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At least 325 records · Page 18

Modular Semantic Tagging of Medline Abstracts and its Use in Inferring Regulatory Networks

We describe MedstractPlus, a resource for mining relations from the Medline bibliographic database that is currently under construction. It was built on the remains of Medstract, a previously created resource that included a biorelation server and an acronym database. MedstractPlus uses simple and scalable natural language processing modules to structure text, is designed with reusability and extendibility in mind, and adheres to the philosophy of the Linguistic Annotation Framework. We show how MedstractPlus has been used to provide seeds for a novel approach to inferring transcriptional regulatory networks from gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗

Jackson, L., Johnson, M.B., Latrach, A., Grimes, D., Martinez, C., and Mclaughlin, J.F., 2024, Multidisciplinary geotechnical data collection, curation, and analysis for conformity with the regulatory framework for geologic carbon storage in Wyoming, USA: Geological Society of America Abstracts with Programs. Vol. 56, No. 5, 2024, doi: 10.1130/abs/2024AM-405024

Title: Multidisciplinary Geotechnical Data Collection, Curation, and Analysis for Conformity with the Regulatory Framework for Geologic Carbon Storage in Wyoming, USA. Text: Construction and operation of wells for geologic sequestration of carbon dioxide necessitate that they are permitted under the Environmental Protection Agency’s Underground Injection Control Class VI requirements. Class VI wells conform to stringent requirements to ensure long-term safety and integrity of the storage site and the protection of Underground Sources of Drinking Water. Entities pursuing Class VI permitting must provide comprehensive geologic site characterization, including regional geologic structure and stratigraphy, aquifer information, reservoir and confining unit geomechanical properties, geochemical analyses, assessment of trapping capacity and mechanisms, and a variety of other of multidisciplinary geotechnical data. The Wyoming Class VI Site Characterization Database Project is focused on developing a geologic site characterization database of geotechnical information, which has been compiled and verified from established, public databases/entities and scientific literature to expedite Class VI permitting in Sweetwater County within the Greater Green River Basin of southern Wyoming. The preliminary suite of compiled data from 14,000 wells includes 8,000 wells with logs and 7,250 wells with formation tops, ~70 wells with core data (e.g., X-Ray diffraction, petrographic, and petrophysical data), ~2,500 water analyses, ~740 seismic events data, and ~520 bottom-hole temperature measurements. Future work on—and stemming from—this project will include new core analyses, calculation and interpolation of subsurface temperature gradients, mechanical earth models, geochemical simulations, storage capacity estimation, stratigraphic column generation and correlation, and construction of subsurface maps. Finally, this work will help to inspire and facilitate subsurface data compilation and curation beyond Sweetwater County, Wyoming.

42 ENGINEERING↗

Delayed Update Algorithms for Quantum Monte Carlo Simulation on GPU: Extended Abstract

QMCPACK is open source scientific software designed to perform Quantum Monte Carlo (QMC) simulation, a first-principles method for describing many-body systems. The evaluation of each Monte Carlo move requires finding the determinant of a dense matrix in the wave functions. This calculation forms a key computational kernel in QMCPACK. After each accepted event, the wave function matrix undergoes a rank-one update to represent a single particle move within the system. The matrix inverse is updated via the Sherman-Morrison formula; occasionally, the explicit inverse must be recomputed to maintain numerical stability.; We propose an alternate approach to this kernel that utilizes QR factorization to maintain stability without refactorization. In addition, algorithms based on a novel delayed update scheme are explored in this effort. This strategy enables probability evaluation for multiple successive Monte Carlo moves, with application of accepted moves to the wave function matrix delayed until an event is denied, or a predetermined limit on acceptances p is reached. Accepted events grouped in this manner are then applied to the matrix en bloc with enhanced arithmetic intensity and computational efficiency. Delayed update Sherman-Morrison probability evaluation algorithms with CPU and GPU-accelerated implementations are tested, profiled, and analyzed. A QR based delayed update algorithm remains in development. Results are evaluated against existing methods for numerical stability and efficiency; emphasis is placed on large systems, for which acceleration is critical.

Computer Science↗

Long term occupancy estimation in a commercial space: an empirical study: poster abstract

Understanding occupancy patterns in a building is very useful to control HVAC systems for improving energy efficiency of the building and occupant comfort. There has been a very little attempt to understand long term occupancy patterns in a commercial space. In this work, we leverage depth sensors (Kinect for XBOX One) to collect occupancy count from an 11,000 square foot commercial space (Bosch office) for nine months. We analyze the collected data and describe key findings that provide deep insights about how a commercial space is used and serve as a guideline to formulate novel and efficient control strategies.

Liu, Kin Sum↗

WiP Abstract: Edge-Based Privacy of Naturalistic Driving Data Collection

Collecting large driving datasets is important for data-driven transportation research and studied in naturalistic driving [3]. Due to the standard implementation of a Controller Area Network (CAN) bus for a vehicle’s inter-module communication, many off-the-shelf devices can easily transform a vehicle into a rich data collection utility [2]. Vehicles with Adaptive Cruise Control (ACC) are an example of a feature resulting in emergent traffic behavior when scaled [4]. While these utilities were designed with particular data use cases, data may be publicly shared to benefit other researchers through online tools like CyVerse [1]. However, such data should only be shared when any private information is removed. This private information may exist as a set of GPS coordinates, since the start and end points of a trip may designate a driver’s place of residence or work. When considering larger continuously-collected data sets with a focus on naturalistic driving, many drivers are needed to make data collection feasible. Removal of private information becomes much more of a challenge since every driver may uniquely define their geographic privacy. This project aims to build upon the foundation of libpanda [2] by adding features of edge-based data privacy enforcement. In it’s current form, libpanda uses a GPS in conjunction with a CAN interface to record data. Libpanda feature s a set of startup and shutdown scripts to perform automatic data collection and upload. With additional support hardware on a Raspberry Pi, the Pi can maintain power on vehicle shutdown to automatically upload data before shutdown.

Bunting, Matt↗

Poster Abstract: Leveraging Large Language Models to Reveal Interpretable Cooling Behaviors from Smart Thermostat Data

Frequent heatwaves and hot summers increasingly challenge occupant comfort, health, and energy grid stability. Addressing these challenges requires a detailed understanding of household cooling behaviors, such as thermostat adjustments and adaptive responses to extreme conditions. Traditional analyses often rely on aggregated numerical metrics that overlook subtle but important household-specific variations. In this study, we introduce a generalizable methodology that integrates large language models (LLMs) with vision capabilities to enable scalable and detailed analysis of residential thermostat data. Using Ecobee's Donate Your Data (DYD) dataset—which provides five-minute records of indoor temperatures, thermostat setpoints, and HVAC runtimes—we focus on two U.S. cities with contrasting summer climates : Austin (TX) and Phoenix (AZ). Because raw time-series data are not well suited for direct LLM analysis, we transform them into visual representations, such as daily indoor temperature trajectories and weekly runtime histograms, to better capture behavioral variations. Leveraging LLMs' visual interpretation, we extract descriptive behavioral features, including temperature preferences, time-of-day cooling orientation, anticipatory versus reactive heatwave responses, and behavioral consistency. These semantic features support unsupervised clustering to identify distinct occupant archetypes at scale, revealing differences—such as morning-centric anticipatory coolers versus households that shift toward warmer setpoints during heatwaves—that can inform demand response, resilience planning, and health-aware interventions. By converting raw numerical data into interpretable behavioral patterns, this methodology enables scalable and practical analysis of occupant behavior, supporting actionable insights for comfort, resilience, and energy management.

Nihar, Kopal↗

Proposing an Abstracted Interface and Protocol for Computer Systems

While it made sense for historical reasons to develop different interfaces and protocols for memory channels, CPU to CPU interactions, and I/O devices, ongoing developments in the computer industry are leading to more converged requirements and physical implementations for these interconnects. As it becomes increasingly common for advanced components to contain a variety of computational devices as well as memory, the distinction between processors, memory, accelerators, and I/O devices becomes increasingly blurred. As a result, the interface requirements among such components are converging. There is also a wide range of new disruptive technologies that will impact the computer market in the coming years, including 3D integration and emerging NVRAM memory. Optimal exploitation of these technologies cannot be done with the existing memory, storage, and I/O interface standards. The computer industry has historically made major advances when industry players have been able to add innovation behind a standard interface. The standard interface provides a large market for their products and enables relatively quick and widespread adoption. To enable a new wave of innovation in the form of advanced memory products and accelerators, we need a new standard interface explicitly designed to provide both the performance and flexibility to support new system integration solutions

97 MATHEMATICS AND COMPUTING↗

Proposing an Abstracted Interface and Protocol for Computer Systems

While it made sense for historical reasons to develop different interfaces and protocols for memory channels, CPU to CPU interactions, and I/O devices, ongoing developments in the computer industry are leading to more converged requirements and physical implementations for these interconnects. As it becomes increasingly common for advanced components to contain a variety of computational devices as well as memory, the distinction between processors, memory, accelerators, and I/O devices become s increasingly blurred. As a result, the interface requirements among such components are converging. There is also a wide range of new disruptive technologies that will impact the computer market in the coming years , including 3D integration and emerging NVRAM memory. Optimal exploitation of these technologies cannot be done with the existing memory, storage, and I/O interface standards. The computer industry has historically made major advances when industry players have been able to add innovation behind a standard interface. The standard interface provides a large market for their products and enables relatively quick and widespread adoption. To enable a new wave of innovation in the form of advanced memory products and accelerators, we need a new standard interface explicitly designed to provide both the performance and flexibility to support new system integration solutions.

97 MATHEMATICS AND COMPUTING↗

Los Alamos National Laboratory Overview of the SAVY-4000 Design: Abstract Meeting the Challenge for Worker Safety

Incidents involving release of nuclear materials stored in containers of convenience such as food pack cans, slip lid taped cans, paint cans, etc. has resulted in defense board concerns over the lack of prescriptive performance requirements for interim storage of nuclear materials. Los Alamos National Laboratory (LANL) has shared in these incidents and in response proactively moved into developing a performance based storage container design, the SAVY-4000. The SAVY-4000 is the first vented general use nuclear material container demonstrated to meet the requirements of DOE M 441.1-1, Nuclear Material Packaging Manual. The SAVY-4000 is an innovative and creative design demonstrated by the fact that it can be opened and closed in a few seconds without torque wrenches or other tools; has a built-in, fire-rated filter that prevents the build-up of hydrogen gas, yet retains 99.97% of plutonium particulates, and prevents release of material even in a 12 foot drop. Finally, it has been tested to 500C for 2 hours, and will reduce the risk to the public in the event of an earthquake/fire scenario. This will allow major nuclear facilities to credit the container towards source term Material at Risk (MAR) reduction. The container was approved for nuclear material storage in theTA-55 Plutonium Facility on March 15, 2011, and the first order of 79 containers was received at LANL on March 21, 2011. The first four SAVY-4000 containers were packaged with plutonium on August 2, 2011. Key aspects of the SAVY-4000 vented storage container design will be discussed which include design qualification and testing, implementation plan development and status, risk ranking methodology for re-packaging, in use implementation with interface to LANMAS, surveillance strategy, the design life extension program as enhanced by surveillance activities and production status with the intent to extend well beyond the current five year design life.

42 ENGINEERING↗

Ion acceleration by laser plasma interaction from liquid cryogenic microjets [Abstract]

Processes that occur in extreme conditions, such as in the center of stars and large planets, can be simulated in the laboratory using facilities such as SLAC National Accelerator Laboratory and the Jupiter Laser Facility (JLF) at Lawrence Livermore National Laboratory (LLNL). These facilities allow scientists to investigate the properties of matter by observing their interactions with high power lasers. Ion acceleration from laser plasma interaction is gaining greater attention today due to its widespread potential applications, including proton beam cancer therapy and fast ignition for energy production. Typically, ion acceleration is achieved by focusing a high power laser on thin foil targets through a mechanism called Target Normal Sheath Acceleration. Based on research and recent experiments, we hypothesized that a pure liquid cryogenic jet would be an ideal target for this type of interaction, capable of producing the highest proton energies possible with todays laser technologies. Furthermore, it would provide a continuous, pure target, unlike metal foils which are consumed in the interaction and easily contaminated. In an effort to test this hypothesis and investigate new, potentially more efficient mechanisms of ion acceleration, we used the 527 nm split beam, frequency-doubled TITAN laser at JLF. Data from the cryogenic jets was limited due to the flow of current up the jet into the nozzle during the interaction, heating the jet and damaging the orifice. However, we acheived a pure proton beam with an indiciation of a monoenergetic feature. Furthermore, data from gold and carbon wires showed surprising and interesting results. Preliminary analysis of data from two ion emission diagnostics, Thomson parabola spectrometers (TPs) and radio chromic films (RCFs), suggests that shockwave acceleration occurred rather than target normal sheath acceleration, the standard mechanism of ion acceleration. Upon completion of the experiment at TITAN, I researched the possibility of transforming our liquid cryogenic jets into droplet streams. This type of target should solve our problems with the jet as it will prevent the flow of exocurrent into the nozzle. It is also highly effective as it is even more mass-limited than standard cryogenic jets. Furthermore, jets break up spontaneously anyway. If we can control the breakup, we can synchronize the droplet emission with the laser pulses. In order to assist the team prepare for an experiment later this year, I familiarized myself with the physics and theory of droplet formation, calculated values for the required parameters, and ordered the required materials for modification of the jet. Future experiments will test these droplet streams and continue towards the goal of ion acceleration using cryogenic targets.

43 PARTICLE ACCELERATORS↗

Investigating the Effect of Pyridine Vapor Treatment on Perovskite Solar Cells (Abstract for a General Audience)

Solar power is an important and increasingly widespread form of renewable energy. If you’ve ever seen solar panels on someone’s roof, they are probably made with crystalline silicon. However, the possibility of creating cheaper and more efficient solar cells motivates scientists to continue searching for alternative materials. Perovskites are one of the newest and most promising solar cell materials: they have seen incredible efficiency gains in just a few years, jumping from 3.8% in 2009 to over 20% in 2014. Even though there’s been progress in improving perovskite-based device efficiency, there are many fundamental aspects of perovskite formation that are still not fully understood. The overall aim of my research is to study these processes and help fill in some of the knowledge gaps.

14 SOLAR ENERGY↗

Pulse Tube Interference in Cryogenic Sensors (General Abstract)

When a voltage is applied to a thin superconducting strip cooled just above its critical temperature, the superconductor becomes its own internal thermostat; an increase in temperature will cause the resistance to rise, which lowers the amount of current and drops the temperature. Likewise, a decrease in temperature causes the resistance to fall, increasing the current and raising the temperature. This change in current due to changes in energy makes the superconductor an ideal energy sensor. Due to the low noise, precise energy resolution, and time stamping of particles, these detectors have several potential applications, ranging from measuring cosmic microwave background, dark matter detection, or measuring the mass of the neutrino. SLAC is currently developing tools to readout data from an array of 10000 of these sensors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Close-out report with links to abstracts

This grant provided A/V support for two technical meetings of the Edge Coordinating Committee: (1) Nov 13, 2013 (co-located with the APS-DPP meeting in Denver, CO) https://ecc.mit.edu/fall-2013-technical-meeting#overlay-context=ecc-meetings; (2) April 28-May 1, 2015 (embedded sessions in the Transport Task Force Meeting, Salem, MA) http://www-internal.psfc.mit.edu/TTF2015/index.html. The ultimate goal of the U.S. Transport Task Force is to develop a physics-based understanding of particle, momentum and heat transport in magnetic fusion devices. This understanding should be of sufficient depth that it allows the development of predictive models of plasma transport that can be validated against experiment, and then used to anticipate the future performance of burning plasmas in ITER, as well as to provide guidance for the design of next-step fusion nuclear science facilities. To achieve success in transport science, it is essential to characterize local fluctuations and transport in toroidal plasmas, to understand the basic mechanisms responsible for transport, and ultimately to control these transport processes. These goals must be pursued in multiple areas, and these topics evolve in order to reflect current interests.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

IC Post-Doctoral Fellowship Abstract and Bio.

Whole cell biosensors (WCBs) utilize an organism’s natural ability to sense and respond to the environment. Through implementation of two different protein engineering methods, I seek to develop a WCB for the detection of important chemical signatures in the environment. I will reengineer the ligand binding profile of proteins known to alter transcription of genes, and I will engineer signal transduction in proteins already known to bind relevant compounds. In both cases, detection of compounds of interest will lead to the production of a measurable fluorescent signal within the organism. These approaches will provide the groundwork for the development of novel chemical sensing technologies that provide a cheap and efficient alternative to traditional methods for detection of compounds.

60 APPLIED LIFE SCIENCES↗