The development of automated techniques for the analysis of image data is an important and active area of research. To make progress, this research requires annotations of image data to build and validate models used for analysis. Given this requirement, the development of software tools that streamline the collection of annotations would be of great benefit to image analysis researchers. Such tools should meet the following requirements: rapid generation of annotations for large data sets, annotation and data management that is straightforward for users, flexibility for application to many diverse image datasets, configurability to allow the collection of annotations to be tuned for a specific research goal, and generation of annotation data in a standardized format so that it can be easily parsed and analyzed. Truthmarker was designed as a tablet computer based image annotation tool to meet these requirements. Researchers can configure Truthmarker to fit the needs of a particular study by specifying an annotation model that fine tunes the user interface and resulting data to fit the annotation task. The quality of annotations generated using Truthmarker was evaluated by recruiting medical experts to annotate ophthalmic images for severity of diabetic retinopathy, a leading cause of blindness. These annotations were compared to annotations of the same images assigned using standard desktop computer based tools. The results, as measured by κ statistics and accuracy, indicate that Truthmarker annotations were of equivalent quality compared to those that were created using desktop-based tools.

Although high-throughput methods exist to identify many small disease causing mutations (e.g. substitutions that alter an amino acid), assays to identify classes of larger mutations such as deletions/duplications are time consuming, laborious and expensive. In addition, no in-silico system exists to identify intragene deletion or duplication candidates. We hypothesize that a computational system, SPeeDD (System to Prioritize Deletion or Duplication candidates), utilizing machine learning techniques can be employed to identify the most likely disease causing deletion or duplication candidates within a gene. Informative sequence based features were obtained from a set of genes with known intragene deletions or duplications for data mining. Machine learning techniques were applied to this data. Sensitivity from 20% to 74.2% varied depending on the specific machine learning model used, but specificity exceeded 90% for all methods evaluated. The logic model tree (LMT) method, which is a combination of decision tree and logistic regression model, yielded the best results. The SPeeDD system also succeeded in accurately predicting a recently published novel BRCA1 deletion. These results suggest that the SPeeDD system provides good sensitivity and specificity and can be used to prioritize candidate genes and gene regions for focused screening. This will reduce the labor and associated costs of the biological assays, and should accelerate the process of mutation discovery.

ABSTRACT SEASONAL AND ANATOMICAL VARIATION IN COMPACT BONE REMODELING IN THE ADULT SHEEP Joseph Calcagno In order to determine whether ovine compact bone is suitable for study of osteoporosis, the remodeling parameters of the untreated animal must be fully characterized. Ovine compact bone is an attractive large animal model due to its similarities in size and bone remodeling to humans. However hormonal, exercise, and dietary changes due to seasonal changes can cause treatment effects to be hidden or superimposed on existing changes in the bone. In order to determine if any seasonal or anatomical variation occurred in the compact bone remodeling, 28 skeletally mature Columbia-Rambouillet cross ewes underwent a sham ovariectomy, OVX, as part of a larger study. The animals were divided into 4 seasonal groups (autumn, winter, spring, and summer) of 7 sheep. Each group underwent surgery and was sacrificed 12 months post-op in their respective seasons. The radii and ulnae were harvested and processed for analysis. Each radius/ulna was divided into 6 anatomical locations (craniolateral, cranial, craniomedial, caudolateral, caudal, and caudomedial). Histomorphometric analysis of the bone volume to tissue volume ratio, the percent of tissue and material remodeling, the mean secondary osteonal radius, and the number of cement line interfaces were quantified. Quantitative microdensitometry analysis was performed to determine the density of each region with respect to an aluminum standard. 2-way repeated measures ANOVAs were performed to determine seasonal and anatomical differences as well as a possible interaction between season and anatomical sectors. Significant seasonal and anatomical differences as well as seasonality within sectors were observed in the remodeling parameters. With the seasonal and anatomical changes in the untreated animal, comparison to other models must ensure treatment and follow up times as well anatomical locations are similar. This research provides a baseline of seasonal and anatomical variations in compact bone remodeling for the untreated adult ovine.

The goal of this study was to understand how arteriogenesis impacts transverse arteriolar tree structure. The previous process involved a vascular casting technique that utilized black India ink as the casting agent and manual measurement of vessel morphology with ImageJ. This study decreased the complexity of the casted samples by using a casting compound called Microfil. Microfil’s viscosity can be adjusted and through experimentation, a viscosity was found that stopped at the capillary level, allowing only the arterial side of the circulation to be casted. A macro in ImageJ was written to help with morphological measurement by bundling vessel length and diameter into one measurement instead of two. These two adjustments were then used in a ligated mouse model to compare healthy and remodeled vascular networks. The analysis revealed that the only significant difference for length and diameter measurements was in the diameters of the collateral. This indicates that it’s possible that stimulating arteriogenesis in a clinical environment should not cause any negative effects in the collateral-containing muscle. However, this observation is potentially limited by the differences between the model and patient.

Previous research 1 on this subject tracked the presumed exact path the HDR source would follow in real-time, during breast brachytherapy treatments in other to ensure accurate dose delivery and effectively confirm actual source position. As a continuation, this research has three objectives. Firstly, we will extract information from patient DICOM file which will be used to perform evaluations, then we will establish communication between our C program and the new Varex Paxscan flat panel detector (FPD). Finally, we will try to embed our C codes into a MATLAB graphical user interface (GUI) This research will attempt to improve the overall existing system in several ways including, code optimization and trying a sample simulation of the process in MATLAB guide app, to check the quality of the new design. Finally, all the algorithms will be integrated into the user-friendly GUI, such that its operation can be implemented easily. The FPD is used to obtain images resulting from the exit radiation of the HDR source, emerging from an organized matrix of markers. The images are processed using in-built functions in MATLAB to obtain projection coordinates, and marker coordinates. Each marker along with its projection constitutes a line in 3D. Using the mathematical solution for near intersection of two 3D lines, N-markers will produce N*(N-1)/2 points of intersection and their mean will produce a more precise source position. The changes in this position as well as the time interval between these changes will be used to confirm the accuracy of our treatment system using the standalone monitoring system built in this research. In the previous study the accuracy of source position detection using the FPD was found to be in sub-millimeter. This study which uses a new FPD with improved features is used to confirm that, but our focus here is improvement of the previous work, as stated earlier.

Graphical information has become a critical method for portraying information for education, work and personal tasks and decisions. Unfortunately there are currently limited means of providing this information to individuals who are blind or visually impaired: alternate text is frequently missing, and accessible tactile diagrams tend to be time consuming to make and require expertise in order for them to be interpretable (which may be costly to the user and/or impossible to get). The aim of this project is to provide an accessible system to automatically generate tactile graphics for those who need to interpret information contained in visual images. Previous automatic conversion methods have not been especially successful and are not used in normal practice, possibly because they have not taken advantage of current advances in the field of image processing. In the preliminary work, we systematically look at the myriad of image segmentation methods that exist as part of the conversion process. For those techniques, previous researchers have often compared the results to the “gold standard” of human segmentation to evaluate their success. However, there are important difference between this “gold standard” and what is needed for tactile graphics. Key steps by professionals who create tactile diagrams are simplification so that the information is manageable to extract through the tactile sense, elimination of perspective as it is difficult to interpret tactually, and possible spreading of information across multiple diagrams. Planned work is to examine more closely the underlying themes to the myriad of algorithm are relevant for tactile diagrams. Future work, will also involve taking the initially segmented image, simplifying it further by removing “unimportant” detail so that it is manageable by the tactile system and removing perspective based on geometric information found in the image.

Ovarian is the leading cause of deaths in women diagnosed with gynecological malignancies. Current treatments include chemotherapy which may cause severe side effects. The purpose of this study was to investigate the combinational therapeutic effect of chemotherapy and hyperthermia to an ovarian cancer cell line and compare the effects of inducing hyperthermia systemically with localized hyperthermia. Cells were seeded in 96-well plates and subjected to different doses of chemotherapy agent; Doxorubicin (DOX). To simulate systemic hyperthermia the 96-well plate was incubated for 60 minutes at 43°C. To simulate localized hyperthermia, Indocyanine Green was added to the seeded cells in 96-well plates, after which the wells were irradiated by 808 nm NIR laser. SRB assay was used at the end of the study to measure cell proliferation. The results showed that cell proliferation was reduced 110% when DOX was combined with localized hyperthermia compared with DOX or systemic hyperthermia alone.

This dissertation project is unique in that it seeks to link two historically independent concepts: mechanical loading of cartilage (1) induces reactive oxygen species (ROS) release from specific mitochondrial complexes, and (2) results in observable metabolic alterations. It is well known that ROS are released from certain loading conditions. It has also been shown that chondrocytes respond favorably to cyclic loading at moderate stresses, as determined metabolically by proteoglycan and collagen production. However, this study aims to demonstrate that these phenomena are interdependent, and in doing so, locates both the source(s) of load-induced ROS and the resultant molecule(s) responsible for metabolic stimulation. To further this investigation, an osteochondral explant mechanical loading platform was built that allowed the imposition of physiological stresses on cartilage explants to further characterize cartilage metabolism. National Instruments hardware and LabVIEW controls a stepper motor driven platen, which when coupled with a load cell, allows for dynamic and static compression stimulation of articular cartilage. Firstly, static stress (0.05 – 1.0 MPa for one hour) induces ROS release, which is mitochondrial in origin, relies on an intact cytoskeletal network, and tracks linearly with bulk tissue strain (r = 0.87). Dissolution of the cytoskeleton with cytochalasin B, blocking complex I of the mitochondria with rotenone, or addition of the cell-permeable SOD mimetic, manganese(III) tetrakis(1-methyl-4-pyridyl)porphyrin (MnTMPyP) reduces this ROS release at 0.25 MPa. Next, under dynamic stress (0.25 MPa/0.5 Hz for one hour), this mitochondrial ROS release was shown to be necessary for stimulating glycolytic energy production 24 hours after stress application. The ROS release from mechanical stimulation was blocked by the addition of rotenone or Mitoquinone (MitoQ10). These treatments also both blocked the increase in intracellular adenosine triphosphate (ATP) content, and therefore show that the ROS from the mitochondria are required for stimulating ATP production. Probing the mitochondria directly with targeted inhibitors in unloaded conditions shows that forcing superoxide generation at ubiquinol: cytochrome c-oxidoreductase (complex III), and efficiently turning this superoxide into hydrogen peroxide, resulted in a dose-dependent increase in ATP content that resembles the response to loading. Here, ATP content increased with increasing doses of antimycin A, which, when accompanied with the SOD mimetic, Galera (m40401), is always higher than antimycin A alone. Finally, if overloading proceeds for too long (three hours at 1.0 MPa or 0.25 MPa at 0.5 Hz for 7 days), ROS-related damage ensues, resulting in significantly impaired mitochondrial function and reduced intracellular ATP content. The damage and deleterious effects are negated by administration of the antioxidant, N-acetylcysteine (NAC). Together, these results show that mechanical stimulation of cartilage produces mitochondrial ROS and resultant products, whose role in articular cartilage is complex. In short term mechanical stimulations, these ROS act to stimulate metabolism. At higher stresses, and over longer durations, ROS cause damage which results in mitochondrial dysfunction and suppressed ATP production. These findings have important implications for the progression of osteoarthritis, which has already been linked to mitochondrial dysfunction

Low back pain is a debilitating condition that afflicts millions of people each year. It is characterized by complex biochemical, morphological, and biomechanical changes. However, most believe low back pain arises due to abnormal mechanical loading, inflammation, and disc degeneration. Several studies have investigated radial back pain, but to date, there is only one in vivo animal model for low back pain. Despite advances in science, the causes of low back pain remain unclear and treatments fail to relieve the pain. To better understand the causative factors of low back pain, a reliable animal model is needed. This study was designed to advance the knowledge of the previous in vivo animal model for low back pain by investigating the effects of shear loading on disc degeneration (for a longer duration of time) and discogenic low back pain (in terms of immunohistochemistry) in hopes developing better treatment strategies for low back pain sufferers and to help elucidate the etiology of low back pain. Adult male Sprague Dawley rats (n=31) were shear loaded for 4- and 8- weeks. Pain behavioral testing was done prior to and after surgery. After sacrifice, immunohistochemistry was used to detect the presence of pain in the intervertebral discs and the spinal cord. Results of this study indicate that the application of an abnormal shear load gives rise to disc degeneration. Histology revealed that all loaded levels as well as the adjacent levels degenerated due to the shear load. Pain behavior testing revealed that the rats did experience pain, however, when combined with the immunohistochemical results, we were able to exclude the pain as pain stemming from the degenerated discs. Surprisingly, we observed that shear loading caused scoliosis of the thoracolumbar spine.

Whole-body vibration (WBV) has been identified as a stressor to supine patients with head and spinal injuries during medical transportation. Limited information is available on the dynamic effects of the long spinal board and stretcher in vibrating environments. This is the first study to investigate the transmission of vibration through the long spinal board, military stretcher, and supine human in relation to a control case with full-rigid support. A sample of eight healthy male participants was used in this study. Each was placed on a vibration platform using spinal immobilization. Random vibration was applied in the fore-aft, lateral, and vertical directions, and the transmission of vibration was computed for the head, sternum, and pelvis. In addition, a novel approach to assess relative motion between segments, called relative transmissibility, was introduced. Compared to full-rigid support, the long spinal board strapped to a standard military litter system showed a 50% increase in transmission of anterior-posterior vibration to the head and a 100% increase to the sternum at its resonance frequency of 5 Hz (p < 0.05, Wilcoxon) for vertical vibration. Use of the cervical collar during immobilization increased the head nodding and the relative head-sternum flexion-extension as a result of the input fore-aft (axial) whole-body vibration. Yet, head nodding was reduced from vertical (anterior-posterior) input vibration. Relative transmissibility has revealed that at 5 Hz, the acceleration difference between the head and sternum was 1.5 times the vertical (anterior-posterior) input acceleration using the spinal board upon the military litter. During air, ground, and hand transportation, WBV may occur around 5 Hz. Patients with head and spinal cord injuries may benefit from vibration-suppression designs that minimize (1) the overall transmission of vibration in each axis and (2) the relative accelerations between segments for the most common vibration frequencies that occur during transportation. Furthermore, vibration applied in each axis independently showed transmissibility results comparable to that of simultaneous stimuli in three axes. Although the effects of vibration are quantified in this study, transient shock type vibration should be investigated and future research should be done to fully understand the clinical significance and application of these results.