Digital Commons Network^™

Stmut: A Framework For Visualizing Somatic Alterations In Spatial Transcriptomics Data Of Cancer, Limin Chen, Darwin Chang, Bishal Tandukar, Delahny Deivendran, Joanna Pozniak, Noel Cruz-Pacheco, Raymond J Cho, Jeffrey Cheng, Iwei Yeh, Chris Marine, Boris C Bastian, Andrew L Ji, A Hunter Shain

Staff and Researcher Publications

Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.

A Practical Low-Dimensional Feature Vector Generation Method Based On Wavelet Transform For Psychophysiological Signals, Erdem Erkan, Yasemi̇n Erkan

Turkish Journal of Electrical Engineering and Computer Sciences

High-dimensional feature vectors entail computational cost and computational complexity. However, a successful classification can be obtained with an optimally sized feature vector consisting of distinctive features. With the widespread use of the internet and mobile devices, the need for systems with low computational costs is increasing day by day. In this study, starting from the idea that each motor imagery is represented as a subject-specific pattern in the brain, we propose a new and practical method that can generate a low-dimensional feature vector based on wavelet transform. The feature vector is obtained from the correlation between each trial and each …

Machine Learning Based Bioinformatics Analysis Of Intron Usage Alterations And Metabolic Regulation In Adipose Browning, Hamza Umut Karakurt, Pinar Pi̇r

Turkish Journal of Electrical Engineering and Computer Sciences

Adipose tissue is the major energy depot of the body and is considered an endocrine organ. Adipose tissue involves many different cell types, first and foremost, the adipocytes. White adipose cells that store fat and brown adipocytes that take part in lipid oxidation and heat generation are the most common cell types in adipose tissue. Even though brown adipocytes which have a high number of mitochondria and high fat-burning capacity are rare in adults, they are abundant in newborns and rodents. White adipocytes can gain a temporal brown-like character with a process called browning, which can be induced with cold …

Camkk2 And Chk1 Phosphorylate Human Stn1 In Response To Replication Stress To Protect Stalled Forks From Aberrant Resection, Rishi Kumar Jaiswal, Kai-Hang Lei, Megan Chastain, Yuan Wang, Olga Shiva, Shan Li, Zhongsheng You, Peter Chi, Weihang Chai

2020-Current year OA Pubs

Keeping replication fork stable is essential for safeguarding genome integrity; hence, its protection is highly regulated. The CTC1-STN1-TEN1 (CST) complex protects stalled forks from aberrant MRE11-mediated nascent strand DNA degradation (NSD). However, the activation mechanism for CST at forks is unknown. Here, we report that STN1 is phosphorylated in its intrinsic disordered region. Loss of STN1 phosphorylation reduces the replication stress-induced STN1 localization to stalled forks, elevates NSD, increases MRE11 access to stalled forks, and decreases RAD51 localization at forks, leading to increased genome instability under perturbed DNA replication condition. STN1 is phosphorylated by both the ATR-CHK1 and the calcium-sensing …

Racial Disparities Among Predicted Bronchopulmonary Dysplasia Risk Outcomes In Premature Infants Born <30 Weeks Gestation, Priyanka Patel, Andrew Ellefson, David A. Paul

Department of Pediatrics Faculty Papers

Background and Objective: There is extensive literature to support eliminating race-based risk stratification. The National Institute of Child Health and Human Development (NICHD) calculator, used to predict risk of bronchopulmonary dysplasia (BPD), includes race as a variable. We sought to investigate how utilizing race in determination of risk for BPD may lead to inequitable care.

Methods: The study included a retrospective cohort of infants born <30 weeks gestation between January 2016 and February 2022. The primary outcome was the difference in predictive risk of BPD for non-Hispanic Black compared to non-Hispanic White infants. The secondary outcome was the disparity in theoretical administration of post-natal corticosteroids when the calculator was applied to the cohort. Analysis included paired T-tests and Chi-Square.

Results: Of the 273 infants studied, 154 were non-Hispanic Black (56%). There was no difference between the groups in gestation or respiratory support on day of life (DOL) 14 or 28. …

World War Two Propaganda: Analyzing And Comparing German And American Strategies, Chandler Schubert '24

Senior Scholarly and Creative Symposium

No abstract provided.

Trees In Our City How A Tree And A Small Patch Of Dirt Inspired A Classroom, Zuleika Hines

Occasional Paper Series

As a new Director in a new school, I knew that I wanted the children to have a curiosity for nature. But to lead the children to a place of discovery, they would need the opportunity to observe, play, and engage in elements of nature that would support hands-on activities both in the classroom and outside. When the opportunity came for me to build my own early childhood program, I knew that I had a unique opportunity to incorporate elements of nature in the design of the classroom. But I wanted nature to be local and the trees of our …

Singing In Dark Times: Improvisational Singing With Children Amidst Ecological Crisis, Stephanie Schuurman-Olson

Occasional Paper Series

Through this research-creation project -- which is represented by a process-driven ten-minute video -- the author asks what ways of knowing emerge when children and adults, more-than-human, and inhuman engage in improvised singing together in an urban park? This project recognizes our current "dark times" within ecological collapse and operates from a space that hopes to build relationality with sonic ecologies through listening-and-singing experiences, while centering the voices of children and other singers within the ecologies we sing in-and-with.

Connecting Children And Young People With Trees, Gill Forrester, Jo Maker, Will Price, Hollie Davison, Heather Gilbert

Occasional Paper Series

Engaging children and young people with the natural world has never been more important. The benefits of outdoor learning span from increased nature connection to improved self-esteem and physical wellbeing. But with so many potential risks and barriers, how can we help practitioners feel confident and capable in an outdoor setting and therefore improve access to green space for children and young people? The education team at the National Forest Company set out to tackle this challenge. The National Forest was established in the early 1990s in a post-industrial area of the English Midlands. It covers 200 square miles and …

Thermo-Kinetic Parameters Governing Decomposition Of Amino Acids: A Computational Study, Mubarak Taleb Alkwradi

Thesis/ Dissertation Defenses

Amino acid model compounds are important nitrogenated species that in various categories of biomass. These compounds exhibit unique fragmentation pathways because of their adjacent amino and hydroxyl groups. Comprehending the decomposition chemistry of amino acids is essential to reduce harmful nitrogen emissions during biomass thermal treatment. This research reports the kinetic and thermodynamic properties of amino acids, and sulfur-containing amino acid, based on accurate density functional theory calculations coupled with kinetic modelling. The first part of the thesis provides comprehensive thermochemical parameters for the complete set of amino acids in the gas phase. The optimized geometries of amino acid compounds …

Towards Strengthening Methods In Design Education And Practice, Jorge Frascara, Paul Gardien, Guillermina Noël, Daniel Rosenberg, Pieter Jan Stappers, Danielle Wilde

Learn X Design Conference Series

No abstract provided.

Neurodesign: A Game-Changer In Educational Contexts, Mario Ivan Zignego, Alessandro Bertirotti, Paolo Andrea Gemelli, Laura Pagani

Learn X Design Conference Series

No abstract provided.

The Flipped Design Classroom: Effectiveness Of Online Lectures, Katja Fleischmann

Learn X Design Conference Series

No abstract provided.

Digital Teaching For Classes In Studios, Practice Rooms, And Labs, Dagmar Steffen

Learn X Design Conference Series

No abstract provided.

Advanced Design Thinking (Adt): A Pathway To Deschooling Design, Ricardo Sosa, Andrew Gibbons, Amabel Hunting

Learn X Design Conference Series

No abstract provided.

From Consumer Capitalism To Wellbeing: Re-Imagining Futures Of Design Education In The View Of Pluriverse, Karina Vissonova, Michael Hohl

Learn X Design Conference Series

No abstract provided.

A Critical Inquiry On Design Cognition And Generative Systems, Aysel Merve Topaloglu

Learn X Design Conference Series

No abstract provided.

Teaching Practices On More-Than-Human Perspectives In Hci Education – Current State And Future Paths, Eva Eriksson, Elisabet M. Nilsson, Tilde Bekker, Daisy Yoo

Learn X Design Conference Series

In times of climate emergency and artificial intelligence affecting everything in life, we must reconsider the way we teach our students how to become responsible designers of future technologies. In recent years we have seen a rise in interest in more-than-human perspectives in human-computer interaction (HCI), where more-than-human things, species, and designers move the field beyond traditional human-centred approaches. In this paper, we set out to explore how this new approach is taught, what we can learn from it, and what challenges remain. The contribution of this paper is an overview of a selection of more-than-human teaching practices and curriculum …

Blood, Sweat And Tears: A Design Education Research Publication Story, Naz Börekçi

Learn X Design Conference Series

No abstract provided.

Teaching Design Ethics Through Tabletop Game Prototyping, Dimitrios Gkouskos, Andrea Resmini, Charlotte Shahlaei, Jonathan Burgos

Learn X Design Conference Series

No abstract provided.

The Decision, Victor Udoewa

Learn X Design Conference Series

No abstract provided.

Unfixing The Studio, James Corazzo, Derek Jones, Frazer Hudson

Learn X Design Conference Series

No abstract provided.

Design From Waste Materials: Situation, Problem, And Solution, Luke Feast, Linda Nhu Laursen

Learn X Design Conference Series

No abstract provided.

Review Of "The North Star: Canada And The Civil War Plots Against Lincoln" By Julian Sher, Tim Cook

Canadian Military History

Review of The North Star: Canada and the Civil War Plots against Lincoln by Julian Sher

Controlled Radiation Capsule For Precision And Rapid Cancer Treatment, Hoseon Lee, Zsolt Kollar, Bailey R. White, Junia Nguyen, David Roque, Sowjanya Palagani

Symposium of Student Scholars

This research aims to transform cancer treatment through the optimization of brachytherapy, with a focus on reducing treatment duration, setup complexities, and financial burdens, all while emphasizing patient safety. Patients living at a distance from radiation clinics, particularly those undergoing extended Low Dose Radiation brachytherapy, often struggle with the formidable financial challenges associated with securing nearby accommodations. In response to these issues, the research introduces a radiation capsule designed to condense the conventional six-month treatment period to approximately just one week, thereby significantly reducing the duration of required accommodations. This capsule is especially relevant considering the construction cost of $40 …

Quantifying The Role Of Water Quality On Nitrogen Cycling In A Trophic Estuary, Kayla Gonzalez-Boy

Symposium of Student Scholars

Jobos Bay Estuary is an intertidal, tropical estuary located in southern Puerto Rico. The estuary covers about 12 km² and has a variety of habitats, such as seagrass beds, mangroves, mud flats, and coral reefs, which play important roles in sediment trapping and water quality maintenance. Seagrasses also serve as nursery and feeding grounds and provide shelter for macrofauna. Currently, the role of seagrasses and water quality on nitrogen (N) cycling in trophic estuaries is not well constrained. Understanding variations in sediment-based effects on N cycling rates and transformations, and how they are associated with water quality, is an …

Culled Lionfish Sexual Maturity Over A Four-Year Timespan​, Christina Bland, Jurgen Hauer, Bilal Saleem, Noelle James

Symposium of Student Scholars

Lionfish are invasive in the Atlantic and the Caribbean. Like many other invasive species, they do not have any natural predators in these areas, so their population can grow unchecked. This can decrease the population of native fish species due to lionfish eating to excess. Because of their impact on native species, resource managers have incentivized lionfish hunting. Hunters were paid $6 USD for every pound of lionfish they brought in, so they possibly favored larger lionfish to increase their reward which would lead to an adaptive advantage for fish of smaller sizes. We hypothesized that the lionfish bounty program …

Spartan Daily, November 29, 2023, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2023

Volume 161, Issue 41

The Family History Of Josiah Noga, Josiah Noga

Your Family in History: HIST 550/700

Josiah Elijah Noga authored this family history as part of the course requirements for HIST 550/700 Your Family in History offered online in Fall 2023 and was submitted to the Pittsburg State University Digital Commons. Please contact the author directly with any questions or comments: [email protected]

The Neuronal Calcium Sensor Ncs-1 Regulates The Phosphorylation State And Activity Of The Gα Chaperone And Gef Ric-8a, Daniel Muñoz-Reyes, Levi J. Mcclelland, Sandra Arroyo-Urea, Sonia Sánchez-Yepes, Juan Sabín, Sara Pérez-Suárez, Margarita Menendez, Alicia Mansilla, Javier García-Nafría, Stephen Sprang, Maria Jose Sanchez-Barrena

Biological Sciences Faculty Publications

The neuronal calcium sensor 1 (NCS-1), an EF-hand Ca binding protein, and Ric-8A coregulate synapse number and probability of neurotransmitter release. Recently, the structures of Ric-8A bound to Gα have revealed how Ric-8A phosphorylation promotes Gα recognition and activity as a chaperone and guanine nucleotide exchange factor. However, the molecular mechanism by which NCS-1 regulates Ric-8A activity and its interaction with Gα subunits is not well understood. Given the interest in the NCS-1/Ric-8A complex as a therapeutic target in nervous system disorders, it is necessary to shed light on this molecular mechanism of action at atomic level. We have reconstituted …