Problem definition and modeling techniques for the study of Kaneohe Bay, Oahu, Hawaii : final report /

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Regional timber yield and cost information for the South : modeling techniques /

"October 1984."

Application of Geographic Modeling Techniques to Quantify Spatial Access to Health Services Before and After an Acute Cardiac Event: The Cardiac ARIA Project

Background: Access to cardiac services is essential for appropriate implementation of evidence-based therapies to improve outcomes. The Cardiac Accessibility and Remoteness Index for Australia (Cardiac ARIA) aimed to derive an objective, geographic measure reflecting access to cardiac services. Methods: An expert panel defined an evidence-based clinical pathway. Using Geographic Information Systems (GIS), a numeric/alpha index was developed at two points along the continuum of care. The acute category (numeric) measured the time from the emergency call to arrival at an appropriate medical facility via road ambulance. The aftercare category (alpha) measured access to four basic services (family doctor, pharmacy, cardiac rehabilitation, and pathology services) when a patient returned to their community. Results: The numeric index ranged from 1 (access to principle referral center with cardiac catheterization service ≤ 1 hour) to 8 (no ambulance service, > 3 hours to medical facility, air transport required). The alphabetic index ranged from A (all 4 services available within 1 hour drive-time) to E (no services available within 1 hour). 13.9 million (71%) Australians resided within Cardiac ARIA 1A locations (hospital with cardiac catheterization laboratory and all aftercare within 1 hour). Those outside Cardiac 1A were over-represented by people aged over 65 years (32%) and Indigenous people (60%). Conclusion: The Cardiac ARIA index demonstrated substantial inequity in access to cardiac services in Australia. This methodology can be used to inform cardiology health service planning and the methodology could be applied to other common disease states within other regions of the world.

An investigation of survey technologies and modeling techniques for improving deepwater surveys of nonindigenous species in the Northwestern Hawaiian Islands

Nonindigenous species (NIS) are a major threat to marine ecosystems, with possible dramatic effects on biodiversity, biological productivity, habitat structure and fisheries. The Papahānaumokuākea Marine National Monument (PMNM) has taken active steps to mitigate the threats of NIS in Northwestern Hawaiian Islands (NWHI). Of particular concern are the 13 NIS already detected in NWHI and two invasive species found among the main Hawaiian Islands, snowflake coral (Carijoa riseii) and a red alga (Hypnea musciformis). Much of the information regarding NIS in NWHI has been collected or informed by surveys using conventional SCUBA or fishing gear. These technologies have significant drawbacks. SCUBA is generally constrained to depths shallower than 40 m and several NIS of concern have been detected well below this limit (e.g., L. kasmira – 256 m) and fishing gear is highly selective. Consequently, not all habitats or species can be properly represented. Effective management of NIS requires knowledge of their spatial distribution and abundance over their entire range. Surveys which provide this requisite information can be expensive, especially in the marine environment and even more so in deepwater. Technologies which minimize costs, increase the probability of detection and are capable of satisfying multiple objectives simultaneously are desired. This report examines survey technologies, with a focus on towed camera systems (TCSs), and modeling techniques which can increase NIS detection and sampling efficiency in deepwater habitats of NWHI; thus filling a critical data gap in present datasets. A pilot study conducted in 2008 at French Frigate Shoals and Brooks Banks was used to investigate the application of TCSs for surveying NIS in habitats deeper than 40 m. Cost and data quality were assessed. Over 100 hours of video was collected, in which 124 sightings of NIS were made among benthic habitats from 20 to 250 m. Most sightings were of a single cosmopolitan species, Lutjanus kasmira, but Cephalopholis argus, and Lutjanus fulvus, were also detected. The data expand the spatial distributions of observed NIS into deepwater habitats, identify algal plain as an important habitat and complement existing data collected using SCUBA and fishing gear. The technology’s principal drawback was its inability to identify organisms of particular concern, such as Carijoa riseii and Hypnea musciformis due to inadequate camera resolution and inability to thoroughly inspect sites. To solve this issue we recommend incorporating high-resolution cameras into TCSs, or using alternative technologies, such as technical SCUBA diving or remotely operated vehicles, in place of TCSs. We compared several different survey technologies by cost and their ability to detect NIS and these results are summarized in Table 3.

Computational modeling techniques for reliability of electronic components on printed circuit boards

This paper describes modeling technology and its use in providing data governing the assembly and subsequent reliability of electronic chip components on printed circuit boards (PCBs). Products, such as mobile phones, camcorders, intelligent displays, etc., are changing at a tremendous rate where newer technologies are being applied to satisfy the demands for smaller products with increased functionality. At ever decreasing dimensions, and increasing number of input/output connections, the design of these components, in terms of dimensions and materials used, is playing a key role in determining the reliability of the final assembly. Multiphysics modeling techniques are being adopted to predict a range of interacting physics-based phenomena associated with the manufacturing process. For example, heat transfer, solidification, marangoni fluid flow, void movement, and thermal-stress. The modeling techniques used are based on finite volume methods that are conservative and take advantage of being able to represent the physical domain using an unstructured mesh. These techniques are also used to provide data on thermal induced fatigue which is then mapped into product lifetime predictions.

Combined use of modeling techniques for the development of the conceptual model in simulation projects

The objective of this paper is to utilize the SIPOC, flowchart and IDEF0 modeling techniques combined to elaborate the conceptual model of a simulation project. It is intended to identify the contribution of these techniques in the elaboration of the computational model. To illustrate such application, a practical case of a high-end technology enterprise is presented. The paper concludes that the proposed approach eases the elaboration of the computational model. © 2008 IEEE.

Analysis and modeling techniques for ultrasonic tissue characterization

This thesis introduces new processing techniques for computer-aided interpretation of ultrasound images with the purpose of supporting medical diagnostic. In terms of practical application, the goal of this work is the improvement of current prostate biopsy protocols by providing physicians with a visual map overlaid over ultrasound images marking regions potentially affected by disease. As far as analysis techniques are concerned, the main contributions of this work to the state-of-the-art is the introduction of deconvolution as a pre-processing step in the standard ultrasonic tissue characterization procedure to improve the diagnostic significance of ultrasonic features. This thesis also includes some innovations in ultrasound modeling, in particular the employment of a continuous-time autoregressive moving-average (CARMA) model for ultrasound signals, a new maximum-likelihood CARMA estimator based on exponential splines and the definition of CARMA parameters as new ultrasonic features able to capture scatterers concentration. Finally, concerning the clinical usefulness of the developed techniques, the main contribution of this research is showing, through a study based on medical ground truth, that a reduction in the number of sampled cores in standard prostate biopsy is possible, preserving the same diagnostic power of the current clinical protocol.

Many-Core Architectures: Hardware-Software Optimization and Modeling Techniques

During the last few decades an unprecedented technological growth has been at the center of the embedded systems design paramount, with Moore’s Law being the leading factor of this trend. Today in fact an ever increasing number of cores can be integrated on the same die, marking the transition from state-of-the-art multi-core chips to the new many-core design paradigm. Despite the extraordinarily high computing power, the complexity of many-core chips opens the door to several challenges. As a result of the increased silicon density of modern Systems-on-a-Chip (SoC), the design space exploration needed to find the best design has exploded and hardware designers are in fact facing the problem of a huge design space. Virtual Platforms have always been used to enable hardware-software co-design, but today they are facing with the huge complexity of both hardware and software systems. In this thesis two different research works on Virtual Platforms are presented: the first one is intended for the hardware developer, to easily allow complex cycle accurate simulations of many-core SoCs. The second work exploits the parallel computing power of off-the-shelf General Purpose Graphics Processing Units (GPGPUs), with the goal of an increased simulation speed. The term Virtualization can be used in the context of many-core systems not only to refer to the aforementioned hardware emulation tools (Virtual Platforms), but also for two other main purposes: 1) to help the programmer to achieve the maximum possible performance of an application, by hiding the complexity of the underlying hardware. 2) to efficiently exploit the high parallel hardware of many-core chips in environments with multiple active Virtual Machines. This thesis is focused on virtualization techniques with the goal to mitigate, and overtake when possible, some of the challenges introduced by the many-core design paradigm.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.