Browsing by Author "Merchant, Fatima Aziz"
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Item 3D Modeling of Chromosomes Territories in Normal and Aneuploid Nuclei(2017) Yen, Fan-Yun; Merchant, Fatima AzizItem An Interactive Pedestrian Re-Identification Tool with Semantic Based Re-Identification(2016-12) Cao, Can 1991-; Shah, Shishir Kirit; Gabriel, Edgar; Merchant, Fatima AzizPerson re-identification is an essential task of recognizing and matching people from non-overlapping cameras. A typical application of person re-identification is identifying a particular person in a gallery of pedestrian images from a camera with one or more given probe images of this person from another camera. This is a chal- lenging and practical task that provides solutions for video-surveillance. In this work, we present a person re-identification software which is called Interactive Pedestrian Re-identification GUI (IPRG), and a semantic-based labelling tool named Reid It (Reidit). According to the growing need for surveillance applications, we develop IPRG to address the person searching and matching problem with the dataset from on-campus security camera videos. From these video frames, we can get semantic in- formation of the candidate such as height, ethnicity, cloth color, etc. By customizing these semantic features in IPRG, we can identify a candidate in the video database rapidly. We also propose a light-labelling tool, Reidit, for labelling pedestrian images with semantic features as the pre-processing for pedestrian recognition. We present an experiment on IPRG with Viewpoint Invariant Pedestrian Recognition (VIPeR) dataset which contains 632 identities. Our experiment shows that our software is more efficient and accurate compared with traditional manual solutions. Moreover, IPRG can handle the situation of missing query person in the database, and it will return the top ten possible individuals. Our software is compatible with different platforms and user-friendly with customizable databases and semantic features.Item An Investigation on Data Plane Programmability and Acceleration Methods(2014-08) Dane, Levent; Gurkan, Deniz; Merchant, Fatima Aziz; Pollonini, LucaProgrammability in networking may span multiple layers of the protocol stack. As cloud networking with resource management (orchestration of workloads), and automation evolved, hardware in computer networks also has also adapted to support better isolation principles while supporting forwarding functions. In this thesis, generic hardware such as servers was assumed to take on the role of legacy switching functions. In order to perform at the line rate, many data plane acceleration methods have been explored. We provided integration of one such data plane acceleration method, namely netmap, to the modular software switch initiative, xDPd (eXtensible Data Plane daemon). We present the measurement results with achieved improvements at levels of about 20% or more. We also present future directions in this paradigm shift.Item Apoptotic Properties of Platinum Antitumor Agents Phosphaplatins(2016-05) Dezvareh, Homa 1989-; Zhang, Xiaoliu Shaun; Chung, Sang-Hyuk; Merchant, Fatima Aziz; Bark, Steven J.Phosphaplatins are a group of non-DNA binding platinum compounds that exhibit excellent in vivo and in vitro efficacies against a variety of cisplatin- and carboplatin-sensitive and resistant ovarian cancers. Although, combinations of cis- or carbo-platin and paclitaxel therapies continue to be the choice of treatment for ovarian cancer, many patients develop resistance to the treatment. Phosphaplatins are pyrophosphate bound platinum-(II) and (IV)-platinum complexes that are bi-negatively charged at or near neutral pH. Both Platinum (II) and platinum (IV) complexes do not induce the overexpress of any DNA repair genes, consistent with the no-DNA binding property of phosphaplatins. In this report, we show the apoptotic properties of two representative compounds, (R, R-1,2-cyclohexanediamine)-(dihydrogen pyrophosphato)platinum (II) (RRD2) and (R,R-1,2-cyclohexanediamine)-trans-dihydroxo(dihydrogen pyrophosphato)platinum (IV) (RRD4) through a variety of experiments as described below. Phosphaplatins are found to activate and upregulate death receptors on cell surface such as FAS, DR5, and TNFR1. These three death receptors follow the common signaling path to trigger apoptosis by an extrinsic pathway via Death Inducing Signaling Complex (DISC) by recruiting FADD and procaspase-8 and activating caspase-8. A direct binding of FAS by platinum is implicated as the platinum compound was found to be co-localized in the lipid rafts. The PTEN-PI3K pathway involvement was confirmed by the down regulation of both PI3K and p-AKT. Phosphoplatins also upregulate tumor suppression genes P53 and PTEN. Apoptosis by p53 signaling follows intrinsic pathways involving BCL-proteins. In particular upregulation of BAX, PUMA, and downregulation of BCL2 were observed. To further confirm p53-signailng, we have identified a number of p53 target genes that include AEN, CYFIP2, TP53I3, TP53INP1, DPYSL4, LRDD, DRAM1, and a few others. Our data shows that phosphaplatins have the potential to not only treat resistant but also advanced metastatic ovarian cancers.Item Automatic Recognition of Buruli Ulcer Images on Smart Handheld Devices(2013-08) Hu, Rui 1984-; Zouridakis, George; Jansen, Ben H.; Chen, Ji; Shih, Wei-Chuan; Merchant, Fatima AzizBuruli ulcer (BU) disease is a devastating flesh eating bacterial infection that each year affects thousands of people in tropical and subtropical regions. Clinically, BU usually starts as a painless subcutaneous nodule, or as other pre-ulcer forms including papule, plaque, and edema; then it evolves into a painless ulcer, and finally leads to extensive scarring, contractures, and deformations with possible total loss of articulation function. However, treatment with antibiotics at an early stage has been very successful in preventing irreversible deformity and long-term functional disability. Therefore, an easily implemented and rapid diagnostic test that can detect the early stages of BU is of high research priority. In this dissertation, a multistage computerized image-analysis system is proposed that can automatically detect BU in multispectral dermoscopic images. The specific contributions of this work focus on the development of techniques for precise lesion segmentation, efficient image sampling for feature extraction, and skin image modeling for accurate lesion classification. For lesion segmentation, a new method is proposed based on fusion of the partial masks derived from separate segmentations of the color and luminance channels of BU images. This procedure outperformed other techniques when tested on a subset of 26 BU images where the ground truth of manual segmentation by domain expert physicians was known. Internally the system represents BU lesions using the Bag-of-Features methodology, where image features are extracted from image patches. A new strategy for nonuniform image sampling was developed based on occurrence of contextual pixel saliency, whereby patches from dermoscopically interesting regions are sampled more densely. Experiments on a set of 197 images demonstrated an advantage of this method compared to classical grid or random sampling. To obtain more accurate statistics and address the problem of class imbalance due to the small number of BU images compared to non-BU controls in the dataset, a new resampling technique was developed, which increased the sample size of the minority class by splitting lesions in the data space, rather than synthesizing new samples in the feature space. Combined with the feature selection metric of Pearson correlation coefficient, this method resulted in a classifier with more discriminative power. Additionally, a new feature representation of the multispectral images based on optical skin modeling was proposed. In this method, the distribution of physiological characteristics of a lesion, such as melanin, blood volume, and blood oxygenation were estimated for all image pixels, and features were extracted from these reconstructed maps. Experimental results with a set of 197 multispectral images showed that the use of multispectral images provided a significant improvement in classification performance compared to classification based on single white light images. Finally, a modular stand-alone application that includes all system stages has been developed in Matlab that can be further implemented on smart handheld devices.Item Characterizing the Optical Response of Human Tissues to Prolonged Pressure(2018-08) Day, Bradford; Pollonini, Luca; Merchant, Fatima Aziz; Yuan, XiaojingPressure Injuries are burdensome to the US healthcare system and significantly impact patient quality of life. Methods for reduction have focused almost exclusively on risk assessment and reductions in pressure and shear stresses. While extensive work has been performed to understand the etiology of pressure injuries, less focus has been placed on the use of non-invasive technologies to monitor tissues and predict injury. This thesis is a step in that direction. The aim of this thesis was to validate a brand new flexible Near Infrared sensing system and model the optical characteristics of tissues under pressure for clinically relevant time periods. The pilot study for this thesis was a descriptive cross-sectional analysis. 5 healthy college aged volunteers lay supine for 2 hours while spectroscopic recordings of their sacral tissues were collected. Results suggested that two physiological process were occurring at different tissue depths. In shallower tissue depths optical signals indicated that relative concentrations of HbO and HbR changed from their initial concentrations, whereas at deeper tissue depths changes in total blood volume occurred. This work is the beginning of a series of exploratory analysis for validating the NIRS device and investigating signals indicative of pressure injury. The NIRS device performed adequately, but multiple improvements to its design have been noted. Specifically, increased flexibility, durability, and sterility of future iterations will need to be addressed.Item Computation of Breast Ptosis from 3D Scans of Torso(2013-08) Li, Danni 1988-; Merchant, Fatima Aziz; Roysam, Badrinath; Ogmen, Haluk; Reece, Gregory P.Ptosis is an important morphological parameter for characterizing breast aesthetics and is frequently used for assessing the outcome of breast surgery. It refers to the extent to which the nipple is lower than the terminus of the inframammary fold (the contour along which the inferior part of the breast attaches to the chest wall). Current clinical assessment of ptosis involves qualitative visualization by observers which is subject to inter- and intra-observer variability. Alternatively, ptosis can be measured anthropometrically from the patient or from clinical photographs, but these methods are error prone. As stereophotography is now finding its niche in clinical breast surgery, in this study we investigated and evaluated the utility of three-dimensional (3D) features such as surface curvature, coronal projection and surface normal for the assessment of breast ptosis using 3D scans of the torso. Experimental results suggest that 3D features are successful for objectively categorizing breast ptosis with high accuracy and precision.Item Computational Modeling of Breast Shape Using Spherical Harmonics(2018-05) Cheong, Audrey; Merchant, Fatima Aziz; Roysam, Badrinath; Mayerich, David; Shah, Shishir Kirit; Reece, Gregory P.As the number of cosmetic and reconstructive breast surgeries performed have been steadily increasing over the years, there is a greater need for improved technologies, such as developing a computational three-dimensional breast model. The breast model will be an invaluable tool for surgeons in surgical planning and during clinical consultations with patients in shared decision making. In this dissertation, a breast model using spherical harmonics is presented. A 3D breast surface image is converted to a spherical harmonic (SPHARM) description, which is represented with three sets of coefficients and can be used to reconstruct a computational model of the breast. Our modeling results demonstrate significantly moderate to strong correlations between specific SPHARM coefficients and breast shape descriptors, such as height, width, projection, and ptosis. We employ these correlations to evaluate breast shape across several subjects and to interactively modify breast shape through these coefficients. We tested the robustness of our method to convert breast image data to SPHARM models and performed classification using the SPHARM coefficients on two types of breast reconstructions: transverse rectus abdominis myocutaneous (TRAM) flap reconstruction and implant reconstruction. Additionally, results were shown on predicting reconstructed breasts from SPHARM models based on preoperative breasts. Contributions of this research: A parametric breast model was developed that can (1) accurately and compactly represent breast data with a set of coefficients (shape descriptors), (2) easily adjust breast shape through modeled coefficients, (3) employ modeling approach to evaluate and differentiate different breast shapes, (4) generate template shape models representative of specific breast shape types, (5) perform classification using the SPHARM description, and (6) perform predictive modeling.Item Deciphering a Novel SUMO-dependent lncRNA Degradation Mechanism on Telomere during Cell Cycle Progression to Impact Aging and Cancer Onset(2021-05) Quttina, Maram Adnan Sami; Bawa-Khalfe, Tasneem; Lin, Chin-Yo; Dauwalder, Brigitte; Merchant, Fatima AzizThe exosome complex component EXOSC9 (Rrp45) is an essential subunit of the RNA degradation machinery in eukaryotic cells. In addition to its supportive role in exosome-based mRNA surveillance, EXOSC9 also exhibits independent catalytic activity to degrade select cytosolic mRNA and is present in the nucleus and chromatin fractions. Like mRNA, long non-protein-coding RNA (lncRNA) is indispensable for normal cell physiology and, consequently, tightly regulated in the cell. Yet, unlike mRNA, substantially less is known about the mechanisms for lncRNA degradation. It is important to delineate the regulatory control of lncRNA degradation, particularly telomeric repeat-containing RNA (TERRA), as the TERRA-telomere R-loops dictate cell cycle progression and genomic stability. Recent studies in our lab indicate that the SUMO-modified heterochromatin protein 1alpha (HP1α) more readily interacts with TERRA than unmodified HP1α. Interestingly, the SUMOylated form of this canonical chromatin remodeling protein also recruits EXOSC9 to the chromatin. During the S/G2 transition of the cell cycle, we observed an accumulation of SUMOylated HP1α, the interaction between HP1α- EXOSC9, and a significant TERRA loss. Hence, we expect that these events support normal cell cycle progression; specifically, chromatin-enriched EXOSC9 requires interaction with SUMO-modified HP1α to degrade TERRA and facilitate telomere replication. Results from this study will delineate for the first-time a cell-cycle driven mechanism for degradation/clearance of chromatin-bound lncRNA. Persistent activation of this lncRNA-clearance system with induction of a SUMO-mimetic HP1α causes accumulation of DNA damage at telomeres. Consistently in normal human cells, SUMO-modification of HP1α is tightly regulated via an active deSUMOylase SENP7 as demonstrated by us and others. The full-length SENP7 (SENP7L) binds and reduces SUMO post-translational modification of HP1α in multiple mouse and human cells including mammary epithelial cells. Unlike other deSUMOylases, SENP7L is enriched at heterochromatin sites and directs condensed chromatin architectures as defined in multiple cell models. While these studies establish a critical role of SENP7L, it is unclear if the enzymatic activity of SENP7L is required for its biological actions. Here, we used a genetically engineered mouse model (GEMM) first established in our lab to evaluate how catalytical activity of SENP7L directs HP1α modification and normal mouse mammary epithelial development. In normal mouse development, we report an induction of SENP7L during the pubertal stage, specifically in mammary hierarchical stem/progenitor cells (MaSC) and the MaSC niche called the terminal end buds. The knockdown of SENP7 catalytic activity in this GEMM increased MG's branching morphogenesis and accelerated differentiation in an ex vivo organoid system. Concurrently, sustained SUMOylated HP1α is enriched in chromatin fraction of this SENP7 dead GEMM. Recent studies in our lab indicate an analogous induction of SUMOylated HP1α with loss of SENP7L in endocrine-resistant hormone receptor positive breast cancer (BCa); this BCa subtype is a therapeutic challenge as patients are unresponsive to conventional endocrine-targeting drugs and readily progress to metastatic disease. Hence, we expect our research could present novel biomarkers to identify endocrine non-responders and identify alternative therapeutic strategies for these BCa patients.Item Design and Evaluation of Different Interaction Techniques for Object Rotation in Mobile VR Applications(2018-05) Karbaschi, Yaser 1987-; Shah, Shishir Kirit; Subhlok, Jaspal; Merchant, Fatima AzizManipulating 3D objects and navigating are the main components when exploring Virtual Reality (VR) content. These tasks can get complex in Mobile-VR due to the limited available inputs. While VR (and specifically Mobile-VR) has the potential to be the next major computing platform, evaluating and defining standards for interaction with VR content is demanding. In this thesis, two mobile applications are proposed to explore interaction techniques in mobile-VR. We evaluated the use of pointer-like controller –implemented using Google Daydream– to allow for 3D rotation of objects on mobile-VR platforms. A user study has been done with 18 participants utilizing the three interaction techniques for a rotation task: Using a reticle to click and drag axis handles or the object for free rotation, adopted from 3D desktop applications (Trackball); Using the remote's inertial sensing alone (Remote); and a hybrid method that combines the remote rotation with the axis handles (Hybrid). Remote and Hybrid were significantly faster than Trackball, while Hybrid was the preferred method and had the lowest average workload. There was no major difference in accuracy between methods. We also discuss our qualitative observations as well as participants' preferences and put our findings into context of the application domain of 3D manipulation in VR environments.Item Detecting Network Intruders by Examining Packet Crossovers in Connections(2014-05) Zhang, Hongyang 1988-; Huang, Stephen; Shi, Weidong; Merchant, Fatima AzizRouting packet traffic through a chain of hosts is a common technique for hackers to attack a victim machine without exposing themselves. Generally, a long connection chain formed is an indication of the presence of an intruder. Previous work has mostly focused on detecting stepping-stone hosts. Few researchers have addressed the issue of long connection chains (especially downstream detection). A challenging issue in this area is to detect users connecting to a server using a long connection chain with only the information at the end of the chain. This thesis presents a solution to the problem of detecting upstream long connection chains. We first observe that the longer a connection chain is, the more packet crossovers are generated. Thus we reduce the problem of detecting long chains to that of detecting unusually large number of packet crossovers along the chain between requests and responses at server side. However, the approach requires the packet information along the whole chain. Since we cannot directly measure the number of crossovers on intermediate nodes, we are forced to study the consequences of large number of crossovers. A detection algorithm has been designed based on the distribution of packet gaps. We validated our algorithm using test data generated on the Internet. The result shows a high detection rate of long connection chains from short ones without too many false positives.Item Determining Nipple Position and Smallest Resolvable Volume for Evaluating Breast Reconstruction Surgery(2020-08) Nowroozilarki, Zhale; Merchant, Fatima Aziz; Zouridakis, George; Pollonini, LucaBreast cancer is one of the most widespread cancers among women globally. Because of recent improvements in cancer treatment and increase in survival rate, more women are living with the consequences of breast removal surgery, known as mastectomy. In order to improve the quality of life, physical and psychological well-being after the cancer treatment process, many women decide to have reconstruction surgery. Metrics of breast aesthetics such as position and volume symmetry are often used for outcome assessment following reconstructive surgery. In order to achieve breast symmetry, many measurements which are difficult for human eyes to precisely estimate need to be done. The first aim of this study is to use a data-driven approach to help surgeons annotate the nipple position on reconstructed breast mounds. A graphical user interface was developed to enable computations of nipple localization and symmetry measurements on 3D surface images of pre- and post-operative patients, and a linear regression model incorporating breast aesthetic measures was developed to provide personalized estimate of nipple localization. Secondly, the smallest measurable volume using 3D imaging was analyzed to quantify the resolution of the 3D imaging system. The computational tools and models developed in this study will assist surgeons with surgical planning and outcome assessment and provide a framework for visualization to support physician-patient communication during clinical consultations. This research aims to benefit breast cancer survivors as well as their care givers.Item Development of an Imaging Tool for Commercial Mushroom Yield and Quality Estimation(2021-05) De La Garza, Alessandro; Merchant, Fatima Aziz; Benhaddou, Driss; Balan, VenkateshCultivation and production of mushrooms has increased during the previous decade. The production increase is due to the development of farms combined with the rise in consumer’s general understanding of the medicinal and dietary benefits of mushrooms consumption. Improvements in mycology and agricultural technology have allowed farmers to increase their mushroom production. Farmers have been able to create microclimates with specific growing conditions that encourage mushroom growth for large-scale harvesting. Although technological advancements have increased production volume, taking measurements of the size and quality of mushrooms is an arduous process that requires a lot of labor hours to complete. Different methods have been used and proposed to assess the size and quality of mushrooms. Computer based image processing is a promising method to tackle this task by implementing image processing and analysis techniques. Computer aided analytical tool can assist farmers by counting, taking measurements, determining the growth rate of mushrooms and calculating the crop yield. Having this information would allow farmers to adjust microclimate conditions and coordinate harvesting schedules to pick mushrooms when quality is at their peak. This thesis takes a different approach to other projects by collecting image data from a large-scale commercial mushroom farm. The main goal of this paper is to develop a system that can support mushroom farmers decision to become more efficient and to evaluate the feasibility of implementing computer vison assistance in an actual mushroom farm.Item Embedding Location-Based Network Connectivity within IPv6 Address(2014-05) Araji, Bahaa; Gurkan, Deniz; Merchant, Fatima Aziz; Lent, RicardoIPv4 (Internet Protocol Version 4) the famous 32-bit address, has been used in networks for many decades [1] and would not have sustained its usability without NAT(Network Address Translation). IPv6 (Internet Protocol version 6) with its 128-bit address, provides slight routing information [2]. In this thesis, we present ESPM (Embedding Switch ID, Port number, MAC address), Embedding Switch Identification number, Port number and MAC (Media Access Control) Address within IPv6 protocol and SDN technology, imposing a device connectivity hierarchy upon the address space. We amend the IPv6 global addressing scheme for hosts to include their MAC address as well as the switch and port numbers that they are connected to. This scheme encodes information that would ordinarily require a lookup or query packets and decrease CAM (Content Addressable Memory) table entries on the switch by forwarding the packets using the ESPM algorithm. After processing ESPM algorithm to check for OF (Open Flow) controller ID, OF switch ID, and the Port ID, the amount of total packets transferred on the network to fulfill an ICMP (Internet Control Message Protocol) request-reply process decreased by 28.1% in 1-switch-2 host. In order to demonstrate the feasibility of such an addressing scheme, we use POF (Protocol Oblivious Forwarding) controller and POF switch [3] to implement ESPM and then measure the impact on the number of network management packets transferred between hosts during connectivity tests.Item Engineering Non-cytotoxic Delivery of Proteins by T cells via Fusion to NPC2(2022-12-14) Saeedi, Arash; Varadarajan, Navin; Willson, Richard C.; Orman, Mehmet A.; Peng, Weiyi; Merchant, Fatima AzizEngineering cellular therapeutics by programming T cells has great potential in immunology. The primary mechanism employed by T cells for the specific transfer of proteins at the immunological synapse is via the lysosomal perforin pathway that facilitates the transfer of cytotoxic granzymes leading to apoptosis in target cells. Facilitating the delivery of non-cytotoxic proteins through perforin oligomers will dramatically expand the range of protein cargos that T cells can traffic to the target cells. Here, we have identified the intralysosomal protein, NPC2, as a chaperone that can facilitate the delivery of T-cell derived reporter proteins through perforin pores at the immunological synapse. Structural and biophysical considerations suggested that NPC2 could traverse through perforin pores and in vitro experiments confirmed the transport of purified NPC2 through perforin pores on cell membranes. To characterize the ability of NPC2 to facilitate the transfer of payloads in T cells, we constructed NPC2-mCherry fusion proteins in T cells. Using confocal microscopy and flow cytometry, we confirmed the colocalization of the NPC2 fused protein with lytic granules and the transfer of the fluorescent protein payload from T cells to target cells in co-culture experiments. The NPC2 fusion enabled the localization of mCherry to secretory lysosomes in mouse TCR CD8+ T cells and human CD4+ and CD8+ chimeric antigen receptor (CAR) T cells. Finally, we introduce a novel method for expression of NPC2 fused toxins within CAR T cells for treating immune resistant tumor cells. These results illustrate that by using NPC2 as a molecular chaperone, the NPC2-perforin pathway can be exploited as a programmable molecular delivery system for cell-based therapies.Item Establishing Quantitative Measures of Quality of Functional Near Infrared Spectroscopy Data(2020-05) Gopal Dhamodaran, Dhanalakshmi; Pollonini, Luca; Zouridakis, George; Merchant, Fatima AzizFunctional Near-Infrared Spectroscopy (fNIRS) is an optical neuroimaging technique that can be used to examine and quantify tissue hemodynamics on the brain. fNIRS signals are contaminated by measurement noises and physiology-based systemic noises, such as a periodic pulsation of optical signals associated with the cardiac activity. Several approaches exist to filter out all sorts of noises and to remove channels with a low signal-to-noise ratio (SNR) that are deemed unreliable to estimate cortical hemodynamics. However, amongst the systemic noises which are undesirable for cerebral hemodynamics, strong cardiac pulsations usually indicate a good contact between the optical probe and the scalp. This thesis aims at evaluating the performance of physiology-based measures of quality of fNIRS data, namely 1) the Scalp Contact Index (SCI) and 2) the Peak Power (PP) of the spectrum, and understand how would they vary as a function of a range of pair of wavelengths, and for experiments conducted with different experimental setups such as 1) the source-detector distance, 2) the integration time of photodetectors and 3) the anatomical location on the head where signals are collected. So, while keeping other parameters constant, we are going to vary only one parameter at a time and collect the data and compute the SCI and PP for that data to compare its quality.Item High Performance fNIRS System Utilizing Microzed Zynq-7000 System on Module Board(2018-12) Szymczyk, Tomasz; Pollonini, Luca; Merchant, Fatima Aziz; Zouridakis, GeorgeCommercial functional near-infrared spectroscopy (fNIRS) instruments used in cognitive neuroscience research tend to be cost prohibitive while also usually suffering from a low signal-to-noise ratio. This thesis describes the design and implementation of an application developed on the Microzed Zynq 7000 series System on Module (SoM) board, which is the core of a custom high performance modular fNIRS device. Utilizing the FPGA capabilities of the Microzed SoM allows improved signal quality by employing digital lock-in demodulation techniques to maximize signal to noise ratio, as well as communication with other electrical components required for an fNIRS system. Software was developed both on the Microzed’s ARM9 processor and external workstation PC to verify the lock-in technique and facilitate data transfer and device configuration. The results verify that the core of a cost effective and portable fNIRS instrument can be developed using an FPGA and processor system on module board.Item How long does it take to offload traffic from firewall?(2013-12) Narisetty, Raja Revanth 1988-; Gurkan, Deniz; Shireen, Wajiha; Merchant, Fatima AzizDemonstration of how intelligent steering of classified application traffic with flows in OpenFlow protocol can alleviate firewall bottleneck issues. Irrespective of the available higher bandwidth capabilities of the network, traffic passing through a firewall, where every packet is statefully inspected and/or deep packet inespected (DPI), causes bottlenecks. Isolation of the classified application traffic from all other traffic by means of VLANs and MPLS has been proposed, and is being implemented. Our demonstration leverages the SDN paradigm and flow isolation is achieved by programming the forwarding plane in conjunction with a dynamic utilization of a firewall’s application-aware DPI capabilities and other analytics. In this respect, as soon as classified application traffic session has been positively identified by the firewall, a flow rule can be written to offload the remainder of the data transfer from the firewall to a fast path on the switch. All sessions are inspected by the firewall, but not all packets of every session need to pass through the firewall. Thus the security is preserved and the throughput constraint is removed. The demonstration utilizes a virtual distributed firewall product from vARMOUR Networks, Inc. to deliver software defined security, SDSec. Once an application is identified for a new session (occurs within a small number of packets, usually less than 10), and the session is to be permitted, the remainder of the session’s packets are steered to a fast path on an OpenFlow switch using as a flow definition that exists for the duration of the session. We present the research investigations on the trade-offs for such a fast path mechanism through the network, considering processing delays introduced by the mechanism. Namely, an optimal session length should be determined for such a fast path mechanism to be worthwhile in a campus network. The main delay components to be measured and presented include: a flow setup requires a controller to push flows respective to programmable, the flow redirection takes time as such a flow should be activated at the programmable switch, and the network delay associated with the setup process. ‘What Is The Ideal Length Of Session To Benefit From The Intelligent Application Steering Based Dpi Offload Solution?’ For the application traffic to benefit from this intelligent offload of deep packet inspection solution, determining the ideal length of the session on the firewall is the objective of this work. In other words, we determine ‘How Long Does It Take to Offload Traffic from the Firewall?’ which is the ideal length of the session on the firewall for this intelligent offload solution.Item IMAGE ANALYSIS FOR ZEBRAFISH VASCULATURE(2015-08) Hans, Charu 1985-; Shah, Shishir Kirit; Merchant, Fatima Aziz; Gabriel, Edgar; Chen, Guoning; Bondesson, MariaZebrafish has become a viable model for various research including vertebrate development, gene expression analysis, human diseases modeling, drug screening and toxicology analysis. Zebrafish have a closed circulatory system, and the mechanisms of vessel formation are highly similar to those in humans. Being able to model the growth of blood vessel in the vasculature system of zebrafish is interesting for understanding both the circulatory system in humans, and for facilitating large scale screening of the influence of various chemicals on vascular development. Zebrafish embryo is an attractive alternative for environmental risk assessment of chemicals since it offers the possibility to perform high throughput analysis in vivo. Intersegmental vessels (ISV) and caudal vein plexus (CVP) undergo active development via angiogenesis. Hence, providing excellent models to study vasculature system. However, the lack of tools for automated analysis of acquired images is a huge bottleneck in utilizing the zebrafish to its full potential. Most of the current research based on ISV observe the presence or absence of ISVs or perturbation of ISV morphology but do not quantify growth dynamics. Moreover, these analyses are done manually; hence, it is tedious and expensive. All of these factors drive the need for automated image processing methods to quantitatively analyze the imaged embryos. In this work, we have focused on developing image processing algorithms to automatically segment and quantify ISVs of zebrafish embryos that have been exposed to various chemicals. We tested the algorithms on images of zebrafish embryos obtained from screening compounds that may act as an ISV disruptor. The efficiency of segmentation and quantification approach is demonstrated by our experiments of the entire zebrafish vasculature recorded using a fluorescence microscope. In this work, we have also presented an approach to segment and detect abnormalities in the CVP region of zebrafish embryos due to exposure to chemicals. Morphological changes due to chemicals exposure are modeled based on the proposed gradient weighted co-occurrence histogram of oriented gradients (gCo-HOG). These features are compared to more commonly use gray level co-occurrence matrix (GLCM), histogram of oriented gradients (HOG) features, and co-occurrence histogram of oriented gradients (Co-HOG) features that utilizes distribution of neighboring pixels to capture spatial structure.Item Investigating Phenotypic Changes in Response to Drug Treatments in Epithelial Ovarian Cancer Using a Novel Si-TiB2 Micropatterned Substrate(2022-05-10) Eisenbrandt, Margaret Ruth; Merchant, Fatima Aziz; Majd, Sheereen; Zagozdzon-Wosik, Wanda; Al-Ubaidi, Muayyad R.Epithelial ovarian cancer (EOC) is one of the most prevalent cancers in women worldwide, with nearly 80% of cases diagnosed in late-stage of disease and an overall survival rate of less than 50%. 3D culture is necessary in order to study the in vivo response of cancer cells to therapeutic agents, in systems that better mimic innate cell-cell and cell-ECM interactions. This study evaluates the potential of a novel micropatterned substrate, fabricated using photolithography to deposit TiB2 micropatterns onto a Si wafer to study the response of EOC to epigenetic and chemotherapeutic drugs. Previous work has validated that the Si-TiB2 substrate enables selective deposition of growth factors and self-assembly of cells onto the TiB2 pattern through differences in stiffness, roughness, wetness, and charge gradient. For EOC cell lines, OVCAR3 (low invasiveness) and SKOV3 (high invasiveness), the Si-TiB2 micropatterned substrate supported cell proliferation and maintained viability, and 3D aggregation for SKOV3 cells. Treating SKOV3 aggregates and OVCAR3 monolayers on patterned substrates, with an epigenetic drug, vorinostat, also known as suberoylanilide hydroxamic acid (SAHA), resulted in decreased diameter and thickness, however viability of the remaining cells was unchanged. Genomic analysis of the treated aggregates suggests a change in phenotype of SKOV3 after treatment with SAHA. While studies show that SAHA alone may not be a sufficient treatment for EOC, it does have the potential to augment the treatment of some cancers when used in combination with chemotherapeutic agents. Treatment of SKOV3 aggregates with a combination of SAHA and Paclitaxel was shown to decrease proliferation and halt growth for an extended period after treatment however these results are not statistically different from the Paclitaxel treatment group, which agrees with a clinical trial of SAHA and Paclitaxel combinatorial treatment. Collectively, data support use of the micropatterned substrate for investigation of potential drug therapies for cancer treatment and cellular changes in response to drug treatment.