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Session Introduction: Graph Representations and Algorithms in Biomedicine

Connectivity is a fundamental property of biological systems: on the cellular level, proteins interact with each other to form protein-protein interaction networks (PPIs); on the organism level, neurons are arranged in a network; and on a community-level, species can have complex relationships with one another that drive the development and balance of an ecosystem. Graphs, representations of systems consisting of entities as vertices and their connections as edges, are a useful structure to characterize many such systems. Such models can be used to understand biological systems that naturally have a network structure, including PPIs, biological neurons, and ecosystems. In today’s information age, graph representations and algorithms (often in combination with machine learning techniques) are used to organize massive amounts of related data, much of which may be heterogeneous or unstructured, and identify patterns that represent novel biological insights. PSB’s 2023 session “Graph Representations and algorithms in Biomedicine,” encompasses modern developments in graph theory and its applications to various fields of biomedicine. This session includes a wide range of research - knowledge graphs built from text-mined health data, heterogeneous networks using multi-omic databases, and graphs refined to represent uncertainty or improve memory usage.

Chrisman, Brianna S.↗

Incorporation of rare earth elements $\text{Sc}$, $\text{Y}$ and $\text{La}$ into gibbsite

Rare earth elements (REE) are increasingly critical resources in technological applications, but the current understanding of their separation by uptake into minerals remains limited. We examined the adsorption and solubilization of scandium (Sc), yttrium (Y), and lanthanum (La) into aluminum hydroxide (gibbsite, Al(OH) 3 ). Based on spectroscopic investigations such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and time of flight-secondary ion mass spectrometry (ToF-SIMS), only Sc exhibited favorable incorporation and adsorption (0.66 and 0.06 atom%, respectively). Analysis of solid state 45 Sc magic angle spinning-nuclear magnetic resonance spectroscopy (MAS-NMR) indicated that Sc exhibits an octahedral coordination consistent with isolated substitutions for Al in the gibbsite structure, leading to a increase in lattice constants detectable by X-ray diffraction. Density functional theory (DFT) calculations reinforced this interpretation by reproducing the detected structural distortion as well as demonstrating the relatively favorable energetic basis for Sc incorporation into gibbsite by substitution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time scales for nonlinear processes in preheating after multifield inflation with nonminimal couplings

We have conducted extensive lattice simulations to study the postinflation dynamics of multifield models involving nonminimal couplings. In this work, we explore the parameter dependence of preheating in these models and describe the various time scales that control such nonlinear processes as energy transfer, rescattering, and the approach to radiation domination and thermalization. In the limit of large nonminimal couplings ($ξ_I$ ~ 100), we find that efficient transfer of energy from the inflaton condensate to radiative degrees of freedom, emergence of a radiation-dominated equation of state, and the onset of thermalization each consistently occur within $N_{\text{reh}} ≲ 3 e$-folds after the end of inflation, largely independent of the values of the other couplings in the models. The exception is the case of negative ellipticity, in which there is a misalignment between the dominant direction in field space along which the system evolves and the larger of the nonminimal couplings $ξ_I$. In those cases, the field-space-driven parametric resonance is effectively shut off. More generally, the competition between the scalar fields’ potential and the field-space manifold structure can yield interesting phenomena such as two-stage resonances. Across many regions of parameter space, we find efficient re-scattering between the distinct fields, leading to a partial memory loss of the shape of the initial fluctuation spectrum. Despite the explosive particle production, which can lead to a quick depletion of the background energy density, the nonlinear processes do not induce any superhorizon correlations after the end of inflation in these models, which keeps predictions for cosmic microwave background observables unaffected by the late-time amplification of isocurvature fluctuations. Hence the excellent agreement between primordial observables and recent observations is preserved for this class of models, even when we consider postinflation dynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Meteorite falls in China and some related human casualty events

Statistics of witnessed and recovered meteorite falls found in Chinese historical texts for the period from 700 B.C. to A.D. 1920 are presented. Several notable features can be seen in the binned distribution as a function of time. An apparent decrease in the number of meteorite reports in the 18th century is observed. An excess of observed meteorite falls in the period from 1840 to 1880 seems to correspond to a similar excess in European data. A chi sq probability test suggest that the association between the two data sets are real. Records of human casualities and structural damage resulting from meteorite falls are also given. A calculation based on the number of casualty events in the Chinese meteorite records suggests that the probability of a meteroite striking a human is far greater than previous estimates. However, it is difficult to verify the accuracy of the reported casualty events.

Yau, Kevin↗

Multireference symmetry-projected variational approximation for the ground state of the doped one-dimensional Hubbard model

The few determinant (FED) approximation introduced in our previous work [Phys. Rev. B 87, 235129 (2013)] is used to describe the ground state, characterized by well-defined spin and space group symmetry quantum numbers as well as doping fractions $N_e/N_{\text{sites}}$, of one-dimensional Hubbard lattices with nearest-neighbor hopping and periodic boundary conditions. Within this multireference scheme, each ground state is expanded in a given number of nonorthogonal and variationally determined symmetry-projected configurations. The results obtained for the ground-state and correlation energies of half-filled and doped lattices with 30, 34, and 50 sites compare well with the exact Lieb-Wu solutions as well as with those obtained with other state-of-the-art approximations. The structure of the intrinsic symmetry-broken determinants resulting from the variational procedure is interpreted in terms of solitons whose translational and breathing motions can be regarded as basic units of quantum fluctuations. It is also shown that in the case of doped one-dimensional lattices, a part of such fluctuations can also be interpreted in terms of polarons. In addition to momentum distributions, both spin-spin and density-density correlation functions are studied as functions of doping. Further, the spectral functions and density of states, computed with an ansatz whose quality can be well controlled by the number of symmetry-projected configurations used to approximate the $N_e$ ± 1 electron systems, display features beyond a simple quasiparticle distribution, as well as spin-charge separation trends.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Hybrid Organic Inorganic Perovskites: Physical Properties and Applications (in 4 Volumes)

This four-volume handbook gives a state-of-the-art overview of hybrid organic inorganic perovskites, both two dimensional (2D) and three dimensional (3D), from synthesis and characterization and simulation to optoelectronic devices (such as solar cells and light emitting diodes), spintronics devices and catalysis application. The editors, coming from academia and national laboratory, are known for their didactic skills as well as their technical expertise. Coordinating the efforts of 30 expert authors in 21 chapters, they construct the story of hybrid perovskite structural and optical properties, electronic and spintronic response, laser action, and catalysis from varied viewpoints: materials science, chemical engineering, and energy engineering. The four volumes are arranged according to the focus material properties. Volume 1 is focused on the material physical properties including structure, deposition characteristic and the structure of the electronic bands and excitons of these compounds. Volume 2 covers the hybrid perovskite optical properties including the ultrafast optical response, photoluminescence and laser action. Volume 3 contains the spin response of these compounds including application such as spin valves, photogalvanic effect, and magnetic response of light emitting diodes and solar cell devices. Finally, and highly relevant to tomorrow's energy challenges, volume 4 is focused on the physics and device properties of the most relevant applications of the hybrid perovskites, namely photovoltaic solar cells. The text contains many high-quality colorful illustrations and examples, as well as thousands of up-to-date references to peer-reviewed articles, reports and websites for further reading. This comprehensive and well-written handbook is a must-have reference for universities, research groups and companies working with the hybrid organic inorganic perovskites.

applications↗

Astrometric and Geodetic Properties of Earth and the Solar System

The mass, size and shape of planets and their satellites and are essential information from which one can consider the balance of gravity and tensile strength, chemical makeup and such factors as internal temperature or porosity. Orbits and planetary rotation are also useful clues concerning origin, internal structure and tidal history. The tables compiled here include some of the latest results such as detection of densities of Pluto-Charon from analysis of HST images and the latest results for Venus' shape, gravity field and pole orientation based on Magellan spacecraft data. Data concerning prominent asteroids, comets and Sun are also included. Most of the material here is presented as tables. They are preceded by brief explanations of the relevant geophysical and orbit parameters. More complete explanations can be found in any of several reference texts on geodesy, geophysics and celestial mechanics.

Yoder, Charles F.↗

Extract useful information from building permits data to profile a city’s building retrofit history

Building retrofit is one of the key strategies for cities to reduce energy use and GHG emissions. The historical information about changes to buildings is crucial to infer the buildings’ current energy system efficiency levels and to identify candidate buildings for retrofit. In general, a building permit is required before the start of any construction activity of a building, such as changing building structure, remodeling, or installing new equipment. Moreover, many large cities provide public datasets of building permits in history. Therefore, the permits are a potentially good resource for mining information on the city’s retrofit history. In this study, we use the permit dataset from the city of San Francisco as a case study. Location and time information from the dataset is also used to depict the retrofit timeline of each building and the whole building stock. The type of work of the permit is inferred from the descriptive text by a machine learning model. At last, the limitations of the current permit dataset and potential improvements on the permit data management are discussed to better utilize the information in the future.

Zhang, Wanni↗

Creating Training Data for Scientific Named Entity Recognition with Minimal Human Effort

Scientific Named Entity Referent Extraction is often more complicated than traditional Named Entity Recognition (NER). For example, in polymer science, chemical structure may be encoded in a variety of nonstandard naming conventions, and authors may refer to polymers with conventional names, commonly used names, labels (in lieu of longer names), synonyms, and acronyms. As a result, accurate scientific NER methods are often based on task-specific rules, which are difficult to develop and maintain, and are not easily generalized to other tasks and fields. Machine learning models require substantial expert-annotated data for training. Here we propose polyNER: a semi-automated system for efficient identification of scientific entities in text. PolyNER applies word embedding models to generate entity-rich corpora for productive expert labeling, and then uses the resulting labeled data to bootstrap a context-based word vector classifier. Evaluation on materials science publications shows that the polyNER approach enables improved precision or recall relative to a state-of-the-art chemical entity extraction system at a dramatically lower cost: it required just two hours of expert time, rather than extensive and expensive rule engineering, to achieve that result. This result highlights the potential for human-computer partnership for constructing domain-specific scientific NER systems.

Crowdsourcing↗

Relative permeability as a stationary process: Energy fluctuations in immiscible displacement

Relative permeability is commonly used to model immiscible fluid flow through porous materials. In this work, we derive the relative permeability relationship from conservation of energy, assuming that the system to be non-ergodic at large length scales and relying on averaging in both space and time to homogenize the behavior. Explicit criteria are obtained to define stationary conditions: (1) there can be no net change for extensive measures of the system state over the time averaging interval; (2) the net energy inputs into the system are zero, meaning that the net rate of work done on the system must balance with the heat removed; and (3) there is no net work performed due to the contribution of internal energy fluctuations. Results are then evaluated based on direct numerical simulation. Dynamic connectivity is observed during steady-state flow, which is quantitatively assessed based the Euler characteristic. We show that even during steady-state flow at low capillary number ([Formula: see text]), typical flow processes will explore multiple connectivity states. The residence time for each connectivity state is captured based on the time-and-space average. The distribution for energy fluctuations is shown to be multi-modal and non-Gaussian when terms are considered independently. However, we demonstrate that their sum is zero. Given an appropriate choice of the thermodynamic driving force, we show that the conventional relative permeability relationship is sufficient to model the energy dissipation in systems with complex pore-scale dynamics that routinely alter the structure of fluid connected pathways.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NEPATEC2.0: NEPA Text Corpus v2.0

The National Environmental Policy Act of 1969, as amended (NEPA), is a major environmental law in the United States, requiring Federal agencies to consider and document potential environmental impacts before deciding on a proposed action. Modernization of NEPA and permitting processes faces significant challenges due to the lack of standardized formats and interoperable systems for organizing and sharing NEPA-related information across agencies. Much of the information gathered during NEPA reviews is written into documents such as categorical exclusions, environmental assessments, and environmental impact statements, then filed in predominately independent agency file stores that may or may not be publicly accessible. The application of metadata and data standards, such as those recommended by the Council on Environmental Quality (CEQ), to NEPA documents offers a shared vocabulary and structure for key entities like projects, processes, and documents that can streamline information exchange and enhance collaboration across systems. In this work, we publicly release NEPATEC2.0, an expanded corpus of NEPA documents with associated metadata. NEPATEC2.0 encompasses approximately 120,000 documents from 60,000 projects prepared by more than 60 different agencies. Modeled to align with CEQ metadata standards, NEPATEC2.0 promotes consistency in environmental reviews and supports the ongoing effort to modernize permitting technologies by facilitating more transparent, efficient, and data-driven decision-making. Importantly, NEPATEC2.0 demonstrates the possibilities and limitations of large language model-based prompting to extract information from NEPA documents at scale.

environmental review↗

Machine Learning and Social Media to Mine and Disseminate Big Scientific Data

One of the challenges in supplying the communities with wider access to scientific databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it might not be practical to make the public aware of the structure of databases. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide a more intuitive method for generating database queries and delivering responses. Through social media, which makes it possible to interact with a wide section of the population, and with the help of natural language processing, researchers at the Atmospheric Radiation Measurement (ARM) Data Center at Oak Ridge National Laboratory (ORNL) have developed a concept to enable easy search and retrieval of data from several environmental data centers for the scientific community through social media.Using a machine learning framework that maps natural language text to thousands of datasets, instruments, variables, and data streams, the prototype system would allow users to request data through Twitter and receive a link (via tweet) to applicable data results on the project's search catalog tailored to their key words. This automated identification of relevant data from various petascale archives at ORNL could increase convenience, access, and use of the project's data by the broader community. In this paper we discuss how some data-intensive projects at ORNL are using innovative ways to help in data discovery.

Devarakonda, Ranjeet↗

Nuclear Data Sheets for A = 195

Experimental structure and decay data for all nuclides with mass number A=195 (Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po, At, Rn) have been revised, updated, and incorporated into the ENSDF data file. All literature available by March 2014 has been considered. This evaluation supersedes the previous one for this mass chain (Zhou Chunmei, Nuclear Data Sheets 86, 645 (1999), 1999Zh11). The detailed level schemes, decay schemes, experimental reaction and decay data on which they are based are summarized and presented here. References, Jπ arguments, and comments are given in the text. No excited state data are yet available for {sup 195}Re and {sup 195}Rn. The adopted levels for {sup 195}At are firstly presented in this evaluation. In addition, Q values have been updated based on 2012Wa38.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Blending Education and Polymer Science: Semiautomated Creation of a Thermodynamic Property Database

Structured databases of chemical and physical properties play a central role in the everyday research activities of scientists and engineers. In materials science, researchers and engineers turn to these databases to quickly query, compare, and aggregate various properties, thereby allowing for the development or application of new materials. The vast majority of these databases have been generated manually, through decades of labor-intensive harvesting of information from the literature, yet while there are many examples of commonly used databases, a significant number of important properties remain locked within the tables, figures, and text of publications. The question addressed in our work is whether and to what extent the process of data collection can be automated. Students of the physical sciences and engineering are often confronted with the challenge of finding and applying property data from the literature, and a central aspect of their education is to develop the critical skills needed to identify such data and discern their meaning or validity. To address shortcomings associated with automated information extraction while simultaneously preparing the next generation of scientists for their future endeavors, we developed a novel course-based approach in which students develop skills in polymer chemistry and physics and apply their knowledge by assisting with the semiautomated creation of a thermodynamic property database.

Collaborative/Cooperative Learning↗

Spinoff 2012

Topics covered include: Water Treatment Technologies Inspire Healthy Beverages; Dietary Formulas Fortify Antioxidant Supplements; Rovers Pave the Way for Hospital Robots; Dry Electrodes Facilitate Remote Health Monitoring; Telescope Innovations Improve Speed, Accuracy of Eye Surgery; Superconductors Enable Lower Cost MRI Systems; Anti-Icing Formulas Prevent Train Delays; Shuttle Repair Tools Automate Vehicle Maintenance; Pressure-Sensitive Paints Advance Rotorcraft Design Testing; Speech Recognition Interfaces Improve Flight Safety; Polymers Advance Heat Management Materials for Vehicles; Wireless Sensors Pinpoint Rotorcraft Troubles; Ultrasonic Detectors Safely Identify Dangerous, Costly Leaks; Detectors Ensure Function, Safety of Aircraft Wiring; Emergency Systems Save Tens of Thousands of Lives; Oxygen Assessments Ensure Safer Medical Devices; Collaborative Platforms Aid Emergency Decision Making; Space-Inspired Trailers Encourage Exploration on Earth; Ultra-Thin Coatings Beautify Art; Spacesuit Materials Add Comfort to Undergarments; Gigapixel Images Connect Sports Teams with Fans; Satellite Maps Deliver More Realistic Gaming; Elemental Scanning Devices Authenticate Works of Art; Microradiometers Reveal Ocean Health, Climate Change; Sensors Enable Plants to Text Message Farmers; Efficient Cells Cut the Cost of Solar Power; Shuttle Topography Data Inform Solar Power Analysis; Photocatalytic Solutions Create Self-Cleaning Surfaces; Concentrators Enhance Solar Power Systems; Innovative Coatings Potentially Lower Facility Maintenance Costs; Simulation Packages Expand Aircraft Design Options; Web Solutions Inspire Cloud Computing Software; Behavior Prediction Tools Strengthen Nanoelectronics; Power Converters Secure Electronics in Harsh Environments; Diagnostics Tools Identify Faults Prior to Failure; Archiving Innovations Preserve Essential Historical Records; Meter Designs Reduce Operation Costs for Industry; Commercial Platforms Allow Affordable Space Research; Fiber Optics Deliver Real-Time Structural Monitoring; Camera Systems Rapidly Scan Large Structures; Terahertz Lasers Reveal Information for 3D Images; Thin Films Protect Electronics from Heat and Radiation; Interferometers Sharpen Measurements for Better Telescopes; and Vision Systems Illuminate Industrial Processes.

Source record↗

Spatially Resolved Recombination Analysis of CuIn $_\text{x}$ Ga $_\text{1-x}$ Se $_{2}$ Absorbers With Alkali Postdeposition Treatments

In this contribution, we probe spatial variations in charge-carrier recombination in CuIn x Ga 1-x Se 2 (CIGS) absorbers grown on soda-lime glass (SLG) and alkali-free sapphire substrates with NaF and KF postdeposition treatments (PDTs). Temperature-and illumination-dependent device measurements are used to track interface recombination and recombination in the quasi-neutral region. The analysis of these data reveals that the benefit of alkali PDTs depends on the substrate: interface recombination is reduced in devices grown on sapphire substrates, whereas recombination in the quasi-neutral regions is reduced in devices grown on SLG substrates. Cathodoluminescence (CL) spectrum imaging is used to study the spatial distribution of recombination with respect to the grain structure. The grain-boundary CL contrast is similar in films with no PDT, NaF PDT, or KF PDT. A reduced grain-boundary contrast is observed with a NaF + KF PDT; however, suggesting a reduced recombination strength at the grain boundaries (GBs) for combined NaF + KF treatment. CL spectra indicate band tailing, consistent with the fluctuating potential model. Fluctuating potentials are believed to reduce open-circuit voltage, but their spatial distribution has not been studied. Here, CL spectrum imaging data are used to generate maps of the root-mean-square value of the potential energy fluctuations-γ. These maps reveal a bimodal ..gamma.. distribution for all samples: ..gamma.. is generally in the range ~15-50 meV or ~100-180 meV. The higher ..gamma.. range is more significantly affected by the PDTs; after the PDTs, it is strongly correlated with GBs. The lower ..gamma.. range is correlated with higher emission intensity regions, typically grain interiors, and increases in area fraction after the PDTs. These results demonstrate how spatially resolved luminescence and device characterization measurements can be used to monitor changes in recombination in CIGS films and photovoltaic devices. Such measurements can complement empirical device optimization and help improve device performance.

14 SOLAR ENERGY↗

RNAcentral: a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality.

Sweeney, Blake A.↗

NEPATEC v2.0: Standardized Metadata and Text Corpus of National Environmental Policy Act Documents

The National Environmental Policy Act of 1969, as amended (NEPA), is a major environmental law in the United States, requiring Federal agencies to consider and document potential environmental impacts before deciding on a proposed action. Modernization of NEPA and permitting processes faces significant challenges due to the lack of standardized formats and interoperable systems for organizing and sharing NEPA-related information across agencies. Much of the information gathered during NEPA reviews is written into documents such as categorical exclusions, environmental assessments, and environmental impact statements, then filed in predominately independent agency file stores that may or may not be publicly accessible. The application of metadata and data standards, such as those recommended by the Council on Environmental Quality (CEQ), to NEPA documents offers a shared vocabulary and structure for key entities like projects, processes, and documents that can streamline information exchange and enhance collaboration across systems. In this work, we publicly release NEPATEC2.0, an expanded corpus of NEPA documents with associated metadata. NEPATEC2.0 encompasses approximately 120,000 documents from 60,000 projects prepared by more than 60 different agencies. Modeled to align with CEQ metadata standards, NEPATEC2.0 promotes consistency in environmental reviews and supports the ongoing effort to modernize permitting technologies by facilitating more transparent, efficient, and data-driven decision-making. Importantly, NEPATEC2.0 demonstrates the possibilities and limitations of large language model-based prompting to extract information from NEPA documents at scale.

54 ENVIRONMENTAL SCIENCES↗