Science. The pre-service teachers recorded their observations using a simple PMI (plus, minus, interesting) matrix which were then coded using the SOLO Taxonomy to look for evidence of their familiarity with and judgements of digital pedagogies. From this, we determined that the majority of preservice teachers we surveyed were using a descriptive rather than a reflective strategy, that is, not extending beyond what was demonstrated in the teaching exemplar or differentiating between action and purpose. We also determined that this method warrants wider trialling as a means of evaluating students’ understandings of the complexity of the digital classroom.

A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family

Background. We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera. Results. Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions. Conclusion. Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages. © 2009 Varsani et al; licensee BioMed Central Ltd.

Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates

Psittacine beak and feather disease (PBFD) has a broad host range and is widespread in wild and captive psittacine populations in Asia, Africa, the Americas, Europe and Australasia. Beak and feather disease circovirus (BFDV) is the causative agent. BFDV has an ~2 kb single stranded circular DNA genome encoding just two proteins (Rep and CP). In this study we provide support for demarcation of BFDV strains by phylogenetic analysis of 65 complete genomes from databases and 22 new BFDV sequences isolated from infected psittacines in South Africa. We propose 94% genome-wide sequence identity as a strain demarcation threshold, with isolates sharing > 94% identity belonging to the same strain, and strain subtypes sharing> 98% identity. Currently, BFDV diversity falls within 14 strains, with five highly divergent isolates from budgerigars probably representing a new species of circovirus with three strains (budgerigar circovirus; BCV-A, -B and -C). The geographical distribution of BFDV and BCV strains is strongly linked to the international trade in exotic birds; strains with more than one host are generally located in the same geographical area. Lastly, we examined BFDV and BCV sequences for evidence of recombination, and determined that recombination had occurred in most BFDV and BCV strains. We established that there were two globally significant recombination hotspots in the viral genome: the first is along the entire intergenic region and the second is in the C-terminal portion of the CP ORF. The implications of our results for the taxonomy and classification of circoviruses are discussed. © 2011 SGM.

A new African streak virus species from Nigeria

The African streak viruses (AfSVs) are a diverse group of mastrevirus species (family Geminiviridae) that infect a wide variety of annual and perennial grass species across the African continent and its nearby Indian Ocean islands. Six AfSV species (of which maize streak virus is the best known) have been described. Here we report the full genome sequences of eight isolates of a seventh AfSV species: Urochloa streak virus (USV), sampled from various locations in Nigeria. Despite there being good evidence of recombination in many other AfSV species, we found no convincing evidence that any of the USV sequences were either inter- or intra-species recombinants. The USV isolates, all of which appear to be variants of the same strain (their genome sequences are all more than 98% identical), share less than 69% nucleotide sequence identity with other currently described AfSV species. © 2008 Springer-Verlag.

A proposal to change existing virus species names to non-Latinized binomials

A proposal has been posted on the ICTV website (2011. 001aG. N. v1. binomial_sp_names) to replace virus species names by non-Latinized binomial names consisting of the current italicized species name with the terminal word "virus" replaced by the italicized and non-capitalized genus name to which the species belongs. If implemented, the current italicized species name Measles virus, for instance, would become Measles morbillivirus while the current virus name measles virus and its abbreviation MeV would remain unchanged. The rationale for the proposed change is presented. © 2010 Springer-Verlag.

The impact of a model of nurse education to improve knowledge and recognition of delirium in older persons by registered nurses

Introduction: Delirium is a serious issue associated with high morbidity and mortality in older hospitalised people. Early recognition enables diagnosis and treatment of underlying cause/s, which can lead to improved patient outcomes. However, research shows knowledge and accurate nurse recognition of delirium and is poor and lack of education appears to be a key issue related to this problem. Thus, the purpose of this randomised controlled trial (RCT) was to evaluate, in a sample of registered nurses, the usability and effectiveness of a web-based learning site, designed using constructivist learning principles, to improve acute care nurse knowledge and recognition of delirium. Prior to undertaking the RCT preliminary phases involving; validation of vignettes, video-taping five of the validated vignettes, website development and pilot testing were completed. Methods: The cluster RCT involved consenting registered nurse participants (N = 175) from twelve clinical areas within three acute health care facilities in Queensland, Australia. Data were collected through a variety of measures and instruments. Primary outcomes were improved ability of nurses to recognise delirium using written validated vignettes and improved knowledge of delirium using a delirium knowledge questionnaire. The secondary outcomes were aimed at determining nurse satisfaction and usability of the website. Primary outcome measures were taken at baseline (T1), directly after the intervention (T2) and two months later (T3). The secondary outcomes were measured at T2 by participants in the intervention group. Following baseline data collection remaining participants were assigned to either the intervention (n=75) or control (n=72) group. Participants in the intervention group were given access to the learning intervention while the control group continued to work in their clinical area and at that time, did not receive access to the learning intervention. Data from the primary outcome measures were examined in mixed model analyses. Results: Overall, the effect of the online learning intervention over time comparing the intervention group and the control group were positive. The intervention groups‘ scores were higher and the change over time results were statistically significant [T3 and T1 (t=3.78 p=<0.001) and T2 and T1 baseline (t=5.83 p=<0.001)]. Statistically significant improvements were also seen for delirium recognition when comparing T2 and T1 results (t=2.58 p=0.012) between the control and intervention group but not for changes in delirium recognition scores between the two groups from T3 and T1 (t=1.80 p=0.074). The majority of the participants rated the website highly on the visual, functional and content elements. Additionally, nearly 80% of the participants liked the overall website features and there were self-reported improvements in delirium knowledge and recognition by the registered nurses in the intervention group. Discussion: Findings from this study support the concept that online learning is an effective and satisfying method of information delivery. Embedded within a constructivist learning environment the site produced a high level of satisfaction and usability for the registered nurse end-users. Additionally, the results showed that the website significantly improved delirium knowledge & recognition scores and the improvement in delirium knowledge was retained at a two month follow-up. Given the strong effect of the intervention the online delirium intervention should be utilised as a way of providing information to registered nurses. It is envisaged that this knowledge would lead to improved recognition of delirium as well as improvement in patient outcomes however; translation of this knowledge attainment into clinical practice was outside the scope of this study. A critical next step is demonstrating the effect of the intervention in changing clinical behaviour, and improving patient health outcomes.

Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

JFA based Speaker Recognition using Delta-Phase and MFCC features

This paper investigates the use of mel-frequency deltaphase (MFDP) features in comparison to, and in fusion with, traditional mel-frequency cepstral coefficient (MFCC) features within joint factor analysis (JFA) speaker verification. MFCC features, commonly used in speaker recognition systems, are derived purely from the magnitude spectrum, with the phase spectrum completely discarded. In this paper, we investigate if features derived from the phase spectrum can provide additional speaker discriminant information to the traditional MFCC approach in a JFA based speaker verification system. Results are presented which provide a comparison of MFCC-only, MFDPonly and score fusion of the two approaches within a JFA speaker verification approach. Based upon the results presented using the NIST 2008 Speaker Recognition Evaluation (SRE) dataset, we believe that, while MFDP features alone cannot compete with MFCC features, MFDP can provide complementary information that result in improved speaker verification performance when both approaches are combined in score fusion, particularly in the case of shorter utterances.

A survey of tagging techniques for music, speech and environmental sound

Sound tagging has been studied for years. Among all sound types, music, speech, and environmental sound are three hottest research areas. This survey aims to provide an overview about the state-of-the-art development in these areas.We discuss about the meaning of tagging in different sound areas at the beginning of the journey. Some examples of sound tagging applications are introduced in order to illustrate the significance of this research. Typical tagging techniques include manual, automatic, and semi-automatic approaches.After reviewing work in music, speech and environmental sound tagging, we compare them and state the research progress to date. Research gaps are identified for each research area and the common features and discriminations between three areas are discovered as well. Published datasets, tools used by researchers, and evaluation measures frequently applied in the analysis are listed. In the end, we summarise the worldwide distribution of countries dedicated to sound tagging research for years.

Automatic Audio Segmentation Using the Generalized Likelihood Ratio

This paper presents a novel technique for segmenting an audio stream into homogeneous regions according to speaker identities, background noise, music, environmental and channel conditions. Audio segmentation is useful in audio diarization systems, which aim to annotate an input audio stream with information that attributes temporal regions of the audio into their specific sources. The segmentation method introduced in this paper is performed using the Generalized Likelihood Ratio (GLR), computed between two adjacent sliding windows over preprocessed speech. This approach is inspired by the popular segmentation method proposed by the pioneering work of Chen and Gopalakrishnan, using the Bayesian Information Criterion (BIC) with an expanding search window. This paper will aim to identify and address the shortcomings associated with such an approach. The result obtained by the proposed segmentation strategy is evaluated on the 2002 Rich Transcription (RT-02) Evaluation dataset, and a miss rate of 19.47% and a false alarm rate of 16.94% is achieved at the optimal threshold.

The backfilled GEI : a cross-capture modality gait feature for frontal and side-view gait recognition

In this paper, we propose a novel direction for gait recognition research by proposing a new capture-modality independent, appearance-based feature which we call the Back-filled Gait Energy Image (BGEI). It can can be constructed from both frontal depth images, as well as the more commonly used side-view silhouettes, allowing the feature to be applied across these two differing capturing systems using the same enrolled database. To evaluate this new feature, a frontally captured depth-based gait dataset was created containing 37 unique subjects, a subset of which also contained sequences captured from the side. The results demonstrate that the BGEI can effectively be used to identify subjects through their gait across these two differing input devices, achieving rank-1 match rate of 100%, in our experiments. We also compare the BGEI against the GEI and GEV in their respective domains, using the CASIA dataset and our depth dataset, showing that it compares favourably against them. The experiments conducted were performed using a sparse representation based classifier with a locally discriminating input feature space, which show significant improvement in performance over other classifiers used in gait recognition literature, achieving state of the art results with the GEI on the CASIA dataset.

Spatio temporal feature evaluation for action recognition

Spatio-Temporal interest points are the most popular feature representation in the field of action recognition. A variety of methods have been proposed to detect and describe local patches in video with several techniques reporting state of the art performance for action recognition. However, the reported results are obtained under different experimental settings with different datasets, making it difficult to compare the various approaches. As a result of this, we seek to comprehensively evaluate state of the art spatio- temporal features under a common evaluation framework with popular benchmark datasets (KTH, Weizmann) and more challenging datasets such as Hollywood2. The purpose of this work is to provide guidance for researchers, when selecting features for different applications with different environmental conditions. In this work we evaluate four popular descriptors (HOG, HOF, HOG/HOF, HOG3D) using a popular bag of visual features representation, and Support Vector Machines (SVM)for classification. Moreover, we provide an in-depth analysis of local feature descriptors and optimize the codebook sizes for different datasets with different descriptors. In this paper, we demonstrate that motion based features offer better performance than those that rely solely on spatial information, while features that combine both types of data are more consistent across a variety of conditions, but typically require a larger codebook for optimal performance.