2023 CompX Recipients

Exploring Watershed Moments Using Virtual Reality

Cottingham

Kathy Cottingham, James Mahoney, Quin Shingai, Monika Roznere, Jess Trout-Haney, Jeff Kerby, John Bell and the DEV studio

Freshwater resources sustain life while serving as economic and cultural infrastructure for societies worldwide, providing food, transportation, drinking water, recreational opportunities, and other valuable ecosystem services that promote human well-being. Despite the critical importance of water to civilization, humans often adversely impact water quality via deforestation, fertilizer overuse, and pollution - impacts that can be exacerbated by the indirect effects of climate change. Unfortunately, the combined direct and indirect anthropogenic effects on lakes and reservoirs can be difficult to understand due to the separation of cause and effect in space and time. We seek to raise awareness of these issues by harnessing virtual reality (VR), a tool which can enhance users' empathy and modify their subsequent behavior.

Mahoney

In this study, we aim to develop a working prototype for an open-source VR simulation of a generalized freshwater lake ("Sim Lake") to serve as a base environment that can be adapted for research, education, and outreach. Specifically, we plan a two-stage, coupled prototype that combines VR simulations of the area around a lake with stereoscopic, photo-based components, above and below the water surface. In stage 1, we will simulate the experience of visualizing abstracted watersheds from a bird's eye view, and also standing on a lake shore, creating an improved version of similar work in Dartmouth extended reality courses. In stage 2, the simulated environment will provide context for a more photorealistic world populated by stereoscopic images closely informed by real-world above water and underwater photos and videos. This more realistic view will facilitate the examination of in-lake conditions, and would include the ability to "tune" properties that cue participants as to the potential water quality and safety of the simulated freshwater lake ecosystem. For example, we can change the clarity and color of the water from a clear blue signaling "clean" water, to a murky blue-green signaling a cyanobacteria bloom, to a murky brown signaling transport of sediment into the lake following a large rainfall event. We can alter the lake bottom from cobble to sand to mud or add and remove particular organisms such as lake trout or invasive Eurasian watermilfoil. Changes to the surrounding land can also be connected to what things look like underwater. Upon completing beta-testing and debugging, the environment will be available open source via a project website, for use by our team and others. Once developed, we plan to gamify "Sim Lake" to communicate the importance of freshwater resources and help users to better understand how their activities on land impact the freshwater ponds, lakes, and reservoirs on which they depend. We also hope to use this tool in research to improve human use and management of these resources. 

"Medium" Data Work: Studying Student Writing Growth via Portfolios

Taine Donahue

In collaboration with Research Computing, this CompX grant will support the quarterly draw of digital portfolio data in the DartWrite research project for the 2023-2024 academic year. This project will pursue, with data already collected, a specific project or more that demonstrate the interest and value of the project's data, and will share results to identify specific fruitful research questions for current and future projects.

DNN modeling of category-selective areas in developmental prosopagnosia 

Brad Duchaine

 In this project, we aim to accelerate research into Developmental Prosopagnosia (DP), a neurodevelopmental disorder causing severe face recognition deficits. We propose to use Deep Convolutional Neural Networks (DNNs) to create computational models of category-selective brain regions. These regions respond selectively to specific visual categories such as faces, places, bodies, and words. 

Our central hypothesis is that by combining intensive scanning of individual participants, high-resolution analysis of responses to individual images, and DNN-based computational modeling of neural responses, we can greatly speed up DP research. We plan to test the accuracy of these models in predicting responses in four individuals with DP. If successful, this approach could transform our approach to investigating visual recognition deficits and could be extended to other neurodevelopmental and psychiatric disorders. 

Our project has two primary objectives: 

1. We aim to determine if models of DP category-selective areas can accurately predict responses to images not used in model training. We will compare the predicted and observed correlations with noise ceilings, which represent the theoretically maximum expected correlation. 

2. We will assess the ability of DP models to predict responses to images designed to test theoretically-motivated questions about DP. We will present stimuli addressing two key theoretical questions to the DPs and compare the predicted and observed responses. 

If our results are promising, they will serve as preliminary data for an R01 proposal. This proposal will test a larger sample of DPs (n=30) to convincingly demonstrate the value of our approach. 

Stimulating brain networks to direct psychedelic induced plasticity

Dwiel

Recent clinical studies have reported beneficial outcomes from pairing psychedelic drugs with psychotherapy. This project will test the theory that the biological mechanisms underpinning these encouraging results will, similarly, create longer-lasting changes in brain activity and behavior when such drugs are paired with brain stimulation. To begin probing the physiological and behavioral consequences of pairing brain stimulation with psychedelic drugs, while avoiding the difficulties associated with human psychedelic trials (e.g., the challenge of an adequate placebo control and strong expectation bias), we have completed preliminary studies administering lysergic acid diethylamide (LSD) to rats. We have shown that LSD alone has acute, detectable effects on brain activity compared to saline; yet, during the known window of enhanced plasticity (~24 hours later) there were no differences in frontal-striatal local field potential oscillations compared to animals given saline, as determined using a machine-learning approach. However, when the rats' infralimbic cortex (IL) was stimulated, this induced more changes in brain activity in the rats that were given LSD 24 hours before stimulation, compared to those given saline 24 hours before stimulation. This physiological evidence supports our hypothesis that psychedelic drugs enhance the ability of brain stimulation to alter frontal-striatal activity in awake, freely-moving rats.

This CompX grant will allow us to implement the Neuropixels system in order to characterize the interaction of LSD and brain stimulation on corticostriatal brain states in rats during a clinically relevant impulsive decision making task. The Neuropixels system will provide high-dimensional single-neuron spiking data and local field potentials (LFPs) from multiple brain regions implicated in decision making. These data will allow us to use computational methods to characterize the effects of brain stimulation and LSD on brain states and their dynamics.

Accelerated discovery and fabrication of robust 3D-printable slide-ring hydrogels

Fe

Natural materials are endowed with exceptional mechanical properties to survive under various extreme conditions. These biomacromolecules and their assemblies are arranged hierarchically to form homo- and heterogeneous 3D architectures across the nano to macro-scales. While defects are ubiquitous in biological systems, biomaterials are more tolerant to defects because of their capability to rearrange in response to stress. In comparison, parts manufactured using synthetic polymers often possess shorter life spans due to the intrinsic nature of polymer networks, material inhomogeneity, as well as defects generated during the manufacturing process. The lack of a comprehensive structure-property-process relationship at the fundamental level limits the advancement of soft materials. Hence, there is an emergent need to weld precise control of soft materials' chemical structures, functions, and hierarchical placements.

To address this problem, we plan to develop a systematic approach by combining the bottom-up slide-ring polymer design with the top-down direct ink writing (DIW) to develop robust polymer hydrogels that are tough and fatigue-resistant. Our work capitalizes on connecting the bottom-up, slide-ring polymer design with the top-down detection and correction of in-line defects during additive manufacturing (AM) through high-throughput synthesis and machine learning (ML) approaches. The research outcome will enable the development and fabrication of next-generation defect-free slide-ring-based resilient materials.

Low Cost Rapid Digital Preservation Documentation Workflows for At-risk Historic Wooden Architecture in Puerto Rico

Brinker Fergason

In recent years Puerto Rico has responded to massive destruction caused by natural disasters with an equally powerful conservation response. In 2022, the Puerto Rico State Historic Preservation Office identified over 100 culturally important wooden vernacular homes as some of the most vulnerable and threatened built heritage on the island. These 19th and 20th century historic properties are unique combinations of European and Creole-vernacular architecture which include the adoption of architectural elements and motifs from other sister islands in the Caribbean. A state-wide "Wooden Architecture Restoration Initiative"  is slated to begin in 2025, but before restoration projects can officially start, precise architectural drawings are needed for baseline conservation documentation. Currently, conservation documentation in Puerto Rico focuses on traditional hand measurements that is costly in both time and expertise. This will delay project start dates making these sites even more vulnerable to incoming hurricanes, which are becoming increasingly severe due to climate change. Thus, developing an accurate and rapid conservation documentation workflow with low-cost and accessible technologies for the creation of architectural drawings is critical for the earlier protection and preservation of these important Puerto Rician cultural sites.

To meet these needs, Dartmouth College in partnership with Centro de Conservación y Restauración de Puerto Rico (CENCOR) and the School of Architecture at the Polytechnic University of Puerto Rico, have been asked to develop and test three new conservation preservation workflows using the latest in digital capture technologies to see how they can increase speed and accessibility compared to traditional hand measurements. The goal of this research is to make headway towards the democratization of digital capture research within the field of cultural heritage preservation.

Leveraging Digital Platforms to Compile Multimedia Chinese Language and Culture Materials in the HTML Format

Mowry

The animation film The Buffalo Boy and His Flute (released in 1963, 22 minutes) is uniquely Chinese: It is in the traditional Chinese water-ink painting style, and has been hailed as a miracle of animation. The Buffalo Boy and His Flute is intentionally delivered as an "international" animated film (i.e., without the limitation of dialogue or exposition in any language, so viewers can interpret and appreciate the film as a primarily visual product) suited to language teaching/learning purposes. I have completed a good portion of the required archival research on, and in-person interviews about, the film's production background—cultural, socio-political, cinematic, artistic, and esthetic. With the support of a 2018-19 CompX grant, my collaborators and I also accomplished about two thirds of the work that is computational in nature. This includes completing the "read along" feature, embedded vocabularies, voiceover and subtitle annotation. Further computational tasks yet to be performed include expounding upon grammatical points visually with clippings from the film, integrating the project's various components into an artistically attractive and pedagogically sound whole, and associated final-phase miscellany.

In addition to The Buffalo Boy and His Flute, we plan to convert a Captivate (v.8) generated digital textbook for intermediate to advanced Chinese language classes, the Snapshots of China, into HTML format. The traditional "paper" version of Snapshots of China, in 30 lessons, has been used as one of the main textbooks at Dartmouth and Dartmouth's Beijing FSP/LSA+ programs since it was written/compiled in 2013. In 2016-17, with the help of two able CS Ph.D. students, we authored the digital version. The creation of the courseware was timely during the first two years of the Covid-19 pandemic, when almost all Dartmouth classes were taught online. While we are not debating the pros and cons of virtual/online classes, my collaborators and I firmly believe that digitalization—and instructional and educational technologies—have positively impacted both the field of education and that of publication.

From Earth to Mars: Atomic Level Probing of Hydrohematite's Magnetism

hautier

Iron minerals are a critical record of planetary processes from planetary formation to plate tectonics to surface processes like nutrient cycling and environmental conditions in both modern and ancient times. In addition to being the most abundant transition metal in terrestrial planets and their crusts, iron has two fundamental properties: a) it is redox sensitive, cycling between +2 and +3 valence states and b) it is ferromagnetic. These properties translate to iron minerals which are being utilized to understand the history of environmental change on Earth as we consider future anthropogenic climate change. Extension to other terrestrial planets like Mars is the next frontier. From a technological perspective, magnetic materials are vital for the alternative energy transition and investigating natural systems could spark new ideas for material synthesis.

slotznick

This project will focus on understanding the magnetism of hydrohematite – a version of the common iron oxide hematite that contains structural water. Hydrohematite could potentially be an unrecognized water reservoir in arid planetary surfaces like Mars and detailed study could provide new clues into both natural magnets and the planet's evolution. The team will perform magnetic measurements and synchrotron-based spectroscopic analyses on natural and synthesized specimens. These results will be compared with computational methods at the atomic and nanometer scale using first-principles calculations and micromagnetic modeling to identify unique magnetic properties of hydrohematite and reveal the physics behind why these occur.

Revealing the Function of the Human Anterior Temporal Lobe with Machine Learning

Steel

The human anterior ventral temporal lobe plays a critical role in memory formation. Prior work has shown that this area, situated on brain's bottom surface, harbors our memories of our family member's faces, sentimental and important objects, and places dear to our hearts. Critically, the anterior ventral temporal cortex is among one of the regions most profoundly impacted by Alzheimer's Disease and frontotemporal dementia, so understanding the functional composition of this area will be necessary to develop therapeutics and interventions for these devastating illnesses. However, our understanding of this region's computational role is limited by technical challenges. Specifically, the most widely used brain imaging technique, functional magnetic resonance imaging (fMRI), fails to adequately image this area because of signal dropout caused by magnetic field distortions. This severely impedes neuroscientific investigation of this brain area and human memory more broadly.

In this project, our central aim is to optimize fMRI acquisition and data processing to study the anterior ventral temporal lobe. First, we will explore novel, advanced multi-echo fMRI acquisition to improve signal dropout artifacts in this region. Second, we will develop new signal processing algorithms to further improve data quality and model fitting. Finally, we will apply this optimized protocol combined with new experimental paradigms to study the computational principles underpinning anterior ventral temporal lobe function. Overall, this project will pave the way to further study of the anterior ventral temporal lobe and reveal new insights into human memory in health and disease.

Epigenomic–Transcriptomic Modeling with Multi-Omic Data and DNA Sequences Leveraging Graph Neural Networks

soroush-vosoughi

Understanding enhancer-target interactions (ETIs) is critical for unraveling the complexities of the human genome. Current experimental methods have limitations, and machine learning (ML) models often overlook the dynamic nature of ETI networks. Our research proposal aims to address this issue by leveraging graph neural networks (GNNs) to predict ETIs, using multi-omic data and DNA sequences.

Wang

Our approach enables the examination of cRE regulation of gene expression and the revelation of how epigenomic profiles of cREs contribute to DNA interactions and gene expressions. This could lead to reduced time and resource consumption for hypothesis construction and promote research in cancer epigenome studies and disease prediction applications. To achieve our objective, we first construct a GNN-based cRE-interaction prediction model with multi-omic data and DNA sequences. Next, we construct an ETI prediction model to jointly examine cRE interactions and gene regulations. Finally, we construct a hypothesis-establishment and validation framework based on the ETI prediction model. By accomplishing these tasks, we expect to gain a better understanding of how intergenic cREs regulate target genes and establish high-quality hypotheses that biological experiments can verify.