A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.
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59 BASIC BIOLOGICAL SCIENCES↗
SEARCH · Engineering Papers
Results for “differential analysis”
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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Genetic and epigenetic signatures of Populus trichocarpa in response to abiotic stresses
Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. We found that ∼5-6% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.
DNA methylation↗
Genetic_and_epigenetic_signatures_of_Populus_Trichocarpa_in_response_to_abiotic_stress
Plants respond to abiotic stresses such as drought, heat, and salinity through both shared and stress-specific regulatory pathways. However, the role of epigenetic mechanisms, particularly DNA methylation, in modulating these responses is still underexplored. Here, we integrated transcriptome profiling with whole-genome bisulfite sequencing (WGBS) to investigate the dynamic relationship between gene expression and DNA methylation in Populus trichocarpa during brief early-stage exposure to abiotic stress. Each stress elicited distinct transcriptional and methylation signatures; however, a subset of conserved stress-responsive genes was commonly regulated across treatments. Approximately 5% of differentially expressed genes also displayed differential methylation patterns, suggesting a coordinated role for DNA methylation in regulating gene expression. Motif enrichment analysis of differentially methylated regions revealed binding sites of key transcription factor families, including ERF, bHLH, and ABF, highlighting potential role for methylation in modulating transcription factor targeting. Furthermore, we identified stress-inducible molecular markers with potential applications in early stress detection and functional dissection of gene regulatory pathways. Together, these findings provide new insights into the coordinated genetic and epigenetic responses to abiotic stress and provide a foundation for developing biosensors and breeding strategies to enhance stress resilience woody plants.
CBI↗
On the Symmetry of Blast Waves
This paper presents a brief historical review of G. I. Taylor’s solution of the point blast wave problem which was applied to the Trinity test of the first atomic bomb. Lie group symmetry techniques (also referred to throughout this paper as geometric techniques) are used to derive Taylor’s famous two-fifths law that relates the position of a blast wave to the time after the explosion and the total energy released. The theory of exterior differential systems is combined with the method of characteristics to demonstrate that the solution of the blast wave problem is directly related to the basic relationships that exist between the symmetry (or geometry) and the physics of wave propagation through the equations of motion. The point blast wave model is cast in terms of two exterior differential systems, and both systems are shown to be integrable with local solutions for the velocity, pressure, and density along curves in space and time behind the blast wave. This work is dedicated to the memory of Professor Roy Axford, who introduced many of his students to the topic of symmetry analysis of differential equations.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
Matrix quadratic solutions.
Matrix quadratic equation solution derivation applied in finding steady state solutions of Riccati differential equations with constant coefficients
OPTIMAL CONTROL↗
Thermal Analysis of High Entropy Rare Earth Oxides
Phase transformations in multicomponent rare earth sesquioxides were studied by splat quenching from the melt, high temperature differential thermal analysis and synchrotron X-ray diffraction on laser-heated samples. Three compositions were prepared by the solution combustion method: (La,Sm,Dy,Er,RE) 2 O 3 , where all oxides are in equimolar ratios and RE is Nd or Gd or Y. After annealing at 800 °C, all powders contained mainly a phase of C-type bixbyite structure. After laser melting, all samples were quenched in a single-phase monoclinic B-type structure. Thermal analysis indicated three reversible phase transitions in the range 1900–2400 °C, assigned as transformations into A, H, and X rare earth sesquioxides structure types. Unit cell volumes and volume changes on C-B, B-A, and H-X transformations were measured by X-ray diffraction and consistent with the trend in pure rare earth sesquioxides. The formation of single-phase solid solutions was predicted by Calphad calculations. The melting point was determined for the (La,Sm,Dy,Er,Nd) 2 O 3 sample as 2456 ± 12 °C, which is higher than for any of constituent oxides. An increase in melting temperature is probably related to nonideal mixing in the solid and/or the melt and prompts future investigation of the liquidus surface in Sm 2 O 3 -Dy 2 O 3 , Sm 2 O 3 -Er 2 O 3 , and Dy 2 O 3 -Er 2 O 3 systems.
36 MATERIALS SCIENCE↗
Developments and Challenges in the Design of the ITER DRGA
We report the ITER Diagnostic Residual Gas Analyzer (DRGA) will measure the distribution of gas species, i.e., deuterium (D), tritium (T), and impurities, in the divertor exhaust stream and in the plasma periphery, with time resolution relevant to fusion plasma–wall particle dynamics. The uniqueness of the DRGA, over previous implementations of plasma dynamics residual gas analysis, is an integrated approach, combining mass and low-temperature plasma-activated optical spectroscopy, in a differentially pumped analysis station. A further unique feature of the ITER divertor-specific DRGA is an ~8-m separation of the analysis station from the sampled pumping duct, while still maintaining a ~1-s response time for hydrogen isotopic concentrations. ITER DRGA final design activities are strongly benefiting from testing of prototypical DRGA components and methods on present fusion devices, most currently on JET and W7-X. DRGA systems are implemented on both these devices and include sensors (and pumping methods) that are directly relevant to the ITER DRGA design. The recent JET-DTE2 campaign has provided the first experience on operating the combined ITER DRGA sensors with D-T plasmas. While enhancing system design for ITER, this experience on operating devices has also revealed additional engineering challenges, which further guide the continuing final design project. Meanwhile, the recent determination that the ITER DRGA, with slight optimization, will resolve the helium isotopes well enough to support an ITER pre-DT, He-3-based heating scheme, has greatly increased ITER Research Program interest in the DRGA and its implementation well ahead of the DT phase.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis
Abstract Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
Plant Sciences↗
Analyses of exobiological and potential resource materials in the Martian soil
Potential Martian soil components relevant to exobiology include water, organic matter, evaporites, clays, and oxides. These materials are also resources for human expeditions to Mars. When found in particular combinations, some of these materials constitute diagnostic paleobiomarker suites, allowing insight to be gained into the probability of life originating on Mars. Critically important to exobiology is the method of data analysis and data interpretation. To that end, methods of analysis of potential biomarker and paleobiomarker compounds and resource materials in soils and rocks pertinent to Martian geology are investigated. Differential thermal analysis coupled with gas chromotography is shown to be a highly useful analytical technique for detecting this wide and complex variety of materials.
Mancinelli, Rocco L.↗
Benchmarking optimization methods for materials research: Gradient descent and Bayesian optimization for lithium-ion battery aging diagnostics
Accurate and efficient parameter estimation is essential for battery diagnostics and aging analysis. Here, in this study, we compare two optimization-based approaches—gradient descent and Bayesian optimization—for extracting parameters from differential voltage analysis in lithium-ion batteries. While these techniques are widely used, their relative strengths and limitations for this application are not well understood. The study evaluates the trade-offs between these methods in terms of result quality, computational cost, and reliability within this specific application. The diagnostic results from our battery data suggest adopting gradient descent as an initial method for rapid and efficient analysis, while employing more stable optimization techniques, such as Bayesian optimization, as a verification step to mitigate potential instability. Comparing the two methods provides information on algorithmic choice, while inspiring further discussions on selecting appropriate techniques for specific research tasks.
Zhao, Ziqing [Boston Univ., MA (United States)] (O↗
Analysis of cured carbon-phenolic decomposition products to investigate the thermal decomposition of nozzle materials
The development of a mass spectrometer/thermal analyzer/computer (MS/TA/Computer) system capable of providing simultaneous thermogravimetry (TG), differential thermal analysis (DTA), derivative thermogravimetry (DTG) and evolved gas detection and analysis (EGD and EGA) under both atmospheric and high pressure conditions is described. The combined system was used to study the thermal decomposition of the nozzle material that constitutes the throat of the solid rocket boosters (SRB).
Thompson, James M.↗
The NEAR-Shoemaker X-Ray Spectrometer: Latest Results and Future Analysis Plans
The NEAR XRS observed the asteroid 433 Eros in low orbit for nearly six months. Elemental ratios are most consistent with a primitive chondrite and give no evidence of global differentiation. Further analysis of this large data set will continue. Additional information is contained in the original extended abstract.
Starr, R. D.↗
An approximate method for solving the single- degree-of-freedom roll equation with time- dependent coefficients
Approximation method for solving singe-degree-of- freedom differential roll equation with time dependent coefficient - ballistic trajectory anallysis
ROLL↗
An algorithm for reducing a linear, time- invariant differential system to state form.
Algorithm for reducing linear time-invariant differential systems to state form applied to systems described by transfer functions
MATRIX ANALYSIS↗
Dysregulation of lung epithelial cell homeostasis and immunity contributes to Middle East respiratory syndrome coronavirus disease severity
Coronaviruses (CoV) emerge suddenly from animal reservoirs to cause novel diseases in new hosts. Discovered in 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in camels in the Middle East and is continually causing local outbreaks and epidemics. While all three newly emerging human CoVs from the past 20 years (SARS-CoV, SARS-CoV-2, and MERS-CoV) cause respiratory disease, each CoV has unique host interactions that drive differential pathogeneses. To better understand the virus and host interactions driving lethal MERS-CoV infection, we performed a longitudinal multi-omics analysis of sublethal and lethal MERS-CoV infection in mice. Significant differences were observed in body weight loss, virus titers, and acute lung injury among lethal and sub-lethal virus doses. Virus-induced apoptosis of type I and II alveolar epithelial cells suggests that loss or dysregulation of these key cell populations was a major driver of severe disease. Omics analysis suggested differential pathogenesis was multi-factorial with clear differences among innate and adaptive immune pathways as well as those that regulate lung epithelial homeostasis. Infection of mice lacking functional T and B cells showed that adaptive immunity was important in controlling viral replication but also increased pathogenesis. In summary, we provide a high-resolution host response atlas for MERS-CoV infection and disease severity. Multi-omics studies of viral pathogenesis offer a unique opportunity to not only better understand the molecular mechanisms of disease but also to identify genes and pathways that can be exploited for therapeutic intervention all of which is important for our future pandemic preparedness.
MERS-CoV↗
Analysis of Material Properties of Aged Rigid Polyurethane Foam
Foams are classified as either rigid or flexible and are commonly used in applications such as pipe insulation, carpet fibers, and chair foam cushions. Polyurethane foams are excellent thermal insulators, have excellent mechanical properties, and are chemically inert. With the addition of fire protective additives, polyurethane foams have the ability to intumescence when exposed to high temperatures. For the future storage of the 9977 nuclear shipping packages, the material properties of the General Plastics 3716 rigid polyurethane foam were evaluated for long term performance by comparing aged samples to unaged samples. General Plastics 3716 rigid polyurethane foam was aged from November 2014 to June 2019 at varying temperatures of: 160 deg. F, 160 deg. F + 50% relative humidity (RH), 185 deg. F, 215 deg. F, and 250 deg. F. The foam was then analyzed via Fourier Transform Infrared Spectroscopy (FTIR), 3D Optical Microscope, Thermal Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC). FTIR and Optical Microscope: No significant change to chemical or physical structure was evident by FTIR or optical microscope analysis. DSC: Decrease of heat capacity over time for all oven temperatures except a slight increase for the 185 deg. F conditioned foams. Largest decrease evident with foams conditioned at 250 deg. F. A slight increase in heat capacity for humid samples. Similar trends in heat capacities at 71 deg. C and 102 deg. C. TGA: As conditioning temperature increased, a decline was evident in the average percent weight loss, onset temperature, and first derivative peak temperature. No significant effect due to humidity except for a decrease in first derivative peak temperature. Unaged samples exhibited strong intumescence. Foams conditioned at 160 deg. F exhibited slight intumescence. Results suggest fire protective additives decomposed at higher temperatures, which contributed to a lower average percent mass loss in higher temperature conditioning. Further thermal degradation testing would be beneficial to evaluate the ability of the conditioned foams to intumesce. Evaluate irradiation dose rate effects on conditioned foam. Possible conditioning in an environment with a known humidity or analyzing a new aliquot of sample for each trial to achieve a more representative heat capacity calculation.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Mef2c regulates bone mass through Sost -dependent and -independent mechanisms
We report Mef2c is a transcription factor that mediates key cellular behaviors that promote endochondral ossification and bone formation. Previously, Mef2c has been shown to regulate Sost transcription via its osteocyte-specific enhancer, ECR5, and conditional deletions of Mef2 cfl/fl with either Col1-Cre or Dmp1-Cre produced generalized high bone mass (HBM) consistent with Van Buchem Disease phenotypes. However, Sost -/- ; Mef2 cfl/fl ; Dmp1-Cre mice produced a significantly higher bone mass phenotype that Sost-/- alone suggesting that Mef2c modulates bone mass through additional mechanisms, independent of Sost. To identify new Mef2c transcriptional targets important in bone metabolism, we profiled gene expression by single-cell RNA sequencing in subpopulations of cells isolated from Mef2 cfl/fl ; Dmp1-Cre and Mef2 cfl/fl ; Bglap-Cre femurs, both strains exhibiting similar high bone mass phenotypes. However, we found Mef2cfl/fl; Bglap-Cre to also display a growth plate defect characterized by an expansion of several osteoprogenitor subpopulations. Differential gene expression analysis identified a total of 96 up- and 2434 down- regulated genes in Mef2 cfl/fl ; Bglap-Cre and 176 up- and 1041 down- regulated genes in Mef2 cfl/fl ; Dmp1-Cre bone cell subpopulations compared to wildtype mice. Mef2c deletion affected the transcriptomes across several cell types including mesenchymal progenitors (MP), osteoprogenitors (OSP), osteoblast (OB), and osteocyte (OCY) subpopulations. Several energy metabolism genes such as Uqcrb, Ndufv2, Ndufs3, Ndufa13, Ndufb9, Ndufb5, Cox6a1, Cox5a, Atp5o, Atp5g2, Atp5b, Atp5 were significantly down regulated in Mef2c-deficient OBs and OCYs, in both strains. Binding motif analysis of promoter regions of differentially expressed genes identified Mef2c binding in Bone Sialoprotein (BSP/Ibsp), a gene known to cause increased trabecular BV/TV in the femurs of Ibsp -/- mice. Immunohistochemical analysis confirmed the absence of Ibsp protein in OBs and OCYs. These findings suggests that the HBM in Sost -/- ; Mef2 cfl/fl ; Dmp1-Cre is caused by a multitude of transcriptional changes in genes that regulate bone formation, two of which are Sost and Ibsp.
59 BASIC BIOLOGICAL SCIENCES↗
Randomized algorithms for generalized singular value decomposition with application to sensitivity analysis
The generalized singular value decomposition (GSVD) is a valuable tool that has many applications in computational science. However, computing the GSVD for large-scale problems is challenging. Motivated by applications in hyper-differential sensitivity analysis (HDSA), in this work we propose new randomized algorithms for computing the GSVD which use randomized subspace iteration and weighted QR factorization. Detailed error analysis is given which provides insight into the accuracy of the algorithms and the choice of the algorithmic parameters. We demonstrate the performance of our algorithms on test matrices and a large-scale model problem where HDSA is used to study subsurface flow.
97 MATHEMATICS AND COMPUTING↗