Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Differentiability”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Identification of Differentially Expressed Genes of Rice Under Cadmium Stress Using DDRT-PCR Approach

Cadmium (Cd) is one of the hazardous environmental pollutants, and it can be harmful to human health through consumption of food-plants capable of bioaccumulating Cd. Therefore, lowering cadmium accumulation in plants is highly desirable. Here, a rice cultivar ‘Qisanzhan’ was studied using differential display reverse transcription-polymerase chain reaction (DDRT-PCR). Fifty-six differentially expressed genes were found in the root tips of 4-leaf stage rice seedlings exposed to 4 and 12 h of 50 µmol/L Cd(NO{sub 3}){sub 2} in a nutrient solution using DDRT-PCR. Further validation using semi-quantitative RT-PCR showed that the expression patterns of 16 genes were consistent with those found in DDRT-PCR. These genes encode receptor-like protein kinase, pleiotropic drug resistance protein, aquaporin protein, plasma membrane ATPase, etc. The differentially genes identified here can be used to obtain a better understanding of the molecular mechanisms of Cd absorption and accumulation in plants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Quantum Spectral Methods for Differential Equations

Recently developed quantum algorithms address computational challenges in numerical analysis by performing linear algebra in Hilbert space. Such algorithms can produce a quantum state proportional to the solution of a d-dimensional system of linear equations or linear differential equations with complexity poly(logd). While several of these algorithms approximate the solution to within ϵ with complexity poly(log(1/ϵ)), no such algorithm was previously known for differential equations with time-dependent coefficients. In this work, we develop a quantum algorithm for linear ordinary differential equations based on so-called spectral methods, an alternative to finite difference methods that approximates the solution globally. Using this approach, we give a quantum algorithm for time-dependent initial and boundary value problems with complexity poly(logd, log(1/ϵ)).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Differentiation of hepatic abscess from metastasis on contrast-enhanced dynamic computed tomography in patients with a history of extrahepatic malignancy: emphasis on dynamic change of arterial rim enhancement

Objectives: The objective of the study is to identify computed tomography (CT) findings that differentiate hepatic abscess from hepatic metastasis in a patient with a history of extrahepatic malignancy. Materials and methods: This retrospective study included 30 patients with 93 hepatic abscesses and 40 patients with 125 hepatic metastases who had a history of extrahepatic malignancy and underwent contrast-enhanced dynamic CT with arterial phase (AP) and portal venous phase (PVP). The diagnosis of hepatic abscess and hepatic metastasis was made using pathological confirmation or clinical diagnosis. Margin, patchy parenchymal enhancement, arterial rim enhancement, dynamic change of arterial rim enhancement, size discrepancy of lesions between arterial and portal phases, bile duct dilatation, perilesional hyperemia, and perilesional low density were evaluated by two radiologists independently. Significant findings for differentiating two groups were identified at univariate and multivariate analysis with nomogram for predicting hepatic abscess. Interobserver agreement was also analyzed for each variable. Results: Multivariate analysis revealed that patchy parenchymal enhancement (P < 0.001), arterial rim enhancement persistent through PVP (P < 0.001), and perilesional hyperemia (P = 0.013) were independent significant findings to predict hepatic abscess than metastasis. Among them, arterial rim enhancement persistent through PVP showed a highest odds ratio (OR 33.73) on multivariate analysis and a highest predictor point on a nomogram for predicting hepatic abscess. When two of these three criteria were combined, 80.7% (75/93) of hepatic abscess were correctly identified, with a specificity of 85.6% (107/125). When all three criteria were satisfied, specificity was up to 100% (125/125). Conclusions: At contrast-enhanced dynamic CT, patchy parenchymal enhancement, arterial rim enhancement persistent through PVP, perilesional hyperemia, and their combinations may be reliable CT features for differentiating hepatic abscess from metastasis in patients with a history of primary extrahepatic malignancy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Can magnetic resonance imaging differentiate among transurethral bulking agent, urethral diverticulum, and periurethral cyst?

Purpose: To evaluate magnetic resonance imaging findings that differentiate among periurethral bulking agents (primarily collagen), urethral diverticulum, and periurethral cyst. Methods: We searched our radiologic database retrospectively from 2001 to 2017 for periurethral cystic lesions, identifying a total of 50 patients with 68 lesions. Final diagnoses in 68 lesions were bulking agents (27), urethral diverticula (29), and periurethral cysts (12). Two abdominal radiologists, blinded to clinical history, independently evaluated T1, T2, and post-contrast images. The readers assessed number, morphological features, location, connection to urethra and mass effect, signal intensity, and enhancement for each lesion. Fisher exact test and logistic regression analysis were performed for each univariate significant feature. The operative and pathologic reports were the reference standard. Results: Magnetic resonance imaging features found more often in bulking agents versus urethral diverticulum were multiple lesions (P = 0.011), upper or upper-mid-urethral location (P ≤ 0.0001), lack of internal fluid/fluid level (P = 0.002), no urethral connection (P = 0.005), T1 isointensity, and T2 mild hyperintensity compared to muscles but lower T2 signal than urine (P < 0.0001). Most cases of urethral diverticula and periurethral cysts were detected at mid- and lower urethra. Urethral diverticula were larger than bulking agents and periurethral cysts (P = 0.005 and P = 0.023) (mean diameter = 24, 16, 15 mm, respectively). Most bulking agents (93%) and urethral diverticula (90%) showed mass effect on urethra, while periurethral cysts (75%) did not (P < 0.0001). Conclusion: Signal intensity and lesion characterization on magnetic resonance imaging can significantly differentiate bulking agent from urethral diverticulum and periurethral cyst. Radiologists should consider differential diagnosis of a bulking agent, especially when distinguishing characteristics described here are present to prevent incorrect diagnosis and ultimately unnecessary surgical intervention.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Apela Promotes Cardiomyocyte Differentiation from Transgenic Human Embryonic Stem Cell Lines

Although embryonic stem (ES) cells (ESCs) may be a promising donor source for the repair of infarcted or ischemic heart tissues, their successful application in regenerative medicine has been hampered by difficulties in enriching, identifying, and selecting cardiomyocytes from the differentiating cells. We established transgenic human ES cell lines by transcriptional control of the α-cardiac myosin heavy chain (α-MHC) promoter driving green fluorescent protein (GFP) expression. Differentiated GFP-expressing cells display the characteristics of cardiomyocytes (CMs). Apela, a recently identified short peptide, up-regulated the expression of the cardiac-restricted transcription factors Tbx5 and GATA4 as well as differentiated the cardiomyocyte markers α-MHC and β-MHC. Flow cytometric analysis showed that apela increased the percentage of GFP-expressing cells in the beating foci of the embryoid bodies. The percentage of cardiac troponin T (TNT)-positive cells and the protein expression of TNT were increased in the ES cell-derived CMs with apela treatment. Functionally, the contractile frequency of the ES-derived CMs responded appropriately to the vasoactive drugs isoprenaline and carbachol. Our work presented a protocol for specially labelling and enriching CMs by combining transgenic human ES cell lines and exogenous growth factor treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

W9 peptide enhanced osteogenic differentiation of human adipose-derived stem cells

W9 is a peptide that abrogates osteoclast differentiation via blockade of nuclear factor-κB ligand (RANKL)-RANK signaling, which activates bone formation. However, W9 stimulated osteogenesis in osteoblasts and mesenchymal stem cells. The present study demonstrated that the W9 peptide promoted osteogenic differentiation of human adipose-derived stem cells (hAdSCs) even under non-osteogenic differentiation culture conditions. W9-treated hAdSCs exhibited several osteocalcin-expressing cells and great mineralization compared to the BMP2-treated hAdSCs, which suggests that the W9 peptide had potent osteogenic potential in hAdSCs. W9 treatment also markedly enhanced the phosphorylation of p38, JNK, Erk1/2, and Akt, and BMP2 treatment only enhanced the phosphorylation of p38 and Erk1/2 in hAdSCs. hAdSCs did not express the RANKL gene, but W9 treatment upregulated Runx2, Collagen type 1A1 and TGF receptor genes and increased Akt phosphorylation. These results suggest that the W9-induced potent osteogenic induction was attributed to activation of TGF and the PI3 kinase/Akt signaling pathway in hAdSCs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

UNC-5 netrin receptor B mediates osteogenic differentiation by modulating bone morphogenetic protein signaling in human adipose-derived stem cells

Highlights: • UNC5B facilitates osteogenic differentiation of human adipose-derived stem cells. • It does so by modulation bone morphogenetic protein signaling. • UNC5B may be useful for bone tissue engineering and therapy for bone defects. UNC-5 netrin receptor B (UNC5B) is a dependence receptor of netrin-1 that plays an essential role in mediating angiogenesis and tumorigenesis. Despite its significant roles, there is limited knowledge about the role played by UNC5B in osteogenesis. In the present study, we first demonstrated that UNC5B was required for osteogenic differentiation of human adipose-derived stem cells (hASCs), both in vitro and in vivo. We also found that mechanistically, UNC5B promotes osteogenic differentiation by activating bone morphogenetic protein signaling. These findings point to a new important function of UNC5B and provide a potential basis for hASCs-mediated bone regeneration.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Effects of connective tissue growth factor (CTGF/CCN2) on condylar chondrocyte proliferation, migration, maturation, differentiation and signalling pathway

Highlights: • It is the first discovery of CCN2 expression in the whole layers of condylar cartilage. • CCN2 promotes condylar chondrocyte migration, maturation and differentiation. • Blocking PI3K/Akt pathway impairs the stimulatory effect of CCN2 on the proliferation of condylar chondrocyte. CCN2, also known as connective tissue growth factor (CTGF), is a 38 kDa cysteine-rich extracellular matrix protein that regulates a sequence of cellular functions and participates in multiple complex biological processes, such as chondrogenesis and osteogenesis. In the present study, we provided the first evidence describing the physiological role of CCN2 in condylar chondrocyte proliferation, migration, maturation and differentiation. CCN2 was widely expressed throughout the whole layers of condylar cartilage and predominantly distributed in the proliferative zone. Recombinant CCN2 promoted the proliferation, migration, proteoglycan synthesis and differentiation capacity of isolated condylar chondrocytes. The stimulatory effect of CCN2 on chondrocyte proliferation was associated with the activation of phosphatidylinositol 3-kinase/Akt signalling pathway. The blocking of this pathway by its inhibitor LY294002 impaired the proliferative effect of CCN2 on chondrocytes. These results suggested a novel physiological role of CCN2 in the development of condylar cartilage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Transcriptional information revealed differentially expressed circular RNAs in facet joint osteoarthritis

Highlights: • A full recognition of circrna changes in FJOA by RNA-seq analysis. • We initial listed Top 20 enriched signaling pathways associated with FJOA. • Seven circRNAs were arbitrarily selected to confirm their differential expression levels by qRT-PCR. • A group of potential miRNAs that might bind to circular RNAs were identified. Circular RNAs are newly identified RNAs that regulate gene expression and execute various biological activities. Facet joint osteoarthritis (FJOA) is a severe facet joint cartilage degeneration disease that induces chronic low back pain to a larger population. The molecular mechanisms of FJOA, especially the presence and changes of circular RNAs in FJOA have not been investigated. In the current study, we analyzed RNA deep sequencing outcomes from healthy control group and FJOA group, identified and annotated circular RNAs, and determined the expressions of circular RNAs. Differentially expressed circular RNAs in the FJOA group were then screened and the host genes of these differentially expressed circular RNAs were functional analyzed by Gene Ontology (GO), Kyoto Enrichment of Genes and Genomes (KEGG), and protein-protein interaction network analysis. Seven circRNAs were arbitrarily selected to confirm the trustworthiness of these profiles by quantitative qRT-PCR. The potential binding sites of microRNAs (miRNAs) and identified circular RNAs were also predicted. Our current study provided valuable bioinformation regarding circular RNAs in FJOA and expanded our knowledge of FJOA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Cyclosporin A inhibits adipogenic differentiation and regulates immunomodulatory functions of murine mesenchymal stem cells

Highlights: • CsA decreased BM-MSCs proliferation and increased cells apoptosis. • CsA inhibited BM-MSCs adipogenic differentiation. • CsA had no effect on the phenotype and osteogenic differentiation of BM-MSCs. • CsA inhibited BM-MSCs secreting IL-6 and promoted the expression of PD-L2. Aplastic anemia (AA) is generally considered as an immune-mediated bone marrow failure syndrome. Several studies show that bone marrow mesenchymal stem cells (BM-MSCs), as key cellular components of the bone marrow microenvironment, are also involved in the pathogenic mechanism of AA. Cyclosporin A (CsA) is a classic immunosuppressive drug for AA, and it specifically inhibits mammalian T cells by preventing activation of transcription factors involved in cytokine gene expression. However, little is known about the effect of CsA on the BM-MSCs. In this study, murine BM-MSCs were stimulated in the presence of CsA. Further, we found that CsA could inhibit murine BM-MSC proliferation and promote BM-MSC apoptosis, what's more CsA could inhibit adipogenic differentiation. Our study also showed that CsA could inhibit interleukin-6 expression in BM-MSCs, while promoting programmed death-ligand 2 expression. In conclusion, our results proposed that CsA may exert an effect on regulating the bone marrow environment by influencing BM-MSCs, which have a beneficial effect on treating AA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Extracellular matrix protein DMP1 suppresses osteogenic differentiation of Mesenchymal Stem Cells

Highlights: • Extracellular matrix protein DMP1 suppresses MSCs osteogenic differentiation. • DMP1 works not only in osteoblasts and osteocytes, but also in MSCs. Mesenchymal Stem Cells (MSCs) are self-renewing and multipotent stem cells which was investigated for diverse clinical applications. However, complex mechanism of MSCs fate determination is still not fully disclosed. Extracellular matrix (ECM) proteins contribute to maintain MSCs stemness by providing extracellular microenvironment. Increasing evidences show that ECM proteins could also regulate the fate of MSCs directly. Dentin matrix protein 1 (DMP1) is an ECM protein enrich in bone tissue and terminal cells, which well-known in promoting osteoblasts and osteocytes maturation, and facilitate mineralization. Recently, our experiment indicated that DMP1 was also expressed in MSCs of long bone. In present study, it is found that DMP1 expressed in Prx1 positive MSCs. And, DMP1 is down-regulated in early osteoblasts and up-regulated again in mature osteoblasts. DMP1 conditional knockout mice model under Prx1cre was generated to explore whether DMP1 regulates MSCs osteogenic differentiation. Specific ablation of DMP1 in Prx1 positive MSCs increased bone mass in vivo and promoted osteoblasts activity in vitro. This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Sanguisorba officinalis L. extracts activate Wnt/β-catenin pathway, and subsequently control adipo-osteogenic differentiation

Highlights: • Identification of herbal extracts as an activator of Wnt/β-catenin pathway. • Activation of Wnt/β-catenin pathway by Sanguisorba officinalis L. extracts (SOE). • Inhibitory effects of SOE on adipogenesis via Wnt/β-catenin pathway activation. • Stimulating effects of SOE on osteogenesis via Wnt/β-catenin pathway activation. • The effectiveness of SOE for accelerating mice calvaroal bone formation ex vivo. Wnt/β-catenin pathway plays an important role in adipogenesis and osteogenesis. To search for novel activators of the Wnt/β-catenin pathway, we screened plant extracts and found that Sangusorba officinalis L. extracts (SOE) could increase β-catenin expression level and nuclear accumulation in 3T3-L1 and MC3T3-E1 cells. It was confirmed that SOE could effectively control adipo-osteogenic differentiation. SOE inhibited adipocyte differentiation of 3T3-L1 cells, markedly decreased intracellular lipid accumulation, and decreased expression levels of key adipogenic transcription factors including PPARγ, C/EBPα, and SREBP-1c. SOE enhanced ALP activity and terminal osteoblast differentiation which was confirmed by Alizarin Red S staining of MC3T3-E1 cells. In ex vivo culture, SOE significantly increased the thickness of calvarial bone in mice. Taken together, our results indicate that SOE could be used as a potential therapeutic agent for dual-treatment of anti-obesity and anti-osteoporosis via activation of Wnt/β-catenin pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Three differential expression profiles of miRNAs as potential biomarkers for lung adenocarcinoma

Highlights: • To identify the differential miRNAs expression between lung cancer and normal tissues. • Data analysis was based on a computational approach to detect survival-associated signatures. • Three-miRNA signature could be used as a prognostic marker in LACA. Owing to the poor prognosis, novel biomarkers for lung adenocarcinoma (LACA) are needed nowadays. The aim of the study was to identify the differential miRNAs expression between lung cancer and normal tissues and evaluate the prognostic values of the miRNAs. Multidimensional data of 528 samples were retrieved from The Cancer Genome Atlas archive. Data analysis was based on a computational approach to detect survival-associated molecular signatures. A total of 191 differentially expressed miRNAs were identified between LACA tissues and normal tissues, including 88 up-regulated and 103 down-regulated miRNAs. The Kaplan-Meier survival method revealed the prognostic function of the three miRNAs (miR-1293, miR-873 and miR-1914). Cox regression analysis showed that the three-miRNA signature was an independent prognostic factor in LACA. The functional enrichment analysis suggested that the target genes of three miRNAs may be involved in various pathways related to the cancer. This study demonstrated that the three-miRNA signature (miR-1293, miR-873 and miR-1914) could be used as a prognostic marker in LACA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

A general approach to seismic inversion with automatic differentiation

Imaging Earth structure or seismic sources from seismic data involves minimizing a target misfit function, and is commonly solved through gradient-based optimization. The adjoint-state method has been developed to compute the gradient efficiently; however, its implementation can be time-consuming and difficult. We develop a general seismic inversion framework to calculate gradients using reverse-mode automatic differentiation. The central idea is that adjoint-state methods and reverse-mode automatic differentiation are mathematically equivalent. Here, the mapping between numerical PDE simulation and deep learning allows us to build a seismic inverse modeling library, ADSeismic, based on deep learning frameworks, which supports high performance reverse-mode automatic differentiation on CPUs and GPUs. We demonstrate the performance of ADSeismic on inverse problems related to velocity model estimation, rupture imaging, earthquake location, and source time function retrieval. ADSeismic has the potential to solve a wide variety of inverse modeling applications within a unified framework.

58 GEOSCIENCES↗
DOE OSTI2018

Hydraulic anatomy affects genotypic variation in plant water use and shows differential organ specific plasticity to drought in Sorghum bicolor

Genotypic variability and plasticity in hydraulic anatomy are not well-understood in herbaceous monocots. In this work, we used Sorghum bicolor , a monocotyledonous, tropical grass model, to understand whether differential plant water use is associated with xylem anatomy and if whole-plant xylem anatomy responds to water stress, justifying differential genotypic sensitivity to drought. In a greenhouse environment, we studied four sorghum genotypes that are known to genetically differ in growth and exhibit differential sensitivity to drought. Under well-watered scenario, transpiration variability and plant growth traits correlated with xylem anatomical traits at both the leaf and stem level, including xylem area and predicted xylem-specific hydraulic conductivity. High water use genotypes had inherently higher hydraulic capacity, but under drought, their transpiration declined at higher fractions of transpirable soil water ( FTSW ) and they showed greater plasticity in hydraulic anatomy. However, lower FTSW thresholds and modest anatomical changes were identified in the low water use genotypes with inherently lower hydraulic conductivity. Drought, induced modular phenotypic plasticity in hydraulic anatomy, whereby plasticity in leaf xylem traits was remarkably higher than stem xylem, while root xylem showed a reverse nature of vascular modification. Xylem traits were in agreement with phloem anatomy, irrespective of water regime. In conclusion, our study indicates that hydraulic anatomy can be critical for herbaceous monocots in determining limits to plant water use and genotypic response to drought with implications on whole-plant functions and habitat ecology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

SubTSBR to tackle high noise and outliers for data-driven discovery of differential equations

Data-driven discovery of differential equations has been an emerging research topic. We propose a novel algorithm subsampling-based threshold sparse Bayesian regression (SubTSBR) to tackle high noise and outliers. The subsampling technique is used for improving the accuracy of the Bayesian learning algorithm. It has two parameters: subsampling size and the number of subsamples. When the subsampling size increases with fixed total sample size, the accuracy of our algorithm goes up and then down. When the number of subsamples increases, the accuracy of our algorithm keeps going up. We demonstrate how to use our algorithm step by step and compare our algorithm with threshold sparse Bayesian regression (TSBR) for the discovery of differential equations. We show that our algorithm produces better results. We also discuss the merits of discovering differential equations from data and demonstrate how to discover models with random initial and boundary condition as well as models with bifurcations. The numerical examples are: (1) predator-prey model with noise, (2) shallow water equations with outliers, (3) heat diffusion with random initial and boundary condition, and (4) fish-harvesting problem with bifurcations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Physics-informed Karhunen-Loeve and Neural Network Approximations for Solving Inverse Differential Equation Problems

Here we present the PI-CKL-NN method for parameter estimation in differential equation (DE) models given sparse measurements of the parameters and states. In the proposed approach, the space- or time-dependent parameters are approximated by Karhunen-Loeve (KL) expansions that are conditioned on the parameters’ measurements, and the states are approximated by deep neural networks (DNNs). The unknown weights in the KL expansions and DNNs are found my minimizing the cost function that enforces the measurements of the states the DE constraint. Regularization is achieved by adding the l2 norm of the conditional KL coefficients into the loss function. Our approach assumes that the parameter fields are correlated in space or time and enforces the statistical knowledge (the mean and the covariance function) in addition to the DE constraints and measurements as opposed to the physics-informed neural network (PINN) and other similar physics-informed machine learning methods where only DE constraints and data are used for parameter estimation. We use the PI-CKL-NN method for parameter estimation in an ordinary differential equation with an unknown time-dependent parameter and the one- and two-dimensional partial differential diffusion equations with unknown space-dependent diffusion coefficients. We also demonstrate that PI-CKL-NN is more accurate than the PINN method, especially when the observations of the parameters are very sparse

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Differential transcription factor expression by human epithelial cells of buccal and urothelial derivation

Identification of transcription factors expressed by differentiated cells is informative not only of tissue-specific pathways, but to help identify master regulators for cellular reprogramming. If applied, such an approach could generate healthy autologous tissue-specific cells for clinical use where cells from the homologous tissue are unavailable due to disease. Normal human epithelial cells of buccal and urothelial derivation maintained in identical culture conditions that lacked significant instructive or permissive signaling cues were found to display inherent similarities and differences of phenotype. Investigation of transcription factors implicated in driving urothelial-type differentiation revealed buccal epithelial cells to have minimal or absent expression of PPARG, GATA3 and FOXA1 genes. Retroviral overexpression of protein coding sequences for GATA3 or PPARy1 in buccal epithelial cells resulted in nuclear immunolocalisation of the respective proteins, with both transductions also inducing expression of the urothelial differentiation-associated claudin 3 tight junction protein. PPARG1 overexpression alone entrained expression of nuclear FOXA1 and GATA3 proteins, providing objective evidence of its upstream positioning in a transcription factor network and identifying it as a candidate factor for urothelial-type transdifferentiation or reprogramming.

60 APPLIED LIFE SCIENCES↗