In vitro and in vivo MMP gene expression localisation by In Situ-RT-PCR in cell culture and paraffin embedded human breast cancer cell line xenografts

Background Members of the matrix metalloproteinase (MMP) family of proteases are required for the degradation of the basement membrane and extracellular matrix in both normal and pathological conditions. In vitro, MT1-MMP (MMP-14, membrane type-1-MMP) expression is higher in more invasive human breast cancer (HBC) cell lines, whilst in vivo its expression has been associated with the stroma surrounding breast tumours. MMP-1 (interstitial collagenase) has been associated with MDA-MB-231 invasion in vitro, while MMP-3 (stromelysin-1) has been localised around invasive cells of breast tumours in vivo. As MMPs are not stored intracellularly, the ability to localise their expression to their cells of origin is difficult. Methods We utilised the unique in situ-reverse transcription-polymerase chain reaction (IS-RT-PCR) methodology to localise the in vitro and in vivo gene expression of MT1-MMP, MMP-1 and MMP-3 in human breast cancer. In vitro, MMP induction was examined in the MDA-MB-231 and MCF-7 HBC cell lines following exposure to Concanavalin A (Con A). In vivo, we examined their expression in archival paraffin embedded xenografts derived from a range of HBC cell lines of varied invasive and metastatic potential. Mouse xenografts are heterogenous, containing neoplastic human parenchyma with mouse stroma and vasculature and provide a reproducible in vivo model system correlated to the human disease state. Results In vitro, exposure to Con A increased MT1-MMP gene expression in MDA-MB-231 cells and decreased MT1-MMP gene expression in MCF-7 cells. MMP-1 and MMP-3 gene expression remained unchanged in both cell lines. In vivo, stromal cells recruited into each xenograft demonstrated differences in localised levels of MMP gene expression. Specifically, MDA-MB-231, MDA-MB-435 and Hs578T HBC cell lines are able to influence MMP gene expression in the surrounding stroma. Conclusion We have demonstrated the applicability and sensitivity of IS-RT-PCR for the examination of MMP gene expression both in vitro and in vivo. Induction of MMP gene expression in both the epithelial tumour cells and surrounding stromal cells is associated with increased metastatic potential. Our data demonstrate the contribution of the stroma to epithelial MMP gene expression, and highlight the complexity of the role of MMPs in the stromal-epithelial interactions within breast carcinoma.

Use of an on-line student response system : an analysis of adoption and continuance

The goal of this project was to initiate the use of an internet-based student response system in a large, first year chemistry class at a typical Australian university, and to verify its popularity and utility. A secondary goal was to influence other academic staff to adopt the system, initiating change at the discipline and Faculty level. The first goal was achieved with a high response rate using a commercial on-line system; however, the number of students engaging with the system dropped gradually during each class and over the course of the semester. Factors affecting student and staff adoption and continuance with technology are explored using established models.

Quantitative and qualitative changes in gene expression patterns characterize the activity of plaques in multiple sclerosis

Multiple sclerosis (MS) is a complex autoimmune disorder of the CNS with both genetic and environmental contributing factors. Clinical symptoms are broadly characterized by initial onset, and progressive debilitating neurological impairment. In this study, RNA from MS chronic active and MS acute lesions was extracted, and compared with patient matched normal white matter by fluorescent cDNA microarray hybridization analysis. This resulted in the identification of 139 genes that were differentially regulated in MS plaque tissue compared to normal tissue. Of these, 69 genes showed a common pattern of expression in the chronic active and acute plaque tissues investigated (Pvalue<0.0001, ρ=0.73, by Spearman's ρ analysis); while 70 transcripts were uniquely differentially expressed (≥1.5-fold) in either acute or chronic active tissues. These results included known markers of MS such as the myelin basic protein (MBP) and glutathione S-transferase (GST) M1, nerve growth factors, such as nerve injury-induced protein 1 (NINJ1), X-ray and excision DNA repair factors (XRCC9 and ERCC5) and X-linked genes such as the ribosomal protein, RPS4X. Primers were then designed for seven array-selected genes, including transferrin (TF), superoxide dismutase 1 (SOD1), glutathione peroxidase 1 (GPX1), GSTP1, crystallin, alpha-B (CRYAB), phosphomannomutase 1 (PMM1) and tubulin β-5 (TBB5), and real time quantitative (Q)-PCR analysis was performed. The results of comparative Q-PCR analysis correlated significantly with those obtained by array analysis (r=0.75, Pvalue<0.01, by Pearson's bivariate correlation). Both chronic active and acute plaques shared the majority of factors identified suggesting that quantitative, rather than gross qualitative differences in gene expression pattern may define the progression from acute to chronic active plaques in MS.

Animated Kolam Patterns

The brief for the creative work was to produce a digital backdrop that would be projected behind and enhance a dance performance. The animation needed to display a static kolam pattern that would then dissolve at a choreographed point in the performance. The dissolving mimics the fragmentation that occurs to physical kolam patterns throughout the day as people interact with the drawings. The final animated work was incorporated into Vanessa Mafe-Keane’s performance titled “Paired Back” performed at the Judith Wright Centre, Brisbane 2013 as part of “Dance. Indie Dance. Through the use of motion capture technology the process of dissolving the pattern is a direct result of the performer’s movements allowing visual and temporal connection between motion of performer and digital graphic to be observed. This creative work presented an opportunity to expand upon experiments conducted in the production of experimental visual forms undertaken at QUT using the Xsens MVN Inertial Motion Capture System. The project took on the form of an investigation into practice with a focus on the additional complexities of capturing, then applying multiple data sources into the production of animated visuals along with bringing to light the considerations taken into account when producing this type of generative art work for live performance. The reported outcomes from this investigation have contributed to a larger study on the use of motion capture in the generative arts, furthering the understanding of and generating theories on practice.

Size characterization of airborne SiO2 nanoparticles with on-line and off-line measurement techniques : an interlaboratory comparison study

Results of an interlaboratory comparison on size characterization of SiO2 airborne nanoparticles using on-line and off-line measurement techniques are discussed. This study was performed in the framework of Technical Working Area (TWA) 34—“Properties of Nanoparticle Populations” of the Versailles Project on Advanced Materials and Standards (VAMAS) in the project no. 3 “Techniques for characterizing size distribution of airborne nanoparticles”. Two types of nano-aerosols, consisting of (1) one population of nanoparticles with a mean diameter between 30.3 and 39.0 nm and (2) two populations of non-agglomerated nanoparticles with mean diameters between, respectively, 36.2–46.6 nm and 80.2–89.8 nm, were generated for characterization measurements. Scanning mobility particle size spectrometers (SMPS) were used for on-line measurements of size distributions of the produced nano-aerosols. Transmission electron microscopy, scanning electron microscopy, and atomic force microscopy were used as off-line measurement techniques for nanoparticles characterization. Samples were deposited on appropriate supports such as grids, filters, and mica plates by electrostatic precipitation and a filtration technique using SMPS controlled generation upstream. The results of the main size distribution parameters (mean and mode diameters), obtained from several laboratories, were compared based on metrological approaches including metrological traceability, calibration, and evaluation of the measurement uncertainty. Internationally harmonized measurement procedures for airborne SiO2 nanoparticles characterization are proposed.

Personal exposure to ultrafine particles : the influence of time-activity patterns

Exposure to ultrafine particles (UFPs) is deemed to be a major risk affecting human health. Therefore, airborne particle studies were performed in the recent years to evaluate the most critical micro-environments, as well as identifying the main UFP sources. Nonetheless, in order to properly evaluate the UFP exposure, personal monitoring is required as the only way to relate particle exposure levels to the activities performed and micro-environments visited. To this purpose, in the present work, the results of experimental analysis aimed at showing the effect of the time-activity patterns on UFP personal exposure are reported. In particular, 24 non-smoking couples (12 during winter and summer time, respectively), comprised of a man who worked full-time and a woman who was a homemaker, were analyzed using personal particle counter and GPS monitors. Each couple was investigated for a 48-h period, during which they also filled out a diary reporting the daily activities performed. Time activity patterns, particle number concentration exposure and the related dose received by the participants, in terms of particle alveolar-deposited surface area, were measured. The average exposure to particle number concentration was higher for women during both summer and winter (Summer: women 1.8×104 part. cm-3; men 9.2×103 part. cm-3; Winter: women 2.9×104 part. cm-3; men 1.3×104 part. cm-3), which was likely due to the time spent undertaking cooking activities. Staying indoors after cooking also led to higher alveolar-deposited surface area dose for both women and men during the winter time (9.12×102 and 6.33×102 mm2, respectively), when indoor ventilation was greatly reduced. The effect of cooking activities was also detected in terms of women’s dose intensity (dose per unit time), being 8.6 and 6.6 in winter and summer, respectively. On the contrary, the highest dose intensity activity for men was time spent using transportation (2.8 in both winter and summer).

Accurate pattern prediction of very closely spaced mismatched antennas using measured active element patterns

A method for prediction of the radiation pattern of N strongly coupled antennas with mismatched sources is presented. The method facilitates fast and accurate design of compact arrays. The prediction is based on the measured N-port S parameters of the coupled antennas and the N active element patterns measured in a 50 ω environment. By introducing equivalent power sources, the radiation pattern with excitation by sources with arbitrary impedances and various decoupling and matching networks (DMN) can be accurately predicted without the need for additional measurements. Two experiments were carried out for verification: pattern prediction for parasitic antennas with different loads and for antennas with DMN. The difference between measured and predicted patterns was within 1 to 2 dB.

Residential dissonance and mode choice

Residential dissonance refers to the mismatch in land-use patterns between individuals’ preferred residential neighbourhood type and the type of neighbourhood in which they currently reside. Current knowledge regarding the impact of residential dissonance is limited to short-term travel behaviours in urban vs. suburban, and rural vs. urban areas. Although the prevailing view is that dissonants adjust their orientation and lifestyle around their surrounding land use over time, empirical evidence is lacking to support this proposition. This research identifies both short-term mode choice behaviour and medium-term mode shift behaviour of dissonants in transit oriented development (TODs) vs. non-TOD areas in Brisbane, Australia. Natural groupings of neighbourhood profiles (e.g. residential density, land use diversity, intersection density, cul-de-sac density, and public transport accessibility levels) of 3957 individuals were identified as living either in a TOD (510 individuals) or non-TOD (3447 individuals) areas in Brisbane using the TwoStep cluster analysis technique. Levels of dissonance were measured based on a factor analysis of 16 items representing the travel attitudes/preferences of individuals. Two multinomial logistic (MNL) regression models were estimated to understand mode choice behaviour of (1) TOD dissonants, and (2) non-TOD dissonants in 2009, controlling for socio-demographics and environmental characteristics. Two additional MNL regression models were estimated to investigate mode shift behaviour of (3) TOD dissonants, and (4) non-TOD dissonants between 2009 and 2011, also controlling for socio-demographic, changes in socio-demographic, and built environmental factors. The findings suggest that travel preference is relatively more influential in transport mode choice decisions compared with built environment features. Little behavioural evidence was found to support the adjustment of a dissonant orientation toward a particular land use feature and mode accessibility they represent (e.g. a modal shift to greater use of the car for non-TOD dissonants). TOD policies should focus on reducing the level of dissonance in TODs in order to enhance transit ridership.

Capping them off! Exploring and explaining the patterns in undergraduate capstone subjects in Australian business schools

Universities are increasingly offering capstone subjects as part of curricula to prepare final year undergraduates for employment through consolidating and integrating their knowledge and skills while bridging the gap between academic learning and professional work. This study investigates capstone subjects offered by Australian business schools, drawing on national survey data collected in 2010-2011, complemented by interviews with associate deans teaching and learning instrumental in course and curricula design. Findings indicate the sector-wide use of capstone subjects in business disciplines, diversity in the patterns of offerings, and instances where subjects labelled as capstones do not meet the definition of capstones. We argue that these features are explained by a range of historic and strategic factors, such as the ad hoc development of subjects and a lack of understanding of the features of capstones. The findings of this paper inform the debate on the design, development, value and use of capstone subjects identifying the implications for staff development and knowledge management in higher education.

IS-RT-PCR assay detection of MT-MMP in a human breast cancer cell line

The in situ-reverse transcription-polymerase chain reaction (IS-RT-PCR) is a method that allows the direct localisation of gene expression. The method utilises the dual buffer mediated activity of the enzyme rTth DNA polymerase enabling both reverse transcription and DNA amplification. Labelled nucleoside triphosphates allow the site of expression to be labelled, rather than the PCR primers themselves, giving a more accurate localisation of transcript expression and decreased background than standard in situ hybridisation (ISH) assays. The MDA-MB-231 human breast carcinoma (HBC) cell line was assayed via the IS-RT-PCR technique, using primers encoding MT-MMP (membrane-type matrix metalloproteinase) and human β-actin. Our results clearly indicate baseline expression of MT-MMP in the relatively invasive MDA-MB-231 cell line at a signal intensity similar to the housekeeping gene β-actin, and results following induction with Concanavalin A (Con A) are consistent with our previous results obtained via Northern blotting.

A concept-based retrieval method for entity-oriented search

Entity-oriented retrieval aims to return a list of relevant entities rather than documents to provide exact answers for user queries. The nature of entity-oriented retrieval requires identifying the semantic intent of user queries, i.e., understanding the semantic role of query terms and determining the semantic categories which indicate the class of target entities. Existing methods are not able to exploit the semantic intent by capturing the semantic relationship between terms in a query and in a document that contains entity related information. To improve the understanding of the semantic intent of user queries, we propose concept-based retrieval method that not only automatically identifies the semantic intent of user queries, i.e., Intent Type and Intent Modifier but introduces concepts represented by Wikipedia articles to user queries. We evaluate our proposed method on entity profile documents annotated by concepts from Wikipedia category and list structure. Empirical analysis reveals that the proposed method outperforms several state-of-the-art approaches.

Quantitative Approaches to Comparing Communication Patterns on Twitter

To date, available literature mainly discusses Twitter activity patterns in the context of individual case studies, while comparative research on a large number of communicative events, their dynamics and patterns is missing. By conducting a comparative study of more than forty different cases (covering topics such as elections, natural disasters, corporate crises, and televised events) we identify a number of distinct types of discussion which can be observed on Twitter. Drawing on a range of communicative metrics, we show that thematic and contextual factors influence the usage of different communicative tools available to Twitter users, such as original tweets, @replies, retweets, and URLs. Based on this first analysis of the overall metrics of Twitter discussions, we also demonstrate stable patterns in the use of Twitter in the context of major topics and events.

An androgen receptor mutation in the MDA-MB-453 cell line model of molecular apocrine breast cancer compromises receptor activity

Recent evidence indicates that the estrogen receptor-a-negative, androgen receptor (AR)- positive molecular apocrine subtype of breast cancer is driven by AR signaling. The MDA-MB-453 cell line is the prototypical model of this breast cancer subtype; its proliferation is stimulated by androgens such as 5a-dihydrotestosterone (DHT) but inhibited by the progestin medroxyprogesterone acetate (MPA) via AR-mediated mechanisms. We report here that the AR gene in MDAMB- 453 cells contains a G-T transversion in exon 7, resulting in a receptor variant with a glutamine to histidine substitution at amino acid 865 (Q865H) in the ligand binding domain. Compared with wild-type AR, the Q865H variant exhibited reduced sensitivity to DHT and MPA in transactivation assays in MDA-MB-453 and PC-3 cells but did not respond to non-androgenic ligands or receptor antagonists. Ligand binding, molecular modeling, mammalian two-hybrid and immunoblot assays revealed effects of the Q865H mutation on ligand dissociation, AR intramolecular interactions, and receptor stability. Microarray expression profiling demonstrated that DHT and MPA regulate distinct transcriptional programs in MDA-MB-453 cells. Gene Set Enrichment Analysis revealed that DHT- but not MPA-regulated genes were associated with estrogen-responsive transcriptomes from MCF-7 cells and the Wnt signaling pathway. These findings suggest that the divergent proliferative responses of MDA-MB-453 cells to DHT and MPA result from the different genetic programs elicited by these two ligands through the AR-Q865H variant. This work highlights the necessity to characterize additional models of molecular apocrine breast cancer to determine the precise role of AR signaling in this breast cancer subtype. Endocrine-Related Cancer (2012) 19 599–613

Privacy oriented access control for electronic health records

Information privacy is a critical success/failure factor in information technology supported healthcare (eHealth). eHealth systems utilise electronic health records (EHR) as the main source of information, thus, implementing appropriate privacy preserving methods for EHRs is vital for the proliferation of eHealth. Whilst information privacy may be a fundamental requirement for eHealth consumers, healthcare professionals demand non-restricted access to patient information for improved healthcare delivery, thus, creating an environment where stakeholder requirements are contradictory. Therefore, there is a need to achieve an appropriate balance of requirements in order to build successful eHealth systems. Towards achieving this balance, a new genre of eHealth systems called Accountable-eHealth (AeH) systems has been proposed. In this paper, an access control model for EHRs is presented that can be utilised by AeH systems to create information usage policies that fulfil both stakeholders’ requirements. These policies are used to accomplish the aforementioned balance of requirements creating a satisfactory eHealth environment for all stakeholders. The access control model is validated using a Web based prototype as a proof of concept.