Complexity and high-end computing in biology and medicine

Biomedical systems involve a large number of entities and intricate interactions between these. Their direct analysis is, therefore, difficult, and it is often necessary to rely on computational models. These models require significant resources and parallel computing solutions. These approaches are particularly suited, given parallel aspects in the nature of biomedical systems. Model hybridisation also permits the integration and simultaneous study of multiple aspects and scales of these systems, thus providing an efficient platform for multidisciplinary research.

Experimental and numerical investigation of strain-rate dependent mechanical properties of single living cells

The objective of this project is to investigate the strain-rate dependent mechanical behaviour of single living cells using both experimental and numerical techniques. The results revealed that living cells behave as porohyperlastic materials and that both solid and fluid phases within the cells play important roles in their mechanical responses. The research reported in this thesis provides a better understanding of the mechanisms underlying the cellular responses to external mechanical loadings and of the process of mechanical signal transduction in living cells. It would help us to enhance knowledge of and insight into the role of mechanical forces in supporting tissue regeneration or degeneration.

Experimental studies of cold-formed steel hollow section columns at elevated temperatures

This paper reports the details of an experimental study of cold-formed steel hollow section columns at ambient and elevated temperatures. In this study the global buckling behaviour of cold-formed Square Hollow Section (SHS) slender columns under axial compression was investigated at various uniform elevated temperatures up to 700℃. The results of these column tests are reported in this paper, which include the buckling/failure modes at elevated temperatures, and ultimate load versus temperature curves. Finite element models of tested columns were also developed and their behaviour and ultimate capacities at ambient and elevated temperatures were studied. Fire design rules given in European and American standards including the Direct Strength Method (DSM) based design rules were used to predict the ultimate capacities of tested columns at elevated temperatures. Elevated temperature mechanical properties and stress-strain models given in European steel design standards and past researches were used with design rules and finite element models to investigate their effects on SHS column capacities. Comparisons of column capacities from tests and finite element analyses with those predicted by current design rules were used to determine the accuracy of currently available column design rules in predicting the capacities of SHS columns at elevated temperatures and the need to use appropriate elevated temperature material stress-strain models. This paper presents the important findings derived from the comparisons of these column capacities.

Dynamics of nitrogen and suspended solids removal in experimental stormwater biofilters under intermittent wetting and drying

This research study comprehensively analyses the dynamics of nitrogen and suspended solids removal in stormwater biofilters. The study focuses on pollutant removal during an event with time, rather than the conventional event-mean analysis. Antecedent dry days (number of days in between rainfall) during which biofilters remain dry and the inflow concentration of pollutants were two other important variables analysed in this study. The research outcome highlights the significance of dry-phase processes and the process of stabilization on filter performance and sets a paradigm shift from the current approach towards an innovative way of performance analysis of biofilters.

Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

Experimental and statistical investigation of Australian native plants for second-generation biodiesel production

This work explores the potential of Australian native plants as a source of second-generation biodiesel for internal combustion engines application. Biodiesels were evaluated from a number of non-edible oil seeds which are grow naturally in Queensland, Australia. The quality of the produced biodiesels has been investigated by several experimental and numerical methods. The research methodology and numerical model developed in this study can be used for a broad range of biodiesel feedstocks and for the future development of renewable native biodiesel in Australia.

Structural complexity in structural health monitoring: Preliminary experimental modal testing and analysis

Many researchers in the field of civil structural health monitoring have developed and tested their methods on simple to moderately complex laboratory structures such as beams, plates, frames, and trusses. Field work has also been conducted by many researchers and practitioners on more complex operating bridges. Most laboratory structures do not adequately replicate the complexity of truss bridges. This paper presents some preliminary results of experimental modal testing and analysis of the bridge model presented in the companion paper, using the peak picking method, and compares these results with those of a simple numerical model of the structure. Three dominant modes of vibration were experimentally identified under 15 Hz. The mode shapes and order of the modes matched those of the numerical model; however, the frequencies did not match.

The molecular structure of kaolinite–potassium acetate intercalation complexes: A combined experimental and molecular dynamic simulation study

The kaolinite (Kaol) intercalated with potassium acetate (Ac) was prepared and characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and thermogravimetry. Molecular dynamic simulation was performed to investigate the structure of Kaol–Ac intercalation complex and the hydrogen bonds between Kaol and intercalated Ac andwater using INTERFACE forcefield. The acetate anions andwater arranged in a bilayer structure in the interlayer space of Kaol. The potassium cations distributed in the interlayer space and strongly coordinated with acetate anions aswell aswater rather than keyed into the ditrigonal holes of tetrahedral surface of Kaol. Strong hydrogen bonds formed between the hydrogen atoms of hydroxyl on the octahedral surface and oxygen atoms of both acetate anions and water. The acetate anions andwater also weakly bonded hydrogen to the silica tetrahedral surface through their hydrogen atoms with the oxygen atoms of silica tetrahedral surface.

A virtual environment for medical radiation collaborative learning

Asoftware-based environment was developed to provide practical training in medical radiation principles and safety. The Virtual Radiation Laboratory application allowed students to conduct virtual experiments using simulated diagnostic and radiotherapy X-ray generators. The experiments were designed to teach students about the inverse square law, half value layer and radiation protection measures and utilised genuine clinical and experimental data. Evaluation of the application was conducted in order to ascertain the impact of the software on students’ understanding, satisfaction and collaborative learning skills and also to determine potential further improvements to the software and guidelines for its continued use. Feedback was gathered via an anonymous online survey consisting of a mixture of Likert-style questions and short answer open questions. Student feedback was highly positive with 80 % of students reporting increased understanding of radiation protection principles. Furthermore 72 % enjoyed using the software and 87 %of students felt that the project facilitated collaboration within small groups. The main themes arising in the qualitative feedback comments related to efficiency and effectiveness of teaching, safety of environment, collaboration and realism. Staff and students both report gains in efficiency and effectiveness associated with the virtual experiments. In addition students particularly value the visualisation of ‘‘invisible’’ physical principles and increased opportunity for experimentation and collaborative problembased learning. Similar ventures will benefit from adopting an approach that allows for individual experimentation while visualizing challenging concepts.

Re-imagining legacy: A woman experimental filmmaker’s response to colonisation

This practice-led research project analyses the creative and critical processes that occur when women visual artists respond to the legacy of colonisation. The research investigates the practices of selected visual artists, interrogates the candidate's creative practice, and analyses interview data. The creative practice component of the research analyses the critical and artistic strategies undertaken to produce an original set of six moving image artworks entitled Sankɔfa Dreaming. The creative practice develops an original artist method, Re-imagining Legacy. This method produces multivalent artworks that express a dynamic set of integrated critical standpoints on legacy and re-imaginings of history.

Experimental evaluation of the performance of 2×2 MIMO-OFDM for vehicle-to-infrastructure communications

In this paper, a novel 2×2 multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) testbed based on an Analog Devices AD9361 highly integrated radio frequency (RF) agile transceiver was specifically implemented for the purpose of estimating and analyzing MIMO-OFDM channel capacity in vehicle-to-infrastructure (V2I) environments using the 920 MHz industrial, scientific, and medical (ISM) band. We implemented two-dimensional discrete cosine transform-based filtering to reduce the channel estimation errors and show its effectiveness on our measurement results. We have also analyzed the effects of channel estimation error on the MIMO channel capacity by simulation. Three different scenarios of subcarrier spacing were investigated which correspond to IEEE 802.11p, Long-Term Evolution (LTE), and Digital Video Broadcasting Terrestrial (DVB-T)(2k) standards. An extensive MIMO-OFDM V2I channel measurement campaign was performed in a suburban environment. Analysis of the measured MIMO channel capacity results as a function of the transmitter-to-receiver (TX-RX) separation distance up to 250 m shows that the variance of the MIMO channel capacity is larger for the near-range line-of-sight (LOS) scenarios than for the long-range non-LOS cases, using a fixed receiver signal-to-noise ratio (SNR) criterion. We observed that the largest capacity values were achieved at LOS propagation despite the common assumption of a degenerated MIMO channel in LOS. We consider that this is due to the large angular spacing between MIMO subchannels which occurs when the receiver vehicle rooftop antennas pass by the fixed transmitter antennas at close range, causing MIMO subchannels to be orthogonal. In addition, analysis on the effects of different subcarrier spacings on MIMO-OFDM channel capacity showed negligible differences in mean channel capacity for the subcarrier spacing range investigated. Measured channels described in this paper are available on request.

Peptide-functionalized polymeric nanoparticles for active targeting of damaged tissue in animals with experimental autoimmune encephalomyelitis

Increased permeability of blood vessels is an indicator for various injuries and diseases, including multiple sclerosis (MS), of the central nervous system. Nanoparticles have the potential to deliver drugs locally to sites of tissue damage, reducing the drug administered and limiting associated side effects, but efficient accumulation still remains a challenge. We developed peptide-functionalized polymeric nanoparticles to target blood clots and the extracellular matrix molecule nidogen, which are associated with areas of tissue damage. Using the induction of experimental autoimmune encephalomyelitis in rats to provide a model of MS associated with tissue damage and blood vessel lesions, all targeted nanoparticles were delivered systemically. In vivo data demonstrates enhanced accumulation of peptide functionalized nanoparticles at the injury site compared to scrambled and naive controls, particularly for nanoparticles functionalized to target fibrin clots. This suggests that further investigations with drug laden, peptide functionalized nanoparticles might be of particular interest in the development of treatment strategies for MS.

The freedom to tinker: Patent law and experimental use

This article considers the origins and the development of the defence of experimental use in patent law - the ’freedom to tinker'. It explores the impact of such an exemption upon a number of important industries - such as agriculture, biotechnology, and pharmaceutical drugs. This article takes a comparative approach in its analysis of patent law and experimental use. It highlights the competing norms, and lack of harmonization between a number of jurisdictions - including the United States, the European Union, and Australia. Section 2 provides a critique of the development of the common law defence of experimental use in the United States. It considers a series of precedents - including Roche Products Inc v Bolar Pharmaceuticals, Madey v Duke University, Integra Lifesciences I Ltd v Merck KgaA, and Applera v MJ Research. Section 3 explores the operation of patent law and experimental use in European jurisdictions. It looks at a number of significant precedents in the United Kingdom, the Netherlands, France, Italy, and Germany. Section 4 considers the policy debate in a number of forums over the defence of experimental use in Australia. It examines the controversy over Genetic Technologies Limited asking research organisations to obtain a licence in respect of its patents associated with non-coding DNA and genomic mapping. It also considers the inquiries of the Australian Law Reform Commission and the Advisory Council on Intellectual Property, as well as the impact of the TRIPS Agreement and the Australia-United States Free Trade Agreement. The conclusion contends that there is a need for a broad-based defence of experimental use for all the member states of the Organisation for Economic Co-operation and Development.

Etapas del cambio en personas inactivas tras un programa de promoción de la actividad física en Atención Primaria

Objetivo El objetivo del estudio fue evaluar las Etapas del cambio en relación con la actividad física y el estado de salud general entre personas que participaron en un Programa de promoción de la actividad física (PPAF) de 12 semanas frente a un grupo control. Diseño Ensayo clínico aleatorizado. Participantes Noventa y ocho personas inactivas de ambos sexos con una edad media de 62,82 años procedentes de 2 centros de Atención Primaria del Distrito Sanitario Costa del Sol. Intervención Un PPAF organizado en grupos y siguiendo los criterios del Colegio Americano de Medicina del Deporte, 2 sesiones semanales de 60 min durante 12 semanas. Mediciones principales La variable principal de resultado fue resistencia al cambio en relación con la actividad física. La variable secundaria fue el estado de salud general (componentes físicos y mentales), determinado con el cuestionario de salud general SF12. Resultados Se encontraron diferencias significativas en las etapas del cambio a favor del grupo experimental (p < 0,05). No se encontraron diferencias estadísticamente significativas entre grupos después de la intervención en el estado general de salud. Conclusión Las etapas del cambio se modificaron en las personas inactivas que realizaron el PPAF en Atención Primaria. Futuros estudios son necesarios para identificar qué factores del entorno de los participantes influyen en la resistencia al cambio de la actividad física. Abstract Objective This study has aimed to evaluate the stages of change in relation to physical activity and overall health status among persons who participated in a 12-week Physical activity promotion program (PAPP) compared to a control group. Design Randomized clinical trial. Participants The study included 98 inactive persons of both sexes with a mean age of 62.82 years from 2 of Primary Care Centers of the Malaga Health Care District. Interventions A PAPP organized in groups according to the American College of Sports Medicine criteria including two weekly sessions of 60 minutes each for 3 months. Main measures The primary outcome was to assess resistance to change in relation to physical activity. The secondary variable was overall health (physical and mental components) determined with the SF12 general health questionnaire. Results Significant differences were found in the stages of change (P<.05). There were no significant differences found in general health status improvement in regards to the initial assessment. Conclusion The stages of change were modified in the inactive persons who carried out the PAPP in Primary Care. Future studies are needed to identify which environmental factors influence the resistance to change in physical activity of the participants.

Cambios hematológicos tras un programa de promoción de actividad física en sujetos inactivos. Ensayo aleatorizado controlado

Objetivo Comparar los cambios antropométricos y bioquímicos en personas inactivas, que realizan un programa de actividad física frente a los que no lo realizan desde los Centros de Atención Primaria. Métodos Cien personas inactivas de ambos sexos, mayores de 55 años fueron aleatorizadas a un grupo experimental (n = 50) y a un grupo control (n = 50). Se realizó un programa de promoción de actividad física siguiendo los criterios del Colegio Americano de Medicina del Deporte, de 60 min cada sesión, 2 sesiones por semana, durante 3 meses. Las medidas antropométricas incluyeron el índice de masa corporal y el porcentaje graso, y como variables bioquímicas el perfil lipídico, hematíes y la creatina kinasa. Resultados Completaron el estudio 75 personas. Esta investigación no presentó cambios significativos a nivel antropométrico, ni en las variables bioquímicas del perfil lipídico. Sí se observaron efectos clínicamente relevantes en la concentración de los hematíes de las mujeres que realizaron dicho programa. Conclusiones El efecto clínico global fue pequeño en las personas que realizaron el programa, pero relevante para la salud de la población. Esta intervención produce efectos a corto plazo en la bioquímica de las personas inactivas. Abstract in English Objective Compare anthropometry and biochemical changes in inactive people who participate in a physical activity program versus those who do not from the Primary Health Care Centers. Methods One hundred inactive subjects of both genders, 55 years and older, from Torremolinos, Spain were randomized into an experimental group (n = 50) and a control group (n = 50). A program promoting physical activity was carried out following the American Medical Society for Sport's Medicine criteria. The program included sessions a week for 3 months. Antropometric measurements included body mass index and fat percentage, and such as biochemical measures: the lipid profile, erythrocytes, and creatine kinase. Results Seventy-five persons completed the study. This research did not show significant changes to anthropometric or biochemical outcomes of the lipid profile. However, there were clinically relevant effects regarding red blood cells concentration in the women who participated in this program. Conclusions Overall clinical effect was small in those participating in the program, but relevant for the health of the population. This program has short-term effects on biochemistry results of inactive subjects.