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This presentation applies open set recognition to classify unknown waveforms, enabling systems to not only identify known types but also reliably detect when waveforms fall outside the training distribution. This approach enhances robustness by avoiding forced misclassification of novel or anomalous signals.
Methanogenic archaea are particularly rich in iron–sulfur proteins, yet their roles remain largely enigmatic. Here, we characterized aMethanococcus voltae(Mvo) protein from the domain of unknown function (DUF) 2193 family, a group of proteins present primarily in archaea and characterized by a conserved cysteine‐rich C‐terminal motif.MvoDUF2193 was heterologously expressed and characterized by a range of spectroscopic and analytical methods. The results demonstrate thatMvoDUF2193 binds a single [4Fe–4S] cluster per subunit and that cluster occupancy regulates the transition from an apo tetramer to a [4Fe–4S] monomeric form. We hypothesize thatMvoDUF2193 serves a regulatory role in the cell, mediated by [Fe–S] cluster binding and changes in oligomeric state.
The lack of available information on the presence and persistence of fentanyl in the environment is a significant gap in the technical literature. Although the origins of the opioid in the environment are well-known because they follow the same pathways of other drug-related environmental contaminants, the downstream effects of fentanyl in the water supply and its retention in soil are less understood. The characterization of fentanyl and its potential degradation products in complex environmental samples such as soil is severely understudied. Very few articles are available that work to identify fentanyl and its degradation products in complex samples or name the possible hazards that may result from environmental exposure and degradation. Therefore, the objectives were to identify available articles focused on environmental fentanyl and its pathways and highlight quantifiable research or results that included specific degradation products or downstream effects. Research articles focused on fentanyl between 2000 and 2024 were identified and reviewed and then filtered using Boolean search terms for environmental parameters. Various studies have determined that trace levels of fentanyl can be found in a variety of environments, and additional data suggest preferential partitioning into soils from water and long-term persistence. Despite this knowledge, very little data exists on the long-term downstream effects of fentanyl or its analogs. As the chronic effects from low-level fentanyl exposure are currently unknown, this lack of insight brings to the forefront the need for further research to improve our understanding of fentanyl persistence, degradation, and toxicity within the environment.
Imposing a boundary condition on a structure can significantly alter its dynamic properties. However, sometimes the specifics of the new boundary conditions are not known. When the effects of a boundary condition are uncertain or there is not enough information, engineers need to excite the complex structure to obtain these modified properties. In order to experimentally obtain the new properties, engineers need multiple experiments and many outputs for interpolation in order to sufficiently represent the entire structure. In this study, the researchers attached a stinger to a cantilever beam, acting as a new transverse restraint of unknown properties. This paper presents a conversion expression that predicts the dynamic behavior of any point in the system with the new boundary condition. This expression relies only on one impact hammer experiment with one output and the model of the stinger-free cantilever beam, referred to as the simple structure. Researchers estimated the Transfer Function (TRF) of the beam and compared it with an experimentally measured TRF to validate the method. The mean absolute error of the estimated TRF compared to the experimental TRF is 1.99 dB. This demonstrates the use of the proposed method for estimating unmeasured TRFs in a system with an uncertain boundary condition using a single input, single output (SISO) test and a model of the simple structure.
In this paper, we consider the frequency synchronization problem in a network of lossless, connected, and network-reduced power system. Frequency synchronization is an important problem in power systems as frequency deviation can lead to degraded power quality, tripping of generators, etc. We present a load-estimator-based consensus algorithm in a network of fourth-order generator models that achieves practical frequency synchronization in the presence of unknown time-varying power demand. We do not assume that the demand is generated by a known model. We follow a multiple time-scale approach for the stability analysis. It is shown that synchronization is achieved for the case of constant power demand, by showing that the system is exponentially stable. Furthermore, for the case of time-varying power demand, we show the error trajectories are ultimately bounded, and the synchronization error is proportional to an upper bound on the derivative of the time-varying power demand. We simulate the controller performance on a four area network which is equivalent to the IEEE New England 39-Bus system.
X-ray ptychography provides exceptional nanoscale resolution and is widely applied in materials science, biology, and nanotechnology. However, its full potential is constrained by the critical challenge of accurately reconstructing images when the illuminating probe is unknown. Conventional iterative methods and deep learning approaches are often suboptimal, particularly under the low-signal conditions inherent to low-dose and high-speed experiments. These limitations compromise reconstruction fidelity and restrict the broader adoption of the technique. In this work, we introduce the Ptychographic Implicit Neural Representation (PtyINR), a self-supervised framework that simultaneously addresses the object- and probe-recovery problem. By parameterizing both as continuous neural representations, PtyINR performs end-to-end reconstruction directly from raw diffraction patterns without requiring any pre-characterization of the probe. Extensive evaluations demonstrate that PtyINR achieves superior reconstruction quality on both simulated and experimental data, with remarkable robustness under challenging low-signal conditions. Furthermore, PtyINR offers a generalizable, physics-informed framework for addressing probe-dependent inverse problems, making it applicable to a wide range of computational microscopy problems.
For decades, researchers have sought to understand how the irreversibility of the surrounding world emerges from the seemingly time-symmetric, fundamental laws of physics. Quantum mechanics conjectured a clue that final irreversibility is set by the measurement procedure and that the time-reversal requires complex conjugation of the wave function, which is overly complex to spontaneously appear in nature. Building on this Landau-Wigner conjecture, it became possible to demonstrate that time-reversal is exponentially improbable in a virgin nature and to design an algorithm artificially reversing a time arrow for a given quantum state on the IBM quantum computer. However, the implemented arrow-of-time reversal embraced only the known states initially disentangled from the thermodynamic reservoir. Here we develop a procedure for reversing the temporal evolution of an arbitrary unknown quantum state. This opens the route for general universal algorithms sending temporal evolution of an arbitrary system backward in time.
Equations of state (EOSs) are a key component in running hydrodynamic simulations as they relate the thermodynamic states for the material. The Davis reactants EOS is commonly used for modeling high explosives (HEs), and the EOS model parameters are calibrated using material specific data. The calibrations are often performed with uncertainty quantification via Bayesian inference to account for uncertainty in the data and generate ensembles of likely parameters. However, there are relatively few HE data sets to use for calibration and many are historical and lack error information. In this work, we simultaneously calibrate the Davis reactants EOS model parameters and unknown data error terms for the high explosive PBX 9501. To quantify the uncertainty in the models and the data, we use a Bayesian framework for the calibration and compute the hierarchical Bayesian posterior distribution with both a posteriori maximization approach and Markov Chain Monte Carlo. In general, we find that, given our assumptions, the two approaches result in similar calibrated parameters, posterior covariance matrices, and insights about the parameters but that the posterior maximization requires far less computational resources.
We present a learning algorithm for discovering conservation laws given as sums of geometrically local observables in quantum dynamics. This includes conserved quantities that arise from local and global symmetries in closed and open quantum many-body systems. The algorithm combines the classical shadow formalism for estimating expectation values of observable and data analysis techniques based on singular value decompositions and robust polynomial interpolation to discover all such conservation laws in unknown quantum dynamics with rigorous performance guarantees. Our method can be directly realized in quantum experiments, which we illustrate with numerical simulations, using closed and open quantum system dynamics in a ℤ 2 gauge theory and in many-body localized spin chains.
Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.
This paper presents a secure reinforcement learning (RL) based control method for unknown linear time-invariant cyber-physical systems (CPSs) that are subjected to compositional attacks such as eavesdropping and covert attack. We consider the attack scenario where the attacker learns about the dynamic model during the exploration phase of the learning conducted by the designer to learn a linear quadratic regulator (LQR), and thereafter, use such information to conduct a covert attack on the dynamic system, which we refer to as doubly learning-based control and attack (DLCA) framework. We propose a dynamic camouflaging based attack-resilient reinforcement learning (ARRL) algorithm which can learn the desired optimal controller for the dynamic system, and at the same time, can inject sufficient misinformation in the estimation of system dynamics by the attacker. The algorithm is accompanied by theoretical guarantees and extensive numerical experiments on a consensus multi-agent system and on a benchmark power grid model.
This paper delves into designing feedback control gains for a continuous-time linear quadratic regulator (LQR) problem that is constrained to certain predefined structure with unknown state matrix. We bring forth the ideas from reinforcement learning (RL) in conjunction with sufficient stability and performance guarantees in order to design these structured gains using the trajectory measurements of states and controls. Here we first formulate a model-based framework using dynamic programming (DP) to embed the structural constraint to the LQR gain computation in the continuous-time setting, and then subsequently, formulate a policy iteration RL algorithm that can alleviate the requirement of known state matrix in conjunction with maintaining the feedback gain structure. The design enables a distributed learning control design which is necessary for many large-scale cyber-physical systems. Theoretical guarantees are provided for stability and convergence of the structured reinforcement learning (SRL) algorithm. We validate our theoretical results with numerical simulations on a multi-agent networked linear time-invariant (LTI) dynamic system.
Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.
Our basic understanding of carbon cycling in the biosphere remains qualitative and incomplete, precluding our ability to effectively engineer novel solutions to climate change. How can we attempt to engineer the unknown? This challenge has been faced before in plant biology, providing a roadmap to guide future efforts. We use examples from over a century of photosynthesis research to illustrate the key principles that will set future plant engineering on a solid footing, namely, an effort to identify the key control variables, quantify the effects of systematically tuning these variables, and use theory to account for these observations. The main contributions of plant synthetic biology will stem not from delivering desired genotypes but from enabling the kind of predictive understanding necessary to rationally design these genotypes in the first place. Only then will synthetic plant biology be able to live up to its promise.
Researchers have recently estimated that Arctic submarine permafrost currently traps 60 billion tons of methane and contains 560 billion tons of organic carbon in seafloor sediments and soil, a giant pool of carbon with potentially large feedbacks on the climate system. Unlike terrestrial permafrost, the submarine permafrost system has remained a “known unknown” because of the difficulty in acquiring samples and measurements. Consequently, this potentially large carbon stock never yet considered in global climate models or policy discussions, represents a real wildcard in our understanding of Earth’s climate. This report summarizes our group’s effort at developing a numerical modeling framework designed to produce a first-of-its-kind estimate of Arctic methane gas releases from the marine sediments to the water column, and potentially to the atmosphere, where positive climate feedback may occur. Newly developed modeling capability supported by the Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories now gives us the ability to probabilistically map gas distribution and quantity in the seabed by using a hybrid approach of geospatial machine learning, and predictive numerical thermodynamic ensemble modeling. The novelty in this approach is its ability to produce maps of useful data in regions that are only sparsely sampled, a common challenge in the Arctic, and a major obstacle to progress in the past. By applying this model to the circum-Arctic continental shelves and integrating the flux of free gas from in situ methanogenesis and dissociating gas hydrates from the sediment column under climate forcing, we can provide the most reliable estimate of a spatially and temporally varying source term for greenhouse gas flux that can be used by global oceanographic circulation and Earth system models (such as DOE’s E3SM). The result will allow us to finally tackle the wildcard of the submarine permafrost carbon system, and better inform us about the severity of future national security threats that sustained climate change poses.
All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.
The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified 14 genes from the DMP family in soybean (Glycine max) and characterized their physiochemical properties, subcellular location, gene structure, and promoter regions using bioinformatics tools. Additionally, their tissue-specific and stress-responsive expressions were analyzed using publicly available transcriptome data. Phylogenetic analysis of 198 DMPs from monocots and dicots revealed six clades, with clade-I encoding senescence-related AtDMP1/2 orthologues and clade-II including pollen-specific AtDMP8/9 orthologues. The largest clade, clade-III, predominantly included monocot DMPs, while monocot- and dicot-specific DMPs were assembled in clade-IV and clade-VI, respectively. Evolutionary analysis suggests that soybean GmDMPs underwent purifying selection during evolution. Using 68 transcriptome datasets, expression profiling revealed expression in diverse tissues and distinct responses to abiotic and biotic stresses. The genes Glyma.09G237500 and Glyma.18G098300 showed pistil-abundant expression by qPCR, suggesting they could be potential targets for female organ-mediated haploid induction. Furthermore, cis-acting regulatory elements primarily related to stress-, hormone-, and light-induced pathways regulate GmDMPs, which is consistent with their divergent expression and suggests involvement in growth and stress responses. Overall, our study provides a comprehensive report on the soybean GmDMP family and a framework for further biological functional analysis of DMP genes in soybean or other crops.
Bayesian inference is used to calibrate a bottom-up home PLC network model with unknown loads and wires at frequencies up to 30 MHz. A network topology with over 50 parameters is calibrated using global sensitivity analysis and transitional Markov Chain Monte Carlo (TMCMC). The sensitivity-informed Bayesian inference computes Sobol indices for each network parameter and applies TMCMC to calibrate the most sensitive parameters for a given network topology. A greedy random search with TMCMC is used to refine the discrete random variables of the network. This results in a model that can accurately compute the transfer function despite noisy training data and a high dimensional parameter space. The model is able to infer some parameters of the network used to produce the training data, and accurately computes the transfer function under extrapolative scenarios.