An efficient framework for photon Monte Carlo treatment planning

Currently photon Monte Carlo treatment planning (MCTP) for a patient stored in the patient database of a treatment planning system (TPS) can usually only be performed using a cumbersome multi-step procedure where many user interactions are needed. This means automation is needed for usage in clinical routine. In addition, because of the long computing time in MCTP, optimization of the MC calculations is essential. For these purposes a new graphical user interface (GUI)-based photon MC environment has been developed resulting in a very flexible framework. By this means appropriate MC transport methods are assigned to different geometric regions by still benefiting from the features included in the TPS. In order to provide a flexible MC environment, the MC particle transport has been divided into different parts: the source, beam modifiers and the patient. The source part includes the phase-space source, source models and full MC transport through the treatment head. The beam modifier part consists of one module for each beam modifier. To simulate the radiation transport through each individual beam modifier, one out of three full MC transport codes can be selected independently. Additionally, for each beam modifier a simple or an exact geometry can be chosen. Thereby, different complexity levels of radiation transport are applied during the simulation. For the patient dose calculation, two different MC codes are available. A special plug-in in Eclipse providing all necessary information by means of Dicom streams was used to start the developed MC GUI. The implementation of this framework separates the MC transport from the geometry and the modules pass the particles in memory; hence, no files are used as the interface. The implementation is realized for 6 and 15 MV beams of a Varian Clinac 2300 C/D. Several applications demonstrate the usefulness of the framework. Apart from applications dealing with the beam modifiers, two patient cases are shown. Thereby, comparisons are performed between MC calculated dose distributions and those calculated by a pencil beam or the AAA algorithm. Interfacing this flexible and efficient MC environment with Eclipse allows a widespread use for all kinds of investigations from timing and benchmarking studies to clinical patient studies. Additionally, it is possible to add modules keeping the system highly flexible and efficient.

Implementation of porous silicon technology for a fluidic flow-through optical sensor for pH measurements

This work presents an innovative integration of sensing and nano-scaled fluidic actuation in the combination of pH sensitive optical dye immobilization with the electro-osmotic phenomena in polar solvents like water for flow-through pH measurements. These flow-through measurements are performed in a flow-through sensing device (FTSD) configuration that is designed and fabricated at MTU. A relatively novel and interesting material, through-wafer mesoporous silica substrates with pore diameters of 20 -200 nm and pore depths of 500 µm are fabricated and implemented for electro-osmotic pumping and flow-through fluorescence sensing for the first time. Performance characteristics of macroporous silicon (> 500 µm) implemented for electro-osmotic pumping include, a very large flow effciency of 19.8 µLmin-1V-1 cm-2 and maximum pressure effciency of 86.6 Pa/V in comparison to mesoporous silica membranes with 2.8 µLmin-1V-1cm-2 flow effciency and a 92 Pa/V pressure effciency. The electrical current (I) of the EOP system for 60 V applied voltage utilizing macroporous silicon membranes is 1.02 x 10-6A with a power consumption of 61.74 x 10-6 watts. Optical measurements on mesoporous silica are performed spectroscopically from 300 nm to 1000 nm using ellipsometry, which includes, angularly resolved transmission and angularly resolved reflection measurements that extend into the infrared regime. Refractive index (n) values for oxidized and un-oxidized mesoporous silicon sample at 1000 nm are found to be 1.36 and 1.66. Fluorescence results and characterization confirm the successful pH measurement from ratiometric techniques. The sensitivity measured for fluorescein in buffer solution is 0.51 a.u./pH compared to sensitivity of ~ 0.2 a.u./pH in the case of fluorescein in porous silica template. Porous silica membranes are efficient templates for immobilization of optical dyes and represent a promising method to increase sensitivity for small variations in chemical properties. The FTSD represents a device topology suitable for application to long term monitoring of lakes and reservoirs. Unique and important contributions from this work include fabrication of a through-wafer mesoporous silica membrane that has been thoroughly characterized optically using ellipsometry. Mesoporous silica membranes are tested as a porous media in an electro-osmotic pump for generating high pressure capacities due to the nanometer pore sizes of the porous media. Further, dye immobilized mesoporous silica membranes along with macroporous silicon substrates are implemented for continuous pH measurements using fluorescence changes in a flow-through sensing device configuration. This novel integration and demonstration is completely based on silicon and implemented for the first time and can lead to miniaturized flow-through sensing systems based on MEMS technologies.

DESIGN AND IMPLEMENTATION OF HOME USE PORTABLE SMART ELECTRONICS

The widespread of low cost embedded electronics makes it easier to implement the smart devices that can understand either the environment or the user behaviors. The main object of this project is to design and implement home use portable smart electronics, including the portable monitoring device for home and office security and the portable 3D mouse for convenient use. Both devices in this project use the MPU6050 which contains a 3 axis accelerometer and a 3 axis gyroscope to sense the inertial motion of the door or the human hands movement. For the portable monitoring device for home and office security, MPU6050 is used to sense the door (either home front door or cabinet door) movement through the gyroscope, and Raspberry Pi is then used to process the data it receives from MPU6050, if the data value exceeds the preset threshold, Raspberry Pi would control the USB Webcam to take a picture and then send out an alert email with the picture to the user. The advantage of this device is that it is a small size portable stand-alone device with its own power source, it is easy to implement, really cheap for residential use, and energy efficient with instantaneous alert. For the 3D mouse, the MPU6050 would use both the accelerometer and gyroscope to sense user hands movement, the data are processed by MSP430G2553 through a digital smooth filter and a complementary filter, and then the filtered data will pass to the personal computer through the serial COM port. By applying the cursor movement equation in the PC driver, this device can work great as a mouse with acceptable accuracy. Compared to the normal optical mouse we are using, this mouse does not need any working surface, with the use of the smooth and complementary filter, it has certain accuracy for normal use, and it is easy to be extended to a portable mouse as small as a finger ring.

Development, implementation, and evaluation of a structured reporting web tool for abdominal aortic aneurysms

BACKGROUND The majority of radiological reports are lacking a standard structure. Even within a specialized area of radiology, each report has its individual structure with regards to details and order, often containing too much of non-relevant information the referring physician is not interested in. For gathering relevant clinical key parameters in an efficient way or to support long-term therapy monitoring, structured reporting might be advantageous. OBJECTIVE Despite of new technologies in medical information systems, medical reporting is still not dynamic. To improve the quality of communication in radiology reports, a new structured reporting system was developed for abdominal aortic aneurysms (AAA), intended to enhance professional communication by providing the pertinent clinical information in a predefined standard. METHODS Actual state analysis was performed within the departments of radiology and vascular surgery by developing a Technology Acceptance Model. The SWOT (strengths, weaknesses, opportunities, and threats) analysis focused on optimization of the radiology reporting of patients with AAA. Definition of clinical parameters was achieved by interviewing experienced clinicians in radiology and vascular surgery. For evaluation, a focus group (4 radiologists) looked at the reports of 16 patients. The usability and reliability of the method was validated in a real-world test environment in the field of radiology. RESULTS A Web-based application for radiological "structured reporting" (SR) was successfully standardized for AAA. Its organization comprises three main categories: characteristics of pathology and adjacent anatomy, measurements, and additional findings. Using different graphical widgets (eg, drop-down menus) in each category facilitate predefined data entries. Measurement parameters shown in a diagram can be defined for clinical monitoring and be adducted for quick adjudications. Figures for optional use to guide and standardize the reporting are embedded. Analysis of variance shows decreased average time required with SR to obtain a radiological report compared to free-text reporting (P=.0001). Questionnaire responses confirm a high acceptance rate by the user. CONCLUSIONS The new SR system may support efficient radiological reporting for initial diagnosis and follow-up for AAA. Perceived advantages of our SR platform are ease of use, which may lead to more accurate decision support. The new system is open to communicate not only with clinical partners but also with Radiology Information and Hospital Information Systems.

Verification of the clinical implementation of the respiratory gated beam delivery technique with synchrotron-based proton irradiation

The clinical advantage for protons over conventional high-energy x-rays stems from their unique depth-dose distribution, which delivers essentially no dose beyond the end of range. In order to achieve it, accurate localization of the tumor volume relative to the proton beam is necessary. For cases where the tumor moves with respiration, the resultant dose distribution is sensitive to such motion. One way to reduce uncertainty caused by respiratory motion is to use gated beam delivery. The main goal of this dissertation is to evaluate the respiratory gating technique in both passive scattering and scanning delivery mode. Our hypothesis for the study was that optimization of the parameters of synchrotron operation and respiratory gating can lead to greater efficiency and accuracy of respiratory gating for all modes of synchrotron-based proton treatment delivery. The hypothesis is tested in two specific aims. The specific aim #1 is to assess the efficiency of respiratory-gated proton beam delivery and optimize the synchrotron operations for the gated proton therapy. A simulation study was performed and introduced an efficient synchrotron operation pattern, called variable Tcyc. In addition, the simulation study estimated the efficiency in the respiratory gated scanning beam delivery mode as well. The specific aim #2 is to assess the accuracy of beam delivery in respiratory-gated proton therapy. The simulation study was extended to the passive scattering mode to estimate the quality of pulsed beam delivery to the residual motion for several synchrotron operation patterns with the gating technique. The results showed that variable Tcyc operation can offer good reproducible beam delivery to the residual motion at a certain phase of the motion. For respiratory gated scanning beam delivery, the impact of motion on the dose distributions by scanned beams was investigated by measurement. The results showed the threshold for motion for a variety of scan patterns and the proper number of paintings for normal and respiratory gated beam deliveries. The results of specific aims 1 and 2 provided supporting data for implementation of the respiratory gating beam delivery technique into both passive and scanning modes and the validation of the hypothesis.

Communication-efficient and crash-quiescent Omega with unknown membership

The failure detector class Omega (Ω) provides an eventual leader election functionality, i.e., eventually all correct processes permanently trust the same correct process. An algorithm is communication-efficient if the number of links that carry messages forever is bounded by n, being n the number of processes in the system. It has been defined that an algorithm is crash-quiescent if it eventually stops sending messages to crashed processes. In this regard, it has been recently shown the impossibility of implementing Ω crash quiescently without a majority of correct processes. We say that the membership is unknown if each process pi only knows its own identity and the number of processes in the system (that is, i and n), but pi does not know the identity of the rest of processes of the system. There is a type of link (denoted by ADD link) in which a bounded (but unknown) number of consecutive messages can be delayed or lost. In this work we present the first implementation (to our knowledge) of Ω in partially synchronous systems with ADD links and with unknown membership. Furthermore, it is the first implementation of Ω that combines two very interesting properties: communication-efficiency and crash-quiescence when the majority of processes are correct. Finally, we also obtain with the same algorithm a failure detector () such that every correct process eventually and permanently outputs the set of all correct processes.

Development of Efficient FPGA-Based Multi-Channel Phase Meters for IR-Interferometers

Infrared (IR) interferometry is a method for measuring the line-electron density of fusion plasmas. The significant performance achieved by FPGAs in solving digital signal processing tasks advocates the use of this type of technology in two-color IR interferometers of modern stellarators, such as the TJ-II (Madrid, Spain) and the future W7-X (Greifswald, Germany). In this work the implementation of a line-average electron density measuring system in an FPGA device is described. Several optimizations for multichannel systems are detailed and test results from the TJ-II as well as from a W7-X prototype are presented.

Area-Efficient Linear Regression Architecture for Real-Time Signal Processing on FPGAs

Linear regression is a technique widely used in digital signal processing. It consists on finding the linear function that better fits a given set of samples. This paper proposes different hardware architectures for the implementation of the linear regression method on FPGAs, specially targeting area restrictive systems. It saves area at the cost of constraining the lengths of the input signal to some fixed values. We have implemented the proposed scheme in an Automatic Modulation Classifier, meeting the hard real-time constraints this kind of systems have.

Cost and energy efficient reconfigurable embedded platform using Spartan-6 FPGAs

Modern FPGAs with run-time reconfiguration allow the implementation of complex systems offering both the flexibility of software-based solutions combined with the performance of hardware. This combination of characteristics, together with the development of new specific methodologies, make feasible to reach new points of the system design space, and make embedded systems built on these platforms acquire more and more importance. However, the practical exploitation of this technique in fields that traditionally have relied on resource restricted embedded systems, is mainly limited by strict power consumption requirements, the cost and the high dependence of DPR techniques with the specific features of the device technology underneath. In this work, we tackle the previously reported problems, designing a reconfigurable platform based on the low-cost and low-power consuming Spartan-6 FPGA family. The full process to develop the platform will be detailed in the paper from scratch. In addition, the implementation of the reconfiguration mechanism, including two profiles, is reported. The first profile is a low-area and low-speed reconfiguration engine based mainly on software functions running on the embedded processor, while the other one is a hardware version of the same engine, implemented in the FPGA logic. This reconfiguration hardware block has been originally designed to the Virtex-5 family, and its porting process will be also described in this work, facing the interoperability problem among different families.

Efficient methodologies for system matrix modelling in iterative image reconstruction for rotating high-resolution PET

A fully 3D iterative image reconstruction algorithm has been developed for high-resolution PET cameras composed of pixelated scintillator crystal arrays and rotating planar detectors, based on the ordered subsets approach. The associated system matrix is precalculated with Monte Carlo methods that incorporate physical effects not included in analytical models, such as positron range effects and interaction of the incident gammas with the scintillator material. Custom Monte Carlo methodologies have been developed and optimized for modelling of system matrices for fast iterative image reconstruction adapted to specific scanner geometries, without redundant calculations. According to the methodology proposed here, only one-eighth of the voxels within two central transaxial slices need to be modelled in detail. The rest of the system matrix elements can be obtained with the aid of axial symmetries and redundancies, as well as in-plane symmetries within transaxial slices. Sparse matrix techniques for the non-zero system matrix elements are employed, allowing for fast execution of the image reconstruction process. This 3D image reconstruction scheme has been compared in terms of image quality to a 2D fast implementation of the OSEM algorithm combined with Fourier rebinning approaches. This work confirms the superiority of fully 3D OSEM in terms of spatial resolution, contrast recovery and noise reduction as compared to conventional 2D approaches based on rebinning schemes. At the same time it demonstrates that fully 3D methodologies can be efficiently applied to the image reconstruction problem for high-resolution rotational PET cameras by applying accurate pre-calculated system models and taking advantage of the system's symmetries.

Efficient local unfolding with ancestor stacks

The most successful unfolding rules used nowadays in the partial evaluation of logic programs are based on well quasi orders (wqo) applied over (covering) ancestors, i.e., a subsequence of the atoms selected during a derivation. Ancestor (sub)sequences are used to increase the specialization power of unfolding while still guaranteeing termination and also to reduce the number of atoms for which the wqo has to be checked. Unfortunately, maintaining the structure of the ancestor relation during unfolding introduces significant overhead. We propose an efficient, practical local unfolding rule based on the notion of covering ancestors which can be used in combination with a wqo and allows a stack-based implementation without losing any opportunities for specialization. Using our technique, certain non-leftmost unfoldings are allowed as long as local unfolding is performed, i.e., we cover depth-first strategies. To deal with practical programs, we propose assertion-based techniques which allow our approach to treat programs that include (Prolog) built-ins and external predicates in a very extensible manner, for the case of leftmost unfolding. Finally, we report on our mplementation of these techniques embedded in a practical partial evaluator, which shows that our techniques, in addition to dealing with practical programs, are also significantly more efficient in time and somewhat more efficient in memory than traditional tree-based implementations. To appear in Theory and Practice of Logic Programming (TPLP).

A generator of efficient abstract machine implementations and its application to emulator minimization

The implementation of abstract machines involves complex decisions regarding, e.g., data representation, opcodes, or instruction specialization levéis, all of which affect the final performance of the emulator and the size of the bytecode programs in ways that are often difficult to foresee. Besides, studying alternatives by implementing abstract machine variants is a time-consuming and error-prone task because of the level of complexity and optimization of competitive implementations, which makes them generally difficult to understand, maintain, and modify. This also makes it hard to genérate specific implementations for particular purposes. To ameliorate those problems, we propose a systematic approach to the automatic generation of implementations of abstract machines. Different parts of their definition (e.g., the instruction set or the infernal data and bytecode representation) are kept sepárate and automatically assembled in the generation process. Alternative versions of the abstract machine are therefore easier to produce, and variants of their implementation can be created mechanically, with specific characteristics for a particular application if necessary. We illustrate the practicality of the approach by reporting on an implementation of a generator of production-quality WAMs which are specialized for executing a particular fixed (set of) program(s). The experimental results show that the approach is effective in reducing emulator size.

Efficient local unfolding with ancestor stacks for full prolog

The integration of powerful partial evaluation methods into practical compilers for logic programs is still far from reality. This is related both to 1) efficiency issues and to 2) the complications of dealing with practical programs. Regarding efnciency, the most successful unfolding rules used nowadays are based on structural orders applied over (covering) ancestors, i.e., a subsequence of the atoms selected during a derivation. Unfortunately, maintaining the structure of the ancestor relation during unfolding introduces significant overhead. We propose an efficient, practical local unfolding rule based on the notion of covering ancestors which can be used in combination with any structural order and allows a stack-based implementation without losing any opportunities for specialization. Regarding the second issue, we propose assertion-based techniques which allow our approach to deal with real programs that include (Prolog) built-ins and external predicates in a very extensible manner. Finally, we report on our implementation of these techniques in a practical partial evaluator, embedded in a state of the art compiler which uses global analysis extensively (the Ciao compiler and, specifically, its preprocessor CiaoPP). The performance analysis of the resulting system shows that our techniques, in addition to dealing with practical programs, are also significantly more efficient in time and somewhat more efficient in memory than traditional tree-based implementations.

Efficient negation using abstract interpretation

While negation has been a very active área of research in logic programming, comparatively few papers have been devoted to implementation issues. Furthermore, the negation-related capabilities of current Prolog systems are limited. We recently presented a novel method for incorporating negation in a Prolog compiler which takes a number of existing methods (some modified and improved by us) and uses them in a combined fashion. The method makes use of information provided by a global analysis of the source code. Our previous work focused on the systematic description of the techniques and the reasoning about correctness and completeness of the method, but provided no experimental evidence to evalúate the proposal. In this paper, we report on an implementation, using the Ciao Prolog system preprocessor, and provide experimental data which indicates that the method is not only feasible but also quite promising from the efficiency point of view. In addition, the tests have provided new insight as to how to improve the proposal further. Abstract interpretation techniques are shown to offer important improvements in this application.

Complete and efficient methods for supporting side effects in independent/restricted and-parallelism

It has been shown that it is possible to exploit Independent/Restricted And-parallelism in logic programs while retaining the conventional "don't know" semantics of such programs. In particular, it is possible to parallelize pure Prolog programs while maintaining the semantics of the language. However, when builtin side-effects (such as write or assert) appear in the program, if an identical observable behaviour to that of sequential Prolog implementations is to be preserved, such side-effects have to be properly sequenced. Previously proposed solutions to this problem are either incomplete (lacking, for example, backtracking semantics) or they force sequentialization of significant portions of the execution graph which could otherwise run in parallel. In this paper a series of side-effect synchronization methods are proposed which incur lower overhead and allow more parallelism than those previously proposed. Most importantly, and unlike previous proposals, they have well-defined backward execution behaviour and require only a small modification to a given (And-parallel) Prolog implementation.