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- All Subjects: Unity
- Creators: Computer Science and Engineering Program
- Creators: Guo, Jia
Description
Measurements of different molecular species from single cells have the potential to reveal cell-to-cell variations, which are precluded by population-based measurements. An increasing percentage of researches have been focused on proteins, for its central roles in biological processes. Immunofluorescence (IF) has been a well-established protein analysis platform. To gain comprehensive insights into cell biology and diagnostic pathology, a crucial direction would be to increase the multiplexity of current single cell protein analysis technologies.
An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of highly multiplexed single cell in situ protein profiling. These highly multiplexed imaging-based platforms have the potential to quantify more than 100 protein targets in cultured cells and more than 50 protein targets in single cells in tissues.
This approach has been successfully applied in formalin-fixed paraffin-embedded (FFPE) brain tissues. Multiplexed protein expression level results reveal neuronal heterogeneity in the human hippocampus.
An azide-based chemical cleavable linker has been introduced to design and synthesis novel fluorescent probes. These probes allow cyclic immunofluorescence staining which leads to the feasibility of highly multiplexed single cell in situ protein profiling. These highly multiplexed imaging-based platforms have the potential to quantify more than 100 protein targets in cultured cells and more than 50 protein targets in single cells in tissues.
This approach has been successfully applied in formalin-fixed paraffin-embedded (FFPE) brain tissues. Multiplexed protein expression level results reveal neuronal heterogeneity in the human hippocampus.
ContributorsLiao, Renjie (Author) / Guo, Jia (Thesis advisor) / Borges, Chad (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2019
Description
Single-cell proteomics and transcriptomics analysis are crucial to gain insights of
healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment.
As an urgent need to advance single-cell analysis, imaging-based technologies have been developed to detect and quantify multiple DNA, RNA and protein molecules in single cell in situ. Novel fluorescent probes have been designed and synthesized, which targets specifically either their nucleic acid counterpart or protein epitopes. These highly multiplexed imaging-based platforms have the potential to detect and quantify 100 different protein molecules and 1000 different nucleic acids in a single cell.
Using novel fluorescent probes, a large number of biomolecules have been detected and quantified in formalin-fixed paraffin-embedded (FFPE) brain tissue at single-cell resolution. By studying protein expression levels, neuronal heterogeneity has been revealed in distinct subregions of human hippocampus.
healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal treatment.
As an urgent need to advance single-cell analysis, imaging-based technologies have been developed to detect and quantify multiple DNA, RNA and protein molecules in single cell in situ. Novel fluorescent probes have been designed and synthesized, which targets specifically either their nucleic acid counterpart or protein epitopes. These highly multiplexed imaging-based platforms have the potential to detect and quantify 100 different protein molecules and 1000 different nucleic acids in a single cell.
Using novel fluorescent probes, a large number of biomolecules have been detected and quantified in formalin-fixed paraffin-embedded (FFPE) brain tissue at single-cell resolution. By studying protein expression levels, neuronal heterogeneity has been revealed in distinct subregions of human hippocampus.
ContributorsMondal, Manas (Author) / Guo, Jia (Thesis advisor) / Gould, Ian (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2018
Description
This paper details the process for designing both a simulation of the board game Jaipur, and an artificial intelligence (AI) agent that can play the game against a human player. When designing an AI for a card game, there are two major problems that can arise. The first is the difficulty of using a search space to analyze every possible set of future moves. Due to the randomized nature of the deck of cards, the search space rapidly leads to an exponentially growing set of potential game states to analyze when one tries to look more than one turn ahead. The second aspect that poses difficulty is the element of uncertainty that exists from opponent feedback. Certain moves are weak to specific opponent reactions, and these are difficult to predict due to hidden information. To circumvent these problems, the AI uses a greedy approach to decision making, attempting to maximize the value of its plays immediately, and not play for future turns. The agent utilizes conditional statements to evaluate the game state and choose a game action that it deems optimal, a heuristic to place an expected value (EV) of the goods it can choose from, and selects the best one based on this evaluation. Initial implementation of the simulation was done using C++ through a terminal application, and then was translated to a graphical interface using Unity and C#.
ContributorsOrr, James Christopher (Author) / Kobayashi, Yoshihiro (Thesis director) / Selgrad, Justin (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The objective of this creative project was to gain experience in digital modeling, animation, coding, shader development and implementation, model integration techniques, and application of gaming principles and design through developing a professional educational game. The team collaborated with Glendale Community College (GCC) to produce an interactive product intended to supplement educational instructions regarding nutrition. The educational game developed, "Nutribots" features the player acting as a nutrition based nanobot sent to the small intestine to help the body. Throughout the game the player will be asked nutrition based questions to test their knowledge of proteins, carbohydrates, and lipids. If the player is unable to answer the question, they must use game mechanics to progress and receive the information as a reward. The level is completed as soon as the question is answered correctly. If the player answers the questions incorrectly twenty times within the entirety of the game, the team loses faith in the player, and the player must reset from title screen. This is to limit guessing and to make sure the player retains the information through repetition once it is demonstrated that they do not know the answers. The team was split into two different groups for the development of this game. The first part of the team developed models, animations, and textures using Autodesk Maya 2016 and Marvelous Designer. The second part of the team developed code and shaders, and implemented products from the first team using Unity and Visual Studio. Once a prototype of the game was developed, it was show-cased amongst peers to gain feedback. Upon receiving feedback, the team implemented the desired changes accordingly. Development for this project began on November 2015 and ended on April 2017. Special thanks to Laura Avila Department Chair and Jennifer Nolz from Glendale Community College Technology and Consumer Sciences, Food and Nutrition Department.
ContributorsNolz, Daisy (Co-author) / Martin, Austin (Co-author) / Quinio, Santiago (Co-author) / Armstrong, Jessica (Co-author) / Kobayashi, Yoshihiro (Thesis director) / Valderrama, Jamie (Committee member) / School of Arts, Media and Engineering (Contributor) / School of Film, Dance and Theatre (Contributor) / Department of English (Contributor) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Herberger Institute for Design and the Arts (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Virtual reality gives users the opportunity to immerse themselves in an accurately
simulated computer-generated environment. These environments are accurately simulated in that they provide the appearance of- and allow users to interact with- the simulated environment. Using head-mounted displays, controllers, and auditory feedback, virtual reality provides a convincing simulation of interactable virtual worlds (Wikipedia, “Virtual reality”). The many worlds of virtual reality are often expansive, colorful, and detailed. However, there is one great flaw among them- an emotion evoked in many users through the exploration of such worlds-loneliness.
The content in these worlds is impressive, immersive, and entertaining. Without other people to share in these experiences, however, one can find themselves lonely. Users discover a feeling that no matter how many objects and colors surround them in countless virtual worlds, every world feels empty. As humans are social beings by nature, they feel lost without a sense of human connection and human interaction. Multiplayer experiences offer this missing element into the immersion of virtual reality worlds. Multiplayer offers users the opportunity to interact with other live people in a virtual simulation, which creates lasting memories and deeper, more meaningful immersion.
simulated computer-generated environment. These environments are accurately simulated in that they provide the appearance of- and allow users to interact with- the simulated environment. Using head-mounted displays, controllers, and auditory feedback, virtual reality provides a convincing simulation of interactable virtual worlds (Wikipedia, “Virtual reality”). The many worlds of virtual reality are often expansive, colorful, and detailed. However, there is one great flaw among them- an emotion evoked in many users through the exploration of such worlds-loneliness.
The content in these worlds is impressive, immersive, and entertaining. Without other people to share in these experiences, however, one can find themselves lonely. Users discover a feeling that no matter how many objects and colors surround them in countless virtual worlds, every world feels empty. As humans are social beings by nature, they feel lost without a sense of human connection and human interaction. Multiplayer experiences offer this missing element into the immersion of virtual reality worlds. Multiplayer offers users the opportunity to interact with other live people in a virtual simulation, which creates lasting memories and deeper, more meaningful immersion.
ContributorsJorgensen, Nicholas Keith (Co-author) / Jorgensen, Caitlin Nicole (Co-author) / Selgrad, Justin (Thesis director) / Ehgner, Arnaud (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Natural Language Processing and Virtual Reality are hot topics in the present. How can we synthesize these together in order to make a cohesive experience? The game focuses on users using vocal commands, building structures, and memorizing spatial objects. In order to get proper vocal commands, the IBM Watson API for Natural Language Processing was incorporated into our game system. User experience elements like gestures, UI color change, and images were used to help guide users in memorizing and building structures. The process to create these elements were streamlined through the VRTK library in Unity. The game has two segments. The first segment is a tutorial level where the user learns to perform motions and in-game actions. The second segment is a game where the user must correctly create a structure by utilizing vocal commands and spatial recognition. A standardized usability test, System Usability Scale, was used to evaluate the effectiveness of the game. A survey was also created in order to evaluate a more descriptive user opinion. Overall, users gave a positive score on the System Usability Scale and slightly positive reviews in the custom survey.
ContributorsOrtega, Excel (Co-author) / Ryan, Alexander (Co-author) / Kobayashi, Yoshihiro (Thesis director) / Nelson, Brian (Committee member) / Computing and Informatics Program (Contributor) / School of Art (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The understanding of normal human physiology and disease pathogenesis shows great promise for progress with increasing ability to profile genomic loci and transcripts in single cells in situ. Using biorthogonal cleavable fluorescent oligonucleotides, a highly multiplexed single-cell in situ RNA and DNA analysis is reported. In this report, azide-based cleavable linker connects oligonucleotides to fluorophores to show nucleic acids through in situ hybridization. Post-imaging, the fluorophores are effectively cleaved off in half an hour without loss of RNA or DNA integrity. Through multiple cycles of hybridization, imaging, and cleavage this approach proves to quantify thousands of different RNA species or genomic loci because of single-molecule sensitivity in single cells in situ. Different nucleic acids can be imaged by shown by multi-color staining in each hybridization cycle, and that multiple hybridization cycles can be run on the same specimen. It is shown that in situ analysis of DNA, RNA and protein can be accomplished using both cleavable fluorescent antibodies and oligonucleotides. The highly multiplexed imaging platforms will have the potential for wide applications in both systems biology and biomedical research. Thus, proving to be cost effective and time effective.
ContributorsSamuel, Adam David (Author) / Guo, Jia (Thesis director) / Liu, Wei (Committee member) / Wang, Xu (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Last Hymn was created by the team of Tyler Pinho, Jefferson Le, and Curtis Spence with the desire to create an eccentric Role Playing Game focused on the exploration of a strange, dying world. Battles in the game are based off of rhythm games like Dance Dance Revolution using a procedural generation algorithm that makes every encounter unique. This is then complemented with the path system where each enemy has unique rhythm patterns to give them different types of combat opportunities. In Last Hymn, the player arrives on a train at the World's End Train Station where they are greeted by a mysterious figure and guided to the Forest where they witness the end of the world and find themselves back at the train station before they left for the Forest. With only a limited amount of time per cycle of the world, the player must constantly weigh the opportunity cost of each decision, and only with careful thought, conviction, and tenacity will the player find a conclusion from the never ending cycle of rebirth. Blending both Shinto architecture and modern elements, Last Hymn used a "fantasy-chic" aesthetic in order to provide memorable locations and dissonant imagery. As the player explores they will struggle against puzzles and dynamic, rhythm based combat while trying to unravel the mystery of the world's looping time. Last Hymn was designed to develop innovative and dynamic new solutions for combat, exploration, and mapping. From this project all three team members were able to grow their software development and game design skills, achieving goals like improved level design, improved asset pipelines while simultaneously aiming to craft an experience that will be unforgettable for players everywhere.
ContributorsPinho, Tyler (Co-author) / Le, Jefferson (Co-author) / Spence, Curtis (Co-author) / Nelson, Brian (Thesis director) / Walker, Erin (Committee member) / Kobayashi, Yoshihiro (Committee member) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The ability to profile proteins allows us to gain a deeper understanding of organization, regulation, and function of different biological systems. Many technologies are currently being used in order to accurately perform the protein profiling. Some of these technologies include mass spectrometry, microarray based analysis, and fluorescence microscopy. Deeper analysis of these technologies have demonstrated limitations which have taken away from either the efficiency or the accuracy of the results. The objective of this project was to develop a technology in which highly multiplexed single cell in situ protein analysis can be completed in a comprehensive manner without the loss of the protein targets. This was accomplished in the span of 3 steps which is referred to as the immunofluorescence cycle. Antibodies with attached fluorophores with the help of novel azide-based cleavable linker are used to detect protein targets. Fluorescence imaging and data storage procedures are done on the targets and then the fluorophores are cleaved from the antibodies without the loss of the protein targets. Continuous cycles of the immunofluorescence procedure can help create a comprehensive and quantitative profile of the protein. The development of such a technique will not only help us understand biological systems such as solid tumor, brain tissues, and developing embryos. But it will also play a role in real-world applications such as signaling network analysis, molecular diagnosis and cellular targeted therapies.
ContributorsGupta, Aakriti (Author) / Guo, Jia (Thesis director) / Liang, Jianming (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
HackerHero is an educational game designed to teach children, especially those from marginalized backgrounds, computation thinking skills needed for STEAM fields. It also teaches children about social injustice. This project was focused on creating an audio visualization for an AI character within the HackerHero game. The audio visualization consisted of a static silhouette of a face and a wave-like form to represent the mouth. Audio content analysis was performed on audio sampled from the character’s voice lines. Pitch and amplitude derived from the analysis was used to animate the character’s visual features such as it’s brightness, color, and mouth movement. The mouth’s movement and color was manipulated with the audio’s pitch. The lights of Wave were controlled by the amplitude of the audio. Design considerations were made to accommodate those with visual disabilities such as color blindness and epilepsy. Overall the final audio visualization satisfied the project sponsor and built upon existing audio visualization work. User feedback will be a necessity for improving the audio visualization in the future.
ContributorsNguyen, Joshep D (Author) / Chavez-Echaegaray, Helen (Thesis director) / Waggoner, Trae (Committee member) / Department of Psychology (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05