Physical Sciences and Mathematics Commons^™

Inference Methods For Token-Level Topic Assignments With Fixed Topics, Stephen Cowley

Theses and Dissertations

Topic modeling, an unsupervised technique used to gain high-level understanding of a large collection of documents, often involves two major goals: The discovery of topics used in the corpus (topic-discovery) and the assignment of topics to individual words (token-level topic assignment). While Latent Dirichlet Allocation (LDA) normally performs both of these steps simultaneously, some situations require only the token-level topic assignments, using fixed topics. We evaluate three topic assignment strategies using fixed topics -- Gibbs sampling, iterated conditional modes, and mean field variational inference -- to determine which should be used when only token-level topic assignment is needed. Among these …

The Fineview Dataset: A 3d Scanned Multi-View Object Dataset Of Fine-Grained Category Instances, Suguru Onda

Theses and Dissertations

In the past decade state-of-the-art deep learning models have shown impressive performance in many computer vision tasks by learning from large and diverse image datasets. Most of these datasets consist of web-scraped image collections. This approach, however, makes it very challenging to obtain desirable data such as multiple views of the same object, 3D geometric information, or camera parameters for a large-scale image dataset. In this paper, we propose a 3D-scanned multi-view 2D image dataset of fine-grained category instances with accurate camera calibration parameters. We describe our bi-directional, multi-camera and 3D scanning system and the data collection pipeline. Our target …

Community Resilience And Creating Capacities For Risk Reduction In First Nations Communities, Case Study In Minegoziibe Anishinabe (Pine Creek First Nation), Brittany S. Lavallee

Capstone Collection

The colonization of Indigenous peoples in Canada has serious consequences on First Nations, including forced removal and displacement from their ancestral lands, environmental degradation, declining resources and capacities, and human rights violations. First Nations communities are currently facing the amplified effects of human-driven climate change. Sustainability of the environment is not just a concept, but a practiced way of life, that recognizes the interdependence of all living things. This deep respect for Aki (earth) is at the foundation of First Nations cultures and continues to guide their actions to insure better futures for Seven Generations. The community of Minegoziibe Anishinabe …

The Magmatic Origin Of The Columbia River Gorge, Usa, Nathaniel Klema, Leif Karlstrom, Charles Cannon, Chengxin Jiang, Jim O'Connor, Ray E. Wells, Brandon Schmandt

Geology Faculty Publications and Presentations

Along subduction zones, high-relief topography is associated with sustained volcanism parallel to the plate margin. However, the relationship between magmatism and mountain building in arcs is poorly understood. Here, we study patterns of surface deformation and correlated fluvial knickpoints in the Columbia River Gorge to link long-term magmatism to the uplift and ensuing topographic development of the Cascade Range. An upwarped paleochannel exposed in the walls of the Gorge constrains unsteady deep magma flux, the ratio of intrusive to extrusive magmatic contributions to topography, and the impact of magmatism on Columbia River incision since 3.5 million years ago. Geophysical data …

Zagamiite, Caal2si3.5o11, The Hexagonal High-Pressure Cas Phase With Dominant Si, As A Mineral From Mars, Chi Ma, Oliver Tschauner, John R. Beckett, Eran Greenberg, Vitali B. Prakapenka

Geoscience Faculty Research

Within the Ca-Al-silicate system, dense, layered hexagonal phases occur at high temperatures and pressures between 20 and 23 GPa. They have been observed both in nature and in experiments. In this study, we describe the endmember with a dominant sixfold coordinated Si as a mineral zagamiite (IMA 2015-022a). This new mineral identified in Martian meteorites has a general formula of (Ca,Na)(Al,Fe,Mg)2(Si,Al,□)4O11, thus defining CaAl2Si3.5O11 as a previously unknown endmember of the hexagonal CAS phases. Zagamiite assumes space group P63/mmc with a unit cell of a = 5.403(2) Å, c = 12.77(3) Å, V = 322.9(11) Å3, and Z = 2. …

Physics I, Kalani Hettiarachchilage

Open Educational Resources

Physics I, class code PHY 116 at College of Staten Island is the first part of a two-semester algebra-based introductory physics course. This course overlaps many topics in the laws of classical mechanics, fluid dynamics, thermodynamics, wave motion, and sound. The important laws of physics in these areas and problem-solving are emphasized. Problem solving is an integral part of the course, all contents are designed to think critically, analytically, and logically. Conceptual understanding is reinforced using interactive computer-based techniques, demonstrations, problem-solving strategies, and laboratory experiences. In this document, all the class materials including lectures, worksheets, homework and group work assignments, …

Creative Physics Syllabus For Online Class, Kalani Hettiarachchilage

Open Educational Resources

Creative Physics syllabus for all information and guidelines will be a big help for students to know about the class structure, expectations, submission, personalized class materials, class ethics, and requirements in one place. This detailed syllabus will be a very effective way of expressing the information to the class. Creating a detailed syllabus and engaging activity of in the learning management system such as syllabus review activity will help students to navigate through important items on the syllabus.

Variables Affecting The Extraction Of Antioxidants In Cold And Hot Brew Coffee: A Review, Brian Yust, Frank Wilkinson, Niny Rao

College of Life Sciences Faculty Papers

Coffee beans are a readily available, abundant source of antioxidants used worldwide. With the increasing interest in and consumption of coffee beverages globally, research into the production, preparation, and chemical profile of coffee has also increased in recent years. A wide range of variables such as roasting temperature, coffee grind size, brewing temperature, and brewing duration can have a significant impact on the extractable antioxidant content of coffee products. While there is no single standard method for measuring all of the antioxidants found in coffee, multiple methods which introduce the coffee product to a target molecule or reagent can be …

The Role Of Colony Morphology And Substratum Inclination On The Distribution Of Eunicella Verrucosa On Shallow Reefs, Luke Thompson

The Plymouth Student Scientist

Eunicella verrucosa plays an important role in shallow reefs, where they produce a complex 'sheet tree' morphology that supports a variety of benthic-dwelling organisms. E. verrucosa is considered 'vulnerable' by the IUCN Red List, which validates the importance of understanding the biotic and abiotic factors influencing the species morphology and survival. This study analyses how horizontal and vertical slope inclinations influence colony morphology. A population of 115 E. verrucosa colonies were observed at Plymouth's inner breakwater fort at 8–13.8m in depth. The influence of inclination on morphology was investigated by observing colony height, encrusting branch diameter and branch complexity for …

A Statistical Analysis Of The Population Of Barbel In The River Teme

The Plymouth Student Scientist

The focus of this project is on the population of barbel (Barbus barbus) living in the River Teme, over a number of years with the objective of examining the fish population size specifically investigating any temporal trend in fish population numbers and, if found, with the further aim of examining any covariates that may be causing the trend. In order to answer these questions, two datasets were investigated and rigorously analysed in order to ascertain whether stocks of barbel are in decline and, if so, to further examine which covariates could be contributing to their depletion. A number of statistical …

Search For Osme Bonds With Π Systems As Electron Donors, Xin Wang, Qingzhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO₄ (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C₂H₂ , C₂H₄ , C₆H₆ , C₄H₅N, C₄H₄O, and C₄H₄S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, …

Interpretable Deep Learning Via Sparse Representation For Protein-Dna Interactions, Shane Kuei-Hsien Chu

McKelvey School of Engineering Graduate Student Theses & Dissertations

A central theme in modeling in regulatory genomics is to consider what representation is suited for DNA sequences that give the most helpful information. Traditionally, there are k-mers, position-weight-matrices, parametric statistical models like Hidden Markov models, and, more recently, deep neural network. In this work, we introduce sparse representations as a principled framework for problems in regulatory genomics. We show that sparse representation is a framework that allows us to build techniques to answer challenging inferential questions in regulatory genomics. Leveraging sparse representations, we reveal that gapped and long motifs are prevalent in in-vivo datasets like ChIP-Seq, often corresponding to …

Culturally Responsive-Sustaining Computational Thinking: Enactment In Elementary Classrooms, Victoria Macann, Aman Yadav

Journal of Computer Science Integration

Technology has increasingly permeated many aspects of everyday life and this evolution raises the need for individuals to understand how the digital world works and what opportunities and risks it brings (Nouri, Zhang, Mannila & Norén, 2019). For this to be an experience for everyone, we need to rethink how we integrate computational thinking (CT) and provide teachers with tools to center their students’ identities, experiences, and cultures in the classroom. In this paper, we present two case studies of primary (elementary) teachers from a full primary (student ages 5–13) semi-rural school in the North Island of New Zealand that …

Cosmic Inflation: Theoretical Exploration And Observational Constraints, Suvedha Suresh Naik

University Departments

No abstract provided.

Computing An Image Of Objects Hiding Behind A Black Hole, Shannon Harding

Honors Program Theses and Projects

Gravitational lensing is the bending of light rays around a black hole. The goal of this project was to produce a computer code that would model light rays coming from a grid of objects set behind a rotating black hole. Using these light rays, we produced an image illustrating how this background of objects would appear to an observer on Earth. This was done by creating a MATLAB code to model the paths of multiple light rays at a time. This code was then used to help check and correct a C++ code that produced an image. Over the semester, …

Difference Of Facial Achromatic Numbers Between Two Triangular Embeddings Of A Graph, Kengo Enami, Yumiko Ohno

Theory & Applications of Graphs

A facial $3$-complete $k$-coloring of a triangulation $G$ on a surface is a vertex $k$-coloring such that every triple of $k$-colors appears on the boundary of some face of $G$. The facial $3$-achromatic number $\psi_3(G)$ of $G$ is the maximum integer $k$ such that $G$ has a facial $3$-complete $k$-coloring. This notion is an expansion of the complete coloring, that is, a proper vertex coloring of a graph such that every pair of colors appears on the ends of some edge.

For two triangulations $G$ and $G'$ on a surface, $\psi_3(G)$ may not be equal to $\psi_3(G')$ even if $G$ …

Cabozantinib Plus Atezolizumab In Previously Untreated Advanced Hepatocellular Carcinoma And Previously Treated Gastric Cancer And Gastroesophageal Junction Adenocarcinoma: Results From Two Expansion Cohorts Of A Multicentre, Open-Label, Phase 1b Trial (Cosmic-021)., Daneng Li, Yohann Loriot, Adam Burgoyne, James Cleary, Armando Santoro, Daniel Lin, Santiago Ponce Aix, Ignacio Garrido-Laguna, Ramu Sudhagoni, Xiang Guo, Svetlana Andrianova, Scott Paulson

Kimmel Cancer Center Faculty Papers

BACKGROUND: Cabozantinib is approved for previously treated advanced hepatocellular carcinoma (aHCC) and has been investigated in gastric cancer (GC) and gastroesophageal junction adenocarcinoma (GEJ). Atezolizumab plus bevacizumab is approved for unresectable or metastatic HCC untreated with prior systemic therapy. We evaluated efficacy and safety of cabozantinib plus atezolizumab in aHCC previously untreated with systemic anticancer therapy or previously treated GC/GEJ.

METHODS: COSMIC-021 (ClinicalTrials.gov, NCT03170960) is an open-label, phase 1b study in solid tumours with a dose-escalation stage followed by tumour-specific expansion cohorts, including aHCC (cohort 14) and GC/GEJ (cohort 15). Eligible patients were aged ≥18 years with measurable locally advanced, …

Cancer Survivorship And Subjective Cognitive Decline In The Us: Results From A Nationally Representative Sample, Monique J. Brown, Ally Hucek, Jingkai Wei, Loretta Anderson, Muzi Na

Faculty Publications

Cancer may be associated with objective cognitive decline. However, studies examining the link between cancer and subjective cognitive decline (SCD), which occurs earlier during cognitive trajectories, are lacking. In addition, research assessing risk factors for SCD among cancer survivors is scant. Therefore, this study aimed to examine the association between cancer and SCD in the past year, and assess the association between age of diagnosis, cancer treatment, and SCD among cancer survivors. Data were obtained from the 2021 Behavioral Risk Factor Surveillance System (N=15,447). Crude and adjusted logistic regression models, controlling for sociodemographic characteristics, were used to determine the association …

2023 December 21 - Tennessee Weekly Drought Summary, Tennessee Climate Office, East Tennessee State University

Tennessee Climate Office Weekly Drought Summaries

No abstract provided.

Long Oligodeoxynucleotides: Chemical Synthesis, Isolation Via Catching-By-Polymerization, Verification Via Sequencing, And Gene Expression Demonstration, Yipeng Yin, Reed Arneson, Alexander Apostle, Adikari M.D.N. Eriyagama, Komal Chillar, Emily Burke, Martina Jahfetson, Yinan Yuan, Shiyue Fang

Michigan Tech Publications

Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex …

Reverse Pseudo-Gours: A New Sub-Type Of Folia Observed In The Nerja Cave (Se Spain), Cristina Liñán Baena, Concepción Jiménez De Cisneros, Yolanda Del Rosal, Paolo Forti

International Journal of Speleology

A new sub-type of folia named “reverse pseudo-gour” has been observed and described in the Nerja Cave, southern Spain. It consists of fairly vertical, thin barriers (about 5 mm high and 2 mm thick) that develop on the underside of a sub-horizontal surface (shelfstone) and grow in the opposite direction to normal gours (rimstone dams), generating sinuous shapes. Their mineral composition is essentially calcium carbonate, although globular aggregates composed of clay and phosphate minerals have also been identified. The genesis and evolution of these reverse pseudo-gours occur just at the air-water interface and are controlled by (1) the sub-horizontality of …

Stereotactic Mr-Guided On-Table Adaptive Radiation Therapy (Smart) For Borderline Resectable And Locally Advanced Pancreatic Cancer: A Multi-Center, Open-Label Phase 2 Study, Michael Chuong, Percy Lee, Daniel Low, Joshua Kim, Kathryn Mittauer, Michael Bassetti, Carri Glide-Hurst, Ann Raldow, Yingli Yang, Lorraine Portelance, Kyle Padgett, Bassem Zaki, Rongxiao Zhang, Hyun Kim, Lauren Henke, Alex Price, Joseph Mancias, Christopher Williams, John Ng, Ryan Pennell, M Raphael Pfeffer, Daphne Levin, Adam Mueller, Karen Mooney, Patrick Kelly, Amish Shah, Luca Boldrini, Lorenzo Placidi, Martin Fuss, Parag Jitendra Parikh

Department of Radiation Oncology Faculty Papers

BACKGROUND AND PURPOSE: Radiation dose escalation may improve local control (LC) and overall survival (OS) in select pancreatic ductal adenocarcinoma (PDAC) patients. We prospectively evaluated the safety and efficacy of ablative stereotactic magnetic resonance (MR)-guided adaptive radiation therapy (SMART) for borderline resectable (BRPC) and locally advanced pancreas cancer (LAPC). The primary endpoint of acute grade ≥ 3 gastrointestinal (GI) toxicity definitely related to SMART was previously published with median follow-up (FU) 8.8 months from SMART. We now present more mature outcomes including OS and late toxicity.

MATERIALS AND METHODS: This prospective, multi-center, single-arm open-label phase 2 trial (NCT03621644) enrolled 136 …

Shock-Wave Tolerant Phase Reconstruction Algorithm For Shack–Hartmann Wavefront Sensor Data, Thomas E. Defoor, Matthew Kalensky, Matthew R. Kemnetz, Timothy J. Bukowski, Mark F. Spencer

Faculty Publications

We develop a phase reconstruction algorithm for the Shack–Hartmann wavefront sensor (SHWFS) that is tolerant to phase discontinuities, such as the ones imposed by shock waves. In practice, this algorithm identifies SHWFS locations where the resultant tilt information is affected by the shock and improves the tilt information in these locations using the local SHWFS observation-plane irradiance patterns. The algorithm was shown to work well over the range of conditions tested with both simulated and experimental data. In turn, the reconstruction algorithm will enable robust wavefront sensing in transonic, supersonic, and hypersonic environments.

The Ricci Curvature On Simplicial Complexes, Taiki Yamada

Theory & Applications of Graphs

We define the Ricci curvature on simplicial complexes modifying the definition of the Ricci curvature on graphs, and prove upper and lower bounds of the Ricci curvature. These properties are generalizations of previous studies. Moreover, we obtain an estimate of the eigenvalues of the Laplacian on simplicial complexes by the Ricci curvature.

Studying The Impact Of The Geospace Environment On Solar Lithosphere Coupling And Earthquake Activity, Dimitar Ouzounov, Galina Khachikyan

Mathematics, Physics, and Computer Science Faculty Articles and Research

In solar–terrestrial physics, there is an open question: does a geomagnetic storm affect earthquakes? We expand research in this direction, analyzing the seismic situation after geomagnetic storms (GMs) accompanied by the precipitation of relativistic electrons from the outer radiation belt to form an additional radiation belt (RB) around lower geomagnetic lines. We consider four widely discussed cases in the literature for long-lived (weeks, months) RBs due to GMs and revealed that the 1/GMs 24 March 1991 with a new RB at L~2.6 was followed by an M7.0 earthquake in Alaska, 30 May 1991, near footprint L = 2.69; the 2/GMs …

Opportunities And Challenges In Monitoring Cultivated Land Red Line In Big Data Era, Jinwei Dong, Yifeng Cui, Yuanyuan Di, Xuan Gao, Xi Chen, Linsheng Yang, Yumei Cai, Jia Ning, Jiyuan Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

The demographic reality of a large population and limited land resources in China necessitates the implementation of the world’s most stringent cultivated land protection system. Effective, timely, and accurate monitoring of the status of cultivated land protection red line is essential to ensuring cultivated land protection and food security. The development of cutting-edge technologies such as remote sensing big data, cloud computing, and artificial intelligence has provided new opportunities for cultivated land control and monitoring. This article systematically elaborates on the current research status and challenges in the field of cultivated land protection redline control and monitoring, including the establishment …

Conception On Asian Elephant Ecological Corridor Planning With Implications For Conservation, Xueyou Li, Qiupeng Yu, Zhechang Hu, Xuelong Jiang

Bulletin of Chinese Academy of Sciences (Chinese Version)

In order to practice the concept of coordinated development of “Lucid Waters and Lush Mountains are Invaluable Assets” and “mountains, rivers, forests, farmlands, lakes, grasslands and deserts are part of the community of life”, this study takes “pursuing green development and promoting harmony between humanity and nature” proposed in the report of the 20th National Congress of the Communist Party of China as the theoretical guidance. With the goal of enhancing ecosystem integrity and connectivity, enhancing population communication, enhancing population viability, and providing a model for the construction of ecological corridors for flagship species, based on the current distribution and …

Effectiveness And Challenges Of Aquatic Ecological Restoration Of Chishui River In Upper Yangtze River, Fei Liu, Huanzhang Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

“To set an example of green development and strength ecological environmental protection in the Chishui River basin” is an important proposal listed in the Outline of the 14th Five-Year Plan (2021--2025) for National Economic and Social Development and Vision 2035 of the People’s Republic of China. Strengthening eco-environmental protection in the Chishui River will play an exemplary and leading role in maintaining fish diversity of the upper Yangtze River, promoting regional high-quality development, and creating a new situation of ecological civilization and Beautiful China. This study interprets the ecological functions of the Chishui River in the upper Yangtze River, expounds …

Market Making In Limit Order Books With Latency And Running Inventory Control, Chang Liu

Arts & Sciences Graduate Student Theses and Dissertations

In this thesis, we delve into the intricate optimization challenges of market making, the concurrent provision of buy and sell prices in financial assets. The focus is particularly on the complexities inherent in high-frequency trading scenarios, addressing optimal market making in the presence of latency and incorporating a running inventory penalty. The initial exploration involves the formulation of a stochastic control model that aptly captures the actions of an electronic market maker navigating a trading environment influenced by latency. The main objective of the market maker lies in the maximization of expected terminal wealth. To systematically address and resolve this …

Prt543, A Protein Arginine Methyltransferase 5 Inhibitor, In Patients With Advanced Adenoid Cystic Carcinoma: An Open-Label, Phase I Dose-Expansion Study, Renata Ferrarotto, Paul Swiecicki, Dan Zandberg, Robert Baiocchi, Robert Wesolowski, Cristina Rodriguez, Meredith Mckean, Hyunseok Kang, Varun Monga, Rajneesh Nath, Neil Palmisiano, Naveen Babbar, William Sun, Glenn Hanna

Department of Medical Oncology Faculty Papers

OBJECTIVES: Currently, no systemic treatments are approved for patients with recurrent and/or metastatic (R/M) adenoid cystic carcinoma (ACC). PRT543, a protein arginine methyltransferase 5 inhibitor that downregulates NOTCH1 and MYB signalling in tumours, is a potential candidate for R/M ACC treatment. We report the safety, tolerability and preliminary efficacy of PRT543 in a dose-expansion cohort of patients with R/M ACC.

MATERIALS AND METHODS: This phase I multicentre, open-label, sequential-cohort, dose-escalation and dose-expansion study (NCT03886831) enrolled patients with advanced solid tumours and select haematologic malignancies. Dose-escalation study design and results were reported previously. In the dose expansion, patients with R/M ACC …