Development and Verification of Control Sequences for Single-Zone Variable Air Volume System Based on ASHRAEGuideline 36
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Zhang, Kun↗
SEARCH · Engineering Papers
Results for “Base Sequence”
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Neutral changes during divergent evolution of hemoglobins
A comparison of the mRNAs for rabbit and human beta-hemoglobins shows that synonymous changes in codons have accumulated three times as rapidly as nucleotide replacements that produced changes in amino acids. This agrees with predictions based on the so-called neutral theory. In addition, seven codon changes that appear to be single-base changes (according to maximum parsimony) are actually two-base changes. This indicates that the construction of primordial sequences is of limited significance when based on inferences that assume minimum base changes for amino acid replacements.
Jukes, T. H.↗
Decoding the protein–ligand interactions using parallel graph neural networks
Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.
59 BASIC BIOLOGICAL SCIENCES↗
Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo -7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA
Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.
59 BASIC BIOLOGICAL SCIENCES↗
A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism
Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2’s flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.
Roell, Garrett W.↗
Developing of Quaternary Pumped Storage Hydropower for Dynamic Studies
Quaternary pumped storage hydropower (Q-PSH) technology, as one of the new advanced-PSH technology, has been developed by taking advantage of Conventional-PSH (C-PSH) and Adjustable Speed-PSH (AS-PSH). By combining adjustable-speed pump unit and conventional hydropower turbine unit in the quaternary configuration, Q-PSH has the more competitive capability of providing fast power support in the future high renewable penetrated power system. Acting as energy storage (ES), Q-PSH provides promising power supply to deal with the uncertainty and variability from renewable energy generation. This paper focuses on the dynamic modeling of Q-PSH technology employing full-converter machine and the impact of Q-PSH on the frequency response in a system. The detailed model of Q-PSH is developed and implemented in the IEEE 14-bus system based on GE Positive Sequence Load Flow (PSLF) platform, which captures the dynamic of multiple operation modes, especially hydraulic short-circuit (HSC) operation mode. Several cases are set up to reveal the advantages of Q-PSH technology when power electronic based renewable energy generation is deployed in the system. Sensitivity studies of the controller in pump governor show the impact of parameters in pump response performance. The comparison case illustrates the impact of frequency response provided by the Q-PSH in the system.
dynamic modeling↗
A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences
The ease with which a particular DNA segment adopts the left-handed Z-conformation depends largely on the sequence and on the degree of negative supercoiling to which it is subjected. We describe a computer program (Z-hunt) that is designed to search long sequences of naturally occurring DNA and retrieve those nucleotide combinations of up to 24 bp in length which show a strong propensity for Z-DNA formation. Incorporated into Z-hunt is a statistical mechanical model based on empirically determined energetic parameters for the B to Z transition accumulated to date. The Z-forming potential of a sequence is assessed by ranking its behavior as a function of negative superhelicity relative to the behavior of similar sized randomly generated nucleotide sequences assembled from over 80,000 combinations. The program makes it possible to compare directly the Z-forming potential of sequences with different base compositions and different sequence lengths. Using Z-hunt, we have analyzed the DNA sequences of the bacteriophage phi X174, plasmid pBR322, the animal virus SV40 and the replicative form of the eukaryotic adenovirus-2. The results are compared with those previously obtained by others from experiments designed to locate Z-DNA forming regions in these sequences using probes which show specificity for the left-handed DNA conformation.
Non-NASA Center↗
Anomaly analysis and visualization for dynamic networks through spatiotemporal graph segmentations
With recent technology advance in Internet of Things (IoT) that involves human, sensors, and mobile devices, networks are not only growing much larger but more complex and dynamic in nature. The spatiotemporal dynamics of networks are represented by both topological changes and temporal shifts of attribute information associated with network components. Understanding the pattern and trend of dynamic networks is increasingly important. While data mining approaches are generally useful in analyzing the statistical properties of networks, there has been recent trend to consider bringing human into the loop, and to examine how feedback from visualizations of large-scale dynamic networks can further improve data mining and machine learning. Traditional visualization methods based on animation and sequences of snapshot graphs are also limited by human cognitive capability. Here, we present a dynamic network analysis and visualization (DNAV) tool which explores the spatiotemporal dimensions of graph components. In particular, nodes and edges are augmented with spatiotemporal segmentation based on both topological and attribute dynamics (e.g., time and locations of connectivity). To further facilitate analysis of large dynamic networks, DNAV includes statistical dynamic overviews alongside graph views, as well as data filtering modules for scalable analysis. Using case studies on public datasets, we demonstrate the effectiveness of DNAV in understanding and analyzing anomalies in dynamic networks such as computer communication networks.
97 MATHEMATICS AND COMPUTING↗
Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses
Switchgrass is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving not only simple additive marker effects but also interactions with genetic backgrounds, e.g., ecotypes, or synergies with other markers. We analyzed plant height, carbon content, nitrogen content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotype. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, but also 83,290 markers for marker-by-ecotype interactions and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected based on marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for carbon content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected based on pairwise marker correlations. Furthermore, one marker-by-ecotype interaction and one pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits in switchgrass. Moreover, they exemplified the importance of interactive effects for the depiction of genetic bases, and illustrated the usefulness of preselection of marker pairs for identifying pairwise marker interactions in association testing.
09 BIOMASS FUELS↗
Impedance Scan of Inverter-Based Resources and Diesel Generator for Stability Analysis
Impedance-based methods are widely used for power system stability analysis with inverter-based resources (IBRs), e.g., assessing dynamic interactions between the power grid and an IBR, control interactions between multiple IBRs, and the sub-synchronous oscillation and damping phenomenon. Since it is difficult to get a numerical model 100% matching with the hardware IBR, using the hardware inverter directly to obtain its output impedance has become a prominent approach nowadays. Therefore, this article presents the impedance scan using hardware IBRs, and also a hardware diesel generator as it still stays with the grid before the grid completely goes to renewable. The devices under test (DuTs) for the impedance scan includes two 3-..phi.., 480 V, 60 Hz commercial grid-forming IBRs (one of 250 kVA and another of 125 kVA rating) in series with ..delta..-Y transformers, one 3-..phi.., 480 V, 60 Hz commercial grid-following IBR (of 125 kVA rating), and a 3-..phi.., 480 V, 60 Hz commercial diesel generator (of 187.5 kVA rating). Using voltage signals perturbed with sub-, inter-, and higher harmonic components, and measuring the current response, the positive-sequence impedances are computed via an offline-based post-analysis. Moreover, best-fit transfer functions are estimated that closely resemble the measured data points of the positive-sequence impedances. Based on the observations from various outcomes of the hardware experiments, this article also provides some fundamental insights on the equivalent positive-sequence impedance of a combination of multiple hardware components by comparing the estimated and the empirically computed impedances. A comparative insight on the damping capability of the DuTs using the positive-sequence impedances of the hardware is also discussed.
current measurement↗
Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development
Conserved non-coding sequences (CNSs) are integral elements of transcriptional regulation. Transcriptional tuning of PLETHORA (PLT) genes that encode master regulators of plant development is vital for embryogenesis and meristematic function. However, how the expression of PLT genes is modulated through CNSs remains unclear. Through motif-based mining of upstream sequences in 120 angiosperm genomes, we identified 21 conserved and lineage-specific CNSs, two of which are unusually long, similar, and colinear within eudicots. Using Arabidopsis thaliana, we demonstrate that these two deeply conserved elements, which we named BOX1 and BOX2, control PLT1 and PLT2 expression. CRISPR mutants within these elements specifically reduced PLT expression levels, and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip, affecting the ability to rescue the plt1 plt2 double mutant. We further show that the influence of these elements on expression patterns is already exerted during embryogenesis and functional in the context of the early embryo. Finally, we reveal the existence of a BOX-mediated autoregulatory feedback loop that, in large part, explains CNS influence on expression patterns. We thus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.
PLETHORA↗
Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
59 BASIC BIOLOGICAL SCIENCES↗
Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1
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Sensitive and error-tolerant annotation of protein-coding DNA with BATH
We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.
59 BASIC BIOLOGICAL SCIENCES↗
Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes
Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.
59 BASIC BIOLOGICAL SCIENCES↗
Solution of eigenvalue problems by Sturm sequence method.
A generalized eigenvalue algorithm is presented herein along with the complete listing of the associated computer program, which may be conveniently utilized for the efficient solution of certain broad classes of eigenvalue problems. Extensive applications of the procedure are envisaged in the analysis of many important engineering problems, such as stability and natural frequency analysis of practical discrete structural systems, idealized by the finite element technique. The procedure based on the Sturm sequence method is accurate and fast, possessing several significant advantages over other known methods of such analysis. Numerical results are also presented for two representative structural engineering problems.
Gupta, K. K.↗
Synchronization Technique For Reception Of Coded Data
Shortest sequence of bits likely to be filled with error bursts examined. Algorithm improves synchronization of frames of noisy binary-coded data signals after Viterbi decoding (recovery from "inner" convolutional code used in transmission channel) and before Reed-Solomon or other decoding (recovery from "outer" error-correcting block code). Based on comparisons of sequences of correct and erroneous Viterbi-decoded received bits with known marker sequence denoting beginning of frame of data. Does not require count of number of bits in received sequence disagreeing with corresponding bits in marker sequence.
Shahshahani, Mehrdad M.↗
MEXEC: An Onboard Integrated Planning and Execution Approach for Spacecraft Commanding
The traditional form of spacecraft commanding is with sequences that specify when commands should execute based on a schedule generated on the ground. Some sequences have control logic and event driven responses to increase flexibility, but it is limited. An approach to increase autonomy is to use goal-based planning and commanding. Using this paradigm, intention and behavior is modeled on board the spacecraft. In this paper we describe MEXEC (Multi-mission EXECutive), a multi-mission, task-based, onboard planning and execution software designed specifically to be used as flight software. As a path to infusion for future flight projects, we describe two experiments performed on the ASTERIA CubeSat and testbed that demonstrate that MEXEC can be integrated and used for spacecraft operations and increase robustness and science return compared to the standard sequences that were being used.
Campuzano, Brian↗