Reforming FOI : time for a new model?

The article discusses the recent developments on Freedom of Information or FOI in Queensland. It mentions the recent calls for a new FOI model, pointing to a radical departure from the old FOI template and the emergence of a significantly different FOI regime. Two of these reforms are the Right to Information Bill 2009 or RTI and the Information Privacy Bill 2009 or IP. It also mentions the new FOI Public Interest Test under the RTI Act.

Hormone-dependent bacterial growth persistence and biofilm formation - A pilot study investigating human follicular fluid collected during IVF cycles

Human follicular fluid, considered sterile, is aspirated as part of an in vitro fertilization (IVF) cycle. However, it is easily contaminated by the trans-vaginal collection route and little information exists in its potential to support the growth of microorganisms. The objectives of this study were to determine whether human follicular fluid can support bacterial growth over time, whether the steroid hormones estradiol and progesterone (present at high levels within follicular fluid) contribute to the in vitro growth of bacterial species, and whether species isolated from follicular fluid form biofilms. We found that bacteria in follicular fluid could persist for at least 28 weeks in vitro and that the steroid hormones stimulated the growth of some bacterial species, specifically Lactobacillus spp., Bifidobacterium spp. Streptococcus spp. and E. coli. Several species, Lactobacillus spp., Propionibacterium spp., and Streptococcus spp., formed biofilms when incubated in native follicular fluids in vitro (18/24, 75%). We conclude that bacteria aspirated along with follicular fluid during IVF cycles demonstrate a persistent pattern of growth. This discovery is important since it can offer a new avenue for investigation in infertile couples.

An analytical method for assessing stage-specific drug activity in Plasmodium vivax malaria : implications for ex vivo drug susceptibility testing

The emergence of highly chloroquine (CQ) resistant P. vivax in Southeast Asia has created an urgent need for an improved understanding of the mechanisms of drug resistance in these parasites, the development of robust tools for defining the spread of resistance, and the discovery of new antimalarial agents. The ex vivo Schizont Maturation Test (SMT), originally developed for the study of P. falciparum, has been modified for P. vivax. We retrospectively analysed the results from 760 parasite isolates assessed by the modified SMT to investigate the relationship between parasite growth dynamics and parasite susceptibility to antimalarial drugs. Previous observations of the stage-specific activity of CQ against P. vivax were confirmed, and shown to have profound consequences for interpretation of the assay. Using a nonlinear model we show increased duration of the assay and a higher proportion of ring stages in the initial blood sample were associated with decreased effective concentration (EC50) values of CQ, and identify a threshold where these associations no longer hold. Thus, starting composition of parasites in the SMT and duration of the assay can have a profound effect on the calculated EC50 for CQ. Our findings indicate that EC50 values from assays with a duration less than 34 hours do not truly reflect the sensitivity of the parasite to CQ, nor an assay where the proportion of ring stage parasites at the start of the assay does not exceed 66%. Application of this threshold modelling approach suggests that similar issues may occur for susceptibility testing of amodiaquine and mefloquine. The statistical methodology which has been developed also provides a novel means of detecting stage-specific drug activity for new antimalarials.

Learning beyond books : strategies for ambient media to improve libraries and collaboration spaces as interfaces for social learning

With the advent of digital media and online information resources, public libraries as physical destinations for information access are being increasingly challenged. As a response, many libraries follow the trend of removing bookshelves in order to provide more floorspace for social interaction and collaboration. Such spaces follow a Commons 2.0 model: they are designed to support collaborative work and social learning. The acquisition of skills and knowledge is facilitated as a result of being surrounded by and interacting with a community of likeminded others. Based on the results of a case study on a Commons 2.0 library space, this paper describes several issues of collaboration and social learning in public library settings. Acknowledging the significance of the architectural characteristics of the physical space, we discuss opportunities for ambient media to better reflect the social attributes of the library as a place; i.e. amplify the sense of other co-present library visitors and provide opportunities for shared encounters and conversations, which would remain invisible otherwise. We present the design of a user check-in system for improving the library as a physical destination for social learning, sharing, and inspiration for and by the community.

Conflict and seduction in the public sphere

In a critical but sympathetic reading of Habermas’s work (1984, 1987a, 1987b, 2003), Luke Goode (2005) recently sought to rework his theory of deliberative democracy in an age of mediated and increasingly digital public spheres. Taking a different approach, Alan McKee (2005) challenged the culture- and class-bound strictures of Habermasian rationalism, instead pursuing a more radically pluralist account of postmodern public spheres. The editors of this special section of Media, Culture & Society invited us to discuss our differing approaches to the public sphere. Goode holds that the institutional bases of contemporary public spheres (political parties, educational institutions or public media) remain of critical importance, albeit in the context of a kaleidoscopic array of unofficial and informal micro-publics, both localized and de-territorialized. In contrast, McKee sustains a ‘hermeneutics of suspicion’ toward the official, hegemonic institutions of the public sphere since they tend to exclude and delegitimize discourses and practices that challenge their polite middle-class norms. McKee’s recent research has focused on sexual cultures, particularly among youth (McKee, 2011). Goode’s recent work has examined new social media spaces, particularly in relation to news and public debate (e.g. Goode, 2009; Goode et al., 2011). Consequently, our discussion turned to a domain which links our interests: after Goode discussed some of his recent research on (in)civility on YouTube as a new media public sphere, McKee challenged him to consider the case of pornographic websites modelled on social media sites.1 He identifies a greater degree of ‘civility’ in these pornographic sibling sites than on YouTube, requiring careful consideration of what constitutes a ‘public sphere’ in contemporary digital culture. Such sites represent an environment that shatters the opposition of public and private interest, affording public engagement on matters of the body, of intimacy, of gender politics, of pleasure and desire – said by many critics to be ruled out of court in Habermasian theory. Such environments also trouble traditional binaries between the cognitive and the affective, and between the performative and the deliberative. In what follows we explore the differences between our approaches in the form of a dialogue. As is often the case, our approaches seemed less at odds after engaging in conversation than may have initially appeared. But important differences of emphasis remain.

An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Factors influencing funding decisions by elected politicians at the state/provincial level : a case study of public libraries in Canada

The purpose of this study was to determine factors (internal and external) that influenced Canadian provincial (state) politicians when making funding decisions about public libraries. Using the case study methodology, Canadian provincial/state level funding for public libraries in the 2009-10 fiscal year was examined. After reviewing funding levels across the country, three jurisdictions were chosen for the case: British Columbia's budget revealed dramatically decreased funding, Alberta's budget showed dramatically increased funding, and Ontario's budget was unchanged from the previous year. The primary source of data for the case was a series of semi-structured interviews with elected officials and senior bureaucrats from the three jurisdictions. An examination of primary and secondary documents was also undertaken to help set the political and economic context as well as to provide triangulation for the case interviews. The data were analysed to determine whether Cialdini's theory of influence (2001) and specifically any of the six tactics of influence (i.e, commitment and consistency, authority, liking, social proof, scarcity and reciprocity) were instrumental in these budget processes. Findings show the principles of "authority", "consistency and commitment" and "liking" were relevant, and that "liking" were especially important to these decisions. When these decision makers were considering funding for public libraries, they most often used three distinct lenses: the consistency lens (what are my values? what would my party do?), the authority lens (is someone with hierarchical power telling me to do this? are the requests legitimate?), and most importantly, the liking lens (how much do I like and know about the requester?). These findings are consistent with Cialdini's theory, which suggests the quality of some relationships is one of six factors that can most influence a decision maker. The small number of prior research studies exploring the reasons for increases or decreases in public library funding allocation decisions have given little insight into the factors that motivate those politicians involved in the process and the variables that contribute to these decisions. No prior studies have examined the construct of influence in decision making about funding for Canadian public libraries at any level of government. Additionally, no prior studies have examined the construct of influence in decision making within the context of Canadian provincial politics. While many public libraries are facing difficult decisions in the face of uncertain funding futures, the ability of the sector to obtain favourable responses to requests for increases may require a less simplistic approach than previously thought. The ability to create meaningful connections with individuals in many communities and across all levels of government should be emphasised as a key factor in influencing funding decisions.

Recent emergence of dengue virus serotype 4 in French Polynesia results from multiple introductions from other south pacific islands

BACKGROUND: Infection by dengue virus (DENV) is a major public health concern in hundreds of tropical and subtropical countries. French Polynesia (FP) regularly experiences epidemics that initiate, or are consecutive to, DENV circulation in other South Pacific Island Countries (SPICs). In January 2009, after a decade of serotype 1 (DENV-1) circulation, the first cases of DENV-4 infection were reported in FP. Two months later a new epidemic emerged, occurring about 20 years after the previous circulation of DENV-4 in FP. In this study, we investigated the epidemiological and molecular characteristics of the introduction, spread and genetic microevolution of DENV-4 in FP. METHODOLOGY/PRINCIPAL FINDINGS: Epidemiological data suggested that recent transmission of DENV-4 in FP started in the Leeward Islands and this serotype quickly displaced DENV-1 throughout FP. Phylogenetic analyses of the nucleotide sequences of the envelope (E) gene of 64 DENV-4 strains collected in FP in the 1980s and in 2009-2010, and some additional strains from other SPICs showed that DENV-4 strains from the SPICs were distributed into genotypes IIa and IIb. Recent FP strains were distributed into two clusters, each comprising viruses from other but distinct SPICs, suggesting that emergence of DENV-4 in FP in 2009 resulted from multiple introductions. Otherwise, we observed that almost all strains collected in the SPICs in the 1980s exhibit an amino acid (aa) substitution V287I within domain I of the E protein, and all recent South Pacific strains exhibit a T365I substitution within domain III. CONCLUSIONS/SIGNIFICANCE: This study confirmed the cyclic re-emergence and displacement of DENV serotypes in FP. Otherwise, our results showed that specific aa substitutions on the E protein were present on all DENV-4 strains circulating in SPICs. These substitutions probably acquired and subsequently conserved could reflect a founder effect to be associated with epidemiological, geographical, eco-biological and social specificities in SPICs.

Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses

Intra-host sequence data from RNA viruses have revealed the ubiquity of defective viruses in natural viral populations, sometimes at surprisingly high frequency. Although defective viruses have long been known to laboratory virologists, their relevance in clinical and epidemiological settings has not been established. The discovery of long-term transmission of a defective lineage of dengue virus type 1 (DENV-1) in Myanmar, first seen in 2001, raised important questions about the emergence of transmissible defective viruses and their role in viral epidemiology. By combining phylogenetic analyses and dynamical modelling, we investigate how evolutionary and ecological processes at the intra-host and inter-host scales shaped the emergence and spread of the defective DENV-1 lineage. We show that this lineage of defective viruses emerged between June 1998 and February 2001, and that the defective virus was transmitted primarily through co-transmission with the functional virus to uninfected individuals. We provide evidence that, surprisingly, this co-transmission route has a higher transmission potential than transmission of functional dengue viruses alone. Consequently, we predict that the defective lineage should increase overall incidence of dengue infection, which could account for the historically high dengue incidence reported in Myanmar in 2001-2002. Our results show the unappreciated potential for defective viruses to impact the epidemiology of human pathogens, possibly by modifying the virulence-transmissibility trade-off, or to emerge as circulating infections in their own right. They also demonstrate that interactions between viral variants, such as complementation, can open new pathways to viral emergence.

Rapid quantification of methamphetamine: using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) and Chemometrics

In Australia and increasingly worldwide, methamphetamine is one of the most commonly seized drugs analysed by forensic chemists. The current well-established GC/MS methods used to identify and quantify methamphetamine are lengthy, expensive processes, but often rapid analysis is requested by undercover police leading to an interest in developing this new analytical technique. Ninety six illicit drug seizures containing methamphetamine (0.1% - 78.6%) were analysed using Fourier Transform Infrared Spectroscopy with an Attenuated Total Reflectance attachment and Chemometrics. Two Partial Least Squares models were developed, one using the principal Infrared Spectroscopy peaks of methamphetamine and the other a Hierarchical Partial Least Squares model. Both of these models were refined to choose the variables that were most closely associated with the methamphetamine % vector. Both of the models were excellent, with the principal peaks in the Partial Least Squares model having Root Mean Square Error of Prediction 3.8, R2 0.9779 and lower limit of quantification 7% methamphetamine. The Hierarchical Partial Least Squares model had lower limit of quantification 0.3% methamphetamine, Root Mean Square Error of Prediction 5.2 and R2 0.9637. Such models offer rapid and effective methods for screening illicit drug samples to determine the percentage of methamphetamine they contain.

Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population

The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup - B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs – B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.

Multiple sclerosis susceptibility-associated SNPs do not influence disease severity measures in a cohort of Australian MS patients

Recent association studies in multiple sclerosis (MS) have identified and replicated several single nucleotide polymorphism (SNP) susceptibility loci including CLEC16A, IL2RA, IL7R, RPL5, CD58, CD40 and chromosome 12q13–14 in addition to the well established allele HLA-DR15. There is potential that these genetic susceptibility factors could also modulate MS disease severity, as demonstrated previously for the MS risk allele HLA-DR15. We investigated this hypothesis in a cohort of 1006 well characterised MS patients from South-Eastern Australia. We tested the MS-associated SNPs for association with five measures of disease severity incorporating disability, age of onset, cognition and brain atrophy. We observed trends towards association between the RPL5 risk SNP and time between first demyelinating event and relapse, and between the CD40 risk SNP and symbol digit test score. No associations were significant after correction for multiple testing. We found no evidence for the hypothesis that these new MS disease risk-associated SNPs influence disease severity.

Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbFAD2 family, NbFAD2.1 and NbFAD2.2, and quantitative RT-PCR (qRT-PCR) confirmed their expression in leaves. FAD2 activities were silenced using hairpin RNAi as monitored by qRT-PCR and biochemical assays. Silencing of endogenous FAD2 activities was combined with overexpression of transgenes via the use of the alternative viral silencing-suppressor protein, V2, from Tomato yellow leaf curl virus. We show that V2 permits maximal overexpression of transgenes but, crucially, also allows hairpin RNAi to operate unimpeded. To illustrate the efficacy of the V2-based leaf assay system, endogenous lipids were shunted from the desaturation of 18:1 to elongation reactions beginning with 18:1 as substrate. These V2-based leaf assays produced ~50% more elongated fatty acid products than p19-based assays. Analyses of small RNA populations generated from hairpin RNAi against NbFAD2 confirm that the siRNA population is dominated by 21 and 22 nt species derived from the hairpin. Collectively, these new tools expand the range of uses and possibilities for metabolic engineering in transient leaf assays. © 2012 Naim et al.

The local library across the digital and physical city : opportunities for economic development

This paper considers the role of the public library as a community hub, engagement space, and entrepreneurial incubator in the context of the city, city governance, and local government planning. It considers this role from the perspective of library experts and their future visions for libraries in a networked knowledge economy. Public libraries (often operated by or on behalf of local governments) potentially play a pivotal role for local governments in positioning communities within the global digital network. Fourteen qualitative interviews with library experts informed the study which investigates how the relationship between digital technology and the physical library space can potentially support the community to develop innovative, collaborative environments for transitioning to a digital future. The study found that libraries can capitalise on their position as community hubs for two purposes: first, to build vibrant community networks and forge economic links across urban localities; and second, to cross the digital divide and act as places of innovation and lifelong learning. Libraries provide a specific combination of community and technology spaces and have significant tangible connection points in the digital age. The paper further discusses the potential benefits for libraries in using ICT networks and infrastructure, such as the National Broadband Network in Australia. These networks could facilitate greater use of library assets and community knowledge, which, in turn, could assist knowledge economies and regional prosperity.

Breast cancer cells induce osteolytic bone lesions in vivo through a reduction in osteoblast activity in mice

Bone metastases are severely debilitating and have a significant impact on the quality of life of women with metastatic breast cancer. Treatment options are limited and in order to develop more targeted therapies, improved understanding of the complex mechanisms that lead to bone lesion development are warranted. Interestingly, whilst prostate-derived bone metastases are characterised by mixed or osteoblastic lesions, breast-derived bone metastases are characterised by osteolytic lesions, suggesting unique regulatory patterns. This study aimed to measure the changes in bone formation and bone resorption activity at two time-points (18 and 36 days) during development of the bone lesion following intratibial injection of MDA-MB-231 human breast cancer cells into the left tibiae of Severely Combined Immuno-Deficient (SCID) mice. The contralateral tibia was used as a control. Tibiae were extracted and processed for undecalcified histomorphometric analysis. We provide evidence that the early bone loss observed following exposure to MDA-MB-231 cells was due to a significant reduction in mineral apposition rate, rather than increased levels of bone resorption. This suggests that osteoblast activity was impaired in the presence of breast cancer cells, contrary to previous reports of osteoclast-dependent bone loss. Furthermore mRNA expression of Dickkopf Homolog 1 (DKK-1) and Noggin were confirmed in the MDA-MB-231 cell line, both of which antagonise osteoblast regulatory pathways. The observed bone loss following injection of cancer cells was due to an overall thinning of the trabecular bone struts rather than perforation of the bone tissue matrix (as measured by trabecular width and trabecular separation, respectively), suggesting an opportunity to reverse the cancer-induced bone changes. These novel insights into the mechanisms through which osteolytic bone lesions develop may be important in the development of new treatment strategies for metastatic breast cancer patients.