Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2)
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99 GENERAL AND MISCELLANEOUS↗
SEARCH · Engineering Papers
Results for “SIGNALS”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage
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Lau, Rebecca K.↗
SIGNALS A Flexible Tool for Radiometry, Sensor Modeling, and Signal Analysis
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Kramer, Cove Jade [Sandia National Laboratories (S↗
From Signal Processing to Signaling Traffic: Using Digital Twins to Improve Traffic and Reduce Our Carbon Footprint
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Brogan, Joel↗
Channel capacity: limitation of entropy rate during cell signal transduction
Cellular signal transduction is mediated through chain activation reactions involving signalling molecules. Information thermodynamics may be a promising approach for quantifying signal transduction. A cell signal is transduced through the signal molecule activation as a step of a signal transduction cascade. In each step, two types of entropy can be defined. First, the signal transduction was defined using thermodynamic entropy production during the chemical activation of signal molecules. Second, the chronology was described as a code string, and the logarithm of the number of signal code strings corresponded to the information entropy. Finally, the total entropy during signal transduction was determined by summing the two entropies. When maximising the total entropy, the total entropy rate per signalling molecule concentration was found to be consistent independently of each transduction step (i.e., signal molecule types). Consequently, the speed limit of the entropy rate can be calculated, providing the capacity, which is an essential property of the signal transduction cascade. The theory introduced here is expected to provide a basic framework for understanding new methods of discovering signal cascades and intracellular signal transduction.
59 BASIC BIOLOGICAL SCIENCES↗
Dimensionally Aligned Signal Projection Algorithms Library
Dimensionally aligned signal projection (DASP) algorithms are used to analyze fast Fourier transforms (FFTs) and generate visualizations that help focus on the harmonics for specific signals. At a high level, these algorithms extract the FFT segments around each harmonic frequency center, and then align them in equally sized arrays ordered by increasing distance from the base frequency. This allows for a focused view of the harmonic frequencies, which, among other use cases, can enable machine learning algorithms to more easily identify salient patterns. This work seeks to provide an effective open-source implementation of the DASP algorithms proposed by Vann et al. (2018) as well as functionality to help explore and test how these algorithms work with an interactive dashboard and signal-generation tool. The DASP library is implemented in Python and contains four types of algorithms for implementing these feature engineering techniques: fixed harmonically aligned signal projection (HASP), decimating HASP, interpolating HASP, and frequency aligned signal projection (FASP). Each algorithm returns a numerical array, which can be visualized as an image. The HASP algorithms are variations of the algorithms originally presented by Vann et al. (2018). For consistency, FASP, which is the terminology used for the short-time Fourier transform (STFT), has been implemented as part of the library to provide a similar interface to the STFT of the raw signal. Additionally, the library contains an algorithm to generate artificial signals with basic customizations such as the base frequency, sample rate, duration, number of harmonics, noise, and number of signals. Finally, the library provides multiple interactive visualizations, each of which is implemented using IPyWidgets and works in a Jupyter environment. A dashboard-style visualization is provided, which contains some common signal-processing visual components (signal, FFT, spectogram) updating in unison with the HASP functions (see Figure 1 below). Separate from the dashboard, an independent visualization is provided for each of the DASP algorithms as well as for the artifical signal generator. These visualizations are included in the library to aid in developing an intuitive understanding how the algorithms are affected by different input signals and parameter selections.
harmonics↗
Epidermal growth factor receptor cascade prioritizes the maximization of signal transduction
Many studies have been performed to quantify cell signaling. Cell signaling molecules are phosphorylated in response to extracellular stimuli, with the phosphorylation sequence forming a signal cascade. The information gain during a signal event is given by the logarithm of the phosphorylation molecule ratio. The average information gain can be regarded as the signal transduction quantity (ST), which is identical to the Kullback–Leibler divergence (KLD), a relative entropy. We previously reported that if the total ST value in a given signal cascade is maximized, the ST rate (STR) of each signaling molecule per signal duration (min) approaches a constant value. To experimentally verify this theoretical conclusion, we measured the STR of the epidermal growth factor (EGF)-related cascade in A431 skin cancer cells following stimulation with EGF using antibody microarrays against phosphorylated signal molecules. The results were consistent with those from the theoretical analysis. Thus, signaling transduction systems may adopt a strategy that prioritizes the maximization of ST. Furthermore, signal molecules with similar STRs may form a signal cascade. In conclusion, ST and STR are promising properties for quantitative analysis of signal transduction.
59 BASIC BIOLOGICAL SCIENCES↗
Automated Signal Timing Plan Reconstruction Using High-Resolution Event-Based Controller Data for Digital Twins
Transportation digital twins are essential tools for evaluating emerging technologies such as connected and automated vehicles, adaptive traffic signal control, and mobility optimization strategies. Realistic digital twins require accurate emulation of real-world signal controllers and detailed signal timing plans. However, signal timing plans are often unavailable or difficult to access, forcing researchers and modelers to rely on assumed fixed timings or halt their analysis. To overcome this challenge, we present a method that directly estimates signal timing plan parameters using high-resolution, event-based data from traffic signal controllers. The proposed method extracts key parameters, including cycle length, offset, phase sequence, coordinated phases, phase-specific minimum and maximum green durations, vehicle extensions, and splits under coordination. A rule-based deterministic signal timing reconstruction algorithm based on traffic signal operation rules, such as those outlined in the Signal Timing Manual, is developed and validated. We evaluate this method, which uses high-resolution controller event logs and verified signal timing plans, on 94 signalized intersections in Nashville, Tennessee, demonstrating their ability to generate accurate, simulation-ready signal timing plans for tools such as SUMO and Vissim.
Saroj, Abhilasha [ORNL] (ORCID:0000000191178063)↗
Signal sequences target enzymes and structural proteins to bacterial microcompartments and are critical for microcompartment formation
ABSTRACT Spatial organization of pathway enzymes has emerged as a promising tool to address several challenges in metabolic engineering, such as flux imbalances and off-target product formation. Bacterial microcompartments (MCPs) are a spatial organization strategy used natively by many bacteria to encapsulate metabolic pathways that produce toxic, volatile intermediates. Several recent studies have focused on engineering MCPs to encapsulate heterologous pathways of interest, but how this engineering affects MCP assembly and function is poorly understood. In this study, we investigated the role of signal sequences, short domains that target proteins to the MCP core, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterized two novel Pdu signal sequences on the structural proteins PduM and PduB, which constitute the first report of metabolosome signal sequences on structural proteins rather than enzymes. We then explored the role of enzymatic and structural Pdu signal sequences on MCP assembly by deleting their encoding sequences from the genome alone and in combination. Deleting enzymatic signal sequences decreased the MCP formation, but this defect could be recovered in some cases by overexpressing genes encoding the knocked-out signal sequence fused to a heterologous protein. By contrast, deleting structural signal sequences caused similar defects to knocking out the genes encoding the full-length PduM and PduB proteins. Our results contribute to a growing understanding of how MCPs form and function in bacteria and provide strategies to mitigate assembly disruption when encapsulating heterologous pathways in MCPs. IMPORTANCE Spatially organizing biosynthetic pathway enzymes is a promising strategy to increase pathway throughput and yield. Bacterial microcompartments (MCPs) are proteinaceous organelles that many bacteria natively use as a spatial organization strategy to encapsulate niche metabolic pathways, providing significant metabolic benefits. Encapsulating heterologous pathways of interest in MCPs could confer these benefits to industrially relevant pathways. Here, we investigate the role of signal sequences, short domains that target proteins for encapsulation in MCPs, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterize two novel signal sequences on structural proteins, constituting the first Pdu signal sequences found on structural proteins rather than enzymes, and perform knockout studies to compare the impacts of enzymatic and structural signal sequences on MCP assembly. Our results demonstrate that enzymatic and structural signal sequences play critical but distinct roles in Pdu MCP assembly and provide design rules for engineering MCPs while minimizing disruption to MCP assembly.
Johnson, Elizabeth R. (ORCID:0000000179236881)↗
Continuous dithered waveform averaging for high-fidelity digitization of repetitive signals
Methods and devices for digitizing an analog repetitive signal using waveform averaging are described. An example method includes generating a time-varying dither signal, receiving the analog repetitive signal comprising multiple instances of a waveform, wherein each waveform has a waveform duration, wherein an average of the time-varying dither signal over multiple waveform durations is substantially zero, and wherein the time-varying dither signal varies over each waveform duration, generating a timing alignment, combining each waveform with the corresponding portion of the time-varying dither signal over each waveform duration to produce an analog output signal, converting the analog output signal to a digital output signal, and producing, based on the timing alignment, a digital averaged signal based on averaging the multiple instances of the waveform in the analog output signal, wherein the timing alignment is used to align the multiple instances of the waveform in the analog output signal.
Buckley, Brandon Walter↗
Scrambling Signal Modularity in Bottom-up Assembled Synthetic Pseudomonas Consortia Reveals Robust Information Transfer
There is immense potential in crafting synthetic microbial communities for application in human health, agriculture, the environment, and even biomanufacturing where an appropriately constructed consortium can be assembled with tremendous biosynthetic or degradative capabilities. In many of these cases, bacterial signaling serves as a form of intercellular information transfer that guides the collective’s behavior. Such communication is complex, as many signals, signal disruptors, microbial species, physical barriers, and spatiotemporal constraints may be involved. Here, in this work, we demonstrate that a multisignal pathway for molecular information transfer within a consortium of several Pseudomonas spp. can be scrambled (genetically and organizationally) while the original message is still effectively conveyed. Assembled from the bottom up, we have employed two types of signaling molecules (i) a redox active secondary metabolite (rhizospheric signal, phloroglucinol), and (ii) a bacterial quorum sensing signal (3-oxo-C12 acylhomoserine lactone, AI-1). These signals can be intraconverted and acted upon by designated community members. We show how the order in which the signals are received, transduced, and subsequently transmitted can be rearranged with minimal impact on the intended outcome. In the consortial context, we found this messaging structure can be remarkably robust. Inspired by rhizospheric molecular signaling mechanisms, this work provides a conceptual framework for designing signaling and information transfer processes within assembled communities.
Biological and medical sciences↗
Kullback–Leibler Divergence of an Open-Queuing Network of a Cell-Signal-Transduction Cascade
Queuing networks (QNs) are essential models in operations research, with applications in cloud computing and healthcare systems. However, few studies have analyzed the cell’s biological signal transduction using QN theory. This study entailed the modeling of signal transduction as an open Jackson’s QN (JQN) to theoretically determine cell signal transduction, under the assumption that the signal mediator queues in the cytoplasm, and the mediator is exchanged from one signaling molecule to another through interactions between the signaling molecules. Each signaling molecule was regarded as a network node in the JQN. The JQN Kullback–Leibler divergence (KLD) was defined using the ratio of the queuing time (λ) to the exchange time (μ), λ/μ. The mitogen-activated protein kinase (MAPK) signal-cascade model was applied, and the KLD rate per signal-transduction-period was shown to be conserved when the KLD was maximized. Our experimental study on MAPK cascade supported this conclusion. This result is similar to the entropy-rate conservation of chemical kinetics and entropy coding reported in our previous studies. Thus, JQN can be used as a novel framework to analyze signal transduction.
97 MATHEMATICS AND COMPUTING↗
A Sparse and Low Rank Penalized Signal Decomposition Model with Constraints: Anomaly Detection in PV Systems
Recently, robust PCA has seen its wide application in various industries for its ability to perform the task of anomaly detection. The essence of robust PCA approach is to break down the signal into a low rank component and sparse component. In many applications, a simple breakdown of the signal without accounting for the signs of low rank components and sparse components would violate the physical constraints of the decomposed signal. In addition, often times, the signals in the real world collected for a long duration has smooth changes within a day and between days. As an example, the power signals collected in a photovoltaic (PV) system are cyclostationary, exhibiting these characteristics. Neglecting the smoothness of signals would result in miss detection of anomalous signals which are smooth within a day but non-smooth between days and vice versa. In this paper, we developed a signal decomposition approach for the purpose of anomaly detection based on the idea of low rank and sparse decomposition taking into consideration the signs of the decomposed low rank and sparse components and the within-day and between-day smooth changes in the original signals. The proposed unsupervised approach for fault detection eliminates the need for faulty samples required by other machine learning methods. It does not require the full I-V characteristics to work. Furthermore, there is no need for complex modelling of PV systems as in the case of power loss analysis. Using Monte Carlo simulations, we demonstrate the ability of our proposed approach for detecting anomalies of different duration and severity in PV systems.
14 SOLAR ENERGY↗
Scalable and Actionable Performance Measures for Traffic Signal Systems using Probe Vehicle Trajectory Data
Scalable and actionable performance measures for traffic signal systems provide opportunities for practitioners to measure and improve the transportation network. Historically, traffic signal improvements have relied on scheduled signal retiming based on limited data collection, or on the public to call and alert engineers of an issue. This inefficient method of improving signal timing led to the creation of automated traffic signal performance measures (ATSPMs). These metrics rely on expensive infrastructure, including detection and communications, which has produced barriers for numerous agencies to fully adopt. Recently, third-party data providers have begun to release vehicle trajectory data, which allows for enhanced signal metrics with no investment in physical equipment. The purpose of this study is to demonstrate the use of these data and summarize the scalability of the created metrics. This work builds on previous efforts to quantify signal performance on nine intersections in Michigan, U.S. Ten signalized corridors in Columbus, Ohio, were chosen to scale a performance assessment using crowdsourced trajectory data. A total of 136 intersections were assessed in 2-h intervals using data from all weekdays in 2017. High-level corridor summary metrics including average percent of vehicles stopping (18%–32%), average delay (9.4–20.5 s), and level of travel time reliability (1.23–2.73) were calculated for each corridor direction. Intersection-level metrics were also introduced, which can be used by practitioners to identify problems, improve signal timings, and prioritize future infrastructure investments.
99 GENERAL AND MISCELLANEOUS↗
Correction for Neutral Pressure-Driven Signal in Radiated Power Measurements on Proto-MPEX
A pinhole camera using four-channel resistive bolometers was designed and implemented on the Prototype Material Plasma Exposure eXperiment (Proto-MPEX) to measure the plasma radiated power. Quantification of the radiated power is required for comprehensive power balance assessments but faces unique challenges on linear plasma devices due to weak absolute signal, compared to typical use in toroidal fusion plasmas, and high neutral pressure changes. Around 1 mTorr, the pressure-driven signal contribution was shown to overwhelm the radiated power signal in Proto-MPEX, found to be ~3 μW . Since the pressure-driven signals could not be predicted from first principle arguments, the signals were corrected using empirical models that take two experimental pressure measurements and the raw bolometer signal to reveal the radiated power signals. Four “gas-only” Proto-MPEX shots were taken, without the radio frequency (rf) plasma discharge, to train, optimize, and validate empirical models. The data included two pressure measurements at different locations along with the bolometer signal. Multiple models were tested; partial least-squares regression with a cross correlation method to account for the time offset in the pressure measurements provided the best combination of accuracy and stability. The model was validated to have a modeling error of 0.0036 V, which was lower than 10% of the expected radiated power signal. The model was tested on a different “gas-only” shot with a complete time-series data. For plasma operation shots, the corrected bolometer measurements were compared with an absolute extreme ultraviolet photodiode measurement and similarities and differences are discussed.
Lee, Seungsup↗
Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant
As sessile organisms, plants have evolved complex signaling mechanisms to sense stress and acclimate. This includes the use of reactive oxygen species (ROS) generated during dysfunctional photosynthesis to initiate signaling. One such ROS, singlet oxygen ( 1 O 2 ), can trigger retrograde signaling, chloroplast degradation, and programmed cell death. However, the signaling mechanisms are largely unknown. Several proteins (e.g. PUB4, OXI1, EX1) are proposed to play signaling roles across three Arabidopsis thaliana mutants that conditionally accumulate chloroplast 1 O 2 (fluorescent in blue light (flu), chlorina 1 (ch1), and plastid ferrochelatase 2 (fc2)). We previously demonstrated that these mutants reveal at least two chloroplast 1 O 2 signaling pathways (represented by flu and fc2/ch1). Here, we test if the 1 O 2 -accumulating lesion mimic mutant, accelerated cell death 2 (acd2), also utilizes these pathways. The pub4–6 allele delayed lesion formation in acd2 and restored photosynthetic efficiency and biomass. Conversely, an oxi1 mutation had no measurable effect on these phenotypes. acd2 mutants were not sensitive to excess light (EL) stress, yet pub4–6 and oxi1 both conferred EL tolerance within the acd2 background, suggesting that EL-induced 1 O 2 signaling pathways are independent from spontaneous lesion formation. Thus, 1 O 2 signaling in acd2 may represent a third (partially overlapping) pathway to control cellular degradation.
59 BASIC BIOLOGICAL SCIENCES↗