• STUDYING RETINA DEVELOPMENT USING SMALL MOLECULE BMP INHIBITORS AND MAKING STABLE MOUSE EMBRYONIC STEM CELL LINES

      Viczian, Andrea; Keshvani, Caezaan (2013)
      Age related macular degeneration results in loss ofconephotoreceptors. Studies have not been able to efficientlytransplant cone cells, possiblydue to their limited numbersand lack of information about their development in the mammalian retina.Our lab has discoveredthat BMP signal inhibition is important for eye developmentin the frogas well as generating retinal cone photoreceptorsin mouse embryonic stem cell cultures. The frog, Xenopus laevis,can grow eyeswithin a few days; it is also amenable to transplantation and genetic alteration. In this study, two small molecule BMP inhibitors, LDN193189 and Dorsomorphin, causedshortened tails(dorsalized) phenotypein Xenopusembryos as well asexpansionofthe neural plate in neural stage embryos. This suggests that these chemical inhibitors can be used in place of the standard BMP antagonist, Noggin, in cell culture experiments. Mouse embryonic stem cell cultures treated with Noggin have been used to generate retinal progenitors that generate cone photoreceptorsin our lab. In order to further study cones indetail,we needed to enrich the population of cone photoreceptors from retinal progenitors by marking these cells in-­‐vitro. We generated stable mouse embryonic stem cells expressing a promoter that drives expression in rod/cone progenitor cells upstream from the mCherry fluorescent protein. This construct also contained aubiquitous promoterdriving an antibiotic resistance genefor antibiotic selection. In future studies, these stable ES celllines could be used to differentiate into rod/cone progenitors selected specifically by FAC sorting. Small molecule BMP inhibitors could be used in place of Noggin and analyzed in the generation of conecells.
    • Style Guide Development For An Internal Reference Library

      Lizardi, Ryan; Bush, Sarah C.; Lizardi, Ryan; First Reader; Jofre, Ana; Second Reader (SUNY Polytechnic Institute, 2020-12)
      This work strives to present information design and user experience (UX) techniques to improve continuity of design and usability, before migrating a cross-functional internal reference library to a new content management system (CMS). Expert-curated content accessed through LinkedIn Learning, combined with scholarly research, result in a complimentary style guide for use in the workplace.
    • Substance Use among ADHD Adults: Implications of Late Onset and Subthreshold Diagnoses

      Faraone, Stephen V.; Wilens, Timothy E.; Petty, Carter; Antshel, Kevin; Spencer, Thomas; Biederman, Joseph (Wiley, 2007-01)
      Diagnosing ADHD in adults is difficult when the diagnostician cannot establish an onset prior to the DSM-IV criterion of age seven or if the number of symptoms does not achieve the DSM threshold for diagnosis. These diagnostic issues are an even larger concern for clinicians faced with adults with substance use disorders (SUD). The present study compared four groups of adults: full ADHD subjects who met all DSM-IV criteria for childhood onset ADHD, late onset ADHD subjects who met all criteria except the age at onset criterion, subthreshold ADHD subjects who did not meet full symptom criteria, and nonADHD subjects who did not meet any of the above criteria. Diagnoses were by the Structured Clinical Interview for DSM-IV, and the Drug Use Severity Index (DUSI) was used for self-report of substance use. Cigarette and marijuana use was significantly greater in all ADHD groups relative to non-ADHD controls. Although usage rates of other drugs failed to reach significance, the ADHD groups were more likely to have used each drug (except alcohol) compared with the non-ADHD group. The late onset and full ADHD groups were more likely to have endorsed ever having a problem due to use of cigarettes, alcohol, or marijuana and reported more trouble resisting use of drugs or alcohol. The full ADHD group was more likely than the other groups to have reported ‘‘getting high’’ as their reason for using their preferred drug. Adults with ADHD have elevated rates of substance use and related impairment. Data about late onset ADHD provides further support for the idea that the DSM-IV age at onset criterion is too stringent. In contrast, subthreshold ADHD seems to be a milder form of the disorder, or perhaps a heterogeneous group of true ADHD cases and false positives.
    • Substance Use Disorders in High-Risk Adolescent Offspring

      Milberger, Stephen V. Faraone, Jose, Sharon (Wiley, 1999-01)
      Objective: To examine the risk for substance use disorders (SUD) in offspring of SUD parents who were not selected due to referral to SUD treatment centers. Method: The original sample was ascertained through two groups of index children: 140 ADHD probands and 120 non-ADHD comparison probands. These groups had 174 and 129 biological siblings and 279 and 240 parents, respectively. Results: We found that: 1) parental SUD was associated with SUD and all SUD subtypes in the offspring; 2) parental alcohol use disorders were associated with alcohol use disorders in the offspring as well as co-occurring alcohol and drug use disorders but not drug use disorders alone in the offspring; and 3) drug use disorders in the parents were associated with drug use disorders but not alcohol use disorders in the offspring. Conclusions: These findings suggest that alcoholism and drug abuse may breed true from parents to their offspring, but further work with larger samples is needed to confirm this idea. Our findings also suggest a possible common diathesis that is expressed as comorbid alcohol and drug use in the offspring of alcoholic parents. If confirmed, these findings may be useful for the development of preventive and early intervention strategies for adolescents at high risk for SUD based on parental history of SUD.
    • Supplemental Teaching Tools: Will They Help Students Improve Their Learning Capabilities?

      Cirillo, Mary Catherine (2012-12-01)
      This project explores the use of supplemental teaching tools as an aid to a traditional lecture course. The website is geared for a community college course in Advertising and/or History of Visual Communication. I also discuss the positives of the use of Google Sites with podcasts, Google Presentation/Docs, Jing, and Prezi as supplemental teaching tools. Using the learning theories of constructivism and cognitivism, I explore how these tools will help students to learn. This paper looks at the learning theories that support the use of these tools to help students learn and fill in gaps that they might have missed in class during the lecture. This work discusses the planning, implementation, and evaluation of the project. A literature review examining different types of supplemental tools and supplemental instruction, as well as the supplemental teaching tool topic, “Women in Advertising,” is also included.
    • Supporting Interactive Fundraising for Gen X Cancer Survivors and Co-Survivors in the New England Area

      Winters, Robert (2015-12)
      Two theories were used in creating the application. The first, Human Centered Design accounts for a number of factors which support a design in being user-friendly and highly functional. The second, Engestrom’s Activity Theory, which stipulates for certain outcomes (goals) it is necessary to produce certain objects (experiences and knowledge). The question under investigation was: Can a mobile application provide interested parties transparent nonprofit financial information and allow them to make a personal contribution? Through the process of prototyping it was found that a mobile application can connect an individual to an organization. It was also found that it is possible for said application to create a connection that results in real world impact by providing clear and easy methods of contributing time and money. In providing this medium of connecting the user to an organization it was also found the organization can provide user impact data through the application to share real time data generating a cycle of application use, impact and reporting which builds over time. The application has been fully prototyped but has not yet been tested in a real world environment. The prototype can be viewed by downloading App Taster (https://itunes.apple.com/app/id518977767) and opening the prototype file (https://www.dropbox.com/sh/ttzg8kv1dwntjyi/AABrcWwi1c23fC0Hm7oOB5hPa?dl=0).
    • Surviving Remote Teaching during a Pandemic

      Stam, Kathryn; Thesis Advisor; Lizardi, Ryan; Second Reader; Van de Bogart, Patty (2020-05)
      On March 11, 2020, the Governor of New York, Andrew Cuomo, announced SUNY and CUNY Colleges of New York would move to online instruction only, as of March 19, 2020. At the same time, school districts throughout the state were moving their curriculum online, and non-essential businesses were being required to have their workers work at home. The headlines across the state were reminding everyone to “stay home” because of the Covid-19. The news was frightening to some of the Professors, Adjuncts and Teachers all across the state, (especially in K-12). In this paper, I will refer to all folks who teach as ‘Instructors’ or ‘Educators.’ These Instructors, who teach in person, and have never taught an online course, were expressing their concern that their course “could not” be taught on line. My Capstone Project is to create a “Guide” with some ideas to help in this stressful time.
    • Swarm Intelligence in the Multi Agent System Environment

      Bollam, Sravani; Sengupta, Saumendra; Adviser; Chiang, Chen-Fu; Reviewer; Rezk, Mohamed; Reviewer (2016-12-20)
      This thesis is focused on the use of naturally occurring concept of “swarm intelligence” to multiagentcsystems, namely the relatively new system-theoretic framework known as Swarm Intelligence Systems (SIS). In this work, outlined is the general framework of an interacting agents behaving as a swarm group on a mission to deliver a service such as transporting a set of goods from a given starting point to a destination. As an example, one could think of a team of drones, for instance, providing a delivery service in a milieu where normal transportation mode may be prohibitively expensive. The entire logistic, in detail as a commercial project, is too involved for our thesis focus; instead, some of the structural interaction issues with a group are outlined and discussed here to articulate the behavior of multi-agent based swarm as a group necessary to function as a distributed entity somewhat different from the standard swarm models found in literature.
    • sxRNA Switches: Hypothesis Through Automated Design Via a Genetic Algorithm Approach

      Tenenbaum, Scott; Chair; Melendez, J.A.; Cady, Nathaniel; Fasullo, Michael; Begley, Thomas; Doyle, Francis J., II (2021-12)
      The following document is meant to represent an overview of my work on structurally interacting RNA (sxRNA), which has already resulted in three publications with another two in preparation. Where appropriate, some text and data from these publications have been reproduced here. Ribonucleic Acid (RNA) is one of the fundamental macromolecules present in living systems. It can be found in all cells as varying length polymer chains composed of four primary bases (adenine, cytosine, guanine, uracil) capable of numerous modifications. Though generally characterized as an information carrier, RNA is a versatile molecule that exhibits both intra and inter-strand base pairing to form complex structures. Similar to protein, the particular shape of an RNA structure in combination with some degree of sequence specificity, can dictate its function (RNA binding protein recognition sites, ribozyme activity, aptameric affinity, etc.). Structurally interacting RNA (sxRNA) is a molecular switch technology that exploits predictable intermolecular RNA base pairing to form an otherwise absent functional structure in one RNA strand when it interacts with a specific, targeted second strand. Originally proposed as a potential regulatory mechanism in natural systems, we used characteristics of predicted pairings in that context to engineer purely synthetic sxRNA switches that have been successfully tested. There are many non-coding RNAs associated with pathological conditions, the ability to use these as triggers for sxRNA opens the door to potential applications ranging from diagnostics to therapeutics. Furthermore, other prospective triggers (including those synthetically designed) may allow use of the technology as a molecular tool for a variety of purposes including as an alternative to antibiotic selection in cell line development. The typical trigger sequences targeted by sxRNA switches are at least 20 bases in length. Combinatorial options with regard to structure positioning and base composition produce an enormous number of potential sxRNA sequences for any given target. Exhaustively examining these for feasible candidates (i.e., analyzing predicted interactions with unintended targets) is computationally impossible with current systems. Evolutionary computing is a subfield of artificial intelligence (AI) that has been inspired by biology. Genetic algorithms are a type of evolutionary algorithm and apply operators (such as recombination and mutation) to find candidate solutions to an optimization problem. The presented dissertation will describe the original sxRNA research as well as the development and testing of a genetic algorithm that automates the production of new sxRNA switch candidates. This algorithm takes into consideration factors that were previously impossible to account for in manual designs.
    • The Synchronological Charting of The Evolution of Electronic Communications

      Conklin, Donald; Kahn, Russell; Thesis Adviser; Stam, Kathryn; Second Reader (SUNY Polytechnic Institute, 2019-05)
      From 1850s to the present time, electronic communications have been evolving from the analog transmission of harmonics over a singular wire connected to boxes with a single hole for transmitting and receiving to texting, FaceTime, Facebook, and twitter. This evolution did not follow a direct path from A to B; instead, it took a winding and interlocking path. This path is represented via a timeline that textually analyzes the data collected, and through graphical interpretation, depicts the history of the path. With this one should be able to see the growth of the enterprises through history, which is shown horizontally, as well as the different variables that affected their growth along the way, depicted vertically. Both of these variables are depicted on one chart, from the same vantage point. This timeline not only shows the path of growth of the technology and its enterprises but also the interrelations of the different enterprises and how either technology, politics, or geographic presence influenced this swath. The online interactive Prezi timeline “Evolution of Electronic Communications” referenced in this abstract can be found at https://prezi.com/vt9673mvbqsa/evolution-of-electronic-communications/ .
    • T Cell Factor-1 (TCF-1) Regulates Mature Alloactivated T Cells to Separate GVHD From GVL

      Mobin Karimi; Harris, Rebecca (2021)
      Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative treatment used for patients with cancer or other hematological malignancies. However, widespread use of this treatment is hindered by development of graft-versus-host disease (GVHD), a life-threatening complication of allo-HSCT. Mature donor T cells in the graft mediate GVHD, but also help kill residual malignant cells in the patient by the graft-versus-leukemia (GVL) effect. Depletion of mature T cells from the graft eliminates this beneficial anti-tumor response. Mature T cells are also needed for proper stem cell engraftment. Therefore, current work has focused on how to modulate T cell signaling and function to separate GVHD from GVL. T Cell Factor-1 (TCF-1) is a T cell developmental transcription factor that is also important in some contexts for T cell activation. The role of TCF-1 in alloactivated mature T cells is completely unknown. To examine the role of TCF-1 in this context, a mouse model of allo-HSCT leading to GVHD/GVL was used to study T cells from mice with a T cell-specific deletion of TCF-1. This work showed that loss of TCF-1 separates GVHD from GVL, with reduced disease severity and persistence yet maintained GVL effects. TCF-1 affects alloactivated T cell phenotypes and suppressive profiles, as well as the major T cell functions (proliferation, migration, and cytokine/cytotoxic mediator production). TCF-1 also controls alloactivated T cell survival, apoptosis, and gene expression programs. The regulation of these functions and programs by TCF-1 is distinct in CD4 versus CD8 T cells. TCF-1 also controls two unique T cell subsets - stem-like CXCR5+ CD8+ T cells, and CD25- noncanonical Tregs. Therefore, TCF-1, or these two unique T cell types, may be a therapeutic target to improve allo-HSCT outcomes by separating GVHD from GVL effects. Expansion of CD25- Tregs during TCF-1 deficiency may also be useful for treatment of other T cell-mediated disorders as well.
    • Targeting wild-type and mutant p53 for cancer treatment

      Stewart N Loh; Blayney, Alan John (2021)
    • Targetingof PIM1 KinaseinMyeloproliferative NeoplasmsInduced by JAK2V617F

      Mohi, Golam; Stuver, Matthew (2017)
      Myeloproliferative neoplasms (MPNs) arestem cell-derivedblood disorders. The most common mutation found in MPN patients is the JAK2V617Fmutation. JAK2 is anon-receptor tyrosine kinase involved in STAT signaling. The JAK2V617F mutation is asingle amino acid substitution of a phenylalanine for valine, whichcauses JAK2 to be constitutively activated. This mutation can cause ahematopoietic transformation. Eventuallythis transformationcan lead to the development of one of thethree different Philadelphia-negative MPN diseases: Polycythemia Vera (PV), Essential Thrombocythemia (ET), and Primary Myelofibrosis (PMF). The JAK2V617F mutationhas been identified in 95% PVpatients,and 50-60% ofETand PMF patients.A JAK1/2 inhibitor (ruxolitinib) has been approved for MF and PV patients and,though it provides initial benefits, it is not effective enough to causelong-termremission in patients. This creates a critical need to identify new therapeutic targets for MPN patients. We found that PIM1 levels were significantly increased inMPN patients, as well asour JAK2V617F mouse modelof MPN.We observedthatknockdown of PIM1 caused a significant decrease in proliferationof JAK2V617F expressing cells. We also found that PIM1 knockdownhad no effect on the proliferation of hematopoietic cells not expressing JAK2V617F, leading us to believe PIM1 is only required in JAK2V617F mediated proliferation. Pharmacological inhibition of PIM kinases,using TP-3654,(kindly provided by Tolero pharmaceuticals)also led to a significant decrease in proliferation of JAK2V617F-expressing cells, but had no effect on cellslacking the mutation. We also found thatthePIM inhibitor,TP-3654,workssynergistically with ruxolitinibto achieve an even greater decrease in proliferation. We found that using the combination of ruxolitiniband TP-3654,we could use both drugs at lower concentrations andachieve an even greater decrease in proliferation and an increase apoptosis. Furthermore,we found that inhibition of PIM kinasesusing TP-3654can resensitize ruxolitinib-resistant cells to ruxolitinibtreatment.These important findingsshow that PIM1 plays animportantrolein the proliferation of hematopoietic cells expressing the JAK2V617F mutation, but is dispensable for the maintenance of cells lacking the mutation. We also found that targeting PIM kinases with TP-3654,significantly decreasedthe proliferation, and increaseapoptosisactivationof JAK2V617Fexpressing cells. We also showedthat TP-3654 and ruxolitinibcan work synergistically. Lastly, we showed that inhibition of PIM kinases,using TP-3654,caused ruxolitinib-resistant cells tobecome resensitized toruxolitinib. These findings helpedus come to the conclusionthatPIM1 kinase, is an importanttherapeutictargetin JAK2V617F-induced MPNs.
    • Teaching of SQL Through a Game

      Ward, Patrick T. (2015-05-01)
      The project seeks to provide an effective alternate method for teaching SQL through the use of a Game. There is value in learning SQL, as SQL skills are still in the top ten list of sought after IT skills for 2015 (Greenspan, 2014). However, lecture based teaching may not fully engage the learner. Therefore, the game was constructed with the MDA framework and Problem-Based Learning in mind. These methods help the learner bridge the gaps between lesson content, problems, and solutions. The game itself was constructed with MSSQL, Adobe Cold Fusion, HTML, CSS, and JavaScript. The game presents lessons on SQL concepts and quiz-based challenges for students to solve. Students faced increasingly difficult challenges as their level SQL knowledge expanded. The project may be found here: http://www.patrickward.net/SQLGame/
    • Technology Case Study in Storage Area Networks

      Marsh, John ; Thesis Advisor; Hash, Larry J.; Climek, David; Bull, Ronny; Pethe, Ameya (2014-05)
      In today's world we need immediate access to data. The demand for networked data access has increased exponentially in the last 20 years. With that demand the importance and volume of networked data has also grown exponentially. The speed at which the data can be accessed has increased and with that the data has moved from individual workstations to a networked location. Over the last decade there has been a trend to move mission critical data away from individual workstations to a centralized data center. A centralized data center removes the location constraint for accessing the data. If critical data is stored on individual servers, a failure will cause the data to be inaccessible. Today, mission critical applications are spanned over multiple servers for redundancy. With this topology, having the data in a central location allows the individual servers to better work with data. With the addition of virtualization, servers can be moved online from one physical server to another. If the data is centralized, it can be presented to all hosts in the cluster. This allows servers to move efficiently between hosts without losing access to the critical data. Many businesses in various industries like finance, airline, hospital, research, etc. depend on the speed and secure availability of their centralized data to function efficiently.
    • A Technology Case Study on Integrating Open Stack with SDN for Internet Connectivity using BGP

      Gonuguntla, Raja Bhushan Rao; Hash, Larry; Advisor (2016-12)
      There were many developments in Internet usage, which resulted in significant increase in Internet routing. With existing networking infrastructure, it is difficult to meet these requirements and causing more cost and less performance. Since network devices are hardware modules, processing them requires more power and more memory. However, if network protocols are developed using software modules, flexibility can be achieved in various programming applications and reduces dependency on hardware. The concept of using networking protocols as a software module can be explained using “Software Defined Networking (SDN).” With SDN, existing infrastructure can be integrated with various applications and centralized control protocols can be developed. One of the key components of SDN is integrating with Cloud Computing, where many applications can be built, which can be used for on-demand services. Integrating cloud computing with SDN will create dynamic networks and reduces infrastructure costs. In this paper, a case was considered for providing better internet connectivity by building public & private networks using Open source cloud technology (OpenStack) and existing distribution environments. For connectivity, BGP was used as routing protocol as it is known to be well- suited for such environments. Both public and private networks were integrated with SDN for centralized control. OpenStack was used to build various network topologies using different plugins through SDN controller. This method allowed to develop SDN controller with global view of OpenStack networks. The same controller was connected to distributed layers using Open Flow protocol. Since, both OpenStack and distributed networks were attached to SDN controller, centralized control of network protocols could be achieved. This model of centralized networks could be very useful in reducing costs and improving network efficiency, especially in large scale deployments.
    • Technology Case Study on Web Real-Time Communications (WebRTC)

      Karnati, Nagarjuna; Hash, Larry; Adviser (2016-05-01)
      Web real-time communication (WebRTC) is the latest technology standard which enables web browsers to communicate directly without having to install any internal or external plug-ins. WebRTC fills a critical gap in the web platform where a native proprietary app like Skype could do something which is media communication that World Wide Web just couldn’t. Now, this can be done form web using WebRTC technology. This paper starts with a brief introduction of WebRTC and how it got started. Moving on, it provides information about the WebRTC technical goals, architecture and protocols involved. This paper highlights the network address translation (NAT) traversal where STUN, TURN and ICE protocols are involved. Also, this paper highlights about the peer to peer to media flows with reference to WebRTC protocol stack and application program interface (API). In the end, this paper discusses about implemented security features, tools available for WebRTC development and provides enterprise use cases.
    • Text Detection from an Image

      Andriamanalimanana, Bruno R.; Thesis Advisor; Novillo, Jorge; Thesis Committee; Spetka, Scott; Thesis Committee; Goda, Piyush Jain (2020-12)
      Recently, a variety of real-world applications have triggered a huge demand for techniques that can extract textual information from images and videos. Therefore, image text detection and recognition have become active research topics in computer vision. The current trend in object detection and localization is to learn predictions with high capacity deep neural networks trained on a very large amount of annotated data and using a high amount of processing power. In this project, I have built an approach for text detection using the object detection technique. Our approach is to deal with the text as objects. We use an object detection method, YOLO (You Only Look Once), to detect the text in the images. We frame object detection as a regression problem to spatially separated bounding boxes and associated class probabilities. YOLO, a single neural network, that predicts bounding boxes and class probabilities directly from full images in one evaluation. Since the whole detection pipeline is a single network, it can be optimized end-to-end directly on detection performance. The MobileNet pre-trained deep learning model architecture was used and modified in different ways to find the best performing model. The goal is to achieve high accuracy in text spotting. Experiments on standard datasets ICDAR 2015 demonstrate that the proposed algorithm significantly outperforms methods in terms of both accuracy and efficiency.