Ernesto Gomez

Space carving and filtered back-projection as preconditioners for proton computed tomography reconstruction

This paper considers how to determine the boundary of an object by comparing two methods: space carving (SC) and filtered back-projection (FBP). Determination of the boundary is an important first step in proton CT. The boundary is used to set up the large sparse linear system of equations, which are then solved to determine the relative stopping power of each element (voxel) in the object. For instance, to find the path of the proton through the object, the entry and exit points on the boundary must first be found. The boundary also becomes important in the iterative reconstruction, as only voxels inside the object are updated, to reduce computational complexity and prevent external artifacts from forming. SC and FBP are compared on speed and boundary results for four cases: (1) noiseless simulated data, (2) noisy simulated data, (3) a real pediatric head phantom, and (4) a real rat. The usefulness and potential of both methods are discussed and future directions are outlined.

A proton simulator for testing implementations of proton CT reconstruction algorithms on GPGPU clusters

Proton computed tomography (pCT) is an image modality that will improve treatment planning for patients receiving proton radiation therapy compared with the current treatment techniques, which are based on X-ray CT. Reconstruction of a pCT image requires solving a large and sparse system of linear equations, which should be accomplished within a few minutes in order to be clinically practical. Analyzing the efficiency of potentially clinical reconstruction implementations requires multiple quality pCT data sets. The purpose of this paper is to describe the simulator that was developed to generate realistic pCT data sets to be used in testing the efficiency of reconstruction algorithms, in particular string-averaging and block-iterative projection algorithms using sparse matrix formats on General Purpose Graphics Processing Units (GPGPU)s.

Patterned Growth in Extreme Environments

Abstract—In the search for life on Mars and other extraterrestrial bodies, one of the biggest problems facing us is, how do we recognize life or the remains of ancient life when we find it? We will need to recognize residual patterns left by life. One approach to recognizing these kinds of patterns is look at patterns created and left by life in extreme environments here on Earth.

Orthogonal and least-squares based coordinate transforms for optical alignment verification in radiosurgery

Radiosurgery is a non-invasive treatment technique applying focused radiation beams. It requires high geometric accuracy as misalignment can cause damage to the surrounding healthy tissues and loss of the therapeutic effect. One promising technique to insure submillimeter alignment accuracy of the radiation beam is to optically monitor the position of the beam axis relative to a frame firmly attached to the patients skull using an optical alignment system. The optical alignment method requires three-dimensional coordinate transforms. This paper compares the standard least squares technique for transforming the coordinate system with an orthogonal transform technique based on the comparison of marker triangles. Orthogonal transforms have good numerical properties and preserve distance, which gives this technique advantages over non-orthogonal techniques. The mathematics behind each technique is covered and alignment results on real test equipment are used to illustrate the differences between the transforms.

A Model for Entropy of Parallel Execution

In this paper we develop a theory of visualizing a parallel execution by the entropy of the phase space induced by its traces. This metric is then shown to be able to both theoretically and practically find program issues, such as starvation due to data in one of its threads.

Preventing deadlock with dynamic message scheduling

Although deadlock is not completely avoidable in distributed and parallel programming, we here describe theory and practice of a system that allows us to limit deadlock to situations in which there are true circular data dependences or failure of processes that compute data needed at other processes. This allows us to guarantee absence of deadlock in SPMD computations absent process failure. Our system guarantees optimal ordering of communication statements. We gratefully acknowledge the support of the US National Science Foundation under Award CISE EIA 9810708 without which this work would not have been possible.

Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert

In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439) and genus (p < 0.006) levels, including multiple biochemical and geochemical trends (p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.

Estimation, Modeling, and Simulation of Patterned Growth in Extreme Environments

In the search for life on Mars and other extraterrestrial bodies or in our attempts to identify biological traces in the most ancient rock record of Earth, one of the biggest problems facing us is how to recognize life or the remains of ancient life in a context very different from our planets modern biological examples. Specific chemistries or biological properties may well be inapplicable to extraterrestrial conditions or ancient Earth environments. Thus, we need to develop an arsenal of techniques that are of broader applicability. The notion of patterning created in some fashion by biological processes and properties may provide such a generalized property of biological systems no matter what the incidentals of chemistry or environmental conditions. One approach to recognizing these kinds of patterns is to look at apparently organized arrangements created and left by life in extreme environments here on Earth, especially at various spatial scales, different geologies, and biogeochemical circumstances.

Algebra of Synchronization with Application to Deadlock and Semaphores

Modern multiprocessor architectures have exacerbated problems of coordinating access to shared data, in particular as regards to the possibility of deadlock. For example semaphores, one of the most basic synchronization primitives, present difficulties. Djikstra defined semaphores to solve the problem of mutual exclusion. Practical implementation of the concept has, however, produced semaphores that are prone to deadlock, even while the original definition is theoretically free of it. This is not simply due to bad programming, but we have lacked a theory that allows us to understand the problem. We introduce a formal definition and new general theory of synchronization. We illustrate its applicability by deriving basic deadlock properties, to show where the problem lies with semaphores and also to guide us in finding some simple modifications to semaphores that greatly ameliorate the problem. We suggest some future directions for deadlock resolution that also avoid resource starvation.

Extensible Simulation of Planets and Comets

The research conducted is intended to enhance the way we view and study our solar system and others, by allowing scientists of astronomy, physics, and computer science to accurately simulate celestial systems. The Extensible Simulator organizes individual groups of celestial bodies, calculates their positions, graphically visualizes their movement using the computed positions, and finally, is extensible, which serves to accommodate additional numerical methods and gravitational functions, body shapes and behaviors, and camera views.