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At least 37 records · Page 2

Identification of drug repurposing candidates for amyotrophic lateral sclerosis using electronic health records: a retrospective cohort study

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a life expectancy of only 3–5 years and few approved treatments. To identify drug repurposing candidates for the treatment of ALS, we analysed the electronic health records (EHRs) of a large cohort of military veterans with ALS. We analysed the EHRs of individuals in the US Veterans Health Administration (VHA) database who were diagnosed with ALS between Jan 1, 2009 and Dec 31, 2019 to assess medication effects. Individuals without recorded prescriptions after the date of diagnosis were excluded. Two sets of criteria were applied to ascertain exposure. Exposure criteria A were met if the dispense date or the end date of the medication was within 12 months of ALS diagnosis and the end date was at least 6 months after the dispense date. Exposure criteria B were met if there were at least two dispenses within 6 months before diagnosis and 12 months after diagnosis. Propensity score-matched control groups were generated on the basis of confounders included in the EHR, with methodology of potential outcomes used to infer treatment effects. The primary outcome was death. A standard Cox proportional hazards analysis was done to assess association with survival. Survival was defined as the time from diagnosis date recorded in the EHR to death reported in the Department for Veterans Affairs Vital Status File. Follow-up survival time was censored on Dec 31, 2020, for those alive on this date. Downstream protein targets of drugs with clinically significant effects were analysed using the protein–protein interaction networks-based algorithm PathFX. The EHRs of 11 003 individuals with ALS in the VHA database were appropriate for analysis. 162 medications with treatment groups of 30 or more individuals were identified. Among these 162 medications, 27 were associated with statistically significant changes (≥0·1) in the hazard ratio (HR) for death. 18 of the medications were associated with a reduced HR for death (prolonged survival), and nine were associated with an increased HR for death (reduced survival). Drugs associated with reduced HR included HMG-CoA reductase inhibitors (simvastatin, pravastatin, lovastatin, and atorvastatin), PDE5 inhibitors (vardenafil and sildenafil), and α-adrenergic antagonists (tamsulosin and terazosin). The medications associated with an increased HR were drugs used either in the management of clinical features of ALS associated with poor outcomes or in end-of-life care. PathFx analysis identified a complex of proteins interacting with several of the identified drugs. To our knowledge, this analysis is the largest EHR-based study for identifying drug repurposing candidates for ALS. We identified several drugs that warrant further assessment as therapeutic options in ALS, as well as a protein network complex that might serve as a therapeutic target for ALS.

Reimer, Richard J. [Stanford Univ., CA (United Sta

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated ß-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-?B signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

proteomics, PTM, automation, SP3, cysteine thiol o

Interconnected nanoconfining pore networks enhance catalyst CO 2 interaction in electrified reactive capture

Systems that sequentially capture and upgrade CO 2 from air to fuels/fuel-intermediates, such as syngas and ethylene, rely on an energy-intensive CO 2 release process. Electrified reactive capture systems transform CO 2 obtained directly from carbonate capture liquid into products. Previous reactive capture systems show a decline in Faradaic efficiencies (FE) at current densities above 200 mA/cm 2 . Here we show the chemical origins of this problem, finding that prior electrocatalyst designs failed to arrest, activate, and reduce in situ-generated CO 2 (i-CO 2 ) before it traversed the catalyst layer and entered the tailgas stream. We develop a templated synthesis to define pore structures and the sites of Ni single atoms, and find that carbon-nitrogen-based nanopores are effective in accumulating i-CO 2 via short-range, non-electrostatic interactions between CO 2 molecules and the nanochannel walls. These interactions confine and enrich i-CO 2 within the pores, enhancing its binding and activation. We report as a result carbonate electrolysis at 300 mA/cm 2 with FE to CO of 50% ± 3%, and with <1% CO 2 in the tailgas outlet stream. This corresponds to a projected energy efficiency (EE) to 2:1 syngas of 46% at 300 mA/cm 2 when H 2 is added using a water electrolyzer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Sparsomycin inhibits translation through a conserved mechanism across all domains of life

Abstract Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts—an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.

Paranjpe, Madhura N [Department of Biological Scie

A simple and highly efficient protocol for 13 C-labeling of plant cell wall for structural and quantitative analyses via solid-state nuclear magnetic resonance

Plant cell walls are made of a complex network of interacting polymers that play a critical role in plant development and responses to environmental changes. Thus, improving plant biomass and fitness requires the elucidation of the structural organization of plant cell walls in their native environment. The 13 C-based multi-dimensional solid-state nuclear magnetic resonance (ssNMR) has been instrumental in revealing the structural information of plant cell walls through 2D and 3D correlation spectral analyses. However, the requirement of enriching plants with 13 C limits the applicability of this method. To our knowledge, there is only a very limited set of methods currently available that achieve high levels of 13 C-labeling of plant materials using 13 CO 2 , and most of them require large amounts of 13 CO 2 in larger growth chambers. In this study, a simplified protocol for 13C-labeling of plant materials is introduced that allows ca 60% labeling of the cell walls, as quantified by comparison with commercially labeled samples. This level of 13 C-enrichment is sufficient for all conventional 2D and 3D correlation ssNMR experiments for detailed analysis of plant cell wall structure. The protocol is based on a convenient and easy setup to supply both 13 C-labeled glucose and 13 CO 2 using a vacuum-desiccator. The protocol does not require large amounts of 13 CO 2 . This study shows that our 13 C-labeling of plant materials can make the accessibility to ssNMR technique easy and affordable. The derived high-resolution 2D and 3D correlation spectra are used to extract structural information of plant cell walls. This helps to better understand the influence of polysaccharide-polysaccharide interaction on plant performance and allows for a more precise parametrization of plant cell wall models.

09 BIOMASS FUELS

Development and transferability of neural-network models for plasma-surface interactions

Plasma-surface interactions are increasingly critical to modern technologies; yet, accurate molecular dynamics simulations remain limited by the capabilities of interatomic potentials. Deep Potentials (DPs) promise to revolutionize the field by providing a systematic method for producing accurate interatomic potentials. The primary challenge of DP development is selecting a dataset, which efficiently spans the set of atomic environments one expects to encounter in the subsequent molecular dynamics simulations. The computational cost of density functional theory calculations, which are the typical basis for DP development, makes it impossible to directly verify the quality of a given DP. To address this challenge, we explore the development of a deep-learned interatomic potential, “DeepREBO,” trained to reproduce the behavior of the REBO2 empirical potential, enabling direct validation of training methodology and transferability. Using an active learning framework, we begin with a minimal dataset and iteratively expand it to train a Deep Potential-Smooth Edition model that faithfully reproduces REBO2 results for 25 eV hydrogen bombardment of diamond (001), a particularly challenging case. We show that small, carefully curated datasets can outperform large, unguided ones, with effective models requiring fewer than 15 000 snapshots. Subsequent transferability tests demonstrate that while DeepREBO generalizes well to diamond (111) surfaces, performance degrades for amorphous carbon or higher-energy impacts, highlighting the need for use-case-specific training data. We also evaluate methods to improve short-range repulsion. This study outlines best practices for training robust deep potentials and underscores the importance of dataset design for predictive plasma simulations.

Ab-initio molecular dynamics

Reconstruction and Selection of Neutrino Interactions in MicroBooNE using Deep Convolutional Neural Networks

In this document, we describe a new reconstruction workflow developed for the MicroBooNE experiment. It features the use of Deep Convolutional Neural Networks trained to recognize key structures within the data sufficient for the 3D reconstruction of neutrino interactions within the detector. As a test of the reconstruction utility, the products of the reconstruction workflow are used to select inclusive charged-current (CC) $\nu_e$ and $\nu_\mu$ interactions in both simulated and real MicroBooNE data. In simulation, our $\nu_e$ and $\nu_\mu$ selections achieve an efficiency of 57% and 68\%, respectively, with a purity of 91% and 96%, respectively. We find that these selections are competitive with the inclusive selections used for the most recent MicroBooNE LEE searches. In particular, the CC-$\nu_e$ inclusive selection efficiency improves by over 20% while also improving sample purity. As a first step in quantifying potential bias, the data and Monte Carlo expectati ons are compared for both selections using the MicroBooNE open data. Within statistical and systematic uncertainties, both the electron and muon CC-inclusive event samples agree. A comparison of the real data events chosen by our work and another reconstruction framework shows that the two analyses each identify a sizeable fraction of events the other does not. This suggests that future analyses integrating the strengths of each could lead to combined gains. This work demonstrates, for the first time on real LArTPC data, state-of-the-art neutrino interaction reconstruction centered around deep learning algorithms.

43 PARTICLE ACCELERATORS

NLML: A Deep Neural Network Emulator for the Exact Nonlinear Interactions in a Wind Wave Model

Nonlinear wave interactions describe the resonant energy transfer between wave components, playing a fundamental role in the evolution of ocean wave spectra. Nonlinear wave interactions significantly influence wave growth and development, making them essential for accurate wave modeling. However, resolving the full six-dimensional Boltzmann integral of the exact nonlinear wave interactions (Webb-Resio-Tracy method, WRT) is computationally expensive, limiting its application in real-time operational wave forecasting and for research purposes. Current approximations, such as the Discrete Interaction Approximation (DIA), prioritize computational speed over accuracy, resulting in significant errors in wave mean parameters. Here, we introduce NLML, a machine learning (ML) emulator designed to approximate the exact nonlinear wave interactions within WAVEWATCH III (WW3), with the goal of achieving the accuracy of WRT while maintaining the stability and computational speed of DIA. By leveraging GPU capabilities such as half precision inference, we achieved substantial speedups, up to 136x mathematical equation faster than the WRT and only a modest 1.04x mathematical equation slowdown relative to DIA, while achieving 2x mathematical equation the accuracy of DIA in global wave spectral energy and mean wave parameters, with up to 7x mathematical equation higher accuracy in some regions. Unlike previous ML approaches, NLML maintained inherent stability throughout model integration in a standalone, year-long WW3 simulation, without requiring additional constraints. Our new ML parameterization bridges the gap between accuracy and efficiency, offering a promising alternative for improving wave modeling in operational settings and research purposes.

16 TIDAL AND WAVE POWER

Exploring the nexus of many-body theories through neural network techniques: the tangent model

Abstract In this paper, we present a physically informed neural network (NN) representation of the effective interactions associated with coupled-cluster downfolding models to describe chemical systems and processes. The NN representation not only allows us to evaluate the effective interactions efficiently for various geometrical configurations of chemical systems corresponding to various levels of complexity of the underlying wave functions, but also reveals that the bare and effective interactions are related by a tangent function of some latent variables. We refer to this characterization of the effective interaction as a tangent model. We discuss the connection between this tangent model for the effective interaction with the previously developed theoretical analysis that examines the difference between the bare and effective Hamiltonians in the corresponding active spaces.

97 MATHEMATICS AND COMPUTING

Optimal Co-Design of Integrated Thermal-Electrical Networks and Control Systems for Grid-interactive Efficient District (GED) Energy Systems

This project advances a unified, open-source framework for the optimal co-design of thermal, electrical, and control systems in grid-interactive efficient districts (GEDs). As communities integrate growing levels of distributed energy resources, traditional approaches that model thermal and electrical networks independently lead to reduced efficiency, limited flexibility, and missed opportunities for coordinated operation. To address these challenges, the research team developed a comprehensive suite of physics-based models, control algorithms, and software tools that enable holistic simulation, optimization, and demonstration of district-scale energy systems.

14 SOLAR ENERGY

Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.

59 BASIC BIOLOGICAL SCIENCES

An integrated experimental–modeling approach to identify key processes for carbon mineralization in fractured mafic and ultramafic rocks

Abstract Controlling atmospheric warming requires immediate reduction of carbon dioxide (CO2) emissions, as well as the active removal and sequestration of CO2 from current point sources. One promising proposed strategy to reduce atmospheric CO2 levels is geologic carbon sequestration (GCS), where CO2 is injected into the subsurface and reacts with the formation to precipitate carbonate minerals. Rapid mineralization has recently been reported for field tests in mafic and ultramafic rocks. However, unlike saline aquifers and depleted oil and gas reservoirs historically considered for GCS, these formations can have extremely low porosities and permeabilities, limiting storage volumes and reactive mineral surfaces to the preexisting fracture network. As a result, coupling between geochemical interactions and the fracture network evolution is a critical component of long-term, sustainable carbon storage. In this paper, we summarize recent advances in integrating experimental and modeling approaches to determine the first-order processes for carbon mineralization in a fractured mafic/ultramafic rock system. We observe the critical role of fracture aperture, flow, and surface characteristics in controlling the quantity, identity, and morphology of secondary precipitates and present where the influence of these factors can be reflected in newly developed thermo-hydro-mechanical–chemical models. Our findings provide a roadmap for future work on carbon mineralization, as we present the most important system components and key challenges that we are overcoming to enable GCS in mafic and ultramafic rocks.

58 GEOSCIENCES

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding the interactions and regulatory relationships among biomolecules is essential for deciphering complex biological systems and elucidating the mechanisms behind diverse biological functions. Traditionally, the collection of such molecular interaction data has relied on expert curation, a process that is both time-consuming and labor-intensive. To address these limitations, this study explores the use of large language models (LLMs) to automate the genome-scale extraction of molecular interaction knowledge. Here, we evaluate the performance of various LLMs on key biological tasks, including the identification of protein-protein interactions, detection of genes associated with pathways influenced by low-dose radiation, and inference of gene regulatory relationships. Our findings demonstrate that larger LLMs tend to perform better, particularly in extracting intricate gene and protein interactions. Despite their strengths, these models face challenges in recognizing functionally diverse gene groups and highly correlated regulatory relationships. Through a comprehensive analysis using established molecular interaction and pathway databases, we show that LLMs possess the potential to identify relevant biomolecules and predict their interactions, offering valuable insights and marking a significant step toward AI-driven biological knowledge discovery.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN

Exact block encoding of imaginary time evolution with universal quantum neural networks

We develop a constructive approach to generate quantum neural networks capable of representing the exact thermal states of all many-body qubit Hamiltonians. The Trotter expansion of the imaginary time propagator is implemented through an exact block encoding by means of a unitary, restricted Boltzmann machine architecture. Marginalization over the hidden-layer neurons (auxiliary qubits) creates the nonunitary action on the visible layer. Then, we introduce a unitary deep Boltzmann machine architecture in which the hidden-layer qubits are allowed to couple laterally to other hidden qubits. We prove that this wave-function is closed under the action of the imaginary time propagator and, more generally, can represent the action of a universal set of quantum gate operations. We provide analytic expressions for the coefficients for both architectures, thus enabling exact network representations of thermal states without stochastic optimization of the network parameters. In the limit of large imaginary time, the yields the ground state of the system. The number of qubits grows linearly with the number of interactions and total imaginary time for a fixed interaction order. Both networks can be readily implemented on quantum hardware via midcircuit measurements of auxiliary qubits. If only one auxiliary qubit is measured and reset, the circuit depth scales linearly with imaginary time and number of interactions, while the width is constant. Alternatively, one can employ a number of auxiliary qubits linearly proportional to the number of interactions, and circuit depth grows linearly with imaginary time only. Every midcircuit measurement has a postselection success probability, and the overall success probability is equal to the product of the probabilities of the midcircuit measurements.

97 MATHEMATICS AND COMPUTING

Machine learning the electric field response of condensed phase systems using perturbed neural network potentials

Abstract The interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å −1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields.

Science & Technology - Other Topics

Simultaneous global and local clustering in multiplex networks with covariate information

Understanding both global and layer-specific group structures is useful for uncovering complex patterns in networks with multiple interaction types. In this work, we introduce a new model, the hierarchical multiplex stochastic blockmodel, which simultaneously detects communities within individual layers of a multiplex network while inferring a global node clustering across the layers. A stochastic blockmodel is assumed in each layer, with probabilities of layer-level group memberships determined by a node’s global group assignment. Our model uses a Bayesian framework, employing a probit stick-breaking process to construct node-specific mixing proportions over a set of shared Griffiths–Engen–McCloseky distributions. These proportions determine layer-level community assignment, allowing for an unknown and varying number of groups across layers, while incorporating nodal covariate information to inform the global clustering. We propose a scalable variational inference procedure with parallelisable updates for application to large networks. Extensive simulation studies demonstrate our model’s ability to accurately recover both global and layer-level clusters in complicated settings, and applications to real data showcase the model’s effectiveness in uncovering interesting latent network structure.

community detection

Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human brain and hiPSC-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 493 synaptic candidates supported by proteomics. We further investigate three such proteins that are associated with neurodevelopmental disorders – the CUL3 E3 ubiquitin ligase, the DDX3X and YBX1 nucleic-acid binding proteins – by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to systematically and more comprehensively resolve the synaptic architecture.

59 BASIC BIOLOGICAL SCIENCES

Belowground cross-trophic networks impact CH4 and CO2 emissions in degraded alpine peatlands

Belowground organisms forming complex cross-trophic ecological networks are essential for maintaining peatland carbon stability and energy flow. However, how peatland degradation affects the biodiversity and cross-trophic ecological networks of soil communities remains poorly understood. Here, we examined the degradation effects on soil prokaryotes (i.e., bacteria, archaea), fungi and nematodes in alpine peatlands on the eastern Tibetan Plateau, characterized by varying water table depths (indicating degradation levels). We found that peatland degradation, accompanied by significant shifts in soil moisture and pH (P < 0.05), reduced the taxonomic richness and phylogenetic diversity of prokaryotes, fungi, and nematodes, particularly in deeper soil layers (20–50 cm). Crucially, peatland degradation weakened potential cross-trophic interactions within bipartite networks of prokaryotes-nematodes and fungi-nematodes, resulting in less than 6.5 %–28.8 % of unchanged modules. Degradation-induced changes in soil moisture and pH were identified as primary drivers of biodiversity loss and network restructuring. Furthermore, such changes of belowground cross-trophic networks (particularly prokaryote-nematode) were significantly correlated with greenhouse gas emissions, such as decreased CO2 emissions, maintained CH4 emissions (leading to a higher CH4/CO2 ratio in deep layers), and reduced temperature sensitivity (Q10) of soil respiration. These findings underscore the critical need to protect soil biodiversity and cross-trophic networks in peatlands, particularly under the threat of climate change, to preserve peatland carbon stocks and maintain ecosystem stability. Our findings highlight that belowground cross-trophic networks are pivotal to decipher soil carbon dynamics of degraded peatlands and project the fate of peatland carbon stocks under future climate change scenarios.

Cross-trophic networks