Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Temporal Integration of Movement: The Time-Course of Motion Streaks Revealed by Masking

Temporal integration in the visual system causes fast-moving objects to leave oriented ‘motion streaks’ in their wake, which could be used to facilitate motion direction perception. Temporal integration is thought to occur over 100 ms in early cortex, although this has never been tested for motion streaks. Here we compare the ability of fast-moving (‘streaky’) and slow-moving fields of dots to mask briefly flashed gratings either parallel or orthogonal to the motion trajectory. Gratings were presented at various asynchronies relative to motion onset (from to ms) to sample the time-course of the accumulating streaks. Predictions were that masking would be strongest for the fast parallel condition, and would be weak at early asynchronies and strengthen over time as integration rendered the translating dots more streaky and grating-like. The asynchrony where the masking function reached a plateau would correspond to the temporal integration period. As expected, fast-moving dots caused greater masking of parallel gratings than orthogonal gratings, and slow motion produced only modest masking of either grating orientation. Masking strength in the fast, parallel condition increased with time and reached a plateau after 77 ms, providing an estimate of the temporal integration period for mechanisms encoding motion streaks. Interestingly, the greater masking by fast motion of parallel compared with orthogonal gratings first reached significance at 48 ms before motion onset, indicating an effect of backward masking by motion streaks

Context Matters: The Illusive Simplicity of Macaque V1 Receptive Fields

Even in V1, where neurons have well characterized classical receptive fields (CRFs), it has been difficult to deduce which features of natural scenes stimuli they actually respond to. Forward models based upon CRF stimuli have had limited success in predicting the response of V1 neurons to natural scenes. As natural scenes exhibit complex spatial and temporal correlations, this could be due to surround effects that modulate the sensitivity of the CRF. Here, instead of attempting a forward model, we quantify the importance of the natural scenes surround for awake macaque monkeys by modeling it non-parametrically. We also quantify the influence of two forms of trial to trial variability. The first is related to the neuron’s own spike history. The second is related to ongoing mean field population activity reflected by the local field potential (LFP). We find that the surround produces strong temporal modulations in the firing rate that can be both suppressive and facilitative. Further, the LFP is found to induce a precise timing in spikes, which tend to be temporally localized on sharp LFP transients in the gamma frequency range. Using the pseudo R[superscript 2] as a measure of model fit, we find that during natural scene viewing the CRF dominates, accounting for 60% of the fit, but that taken collectively the surround, spike history and LFP are almost as important, accounting for 40%. However, overall only a small proportion of V1 spiking statistics could be explained (R[superscript 2]~5%), even when the full stimulus, spike history and LFP were taken into account. This suggests that under natural scene conditions, the dominant influence on V1 neurons is not the stimulus, nor the mean field dynamics of the LFP, but the complex, incoherent dynamics of the network in which neurons are embedded.National Institutes of Health (U.S.) (K25 NS052422-02)National Institutes of Health (U.S.) (DP1 ODOO3646

Modern Structural Analysis of Subsurface Provinces: A Case Study on the Cooper and Eromanga Basins, Australia

The Cooper‐Eromanga Basin is Australia’s largest onshore hydrocarbon province with significant unconventional hydrocarbon potential; however, due to the lack of outcrop, geological data is not easily measured. To mitigate this issue, an approach that can be used to provide a modern structural analysis of subsurface provinces with limited outcrop is presented in this thesis. A holistic approach integrating many datasets, techniques, methodologies, and software has provided better constraints on the structural geology, geophysics and tectonic evolution of the province. Hydrocarbon exploration in the basin has transitioned to technically challenging plays (pinch‐out traps, low relief structures, basin centred gas, etc.), but these programs have been somewhat hampered by a poor understanding of the structural geology, geophysics and tectonic evolution of the basin, with previous work using low resolution and sparse 2D seismic data that remained in the time‐domain. Apart from this approach, the key deliverable of this project was constraining the orientation and magnitude of six tectonic events (N‐S Alice Springs, SE‐NW Mid‐Permian, NE‐SW Daralingie, E‐W Hunter‐Bowen, E‐W Late Cretaceous, and N‐S Paleogene Events) that have controlled the evolution of the Cooper‐Eromanga Basin. The integration of geophysical data, calcite twin stress inversion analysis and rock mechanics presented a new combination of data to constrain the tectonic evolution of subsurface provinces. These complete paleo‐stress tensors were integrated with six geomechanical models to constrain hydrocarbon migration pathways through time, finding that since the critical moment (90 Ma), NE‐SW striking high angle (60ᵒ) faults were likely facilitating hydrocarbon migration. Under contemporary stresses, the regional SE‐NW strike‐slip faults are most likely to reactivate and complicate hydraulic fracture stimulation treatments. Considering that a detailed structural architecture map was not available in literature, all available 2D seismic lines and 12 3D seismic surveys were interpreted to generate a modern basement fault map and detailed fault models for each seismic survey. Four of these surveys cover major basin ridges and were used to constrain the tectonostratigraphic evolution of the basin. Extensive on‐lapping features were created along major structures during the structural events, particularly within Permian stratigraphy. The timing of structural movement is important; however, for economic production of hydrocarbons, a detailed understanding of the natural fracture network in tight sand reservoirs is fundamental. This led to a study that would map the distribution of >6000 temperature samples, >8000 pressure samples, and natural fracture data from 11 borehole image logs across the basin. Following this, the spatial and temporal distribution of subsurface permeable natural fracture networks was presented for five 3D seismic surveys using seismic curvature analysis and a geomechanical model. This model found that E‐W striking natural fractures are optimally oriented to form structural sweet‐spots and are commonly associated with E‐W elongate structures. To better understand the seismic time‐to‐depth conversion accuracy within the basin, an automated cross‐validation method was developed to generate a significant statistical database from 13 D seismic surveys, 73 interpreted horizons, and 657 wells. The results showed that a single method should not be used for the entire basin, as the most accurate method and expected error changes depending on the unique dataset. To conclude this research, a thorough literature review was carried out to synthesis the new research and integrate it with previous literature. The approach used in this thesis has significant value to all subsurface provinces with limited outcrop that has prevented detailed structural and geomechanical analysis, leaving significant research gaps.Thesis (Ph.D.) -- University of Adelaide, Australian School of Petroleum, 201