Transcriptome analyses of amoebic gill disease-affected atlantic salmon (Salmo salar) tissues reveal localized host gene suppression

The transcriptome response of Atlantic salmon (Salmo salar) displaying advanced stages of amoebic gill disease (AGD) was investigated. Naïve smolt were challenged with AGD for 19 days, at which time all fish were euthanized and their severity of infection quantified through histopathological scoring. Gene expression profiles were compared between heavily infected and naïve individuals using a 17 K Atlantic salmon cDNA microarray with real-time quantitative RT-PCR (qPCR) verification. Expression profiles were examined in the gill, anterior kidney, and liver. Twenty-seven transcripts were significantly differentially expressed within the gill; 20 of these transcripts were down-regulated in the AGD-affected individuals compared with naïve individuals. In contrast, only nine transcripts were significantly differentially expressed within the anterior kidney and five within the liver. Again the majority of these transcripts were down-regulated within the diseased individuals. A down-regulation of transcripts involved in apoptosis (procathepsin L, cathepsin H precursor, and cystatin B) was observed in AGD-affected Atlantic salmon. Four transcripts encoding genes with antioxidant properties also were down-regulated in AGD-affected gill tissue according to qPCR analysis. The most up-regulated transcript within the gill was an unknown expressed sequence tag (EST) whose expression was 218-fold (± SE 66) higher within the AGD affected gill tissue. Our results suggest that Atlantic salmon experiencing advanced stages of AGD demonstrate general down-regulation of gene expression, which is most pronounced within the gill. We propose that this general gene suppression is parasite-mediated, thus allowing the parasite to withstand or ameliorate the host response. © 2008 Springer Science+Business Media, LLC.

Scale adaptive tracking using mean shift and efficient feature matching

The mean shift tracker has achieved great success in visual object tracking due to its efficiency being nonparametric. However, it is still difficult for the tracker to handle scale changes of the object. In this paper, we associate a scale adaptive approach with the mean shift tracker. Firstly, the target in the current frame is located by the mean shift tracker. Then, a feature point matching procedure is employed to get the matched pairs of the feature point between target regions in the current frame and the previous frame. We employ FAST-9 corner detector and HOG descriptor for the feature matching. Finally, with the acquired matched pairs of the feature point, the affine transformation between target regions in the two frames is solved to obtain the current scale of the target. Experimental results show that the proposed tracker gives satisfying results when the scale of the target changes, with a good performance of efficiency.

Weak acid extractable metals in Bramble Bay, Queensland, Australia : temporal behaviour, enrichment and source apportionment

Sediment samples were taken from six sampling sites in Bramble Bay, Queensland, Australia between February and November in 2012. They were analysed for a range of heavy metals including Al, Fe, Mn, Ti, Ce, Th, U, V, Cr, Co, Ni, Cu, Zn, As, Cd, Sb, Te, Hg, Tl and Pb. Fraction analysis, enrichment factors and Principal Component Analysis –Absolute Principal Component Scores (PCA-APCS) were carried out in order to assess metal pollution, potential bioavailability and source apportionment. Cr and Ni exceeded the Australian Interim Sediment Quality Guidelines at some sampling sites, while Hg was found to be the most enriched metal. Fraction analysis identified increased weak acid soluble Hg and Cd during the sampling period. Source apportionment via PCA-APCS found four sources of metals pollution, namely, marine sediments, shipping, antifouling coatings and a mixed source. These sources need to be considered in any metal pollution control measure within Bramble Bay.

Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis

Systems-level identification and analysis of cellular circuits in the brain will require the development of whole-brain imaging with single-cell resolution. To this end, we performed comprehensive chemical screening to develop a whole-brain clearing and imaging method, termed CUBIC (clear, unobstructed brain imaging cocktails and computational analysis). CUBIC is a simple and efficient method involving the immersion of brain samples in chemical mixtures containing aminoalcohols, which enables rapid whole-brain imaging with single-photon excitation microscopy. CUBIC is applicable to multicolor imaging of fluorescent proteins or immunostained samples in adult brains and is scalable from a primate brain to subcellular structures. We also developed a whole-brain cell-nuclear counterstaining protocol and a computational image analysis pipeline that, together with CUBIC reagents, enable the visualization and quantification of neural activities induced by environmental stimulation. CUBIC enables time-course expression profiling of whole adult brains with single-cell resolution.

Family-based programmes for preventing smoking by children and adolescents (Review)

Background There is evidence that family and friends influence children's decisions to smoke. Objectives To assess the effectiveness of interventions to help families stop children starting smoking. Search methods We searched 14 electronic bibliographic databases, including the Cochrane Tobacco Addiction Group specialized register, MEDLINE, EMBASE, PsycINFO, CINAHL unpublished material, and key articles' reference lists. We performed free-text internet searches and targeted searches of appropriate websites, and hand-searched key journals not available electronically. We consulted authors and experts in the field. The most recent search was 3 April 2014. There were no date or language limitations. Selection criteria Randomised controlled trials (RCTs) of interventions with children (aged 5-12) or adolescents (aged 13-18) and families to deter tobacco use. The primary outcome was the effect of the intervention on the smoking status of children who reported no use of tobacco at baseline. Included trials had to report outcomes measured at least six months from the start of the intervention. Data collection and analysis We reviewed all potentially relevant citations and retrieved the full text to determine whether the study was an RCT and matched our inclusion criteria. Two authors independently extracted study data for each RCT and assessed them for risk of bias. We pooled risk ratios using a Mantel-Haenszel fixed effect model. Main results Twenty-seven RCTs were included. The interventions were very heterogeneous in the components of the family intervention, the other risk behaviours targeted alongside tobacco, the age of children at baseline and the length of follow-up. Two interventions were tested by two RCTs, one was tested by three RCTs and the remaining 20 distinct interventions were tested only by one RCT. Twenty-three interventions were tested in the USA, two in Europe, one in Australia and one in India. The control conditions fell into two main groups: no intervention or usual care; or school-based interventions provided to all participants. These two groups of studies were considered separately. Most studies had a judgement of 'unclear' for at least one risk of bias criteria, so the quality of evidence was downgraded to moderate. Although there was heterogeneity between studies there was little evidence of statistical heterogeneity in the results. We were unable to extract data from all studies in a format that allowed inclusion in a meta-analysis. There was moderate quality evidence family-based interventions had a positive impact on preventing smoking when compared to a no intervention control. Nine studies (4810 participants) reporting smoking uptake amongst baseline non-smokers could be pooled, but eight studies with about 5000 participants could not be pooled because of insufficient data. The pooled estimate detected a significant reduction in smoking behaviour in the intervention arms (risk ratio [RR] 0.76, 95% confidence interval [CI] 0.68 to 0.84). Most of these studies used intensive interventions. Estimates for the medium and low intensity subgroups were similar but confidence intervals were wide. Two studies in which some of the 4487 participants already had smoking experience at baseline did not detect evidence of effect (RR 1.04, 95% CI 0.93 to 1.17). Eight RCTs compared a combined family plus school intervention to a school intervention only. Of the three studies with data, two RCTS with outcomes for 2301 baseline never smokers detected evidence of an effect (RR 0.85, 95% CI 0.75 to 0.96) and one study with data for 1096 participants not restricted to never users at baseline also detected a benefit (RR 0.60, 95% CI 0.38 to 0.94). The other five studies with about 18,500 participants did not report data in a format allowing meta-analysis. One RCT also compared a family intervention to a school 'good behaviour' intervention and did not detect a difference between the two types of programme (RR 1.05, 95% CI 0.80 to 1.38, n = 388). No studies identified any adverse effects of intervention. Authors' conclusions There is moderate quality evidence to suggest that family-based interventions can have a positive effect on preventing children and adolescents from starting to smoke. There were more studies of high intensity programmes compared to a control group receiving no intervention, than there were for other compairsons. The evidence is therefore strongest for high intensity programmes used independently of school interventions. Programmes typically addressed family functioning, and were introduced when children were between 11 and 14 years old. Based on this moderate quality evidence a family intervention might reduce uptake or experimentation with smoking by between 16 and 32%. However, these findings should be interpreted cautiously because effect estimates could not include data from all studies. Our interpretation is that the common feature of the effective high intensity interventions was encouraging authoritative parenting (which is usually defined as showing strong interest in and care for the adolescent, often with rule setting). This is different from authoritarian parenting (do as I say) or neglectful or unsupervised parenting.

Ants, apples and the ABCs: The use of commercial phonics programmes in prior-to-school children's services

Commercial phonics programmes (e.g. Jolly Phonics and Letterland) are becoming widely used in the early years of school. These programmes claim to use a systematic explicit approach, considered as the preferred method of phonics instruction for teaching alphabetic code-breaking skills in Australia and the UK in the first years of school (Department of Education, Science and Training, 2005; Rose, 2006). However, little is known about the extent to which they are being used in prior-to-school settings, and the reasons behind decisions to use them. This study surveyed 283 early childhood staff in Sydney, Australia and found that commercial phonics programmes were being used in 36% of the early childhood settings surveyed. Staff with early childhood univer- sity qualifications and staff working in not-for-profit service types were less likely to use a commercial phonics programme than staff without university qualifications and staff working in for-profit services. Staff with less than 10 years’ experience were also more likely to use a commercial phonics programme. The rationale behind decisions deter- mining whether or not staff used the programmes ranged from pragmatic reasons, such as parent pressure or higher management decisions, to pedagogical reasons, such as teacher beliefs about how children learn to read and write. The practices staff engage in to teach phonics are explored.

Extending the validity of the Feeding Practices and Structure Questionnaire

Background Feeding practices are commonly examined as potentially modifiable determinants of children’s eating behaviours and weight status. Although a variety of questionnaires exist to assess different feeding aspects, many lack thorough reliability and validity testing. The Feeding Practices and Structure Questionnaire (FPSQ) is a tool designed to measure early feeding practices related to non-responsive feeding and structure of the meal environment. Face validity, factorial validity, internal reliability and cross-sectional correlations with children’s eating behaviours have been established in mothers with 2-year-old children. The aim of the present study was to further extend the validity of the FPSQ by examining factorial, construct and predictive validity, and stability. Methods Participants were from the NOURISH randomised controlled trial which evaluated an intervention with first-time mothers designed to promote protective feeding practices. Maternal feeding practices (FP) and child eating behaviours were assessed when children were aged 2 years and 3.7 years (n=388). Confirmatory Factor analysis, group differences, predictive relationships, and stability were tested. Results The original 9-factor structure was confirmed when children were aged 3.7±0.3 years. Cronbach’s alpha was above the recommended 0.70 cut-off for all factors except Structured Meal Timing, Over Restriction and Distrust in Appetite which were 0.58, 0.67 and 0.66 respectively. Allocated group differences reflected behaviour consistent with intervention content and all feeding practices were stable across both time points (range of r= 0.45-0.70). There was some evidence for the predictive validity of factors with 2 FP showing expected relationships, 2 FP showing expected and unexpected relationships and 5 FP showing no relationship. Conclusions Reliability and validity was demonstrated for most subscales of the FPSQ. Future validation is warranted with culturally diverse samples and with fathers and other caregivers. The use of additional outcomes to further explore predictive validity is recommended as well as testing construct validity and test-retest reliability of the questionnaire.

Perubahan bahasa dalam perspektif Pre neogrammarian dan Neogrammarian dan Pengajaran bahasa dalam konteks EFL (Pre-Neogrammarian and Neogrammarians’ language change and English language pedagogy in EFL contexts)

This article describes different perspectives in response to language change, and aligns the perspectives of language change to English language pedagogy in non-English speaking contexts. The Pre-Neogrammarian and Neo-grammarian linguists that believe the change leads to respectively language decay or language existence will be outlined. This article suggests that the theories derived from both perspectives can be applied to any language. Once there is cultural contact between languages, the dominant language tends to suppress the non-dominant language. Hence, besides focusing on changes that happen in English and the effects of the changes into this language, this article also considers that other language—in this case EFL teachers’ “local language”—experiences an adverse change as the result of the speakers’ interaction with English. Then, this article also describes how the changes might lead to EFL teachers’ adaptation in their practice and cause teachers’ dilemmas.

Submission on the Hawke Interim Review of the Environment Protection and Biodiversity Conservation Act 1999 (Cth)

There are currently no regulatory mechanisms, laws or policies that specifically provide rights to Indigenous peoples over their Indigenous knowledge and intellectual property. We strongly recommend that the commonwealth take the lead to ensure that national sui generis laws are developed (perhaps to operate initially in areas of Cth jurisdiction, such as IPAs and national parks). The development of such laws should be in tandem with practical guidelines to assist their implementation. A comprehensive, nationally consistent scheme for access to genetic resources, which offers meaningful protection of traditional knowledge and substantive benefit-sharing with Indigenous communities, has to be developed. There are already a range of reports/resources that urge these same reforms and that we direct the Enquiry to again; these include the Voumard Report (2000) – especially Fourmile’s Appendix 10 – “Indigenous Interests”, and Terri Jankes “Our Culture, Our Future (1998).

Working the story : News curation in social media as a second save of citizen journalism

For the first decade of its existence, the concept of citizen journalism has described an approach which was seen as a broadening of the participant base in journalistic processes, but still involved only a comparatively small subset of overall society – for the most part, citizen journalists were news enthusiasts and “political junkies” (Coleman, 2006) who, as some exasperated professional journalists put it, “wouldn’t get a job at a real newspaper” (The Australian, 2007), but nonetheless followed many of the same journalistic principles. The investment – if not of money, then at least of time and effort – involved in setting up a blog or participating in a citizen journalism Website remained substantial enough to prevent the majority of Internet users from engaging in citizen journalist activities to any significant extent; what emerged in the form of news blogs and citizen journalism sites was a new online elite which for some time challenged the hegemony of the existing journalistic elite, but gradually also merged with it. The mass adoption of next-generation social media platforms such as Facebook and Twitter, however, has led to the emergence of a new wave of quasi-journalistic user activities which now much more closely resemble the “random acts of journalism” which JD Lasica envisaged in 2003. Social media are not exclusively or even predominantly used for citizen journalism; instead, citizen journalism is now simply a by-product of user communities engaging in exchanges about the topics which interest them, or tracking emerging stories and events as they happen. Such platforms – and especially Twitter with its system of ad hoc hashtags that enable the rapid exchange of information about issues of interest – provide spaces for users to come together to “work the story” through a process of collaborative gatewatching (Bruns, 2005), content curation, and information evaluation which takes place in real time and brings together everyday users, domain experts, journalists, and potentially even the subjects of the story themselves. Compared to the spaces of news blogs and citizen journalism sites, but also of conventional online news Websites, which are controlled by their respective operators and inherently position user engagement as a secondary activity to content publication, these social media spaces are centred around user interaction, providing a third-party space in which everyday as well as institutional users, laypeople as well as experts converge without being able to control the exchange. Drawing on a number of recent examples, this article will argue that this results in a new dynamic of interaction and enables the emergence of a more broadly-based, decentralised, second wave of citizen engagement in journalistic processes.

Decisions and actions of distracted drivers at the onset of yellow light

Driving on an approach to a signalized intersection while distracted is relatively risky, as potential vehicular conflicts and resulting angle collisions tend to be relatively more severe compared to other locations. Given the prevalence and importance of this particular scenario, the objective of this study was to examine the decisions and actions of distracted drivers during the onset of yellow lights. Driving simulator data were obtained from a sample of 69 drivers under baseline and handheld cell phone conditions at the University of Iowa – National Advanced Driving Simulator. Explanatory variables included age, gender, cell phone use, distance to stop-line, and speed. Although there is extensive research on drivers’ responses to yellow traffic signals, the examinations have been conducted from a traditional regression-based approach, which do not necessary provide the underlying relations and patterns among the sampled data. In this paper, we exploit the benefits of both classical statistical inference and data mining techniques to identify the a priori relationships among main effects, non-linearities, and interaction effects. Results suggest that the probability of yellow light running increases with the increase in driving speed at the onset of yellow. Both young (18–25 years) and middle-aged (30–45 years) drivers reveal reduced propensity for yellow light running whilst distracted across the entire speed range, exhibiting possible risk compensation during this critical driving situation. The propensity for yellow light running for both distracted male and female older (50–60 years) drivers is significantly higher. Driver experience captured by age interacts with distraction, resulting in their combined effect having slower physiological response and being distracted particularly risky.

Knowledge transfer through a transnational program partnership between Indonesian and Australian universities

As transnational programs are often advocated as a knowledge transfer opportunity between the partner universities, this case study investigated the knowledge transfer (KT) processes between Indonesian and Australian universities through an undergraduate transnational program partnership (TPP). An inter-organisational KT theoretical framework from the business sector was adapted and used to guide the study. The data were generated through semi-structured interviews with key university officers and document analysis from two partner universities. Based on the thematic analysis of the data, the findings demonstrated that the curriculum mapping process facilitated KT. However, different intentions of the partner universities in establishing the program led to declining interest to conduct more KT when expectations were not met. The Indonesian university’s existing knowledge, acquired from other sources through processes that were serendipitous and based on individual lecturers’ personal experience, meant that KT opportunities through the TPP were not always pursued despite written agreement to exchange knowledge with the Australian partner. While KT most evidently resulted in institutional capacity development for the Indonesian university’s school that managed the TPP, dissemination of knowledge to other units within the university was more challenging due to communication problems between the units. Hence, other universities seeking to conduct KT through TPPs need to understand each partner university's intention in establishing the partnerships, identify the institutions' needs before seeking knowledge input from the partner university and improve the communication between and within the universities for sustainable benefits.

PTHR1 polymorphisms influence BMD variation through effects on the growing skeleton

We investigated whether polymorphisms in PTHR1 are associated with bone mineral density (BMD), to determine whether the association of this gene with BMD was due to effects on attainment of peak bone mass or effects on subsequent bone loss. The PTHR1 gene, including its 14 exons, their exon-intron boundaries, and 1,500 bp of its promoter region, was screened for polymorphisms by denaturing high-performance liquid chromatography (dHPLC) and sequencing in 36 osteoporotic cases. Eleven single-nucleotide polymorphisms (SNPs), one tetranucleotide repeat, and one tetranucleotide deletion were identified. A cohort of 634 families, including 1,236 men (39%) and 1,926 women (61%) ascertained with probands with low BMD (Z< -2.0) and the Children in Focus subset of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort (785 unrelated individuals, mean age 118 months), were genotyped for the five most informative SNPs (minor allele frequency >5%) and the tetranucleotide repeat. In our osteoporosis families, association was noted between lumbar spine BMD and alleles of a known functional tetranucleotide repeat (U4) in the PTHR1 promoter region (P = 0.042) and between two and three marker haplotypes of PTHR1 polymorphisms with lumbar spine, femoral neck, and total hip BMD (P = 0.021-0.047). This association was restricted to the youngest tertile of the population (age 16-39 years, P = 0.013-0.048). A similar association was found for the ALSPAC cohort: two marker haplotypes of SNPs A48609T and C52813T were associated with height (P = 0.006) and total body less head BMD (P = 0.02), corrected for age and gender, confirming the family findings. These findings suggest a role for PTHR1 variation in determining peak BMD.

Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1

We report a genome-wide association study for open-angle glaucoma (OAG) blindness using a discovery cohort of 590 individuals with severe visual field loss (cases) and 3,956 controls. We identified associated loci at TMCO1 (rs4656461[G] odds ratio (OR) = 1.68, P = 6.1 × 10-10) and CDKN2B-AS1 (rs4977756[A] OR = 1.50, P = 4.7 × 10-9). We replicated these associations in an independent cohort of cases with advanced OAG (rs4656461 P = 0.010; rs4977756 P = 0.042) and two additional cohorts of less severe OAG (rs4656461 combined discovery and replication P = 6.00 × 10-14, OR = 1.51, 95% CI 1.35-1.68; rs4977756 combined P = 1.35 × 10-14, OR = 1.39, 95% CI 1.28-1.51). We show retinal expression of genes at both loci in human ocular tissues. We also show that CDKN2A and CDKN2B are upregulated in the retina of a rat model of glaucoma. © 2011 Nature America, Inc. All rights reserved.