78,440 results on '"Dougherty BE"'
Search Results
2. An Empirical Analysis of Speech Self-Supervised Learning at Multiple Resolutions
- Author
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Clark, Theo, Cevoli, Benedetta, de Jong, Eloy, Abramski, Timofey, and Dougherty, Jamie
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Electrical Engineering and Systems Science - Audio and Speech Processing ,Computer Science - Machine Learning ,I.2.0 - Abstract
Self-supervised learning (SSL) models have become crucial in speech processing, with recent advancements concentrating on developing architectures that capture representations across multiple timescales. The primary goal of these multi-scale architectures is to exploit the hierarchical nature of speech, where lower-resolution components aim to capture representations that align with increasingly abstract concepts (e.g., from phones to words to sentences). Although multi-scale approaches have demonstrated some improvements over single-scale models, the precise reasons for these enhancements have poor empirical support. In this study, we present an initial analysis of layer-wise representations in multi-scale architectures, with a focus on Canonical Correlation Analysis (CCA) and Mutual Information (MI). We apply this analysis to Multi-Resolution HuBERT (MR-HuBERT) and find that (1) the improved performance on SUPERB tasks is primarily due to the auxiliary low-resolution loss rather than the downsampling itself, and (2) downsampling to lower resolutions neither improves downstream performance nor correlates with higher-level information (e.g., words), though it does improve computational efficiency. These findings challenge assumptions about the multi-scale nature of MR-HuBERT and motivate the importance of disentangling computational efficiency from learning better representations.
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- 2024
3. The (Symbolic and Numeric) Computational Challenges of Counting 0-1 Balanced Matrices
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Dougherty-Bliss, Robert, Koutschan, Christoph, Ter-Saakov, Natalya, and Zeilberger, Doron
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Mathematics - Combinatorics ,05A05 - Abstract
A chessboard has the property that every row and every column has as many white squares as black squares. In this mostly methodological note, we address the problem of counting such rectangular arrays with a fixed (numeric) number of rows, but an arbitrary (symbolic) number of columns. We first address the ``vanilla" problem where there are no restrictions, and then go on to discuss the still-more-challenging problem of counting such binary arrays that are not permitted to contain a specified (finite) set of horizontal patterns, and a specified set of vertical patterns. While we can rigorously prove that each such sequence satisfies some linear recurrence equation with polynomial coefficients, actually finding these recurrences poses major {\it symbolic}-computational challenges, that we can only meet in some small cases. In fact, just generating as many as possible terms of these sequences is a big {\it numeric}-computational challenge. This was tackled by computer whiz Ron H. Hardin, who contributed several such sequences, and computed quite a few terms of each. We extend Hardin's sequences quite considerably. We also talk about the much easier problem of counting such restricted arrays without balance conditions.
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- 2024
4. Geometric Combinatorics of Polynomials II: Polynomials and Cell Structures
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Dougherty, Michael and McCammond, Jon
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Mathematics - Geometric Topology ,Mathematics - Combinatorics ,Mathematics - Complex Variables ,Mathematics - Group Theory - Abstract
This article introduces a finite piecewise Euclidean cell complex homeomorphic to the space of monic centered complex polynomials of degree $d$ whose critical values lie in a fixed closed rectangular region. We call this the branched rectangle complex since its points are indexed by marked $d$-sheeted planar branched covers of the fixed rectangle. The vertices of the cell structure are indexed by the combinatorial "basketballs" studied by Martin, Savitt and Singer. Structurally, the branched rectangle complex is a full subcomplex of a direct product of two copies of the order complex of the noncrossing partition lattice. Topologically, it is homeomorphic to the closed $2n$-dimensional ball where $n=d-1$. Metrically, the simplices in each factor are orthoschemes. It can also be viewed as a compactification of the space of all monic centered complex polynomials of degree $d$. We also introduce a finite piecewise Euclidean cell complex homeomorphic to the space of monic centered complex polynomials of degree $d$ whose critical values lie in a fixed closed annular region. We call this the branched annulus complex since its points are indexed by marked $d$-sheeted planar branched covers of the fixed annulus.It can be constructed from the branched rectangle complex as a cellular quotient by isometric face identifications. And it can be viewed as a compactification of the space of all monic centered complex polynomials of degree $d$ with distinct roots. Finally, the branched annulus complex deformation retracts to the branched circle complex, which we identify with the dual braid complex. Our explicit embedding of the dual braid complex as a spine for the space of polynomials with distinct roots provides a direct proof that these two classifying spaces for the braid group are homotopy equivalent., Comment: 82 pages, 36 figures
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- 2024
5. Scaffolding Research Projects in Theory of Computing Courses
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Dougherty, Ryan E.
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Computer Science - Computers and Society - Abstract
Theory of Computing (ToC) is an important course in CS curricula because of its connections to other CS courses as a foundation for them. Traditional ToC course grading schemes are mostly exam-based, and sometimes a small weight for traditional proof-type assignments. Recent work experimented with a new type of assignment, namely a ``mock conference'' project wherein students approach and present ToC problems as if they were submitting to a ``real'' CS conference. In this paper we massively scaffold this existing project and provide our experiences in running such a conference in our own ToC course.
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- 2024
6. Midpoint Reading: Collaborative Student Annotation in the Humanities Classroom
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Daniel Dougherty
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In the era of remote learning courses, the humanities instructor struggled more than most to translate the many familiar techniques of close reading to the unfamiliar realm of technology. Oftentimes instructors have depended on facsimiles of traditional methods: a shared passage annotated by the class digitally, or small groups sent to individual breakout rooms which will eventually rejoin the class and share their findings. This article offers a methodology which incorporates the beneficial technologies which were necessary in remote classrooms into the traditional classroom, encouraging students to collaborate and debate through the shared digital annotation of primary texts.
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- 2024
7. Extension Efforts to Address the Current National Housing Crisis
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Michael J. Dougherty, Melissa B. Hamilton, and Bradley Neumann
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Housing is a basic need. The National Association of Community Development Extension Professionals (NACDEP), Land Use Planning Community of Practice held a virtual forum in December 2021 on the national housing crisis. The session revealed common challenges communities face when addressing these issues locally. As a follow-up to that session, this paper summarizes Extension perspectives on community housing issues discussed during the session, reviews the literature on Extension programs related to housing, and makes the case for a national peer learning and communications network to address these difficult and urgent community housing challenges.
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- 2024
8. Graphic Novels as the Forger's Tool for Literacy
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Cailyn N. Dougherty and Cori Robinson Gregg
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Exploring the realm of literacy involves understanding how graphic novels shape students' reading and writing journeys. Through scholarly research, the authors delve into the significant impact of graphic novels on education while highlighting their appeal to students through visual features and engaging storytelling. Included is a discussion of lesson planning using eighth-grade English Language Arts and Reading (ELAR) Texas Essential Knowledge and Skills (TEKS) focused on exploring the role setting has on a character's motivations, values, and beliefs through the graphic novel "When Stars Are Scattered" by Victoria Jamieson and Omar Mohamed. This approach empowers students to become proficient readers and writers in today's visual society.
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- 2024
9. Finite State Machine with Input and Process Render
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Bennett-Manke, Sierra Zoe, Neumann, Sebastian, and Dougherty, Ryan E.
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Computer Science - Computers and Society - Abstract
Finite State Machines are a concept widely taught in undergraduate theory of computing courses. Educators typically use tools with static representations of FSMs to help students visualize these objects and processes; however, all existing tools require manual editing by the instructor. In this poster, we created an automatic visualization tool for FSMs that generates videos of FSM simulation, named Finite State Machine with Input and Process Render (FSMIPR). Educators can input any formal definition of an FSM and an input string, and FSMIPR generates an accompanying video of its simulation. We believe that FSMIPR will be beneficial to students who learn difficult computer theory concepts. We conclude with future work currently in-progress with FSMIPR., Comment: Accepted to SIGCSE Virtual 2024
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- 2024
10. The Comma Sequence is Finite in Other Bases
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Dougherty-Bliss, Robert and Ter-Saakov, Natalya
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Mathematics - Number Theory ,Mathematics - Combinatorics ,11B37, 11B75 - Abstract
The comma sequence (1, 12, 35, 94, ...) is the lexicographically earliest sequence such that the difference of consecutive terms equals the concatenation of the digits on either side of the comma separating them. The behavior of a "generalized comma sequence" depends on the base the numbers are written in, as well as the sequence's initial values. We provide a computational proof that all comma sequences in bases 3 through 633 are finite. Relying on a combinatorial conjecture, Angelini et al. estimated that the final element of a comma sequence in base b should be roughly exp(O(b)). We prove their conjecture, but provide evidence that the correct estimate is actually exp(O(b log b))., Comment: This version handles much larger bases by using a superior cycle-detection algorithm suggested by Luke Pebody
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- 2024
11. Can ChatGPT Pass a Theory of Computing Course?
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Golesteanu, Matei A., Vowinkel, Garrett B., and Dougherty, Ryan E.
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Computer Science - Computers and Society - Abstract
Large Language Models (LLMs) have had considerable difficulty when prompted with mathematical questions, especially those within theory of computing (ToC) courses. In this paper, we detail two experiments regarding our own ToC course and the ChatGPT LLM. For the first, we evaluated ChatGPT's ability to pass our own ToC course's exams. For the second, we created a database of sample ToC questions and responses to accommodate other ToC offerings' choices for topics and structure. We scored each of ChatGPT's outputs on these questions. Overall, we determined that ChatGPT can pass our ToC course, and is adequate at understanding common formal definitions and answering "simple"-style questions, e.g., true/false and multiple choice. However, ChatGPT often makes nonsensical claims in open-ended responses, such as proofs., Comment: Accepted to SIGCSE Virtual 2024
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- 2024
12. Cholesterol-dependent LXR transcription factor activity represses pronociceptive effects of estrogen in sensory neurons and pain induced by myelin basic protein fragments.
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Hullugundi, Swathi, Dolkas, Jennifer, Chernov, Andrei, Yaksh, Tony, Eddinger, Kelly, Angert, Mila, Catroli, Glaucilene, Strongin, Alex, Dougherty, Patrick, Li, Yan, Quehenberger, Oswal, Armando, Aaron, and Shubayev, Veronica
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Cholesterol ,DRG culture ,Estrogen ,Interleukin 6 ,LXR ,Liver x receptor ,Myelin basic protein ,Neuropathic pain ,Oxysterol ,Sensory neuron - Abstract
BACKGROUND: A bioactive myelin basic protein (MBP) fragment, comprising MBP84-104, is released in sciatic nerve after chronic constriction injury (CCI). Intraneural injection (IN) of MBP84-104 in an intact sciatic nerve is sufficient to induce persistent neuropathic pain-like behavior via robust transcriptional remodeling at the injection site and ipsilateral dorsal root ganglia (DRG) and spinal cord. The sex (female)-specific pronociceptive activity of MBP84-104 associates with sex-specific changes in cholesterol metabolism and activation of estrogen receptor (ESR)1 signaling. METHODS: In male and female normal and post-CCI rat sciatic nerves, we assessed: (i) cholesterol precursor and metabolite levels by lipidomics; (ii) MBP84-104 interactors by mass spectrometry of MBP84-104 pull-down; and (iii) liver X receptor (LXR)α protein expression by immunoblotting. To test the effect of LXRα stimulation on IN MBP84-104-induced mechanical hypersensitivity, the LXRα expression was confirmed along the segmental neuraxis, in DRG and spinal cord, followed by von Frey testing of the effect of intrathecally administered synthetic LXR agonist, GW3965. In cultured male and female rat DRGs exposed to MBP84-104 and/or estrogen treatments, transcriptional effect of LXR stimulation by GW3965 was assessed on downstream cholesterol transporter Abc, interleukin (IL)-6, and pronociceptive Cacna2d1 gene expression. RESULTS: CCI regulated LXRα ligand and receptor levels in nerves of both sexes, with cholesterol precursors, desmosterol and 7-DHC, and oxysterol elevated in females relative to males. MBP84-104 interacted with nuclear receptor coactivator (Ncoa)1, known to activate LXRα, injury-specific in nerves of both sexes. LXR stimulation suppressed ESR1-induced IL-6 and Cacna2d1 expression in cultured DRGs of both sexes and attenuated MBP84-104-induced pain in females. CONCLUSION: The injury-released bioactive MBP fragments induce pronociceptive changes by selective inactivation of nuclear transcription factors, including LXRα. By Ncoa1 sequestration, bioactive MBP fragments render LXRα function to counteract pronociceptive activity of estrogen/ESR1 in sensory neurons. This effect of MBP fragments is prevalent in females due to high circulating estrogen levels in females relative to males. Restoring LXR activity presents a promising therapeutic strategy in management of neuropathic pain induced by bioactive MBP.
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- 2024
13. Mapping Interfacial Energetic Landscape in Organic Solar Cells Reveals Pathways to Reducing Nonradiative Losses
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Thapa, Gaurab J., Chauhan, Mihirsinh, Mauthe, Jacob P., Dougherty, Daniel B., and Amassian, Aram
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Condensed Matter - Materials Science ,Condensed Matter - Soft Condensed Matter - Abstract
Bulk heterojunction (BHJ) organic solar cells have made remarkable inroads towards 20% efficiency, yet nonradiative recombination losses ({\Delta}Vnr) remain high compared to silicon and perovskite photovoltaics. Interfaces buried within BHJ blends hold the key to recombination losses but access to their energetic landscape underpinning charge transfer (CT) states and their disorder remain elusive. Here, we reveal the energetic landscape and CT state manifold of modern BHJs with both spatial and energetic resolutions and link the offset between singlet (ES1) and CT energy (ES1-CT) and interfacial energetic disorder with {\Delta}Vnr. We do so by locally mapping the energy distributions of modern PM6-based BHJs with IT4F, Y6 and PC71BM acceptors and combine it, for the first time, with sensitive EQE measurements, to visualize and quantify donor (D) and acceptor (A) energetics at interfaces and associated them with CT states within a modified Marcus framework. A key new ability is the identification of the specific BHJ interfaces associated with the CT manifold, including where the lowest energy CT states reside. Moreover, we quantify energy levels and electronic disorders directly at these and other interfaces and connect these contributions to the energy losses. We delineate the influences of S1-CT offset and interfacial energetic disorder on {\Delta}Vnr across morphologically varied BHJs. Our results show both factors influencing energy losses in different ways. We demonstrate that PM6:Y6 can achieve low {\Delta}Vnr by forming a nominally sharp D/A interface with exceptionally low interfacial disorder via judicious processing combined with a low S1 to CT offset. This provides a design rule to minimize {\Delta}Vnr for modern NFAs: sharp D/A interfaces with low S1 to CT offset exhibiting minimal interfacial disorder., Comment: Manuscript: 30 pages, 4 figures, 2 tables Supplementary information: 41 pages, 24 figures, 7 tables
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- 2024
14. Quantum optimization using a 127-qubit gate-model IBM quantum computer can outperform quantum annealers for nontrivial binary optimization problems
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Sachdeva, Natasha, Hartnett, Gavin S., Maity, Smarak, Marsh, Samuel, Wang, Yulun, Winick, Adam, Dougherty, Ryan, Canuto, Daniel, Chong, You Quan, Hush, Michael, Mundada, Pranav S., Bentley, Christopher D. B., Biercuk, Michael J., and Baum, Yuval
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Quantum Physics - Abstract
We introduce a comprehensive quantum solver for binary combinatorial optimization problems on gate-model quantum computers that outperforms any published alternative and consistently delivers correct solutions for problems with up to 127 qubits. We provide an overview of the internal workflow, describing the integration of a customized ansatz and variational parameter update strategy, efficient error suppression in hardware execution, and QPU-overhead-free post-processing to correct for bit-flip errors. We benchmark this solver on IBM quantum computers for several classically nontrivial unconstrained binary optimization problems -- the entire optimization is conducted on hardware with no use of classical simulation or prior knowledge of the solution. First, we demonstrate the ability to correctly solve Max-Cut instances for random regular graphs with a variety of densities using up to 120 qubits, where the graph topologies are not matched to device connectivity. Next, we apply the solver to higher-order binary optimization and successfully search for the ground state energy of a 127-qubit spin-glass model with linear, quadratic, and cubic interaction terms. Use of this new quantum solver increases the likelihood of finding the minimum energy by up to $\sim1,500\times$ relative to published results using a DWave annealer, and it can find the correct solution when the annealer fails. Furthermore, for both problem types, the Q-CTRL solver outperforms a heuristic local solver used to indicate the relative difficulty of the problems pursued. Overall, these results represent the largest quantum optimizations successfully solved on hardware to date, and demonstrate the first time a gate-model quantum computer has been able to outperform an annealer for a class of binary optimization problems., Comment: 19 pages, 8 figures
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- 2024
15. Ligand Field Exciton Annihilation in Bulk CrCl3
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Sridhar, Samanvitha, Khansari, Ario, O'Donnell, Shaun, Barth, Alexandra T., Danilov, Evgeny O., Castellano, Felix N., Maggard, Paul A., and Dougherty, Daniel B.
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Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
The layered van der Waals material CrCl3 exhibits very strongly bound ligand field excitons that control optoelectronic applications and are connected with magnetic ordering by virtue of their d-orbital origin. Time-resolved photoluminescence of these exciton populations at room temperature shows that their relaxation is dominated by exciton-exciton annihilation and that the spontaneous decay lifetime is very long. These observations allow the rough quantification of the exciton annihilation rate constant and contextualization in light of a recent theory of universal scaling behavior of the annihilation process.
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- 2024
16. Clio: Real-time Task-Driven Open-Set 3D Scene Graphs
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Maggio, Dominic, Chang, Yun, Hughes, Nathan, Trang, Matthew, Griffith, Dan, Dougherty, Carlyn, Cristofalo, Eric, Schmid, Lukas, and Carlone, Luca
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Computer Science - Robotics - Abstract
Modern tools for class-agnostic image segmentation (e.g., SegmentAnything) and open-set semantic understanding (e.g., CLIP) provide unprecedented opportunities for robot perception and mapping. While traditional closed-set metric-semantic maps were restricted to tens or hundreds of semantic classes, we can now build maps with a plethora of objects and countless semantic variations. This leaves us with a fundamental question: what is the right granularity for the objects (and, more generally, for the semantic concepts) the robot has to include in its map representation? While related work implicitly chooses a level of granularity by tuning thresholds for object detection, we argue that such a choice is intrinsically task-dependent. The first contribution of this paper is to propose a task-driven 3D scene understanding problem, where the robot is given a list of tasks in natural language and has to select the granularity and the subset of objects and scene structure to retain in its map that is sufficient to complete the tasks. We show that this problem can be naturally formulated using the Information Bottleneck (IB), an established information-theoretic framework. The second contribution is an algorithm for task-driven 3D scene understanding based on an Agglomerative IB approach, that is able to cluster 3D primitives in the environment into task-relevant objects and regions and executes incrementally. The third contribution is to integrate our task-driven clustering algorithm into a real-time pipeline, named Clio, that constructs a hierarchical 3D scene graph of the environment online using only onboard compute, as the robot explores it. Our final contribution is an extensive experimental campaign showing that Clio not only allows real-time construction of compact open-set 3D scene graphs, but also improves the accuracy of task execution by limiting the map to relevant semantic concepts.
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- 2024
17. Wasserstein Wormhole: Scalable Optimal Transport Distance with Transformers
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Haviv, Doron, Kunes, Russell Zhang, Dougherty, Thomas, Burdziak, Cassandra, Nawy, Tal, Gilbert, Anna, and Pe'er, Dana
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Computer Science - Machine Learning ,Computer Science - Computational Geometry ,Quantitative Biology - Genomics - Abstract
Optimal transport (OT) and the related Wasserstein metric (W) are powerful and ubiquitous tools for comparing distributions. However, computing pairwise Wasserstein distances rapidly becomes intractable as cohort size grows. An attractive alternative would be to find an embedding space in which pairwise Euclidean distances map to OT distances, akin to standard multidimensional scaling (MDS). We present Wasserstein Wormhole, a transformer-based autoencoder that embeds empirical distributions into a latent space wherein Euclidean distances approximate OT distances. Extending MDS theory, we show that our objective function implies a bound on the error incurred when embedding non-Euclidean distances. Empirically, distances between Wormhole embeddings closely match Wasserstein distances, enabling linear time computation of OT distances. Along with an encoder that maps distributions to embeddings, Wasserstein Wormhole includes a decoder that maps embeddings back to distributions, allowing for operations in the embedding space to generalize to OT spaces, such as Wasserstein barycenter estimation and OT interpolation. By lending scalability and interpretability to OT approaches, Wasserstein Wormhole unlocks new avenues for data analysis in the fields of computational geometry and single-cell biology., Comment: Published at the Forty-first International Conference on Machine Learning (ICML2024)
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- 2024
18. Creating Decidable Diophantine Equations
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Dougherty-Bliss, Robert, Kenney, Charles, and Zeilberger, Doron
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Mathematics - Number Theory ,11D72 - Abstract
Generalizing an argument of Matiyasevich, we illustrate a method to generate infinitely many diophantine equations whose solutions can be completely described by linear recurrences. In particular, we provide an integer-coefficient polynomial $p(x, y, z)$ whose only integer roots are consecutive triples of Tribonacci numbers., Comment: This version corrects a misstated date
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- 2024
19. Climate-Related Displacement and U.S. Refugee Protection
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Neusner, Julia, Cremins, David, Dougherty, Ana Cutts, Freeman, Kelsey, Lebel, Rosie, Diaz, Milena, and Chavez, Nicole
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Government regulation ,Forced migration -- Environmental aspects -- Laws, regulations and rules ,Immigration policy -- Environmental aspects -- Evaluation ,Asylum, Right of -- Laws, regulations and rules ,Political persecution -- Laws, regulations and rules ,Refoulement -- Laws, regulations and rules ,Climatic changes -- Laws, regulations and rules ,Environmental refugees -- Laws, regulations and rules ,United Nations Convention Relating to the Status of Refugees ,Immigration and Nationality Act of 1952 (8 U.S.C. 1101(a)(42)) ,Refugee Act of 1980 - Abstract
In an era defined by climate crises and mounting barriers to cross-border movement, this Article examines the intricate relationships between climate change, displacement, and refugee protection in the United States. Through a comprehensive analysis, incorporating insights from interviews with asylum seekers from Mexico and Central America at the U.S.-Mexico border, we present case examples that highlight the convergence of climate change impacts with other drivers of displacement. Our assessment reveals how some individuals affected by climate-related displacement may qualify for refugee protection when climate change impacts intersect with and exacerbate persecution based on protected grounds under U.S. law. Nevertheless, the significant protection gaps for climate-displaced people underscore the urgent need for the development of additional protection pathways as climate change impacts increasingly drive movement across borders., TABLE OF CONTENTS I. INTRODUCTION 178 II. METHODOLOGY 186 III. FINDINGS: DOCUMENTING CLIMATE HARMS ON THE GROUND 187 A. Climate change exacerbates economic harms to affected 187 communities B. Climate [...]
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- 2024
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20. Rural Early Childhood Programs & School Readiness: An Evaluation of the Early Steps to School Success Program. EdWorkingPaper No. 23-842
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Annenberg Institute for School Reform at Brown University, Shaun M. Dougherty, Mary M. Smith, and Beth Kelly
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Prior research has clearly established the substantial expected payoffs to investments in early childhood education. However, the ability to deliver early childhood programs differs across communities with access to high quality programing especially hard to establish in rural communities. We study one program, Early Steps to School Success, to understand whether the provision of home visiting and book exchange programs in rural Kentucky can influence kindergarten readiness. Linking program data with the state longitudinal data system in Kentucky we create multiple comparison groups by matching children on known program qualification indicators to estimate whether Early Steps program participation was related to school readiness. Our estimates suggest that program participation resulted in small improvements to children's kindergarten readiness, as measured by the Brigance kindergarten readiness assessment overall score and sub-scores in language, cognitive, and physical development. Results are not sensitive to our choice of comparison group, though they appear driven by the experiences of children who participate from birth through age five or from ages three-to-five only. Our findings suggest that the Early Steps home visiting intervention may be a worthwhile intervention for improving kindergarten preparedness for children living in rural contexts.
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- 2023
21. Relationship between skeletal mitochondrial function and digital markers of free-living physical activity in older adults
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Wanigatunga, Amal A., Liu, Fangyu, Dougherty, Ryan J., Roche, Karen Bandeen, Urbanek, Jacek K., Zampino, Marta, Simonsick, Eleanor M., Tian, Qu, Schrack, Jennifer A., and Ferrucci, Luigi
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- 2024
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22. Correction: Rehabilitation Protocols Following Platelet-Rich Plasma Injections in the Hip
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Raja, Altamash E., Pigott, Tyler, Pope, Daniel, Tunis, Brandon, Dougherty, Jaime, Catapano, Michael, and Robinson, David M.
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- 2024
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23. Choice Is Not Always Good: Reducing the Role of Informational Inequality in Producing and Legitimating Higher Education Inequality. CCRC Working Paper No. 133
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Columbia University, Community College Research Center (CCRC) and Dougherty, Kevin J.
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This paper examines how the process of making higher education choices in the United States--whether to enter higher education, attend a particular college, or follow a particular path through college--produces and legitimates social inequality. The paper's central thesis is that a societal regime of many choices--while serving individual freedom and producing social well-being--"produces" societal inequality in a way that obscures that process of social reproduction for virtually all who participate in that choice regime. Students often make choices that do not serve their interests as well as they might wish, particularly if students are faced with many choices and do not have adequate information. The incidence of those suboptimal choices is not random but is socially stratified. It is higher for less advantaged people, and unequal provision of good information plays a crucial role in producing those socially stratified suboptimal choices. Secondly, the provision of many choices "legitimates" social inequality. Seemingly offered many choices in life, both the fortunate and unfortunate in society come to feel that much of the inequality they experience is due to their own actions and therefore is legitimate. The paper concludes by offering various prescriptions for reducing the socially stratifying impacts and ideological consequences of a high-choice regime. It lays out how we could more equally distribute high-quality information, nudge students toward better choice making, reduce the costs to students of suboptimal choices, and mitigate blaming self and others by demystifying the nature of choice. In making these arguments, this paper draws on the research literature in sociology of education, behavioral economics, cognitive psychology, and social psychology of inequality.
- Published
- 2023
24. The Politics of the Gender Gap in COVID-19: Partisanship, Health Behavior, and Policy Preferences in the US
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Burton, Colleen Dougherty, Gadarian, Shana Kushner, Goodman, Sara Wallace, and Pepinsky, Thomas B
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Political Science ,Human Society ,Infectious Diseases ,Clinical Research ,Emerging Infectious Diseases ,Coronaviruses ,Basic Behavioral and Social Science ,Behavioral and Social Science ,Gender Equality ,Humans ,COVID-19 ,United States ,Female ,Male ,Politics ,Health Behavior ,Sex Factors ,Health Policy ,Adult ,Middle Aged ,gender gap ,partisanship ,health behavior ,public opinion ,Public Health and Health Services ,Policy and Administration ,Law ,Health Policy & Services ,Policy and administration ,Political science - Abstract
Several studies demonstrate gender and partisan differences among Americans in COVID-19 socioeconomic consequences, attitudes, and behaviors. The authors of this study use six waves of panel survey data to explore the intersection of gender and party across COVID-19 mitigation behaviors, concerns, and policy preferences. The authors observe small gender gaps on several measures; however, partisan differences are larger than gender differences when considering the interaction between gender and partisanship. Democratic women are more similar to Democratic men on these measures than to Republican women. On virtually all measures, Republican women report lower levels of mitigation behaviors, worries, and support for expansive government policies compared to Democratic women and men. Analyzing the interaction of gender and partisanship illuminates how individuals navigated the pandemic with respect to identity factors that often pull in different directions. These findings suggest that one's partisan identity is more consequential than gender when it comes to COVID behaviors, concerns, and policy preferences.
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- 2024
25. Perceived Pubertal Timing and Deviant Peer Processes Predicting Substance Use Initiation: The Moderating Role of Impulsiveness
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A. M. Wasserman, T. E. Karns-Wright, C. W. Mathias, T. J. Moon, N. Hill-Kapturczak, and D. M. Dougherty
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The present study aimed to test if perceived pubertal timing was related to marijuana and alcohol use through deviant peer affiliation. Additionally, we examined if the deviant peer pathway was moderated by impulsiveness, gender, or both. Data were collected from 342 youth, most of whom had a family history of substance use disorder. Youth completed assessments every six months from age 13 to 16. For girls only, longitudinal analyses revealed that perceived pubertal timing was indirectly related to substance use through higher levels of deviant peer affiliation. This pathway was moderated by impulsiveness such that the association between perceived pubertal timing and deviant peer affiliation was only present for girls with average to high levels of impulsiveness. These findings elucidate a developmental pathway from perceived pubertal timing to substance use through deviant peer affiliation for high-risk girls, although low levels of impulsiveness were protective.
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- 2024
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26. Misattributions in the Downstream Marcan Literature: A Forty-Year Perspective
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Dougherty, M. V.
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- 2024
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27. Let the Light Shine Through
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Dougherty, Stephen
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- 2024
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28. Does High School STEMM Career Coursework Align with College Employment?
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Michael Gottfri, Jennifer A. Freeman, Taylor K. Odle, Jay S. Plasman, Daniel Klasik, and Shaun M. Dougherty
- Abstract
Background/Context: Career and technical education (CTE) coursework in science, technology, engineering, mathematics, and medical/health (STEMM) fields has been supported by policy makers as a way to align the secondary-to-postsecondary-to-career pipeline. Yet, in the research, the focus has been on whether STEMM CTE coursetaking in high school predicts college-going or whether it predicts employment for non-college goers. Little attention has been paid to whether STEMM CTE coursetaking in high school aligns with college employment opportunities. Purpose/Objective/Research Question/Focus of Study: This study investigates the relationship between one promising educational practice--STEMM career and technical education (STEMM CTE) coursetaking--and outcomes along students' college employment pathways. Specifically, we asked the following research questions: Does taking more STEMM CTE courses in high school link to "general" college employment outcomes? Does taking more STEMM CTE courses in high school link to "STEMM-specific" college employment outcomes? How do these relationships vary across important student subgroups, namely, those identified by the National Science Foundation as traditionally underrepresented in STEMM fields: low-income students, students with learning disabilities, women, and Black and Hispanic students? Research Design: We relied on data from the High School Longitudinal Study of 2009 (HSLS). Administered by the National Center for Education Statistics (NCES), HSLS is the most current, nationally representative data set that follows a cohort of more than 20,000 ninth-grade students across the United States throughout high school and after graduation. Our regression analyses relied on data collected during the baseline year school-level survey (2009), the high school transcript update (2013), and student-level surveys from all four data-collection waves (2009, 2012, 2013, 2016). Conclusions/Recommendations: Using these national data, we find that taking more STEMM CTE courses was associated with a higher chance of having a STEMM job during college and having higher expectations for future STEMM employment, though not with general employment outcomes such as wages. The findings were different for students from some underrepresented backgrounds in STEMM fields, and implications are discussed.
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- 2023
29. Teaching Literacy Boldly: Talk Nerdy to Me
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Cailyn N. Dougherty and Michelle Parker
- Abstract
Video games' popularity has continued to increase from their origins within a niche community to something engaged in by the general public. This field of literacy-making has a plethora of benefits to bridging skills both within and outside of the ELAR classroom for students of various backgrounds and skill sets, including language learners and students with disabilities as well as our high-performing honors students. Video games align with pedagogical best practices and our ELAR TEKS, making this the perfect combination for literacy building, risk-taking, and skill mastery.
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- 2023
30. A bilingual speech neuroprosthesis driven by cortical articulatory representations shared between languages
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Silva, Alexander B., Liu, Jessie R., Metzger, Sean L., Bhaya-Grossman, Ilina, Dougherty, Maximilian E., Seaton, Margaret P., Littlejohn, Kaylo T., Tu-Chan, Adelyn, Ganguly, Karunesh, Moses, David A., and Chang, Edward F.
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- 2024
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31. Clinical Characteristics of Youth with Trichotillomania (Hair-Pulling Disorder) and Excoriation (Skin-Picking) Disorder
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Ricketts, Emily J., Peris, Tara S., Grant, Jon E., Valle, Stephanie, Cavic, Elizabeth, Lerner, Juliette E., Lochner, Christine, Stein, Dan J., Dougherty, Darin D., O’Neill, Joseph, Woods, Douglas W., Keuthen, Nancy J., and Piacentini, John
- Published
- 2024
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32. Evaluation of direct point dose estimation based on the distribution of the size-specific dose estimate
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Anam, Choirul, Sutanto, Heri, Amilia, Riska, Marini, Rini, Barokah, Sinta Nur, Osman, Noor Diyana, and Dougherty, Geoff
- Published
- 2024
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33. Noncrossing Partition Lattices from Planar Configurations
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Cohen, Stella, Dougherty, Michael, Harsh, Andrew D., and Martin, Spencer Park
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- 2024
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34. Early Predictors and Concurrent Correlates of Tonic and Phasic Irritability in Adolescence
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Sorcher, Leah K., Silver, Jamilah, Chad-Friedman, Emma, Carlson, Gabrielle A., Klein, Daniel N., and Dougherty, Lea R.
- Published
- 2024
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35. Molly: A Verified Compiler for Cryptoprotocol Roles
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Dougherty, Daniel J. and Guttman, Joshua D.
- Subjects
Computer Science - Cryptography and Security - Abstract
Molly is a program that compiles cryptographic protocol roles written in a high-level notation into straight-line programs in an intermediate-level imperative language, suitable for implementation in a conventional programming language. We define a denotational semantics for protocol roles based on an axiomatization of the runtime. A notable feature of our approach is that we assume that encryption is randomized. Thus, at the runtime level we treat encryption as a relation rather than a function. Molly is written in Coq, and generates a machine-checked proof that the procedure it constructs is correct with respect to the runtime semantics. Using Coq's extraction mechanism, one can build an efficient functional program for compilation.
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- 2023
36. Creation of a CS1 Course with Modern C++ Principles
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Dougherty, Ryan E.
- Subjects
Computer Science - Computers and Society - Abstract
Best practices in programming need to be emphasized in a CS1 course as bad student habits persist if not reinforced well. The C++ programming language, although a relatively old language, has been regularly updated with new versions since 2011, on the pace of once every three years. Each new version contains important features that make the C++ language more complex for backwards compatibility, but often introduce new features to make common use cases simpler to implement. This poster contains experiences in designing a CS1 course that uses the C++ programming language that incorporates ``modern'' versions of the language from the start, as well as recent conferences about the language. Our goals were to prevent many common bad habits among C++ programmers., Comment: Accepted to SIGCSE TS 2024 (poster)
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- 2023
37. Designing Theory of Computing Backwards
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Dougherty, Ryan E.
- Subjects
Computer Science - Computers and Society - Abstract
The design of any technical Computer Science course must involve its context within the institution's CS program, but also incorporate any new material that is relevant and appropriately accessible to students. In many institutions, theory of computing (ToC) courses within undergraduate CS programs are often placed near the end of the program, and have a very common structure of building off previous sections of the course. The central question behind any such course is ``What are the limits of computers?'' for various types of computational models. However, what is often intuitive for students about what a ``computer'' is--a Turing machine--is taught at the end of the course, which necessitates motivation for earlier models. This poster contains our experiences in designing a ToC course that teaches the material effectively ``backwards,'' with pedagogic motivation of instead asking the question ``What suitable restrictions can we place on computers to make their problems tractable?'' We also give recommendations for future course design., Comment: Accepted to SIGCSE TS 2024 (poster)
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- 2023
38. Next-generation MRD assays: do we have the tools to evaluate them properly?
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Stetson, Dan, Labrousse, Paul, Russell, Hugh, Shera, David, Abbosh, Chris, Dougherty, Brian, Barrett, J. Carl, Hodgson, Darren, and Hadfield, James
- Subjects
Quantitative Biology - Other Quantitative Biology - Abstract
Circulating tumour DNA (ctDNA) detection of molecular residual disease (MRD) in solid tumours correlates strongly with patient outcomes and is being adopted as a new clinical standard. ctDNA levels are known to correlate with tumor volume, and although the absolute levels vary across indication and histology, its analysis is driving the adoption of MRD. MRD assays must detect tumor when imaging cannot and, as such, require very high sensitivity to detect the low levels of ctDNA found after curative intent therapy. The minimum threshold is 0.01% Tumour Fraction but current methods like Archer and Signatera are limited by detection sensitivity resulting in some patients receiving a false negative call thereby missing out on earlier therapeutic intervention. Multiple vendors are increasing the number of somatic variants tracked in tumour-informed and personalized NGS assays, from tens to thousands of variants. Most recently, assays using other biological features of ctDNA, e.g methylation or fragmentome, have been developed at the LOD required for clinical utility. These uniformed, or tumour-naive and non-personalised assays may be more easily, and therefore more rapidly, adopted in the clinic. However, this rapid development in MRD assay technology results in significant challenges in benchmarking these new technologies for use in clinical trials. This is further complicated by the fact that previous reference materials have focused on somatic variants, and do not retain all of the epigenomic features assessed by newer technologies. In this Comments and Controversy paper, we detail what is known and what remains to be determined for optimal reference materials of MRD methods and provide opinions generated during three-years of MRD technology benchmarking in AstraZeneca Translational Medicine to help guide the community conversation.
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- 2023
39. Hausdorff reflections and bifurcate curves
- Author
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Dougherty, John
- Subjects
Mathematics - General Topology - Abstract
A manifold is a space that locally looks like the smooth space $\mathbf{R}^{n}$. It is usually also assumed that the underlying topological space of a manifold is hausdorff. However, there are natural examples of manifolds for which the hausdorff conditions fails. Some but not all of these examples contain bifurcate pairs of curves: pairs of curves that agree on some initial interval but disagree on a later interval. The first part of this note proves that a manifold $M$ is hausdorff if and only if (i) it contains no bifurcate curves and (ii) there is a hausdorff manifold $N$ with the same algebra of smooth real-valued functions as $M$; this confirms a conjecture of Wu and Weatherall. The second part of this note shows that a hausdorff manifold $N$ satisfying (ii) is a certain quotient of $M$., Comment: 11 pages, 0 figures
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- 2023
40. Faster Location in Combinatorial Interaction Testing
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Dougherty, Ryan E., Green, Dylan N., and Kim, Grace M.
- Subjects
Computer Science - Discrete Mathematics ,Mathematics - Combinatorics - Abstract
Factors within a large-scale software system that simultaneously interact and strongly impact the system's response under a configuration are often difficult to identify. Although screening such a system for the existence of such interactions is important, determining their location is more useful for system engineers. Combinatorial interaction testing (CIT) concerns creation of test suites that nonadaptively either detect or locate the desired interactions, each of at most a specified size or show that no such set exists. Under the assumption that there are at most a given number of such interactions causing such a response, locating arrays (LAs) guarantee unique location for every such set of interactions and an algorithm to deal with outliers and nondeterministic behavior from real systems, we additionally require the LAs to have a "separation" between these collections. State-of-the-art approaches generate LAs that can locate at most one interaction of size at most three, due to the massive number of interaction combinations for larger parameters if no constraints are given. This paper presents LocAG, a two-stage algorithm that generates (unconstrained) LAs using a simple, but powerful partitioning strategy of these combinations. In particular, we are able to generate LAs with more factors, with any desired separation, and greater interaction size than existing approaches.
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- 2023
41. Experiences with Research Processes in an Undergraduate Theory of Computing Course
- Author
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Dougherty, Ryan E.
- Subjects
Computer Science - Computers and Society - Abstract
Theory of computing (ToC) courses are a staple in many undergraduate CS curricula as they lay the foundation of why CS is important to students. Although not a stated goal, an inevitable outcome of the course is enhancing the students' technical reading and writing abilities as it often contains formal reasoning and proof writing. Separately, many undergraduate students are interested in performing research, but often lack these abilities. Based on this observation, we emulated a common research environment within our ToC course by creating a mock conference assignment, where students (in groups) both wrote a technical paper solving an assigned problem and (individually) anonymously refereed other groups' papers. In this paper we discuss the details of this assignment and our experiences, and conclude with reflections and future work about similar courses., Comment: Accepted to SIGCSE TS 2024
- Published
- 2023
42. Device Neuromodulation and Brain Stimulation Therapies
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Luccarelli, James, primary, Henry, Michael E., additional, Fernandez-Robles, Carlos, additional, Cusin, Cristina, additional, Camprodon, Joan A., additional, and Dougherty, Darin D., additional
- Published
- 2025
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43. Contributors
- Author
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Acampora, Gregory Alexander, primary, Ahmad, Zeba N., additional, Alpay, Menekse, additional, Alpert, Jonathan E., additional, Babadi, Baktash, additional, Baek, Ji Hyun, additional, Baig, Mizra, additional, Bains, Ashika, additional, Baker, Amanda Waters, additional, Baldi, Olivia, additional, Beach, Scott R., additional, Beck, BJ, additional, Beckwith, Noor, additional, Benedek, David M., additional, Beresin, Eugene V., additional, Biederman, Joseph, additional, Bird, Suzanne A., additional, Blais, Mark A., additional, Bosson, Rahel, additional, Brendel, Rebecca Weintraub, additional, Bui, Eric, additional, Camprodon, Joan A., additional, Capawana, Michael R., additional, Caplan, Jason P., additional, Carter, Christopher, additional, Cassano, Paolo, additional, Cather, Corinne, additional, Celano, Christopher M., additional, Chang, Trina E., additional, Charoenpong, Prangthip, additional, Chemali, Zeina N., additional, Chen, Justin, additional, Chopra, Amit, additional, Choukas, Nathaniel, additional, Chung, Sun Young, additional, Cohen, Jonah, additional, Cohen, Lee S., additional, Colvin, Mary K. (Molly), additional, Conteh, Nkechi, additional, Crain, Laura D., additional, Cremens, M. Cornelia, additional, Cusin, Cristina, additional, Dekel, Sharon, additional, Denysenko, Lex, additional, Dickerson, Bradford C., additional, Donovan, Abigail L., additional, Doorley, James, additional, Dougherty, Darin D., additional, Ducharme, Simon, additional, Eddy, Kamryn T., additional, Edersheim, Judith G., additional, Evanoff, Anastasia B., additional, Fava, Maurizio, additional, Finn, Christine T., additional, Fernandez-Robles, Carlos, additional, Fishel, Anne K., additional, Forchelli, Gina, additional, Freudenreich, Oliver, additional, Fricchione, Gregory L., additional, Friedman, Nora D.B., additional, Gatchel, Jennifer R., additional, Gelaye, Bizu, additional, Georgiopoulos, Anna M., additional, Ghaznavi, Sharmin, additional, Ginsburg, Richard, additional, Gold, Alexandra K., additional, Gordon, Christopher D., additional, Gray, Caroline A., additional, Greenberg, Donna B., additional, Greer, Joseph, additional, Hazen, Eric P., additional, Henry, Michael E., additional, Herman, John B., additional, Himes, Susan, additional, Hogan, Charlotte, additional, Holt, Daphne J., additional, Huffman, Jeffery C., additional, Huguenel, Brynn, additional, Ipek, Simay, additional, Irwin, Kelly Edwards, additional, Ivkovic, Ana, additional, Jacobs, Jamie, additional, Jagodnik, Kathleen M., additional, Jain, Felipe A., additional, Jankauskaite, Greta, additional, Januzzi, James L., additional, Jenike, Michael A., additional, Jenkins, Jonathan, additional, Johnson, Justin M., additional, Julian, John N., additional, Kamali, Masoud, additional, Kaneko, Yoshio A., additional, Katz, Tamar C., additional, Keuroghlian, Alex, additional, Keuthen, Nancy J., additional, Khoshbin, Shahram, additional, Kim, Hyun-Hee, additional, Kim, Youngjung R., additional, Koh, Katherine A., additional, Kohrman, Samuel I., additional, Kontos, Nicholas, additional, Lagomasino, Isabel T., additional, Leval, Rebecca, additional, Leveroni, Catherine, additional, Lim, Carol, additional, Luccarelli, James, additional, Madarasmi, Saira, additional, Madva, Elizabeth N., additional, McCoy, Thomas H., additional, Milosavljevic, Nada, additional, Mischoulon, David, additional, Miyares, Peyton, additional, Morelli, Leah W., additional, Rodriguez, Alejandra E. Morfin, additional, Murray, Evan D., additional, Murray, Helen Burton, additional, Nejad, Shamim H., additional, Newhouse, Amy L., additional, Nicolson, Stephen E., additional, Nierenberg, Andrew A., additional, Nisavic, Mladen, additional, Nonacs, Ruta M., additional, Öngür, Dost, additional, Onyeaka, Henry, additional, Orr, Scott P., additional, Ostacher, Michael J., additional, Pace-Schott, Edward F., additional, Papakostas, George I., additional, Paudel, Shreedhar, additional, Peay, Celeste, additional, Pederson, Aderonke Bamgbose, additional, Penava, Susan J., additional, Perez, David L., additional, Perlis, Roy H., additional, Peters, Amy T., additional, Pinsky, Elizabeth G., additional, Pollak, Lauren Norton, additional, Pollastri, Alisha R., additional, Post, Loren M., additional, Powell, Alicia D., additional, Prager, Laura M., additional, Praschan, Nathan, additional, Price, Bruce H., additional, Prince, Jefferson B., additional, Probert, Julia M., additional, Prom, Maria C., additional, Punko, Diana, additional, Rauch, Scott L., additional, Raviola, Giuseppe J., additional, Reilly-Harrington, Noreen A., additional, Ritchie, Elspeth Cameron, additional, Rivas-Vazquez, Rafael, additional, Robinson, Ellen M., additional, Roffman, Joshua L., additional, Rubin, David H., additional, Ruchensky, Jared R., additional, Salvi, Joshua D., additional, Sanders, Kathy M., additional, Sanders, Wesley M., additional, Schlozman, Steven C., additional, Schouten, Ronald, additional, Schuster, Randi, additional, Shafer, Linda C., additional, Sheets, Jennifer, additional, Sher, Yelizaveta, additional, Sherman, Janet Cohen, additional, Sinclair, Samuel Justin, additional, Smith, Felicia A., additional, Sockalingam, Sanjeev, additional, Sogg, Stephanie, additional, Sorg, Emily M., additional, Sprich, Susan E., additional, Stein, Michelle B., additional, Stern, Theodore A., additional, Stoler, Joan M., additional, Stone, Mira, additional, Surman, Craig B.H., additional, Sylvia, Louisa G., additional, Tanev, Kaloyan S., additional, Tayeb, Haythum O., additional, Taylor, John B., additional, Thom, Robyn P., additional, Thomas, Jennifer J., additional, Tillman, Emma M., additional, Traeger, Lara, additional, Trinh, Nhi-Ha, additional, Uchida, Mai, additional, Ulman, Kathleen Hubbs, additional, Valera, Eve M., additional, Van Alphen, Manjola U., additional, Vazquez, Rafael, additional, Viguera, Adele C., additional, Wang, Betty, additional, Weilburg, Jeffrey B., additional, Weinberg, Marc, additional, Weinstein, Sylvie J., additional, Weisholtz, Daniel, additional, Wilens, Timothy E., additional, Wilhelm, Sabine, additional, Winkelman, John W., additional, Wright, Christopher L., additional, Wynn, Gary H., additional, Yeung, Albert, additional, Zakhary, Lisa, additional, and Zambrano, Juliana, additional
- Published
- 2025
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44. Neuroimaging in Psychiatry
- Author
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Camprodon, Joan A., primary, Dougherty, Darin D., additional, and Rauch, Scott L., additional
- Published
- 2025
- Full Text
- View/download PDF
45. Mapping dysfunctional circuits in the frontal cortex using deep brain stimulation.
- Author
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Hollunder, Barbara, Ostrem, Jill, Sahin, Ilkem, Rajamani, Nanditha, Oxenford, Simón, Butenko, Konstantin, Neudorfer, Clemens, Reinhardt, Pablo, Zvarova, Patricia, Polosan, Mircea, Akram, Harith, Vissani, Matteo, Zhang, Chencheng, Sun, Bomin, Navratil, Pavel, Reich, Martin, Volkmann, Jens, Yeh, Fang-Cheng, Baldermann, Juan, Dembek, Till, Visser-Vandewalle, Veerle, Alho, Eduardo, Franceschini, Paulo, Nanda, Pranav, Finke, Carsten, Kühn, Andrea, Dougherty, Darin, Richardson, R, Bergman, Hagai, DeLong, Mahlon, Mazzoni, Alberto, Romito, Luigi, Tyagi, Himanshu, Zrinzo, Ludvic, Joyce, Eileen, Chabardes, Stephan, Li, Ningfei, Horn, Andreas, and Starr, Philip
- Subjects
Humans ,Deep Brain Stimulation ,Brain ,Motor Cortex ,Parkinson Disease ,Brain Mapping - Abstract
Frontal circuits play a critical role in motor, cognitive and affective processing, and their dysfunction may result in a variety of brain disorders. However, exactly which frontal domains mediate which (dys)functions remains largely elusive. We studied 534 deep brain stimulation electrodes implanted to treat four different brain disorders. By analyzing which connections were modulated for optimal therapeutic response across these disorders, we segregated the frontal cortex into circuits that had become dysfunctional in each of them. Dysfunctional circuits were topographically arranged from occipital to frontal, ranging from interconnections with sensorimotor cortices in dystonia, the primary motor cortex in Tourettes syndrome, the supplementary motor area in Parkinsons disease, to ventromedial prefrontal and anterior cingulate cortices in obsessive-compulsive disorder. Our findings highlight the integration of deep brain stimulation with brain connectomics as a powerful tool to explore couplings between brain structure and functional impairments in the human brain.
- Published
- 2024
46. Epigenetic reprogramming shapes the cellular landscape of schwannoma.
- Author
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Liu, S, Casey-Clyde, Tim, Cho, Nam, Swinderman, Jason, Pekmezci, Melike, Dougherty, Mark, Foster, Kyla, Chen, William, Villanueva-Meyer, Javier, Swaney, Danielle, Vasudevan, Harish, Choudhury, Abrar, Pak, Joanna, Breshears, Jonathan, Lang, Ursula, Eaton, Charlotte, Hiam-Galvez, Kamir, Stevenson, Erica, Chen, Kuei-Ho, Lien, Brian, Wu, David, Braunstein, Steve, Sneed, Penny, Magill, Stephen, Lim, Daniel, McDermott, Michael, Berger, Mitchel, Perry, Arie, Krogan, Nevan, Hansen, Marlan, Spitzer, Matthew, Gilbert, Luke, Theodosopoulos, Philip, and Raleigh, David
- Subjects
Humans ,Neurilemmoma ,Epigenesis ,Genetic ,Cellular Reprogramming ,Tumor Microenvironment - Abstract
Mechanisms specifying cancer cell states and response to therapy are incompletely understood. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas, the most common tumors of the peripheral nervous system. We find schwannomas are comprised of 2 molecular groups that are distinguished by activation of neural crest or nerve injury pathways that specify tumor cell states and the architecture of the tumor immune microenvironment. Moreover, we find radiotherapy is sufficient for interconversion of neural crest schwannomas to immune-enriched schwannomas through epigenetic and metabolic reprogramming. To define mechanisms underlying schwannoma groups, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of tumor evolution and establish a paradigm of epigenetic and metabolic reprograming of cancer cells that shapes the immune microenvironment in response to radiotherapy.
- Published
- 2024
47. A revised model of energy transactions and body composition in sheep.
- Author
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Oddy, Victor, Dougherty, James, Evered, Mark, Clayton, Edward, and Oltjen, James
- Subjects
body composition ,growth ,metabolism ,modeling ,nutrition ,ruminant ,Humans ,Animals ,Sheep ,Energy Metabolism ,Australia ,Energy Intake ,Body Composition ,Proteins ,Body Weight ,Sheep ,Domestic ,Animal Feed ,Diet - Abstract
A mechanistic, dynamic model was developed to calculate body composition in growing lambs by calculating heat production (HP) internally from energy transactions within the body. The model has a fat pool (f) and three protein pools: visceral (v), nonvisceral (m), and wool (w). Heat production is calculated as the sum of fasting heat production, heat of product formation (HrE), and heat associated with feeding (HAF). Fasting heat production is represented as a function of visceral and nonvisceral protein mass. Heat associated with feeding (HAF) is calculated as ((1 - km) x MEI), where km is partial efficiency of ME use for maintenance, and MEI = metabolizable energy intake) applies at all levels above and below maintenance. The value of km derived from data where lambs were fed above maintenance was 0.7. Protein change (dp/dt) is the sum of change in the m, v, and w pools, and change in fat is equal to net energy available for gain minus dp/dt. Heat associated with a change in body composition (HrE) is calculated from the change in protein and fat with estimated partial efficiencies of energy use of 0.4 and 0.7 for protein and fat, respectively. The model allows for individuals to gain protein while losing fat or vice versa. When evaluated with independent data, the model performed better than the current Australian feeding standards (Freer et al., 2007) for predicting protein gain in the empty body but did not perform as well as for gain of fat and fleece-free empty body weight. Models performed similarly for predicting clean wool growth. By explicit representation of the major energy using processes in the body, and through simplification of the way body composition is computed in growing animals, the model is more transparent than current feeding systems while achieving similar performance. An advantage of this approach is that the model has the potential for wider applicability across different growth trajectories and can explicitly account for the effects of systematic changes on energy transactions, such as the effects of selective breeding, growth manipulation, or environmental changes.
- Published
- 2024
48. Catalyzing communities of research rigour champions.
- Author
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Brumback, Audrey, Ngiam, William, Lapato, Dana, Allison, David, Daniels, Christin, Dougherty, Michael, Hazlett, Haley, Kerr, Kara, Pusek, Susan, and Schrag, Naomi
- Subjects
open science ,reproducibility ,scientific rigour - Abstract
The biomedical sciences must maintain and enhance a research culture that prioritizes rigour and transparency. The US National Institute of Neurological Disorders and Stroke convened a workshop entitled Catalyzing Communities of Research Rigor Champions that brought together a diverse group of leaders in promoting research rigour and transparency (identified as rigour champions) to discuss strategies, barriers and resources for catalyzing technical, cultural and educational changes in the biomedical sciences. This article summarizes 2 days of panels and discussions and provides an overview of critical barriers to research rigour, perspectives behind reform initiatives and considerations for stakeholders across science. Additionally, we describe applications of network science to foster, maintain and expand cultural changes related to scientific rigour and opportunities to embed rigourous practices into didactic courses, training experiences and degree programme requirements. We hope this piece provides a primer for the wider research community on current discussions and actions and inspires individuals to build, join or expand collaborative networks within their own institutions that prioritize rigourous research practices.
- Published
- 2024
49. Pharmacologic interventions for the treatment of equine herpesvirus-1 in domesticated horses: A systematic review.
- Author
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Goehring, Lutz, Dorman, David, Osterrieder, Klaus, Burgess, Brandy, Dougherty, Kelsie, Gross, Peggy, Neinast, Claire, Pusterla, Nicola, Soboll-Hussey, Gisela, and Lunn, David
- Subjects
chemotherapy ,equine ,equine herpesvirus myeloencephalopathy ,herpesvirus‐1 ,Animals ,Horses ,Herpesvirus 1 ,Equid ,Horse Diseases ,Herpesviridae Infections ,Antiviral Agents ,Valacyclovir - Abstract
BACKGROUND: Equine herpes virus type 1 (EHV-1) infection in horses is associated with upper respiratory disease, neurological disease, abortions, and neonatal death. REVIEW QUESTION: Does pharmacological therapy decrease either the incidence or severity of disease or infection caused by EHV-1 in domesticated horses? METHODS: A systematic review was preformed searching AGRICOLA, CAB Abstracts, Cochrane, PubMed, Web of Science, and WHO Global Health Index Medicus Regional Databases to identify articles published before February 15, 2021. Selection criteria were original research reports published in peer reviewed journals, and studies investigating in vivo use of therapeutic agents for prevention or treatment of EHV-1 in horses. Outcomes assessed included measures related to clinical outcomes that reflect symptomatic EHV-1 infection or virus infection. We evaluated risk of bias and performed a GRADE evaluation of the quality of evidence for interventions. RESULTS: A total of 7009 unique studies were identified, of which 9 met the inclusion criteria. Two studies evaluated valacyclovir or small interfering RNAs, and single studies evaluated the use of a Parapoxvirus ovis-based immunomodulator, human alpha interferon, an herbal supplement, a cytosine analog, and heparin. The level of evidence ranged between randomized controlled studies and observational trials. The risk of bias was moderate to high and sample sizes were small. Most studies reported either no benefit or minimal efficacy of the intervention tested. CONCLUSIONS AND CLINICAL IMPORTANCE: Our review indicates minimal or limited benefit either as a prophylactic or post-exposure treatment for any of the studied interventions in the mitigation of EHV-1-associated disease outcome.
- Published
- 2024
50. Advancing scaling science in health and social care: a scoping review and appraisal of scaling frameworks
- Author
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Kothari, Anita, Graham, Ian D., Dougherty, Madeline, de Carvalho Corôa, Roberta, Mochcovitch, Diogo G. V., Cassidy, Christine, Etherington, Amy, Ingabire, Marie-Gloriose, Gittings, Lesley, Gogovor, Amede, Légaré, France, Nassar, Elsa-Lynn, Tinuoye, Oluwabambi, Volmink, Heinrich Cyril, and McLean, Robert K. D.
- Published
- 2024
- Full Text
- View/download PDF
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