gebhart/patrepeval huggingface dataset:
Fast Prediction of HCCI Combustion with an Artificial Neural Network Linked to a Fluid Mechanics Code (2006)

<div class="htmlview paragraph">We have developed an artificial neural network (ANN) based combustion model and have integrated it into a fluid mechanics code (KIVA3V) to produce a new analysis tool (titled KIVA3V-ANN) that can yield accurate HCCI predictions at very low computational cost. The neural network predicts ignition delay as a function of operating parameters (temperature, pressure, equivalence ratio and residual gas fraction). KIVA3V-ANN keeps track of the time history of the ignition delay during the engine cycle to evaluate the ignition integral and predict ignition for each computational cell. After a cell ignites, chemistry becomes active, and a two-step chemical kinetic mechanism predicts composition and heat generation in the ignited cells.</div> <div class="htmlview paragraph">KIVA3V-ANN has been validated by comparison with isooctane HCCI experiments in two different engines. The neural network provides reasonable predictions for HCCI combustion and emissions that, although typically not as good as obtained with the more physically representative multi-zone model, are obtained at a much reduced computational cost. KIVA3V-ANN can perform reasonably accurate HCCI calculations while requiring only 10% more computational effort than a motored KIVA3V run. It is therefore considered a valuable tool for evaluation of engine maps or other performance analysis tasks requiring multiple individual runs.</div>
Expanding the computable reactome in Pseudomonas putida reveals metabolic cycles providing robustness (2017)

Abstract Genome-scale network reconstructions are organism-specific representations of metabolism and powerful tools for analyzing systemic metabolic properties. The use of reconstructions is limited by the lack of coverage of the metabolic reactome. We present an exhaustive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440, greatly expanding its computable metabolic states. The reconstruction, i JN1411, represents a significant expansion over other reconstructed bacterial metabolic networks. Computations based on the reconstruction exhibit high accuracy in predicting nutrient sources, growth rates, carbon flux distributions, and gene essentiality, thus providing a deep understanding of Pseudomonas metabolism. i JN1411 was used for: i) the assessment of the metabolic capabilities of P. putida as a species through multi-strain modeling, ii) deciphering the molecular mechanisms underlying metabolic robustness, and iii) identification of metabolic “capacitors” based on ATP-fueled metabolic cycles. This study represents the most complete and comprehensive bacterial metabolic reconstruction built to date, while providing computational and experimental evidence about how bacteria increase metabolic robustness, paving the way for engineering more robust biocatalysts and searching for drug targets in robust pathogens.
Defect Activity in InGaN/GaN LEDs (invited). (2020)

Abstract not provided.
Nonlinear performance of 200Gb/s, 400Gb/s and 1Tb/s PM-16QAM superchannels in dynamic WDM traffic scenario (2015)

We experimentally evaluate flex-grid network upgrade scenarios, employing variable data rates and modulation formats and show that optical channel power should be assigned with knowledge of existing neighboring traffic to achieve best performance in WDM transmission.
Transcriptional profiling by cDNA‐AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis (2004)

A comprehensive transcriptome analysis by means of cDNA-amplified fragment length polymorphism (AFLP) and cDNA-microarray technology was performed in order to gain further understanding of the molecular mechanisms of immediate transcriptional response to ethylene. Col-0 plants were treated with exogenous ethylene and sampled at six different time-points ranging from 10 min until 6 h. In order to isolate truly ethylene-responsive genes, both the ethylene-insensitive mutant ein2-1 and the constitutive mutant (ctr1-1) were analysed in parallel by cDNA-AFLP while ein2-1 was included for the microarray experiment. Out of the cDNA-transcript profiling covering about 5% of the Arabidopsis transcriptome, 46 ethylene-responsive genes were isolated, falling in different classes of expression pattern and including a number of novel genes. Out of the 6008 genes present on the chip, 214 genes were significantly (alpha = 0.001) differentially expressed between Col-0 and ein2-1 over time. Cluster analysis and functional grouping of co-regulated genes allowed to determine the major ethylene-regulated classes of genes. In particular, a large number of genes involved in cell rescue, disease and defence mechanisms were identified as early ethylene-regulated genes. Furthermore, the data provide insight into the role of protein degradation in ethylene signalling and ethylene-regulated transcription and protein fate. Novel interactions between ethylene response and responses to several other signals have been identified by this study. Of particular interest is the overlap between ethylene response and responses to abscisic acid, sugar and auxin. In conclusion, the data provide unique insight into early regulatory steps of ethylene response.
<title>Aspects of satellite imagery exploration in GIS-based command and control real-time technologies</title> (2002)

The tremendous increase in satellite imagery resolution and accuracy has made it reasonable to exploit such imagery in GIS-based command and control, fusing data streams from UAV/UGV and satellite sensors for C4ISR systems. To fuse imagery from satellite and tactical sensors in real time, the authors apply probabilistic analysis, polyquadrically interpolating evidential reasoning about non-numeric tactical factors and superimposing them on Digital Terrain Models and satellite imagery. Doing this in real time for C4ISR requires highly parallel computation, implemented on Video/Imagery Super-Parallel and Supercomputer-Path (VISP) hardware. Another approach is integrated view analysis for purposes of command decision making missions, making use of GIS environments, Dynamic Time Multiplexed Holographic (DTMH) screens, and 3-D projection for precise visualization of accurate GIS-based imagery. This technology incorporates non-numeric real-time information into the command and control processes with simultaneous integrated 3-D views. Theory and experiment both indicate that the methods and algorithms described here are feasible.
Current research on chronic active Epstein–Barr virus infection in Japan (2014)

Epstein-Barr virus (EBV) infection is usually asymptomatic and persists lifelong. Although EBV-infected B cells have the potential for unlimited proliferation, they are effectively removed by the virus-specific cytotoxic T cells, and EBV-associated lymphoproliferative disease develops only in immunocompromised hosts. Rarely, however, individuals without apparent immunodeficiency develop chronic EBV infection with persistent infectious mononucleosis-like symptoms. These patients have high EBV-DNA load in the peripheral blood and systemic clonal expansion of EBV-infected T cells or natural killer (NK) cells. Their prognosis is poor with life-threatening complications including hemophagocytic lymphohistiocytosis, organ failure, and malignant lymphomas. The term "chronic active EBV infection" (CAEBV) is now generally used for this disease. The geographical distribution of CAEBV is markedly uneven and most cases have been reported from Japan and other East Asian countries. Here we summarize the current understanding of CAEBV and describe the recent progress of CAEBV research in Japan.
A wheat kinase and immune receptor form host-specificity barriers against the blast fungus (2023)

Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. Here we show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes will enable study of the molecular interaction between pathogen effector and host resistance genes.
Hepatitis C Virus Glycoprotein Complex Localization in the Endoplasmic Reticulum Involves a Determinant for Retention and Not Retrieval (1998)

The hepatitis C virus (HCV) genome encodes two envelope glycoproteins (E1 and E2). These glycoproteins interact to form a noncovalent heterodimeric complex which in the cell accumulates in endoplasmic reticulum (ER)-like structures. The transmembrane domain of E2, at least, is involved in HCV glycoprotein complex localization in this compartment. In principle, ER localization of a protein can be the consequence of actual retention in this organelle or of retrieval from the Golgi. To determine which of these two mechanisms is responsible for HCV glycoprotein complex accumulation in the ER, the precise localization of these proteins was studied by immunofluorescence, and the processing of their glycans was analyzed. Immunolocalization of HCV glycoproteins after nocodazole treatment suggested an ER retention. In addition, HCV glycoprotein glycans were not modified by Golgi enzymes, indicating that the ER localization of these proteins is not because of their retrieval from the cis Golgi. Retention of HCV glycoprotein complexes in the ER without retrieval suggests that this compartment plays an important role for the acquisition of the envelope of HCV particles. A true retention in the ER was also observed for E2 expressed in the absence of E1 or for a chimeric protein containing the ectodomain of CD4 in fusion with the transmembrane domain of E2. These data indicate that, in HCV glycoprotein complex, the transmembrane domain of E2, at least, is responsible for true retention in the ER, without recycling through the Golgi.
Computer Platform Adaptive Interference Cancellation Using Higher-Order Statistics (2015)

Broadband wireless interference in a computer platform is the result of multiple dynamic electromagnetic emission sources. This interference is non-Gaussian and a receiver design based on the Gaussian assumption will yield suboptimal performance. In fact, it has a double-sided K-distribution and needs to be treated differently in the design process. When dealing with this type of interference in the presence of white Gaussian noise, traditional interference/noise cancellation schemes do not produce satisfactory results. In this paper, we present an interference mitigation method which improves BER performance. We do this by using the cross-cumulant as the criterion of goodness. Specifically, our algorithm is based on higher order statistics (HOS) and is designed to reconstruct and to cancel the interference in a recursive fashion. The algorithm is tested on both BPSK and OFDM communication environments. We compare performance in terms of BER against other cancellation methods.
Mouse B cells do not proliferate in human interleukin 2 (1986)

By pre-activation with a monoclonal anti-IgM antibody coupled to Sepharose, either in the absence or presence of low doses of lipopolysaccharide, mouse B cell populations were rendered responsive to recombinant DNA derived human interleukin 2 (IL 2). However, if the B cell populations were subjected to separation based on their buoyant density before pre-activation, only low but not high buoyant density cells became responsive to IL 2. Both cell populations subsequent to anti-IgM pre-activation were equally responsive to a Sephadex G-100 fraction of supernatants from rat spleen cells stimulated with concanavalin A. Furthermore, the differences in the IL 2 titration curves on T and B cell populations indicate that only a subpopulation of cells are responding to IL 2 in the B cell populations. In B cell populations that did respond to IL 2, a population of Thy-1.2-positive cells appeared. The proportion of IL 2-responsive T cells needed to give a significant signal when admixed with nonresponding B cell populations was quantitated to be less than 1%.
Stimuli-Responsive Surface Ligands for Direct Lithography of Functional Inorganic Nanomaterials (2023)

ConspectusColloidal nanocrystals (NCs) have emerged as a diverse class of materials with tunable composition, size, shape, and surface chemistry. From their facile syntheses to unique optoelectronic properties, these solution-processed nanomaterials are a promising alternative to materials grown as bulk crystals or by vapor-phase methods. However, the integration of colloidal nanomaterials in real-world devices is held back by challenges in making patterned NC films with the resolution, throughput, and cost demanded by device components and applications. Therefore, suitable approaches to pattern NCs need to be established to aid the transition from individual proof-of-concept NC devices to integrated and multiplexed technological systems.In this Account, we discuss the development of stimuli-sensitive surface ligands that enable NCs to be patterned directly with good pattern fidelity while retaining desirable properties. We focus on rationally selected ligands that enable changes in the NC dispersibility by responding to light, electron beam, and/or heat. First, we summarize the fundamental forces between colloidal NCs and discuss the principles behind NC stabilization/destabilization. These principles are applied to understanding the mechanisms of the NC dispersibility change upon stimuli-induced ligand modifications. Six ligand-based patterning mechanisms are introduced: ligand cross-linking, ligand decomposition, ligand desorption, <i>in situ</i> ligand exchange, ion/ligand binding, and ligand-aided increase of ionic strength. We discuss examples of stimuli-sensitive ligands that fall under each mechanism, including their chemical transformations, and address how these ligands are used to pattern either sterically or electrostatically stabilized colloidal NCs. Following that, we explain the rationale behind the exploration of different types of stimuli, as well as the advantages and disadvantages of each stimulus.We then discuss relevant figures-of-merit that should be considered when choosing a particular ligand chemistry or stimulus for patterning NCs. These figures-of-merit pertain to either the pattern quality (e.g., resolution, edge and surface roughness, layer thickness), or to the NC material quality (e.g., photo/electro-luminescence, electrical conductivity, inorganic fraction). We outline the importance of these properties and provide insights on optimizing them. Both the pattern quality and NC quality impact the performance of patterned NC devices such as field-effect transistors, light-emitting diodes, color-conversion pixels, photodetectors, and diffractive optical elements. We also give examples of proof-of-concept patterned NC devices and evaluate their performance. Finally, we provide an outlook on further expanding the chemistry of stimuli-sensitive ligands, improving the NC pattern quality, progress toward 3D printing, and other potential research directions. Ultimately, we hope that the development of a patterning toolbox for NCs will expedite their implementation in a broad range of applications.
Association of Sodium Channel γ-Subunit Promoter Variant With Blood Pressure (2001)

The SCNN1G gene, located on human chromosome 16p12, encodes the gamma subunit of the amiloride-sensitive epithelial sodium channel, and mutations in SCNN1G can result in Liddle's syndrome or pseudohypoaldosteronism type I. We identified sequence variations in the promoter region of SCNN1G and examined the association between this polymorphism and blood pressure in a large cohort (n=4075) representing the general population in Japan. We found T(-1290)C, T(-501)G, G(-173)A, and G(-104)T polymorphisms in the promoter region of SCNN1G and confirmed the existence of T387C and T474C polymorphisms in exon 3 and the C1947G polymorphism in exon 13. Because the genotypes of the T(-1290)C, T(-501)G, G(-104)T, and T474C polymorphisms were in tight linkage disequilibrium, we selected the T474C and G(-173)A polymorphisms for an association study. The G(-173)A polymorphism of SCNN1G had a significant effect on systolic pressure (P=0.0050) and pulse pressure (P=0.0050). The AA genotype was associated with an 11 mm Hg drop in systolic pressure and an 8 mm Hg drop in pulse pressure and with a higher prevalence of hypotension (P=0.0195). A transient transfection assay using MDCK cells and human renal epithelial cells indicated that the promoter activity of the G(-173) allele was higher than that of the A(-173) allele. Although the effects of the A(-173) allele were recessive and although the AA genotype was found in just 0.7% of our study population, we observed that this variation of human SCNN1G had significant effects on blood pressure.
Real-time restriction mapping of DNA stretched in nanofluidic devices (2005)

The recovery of symmetric and efficient walking is one of the key goals of a rehabilitation program in patients with stroke. The use of overground exoskeletons alongside conventional gait training might help foster rhythmic muscle activation in the gait cycle toward a more efficient gait. About twenty-nine patients with subacute stroke have been recruited and underwent either conventional gait training or experimental training, including overground gait training using a wearable powered exoskeleton alongside conventional therapy. Before and after the rehabilitation treatment, we assessed: (i) gait functionality by means of clinical scales combined to obtain a Capacity Score, and (ii) gait neuromuscular lower limbs pattern using superficial EMG signals. Both groups improved their ability to walk in terms of functional gait, as detected by the Capacity Score. However, only the group treated with the robotic exoskeleton regained a controlled rhythmic neuromuscular pattern in the proximal lower limb muscles, as observed by the muscular activation analysis. Coherence analysis suggested that the control group (CG) improvement was mediated mainly by spinal cord control, while experimental group improvements were mediated by cortical-driven control. In subacute stroke patients, we hypothesize that exoskeleton multijoint powered fine control overground gait training, alongside conventional care, may lead to a more fine-tuned and efficient gait pattern.
Biosensor-based engineering of biosynthetic pathways (2016)

Biosynthetic pathways provide an enzymatic route from inexpensive renewable resources to valuable metabolic products such as pharmaceuticals and plastics. Designing these pathways is challenging due to the complexities of biology. Advances in the design and construction of genetic variants has enabled billions of cells, each possessing a slightly different metabolic design, to be rapidly generated. However, our ability to measure the quality of these designs lags by several orders of magnitude. Recent research has enabled cells to report their own success in chemical production through the use of genetically encoded biosensors. A new engineering discipline is emerging around the creation and application of biosensors. Biosensors, implemented in selections and screens to identify productive cells, are paving the way for a new era of biotechnological progress.
Sensitivity Analysis of the Vehicle Model Mass for Model Predictive Control Based Power Management System of a Plug-in Hybrid Electric Vehicle (2018)

Model predictive control strategy (MPC) has been identified as an efficient path for reducing fuel consumption, greenhouse gasses (GHG) emission, or degradation of power-train components for electrified vehicles. MPC is an optimization-based control strategy that aims at finding the optimal control actions of a system by predicting its future behaviors. As a main contribution, this paper investigate, identify, and quantify the effects of inaccuracy on the vehicle model mass estimation on the performance of the MPC controller when the plug hybrid electric vehicle (PHEV) is in the charge sustaining (CS) mode. Simulations show that error in the vehicle mass estimation degrades the performance of the MPC controller regarding the equivalent fuel consumption, the battery aging, and the objective function.
Frequency dependence of average phase shift from human calcaneusin vitro (2009)

If dispersion in a medium is weak and approximately linear with frequency (over the experimental band of frequencies), then it can be shown that the constant term in a polynomial representation of phase shift as a function of frequency can produce errors in measurements of phase-velocity differences in through-transmission, substitution experiments. A method for suppressing the effects of the constant phase shift in the context of the single-wave-model was tested on measurements from 30 cancellous human calcaneus samples in vitro. Without adjustment for constant phase shifts, the estimated phase velocity at 500 kHz was 1516+/-6 m/s (mean+/-standard error), and the estimated dispersion was -24+/-4 m/s MHz (mean+/-standard error). With adjustment for constant phase shifts, the estimated mean velocity decreased by 4-9 m/s, and the estimated magnitude of mean dispersion decreased by 50%-100%. The average correlation coefficient between the measured attenuation coefficient and frequency was 0.997+/-0.0026 (mean+/-standard deviation), suggesting that the signal for each sample was dominated by one wave. A single-wave, linearly dispersive model conformed to measured complex transfer functions from the 30 cancellous-bone samples with an average root-mean-square error of 1.9%+/-1.0%.
The Xanthate Route to Amino Acids (2020)

The degenerative xanthate addition transfer to alkenes allows the synthesis of a broad range of protected, and in some cases enantiopure, α, β, and γ-amino acids, including proline and pipecolic derivatives, as well as fluorinated congeners and β-lactams. The radical addition furnishes naturally latent mercapto-α-amino acids that are ideally equipped for native chemical ligation. Most of the amino acid structures accessible rapidly by this chemistry would otherwise require tedious multi-step syntheses.
Efficient Engineering of Vascularized Ectopic Bone from Human Embryonic Stem Cell–Derived Mesenchymal Stem Cells (2012)

Human mesenchymal stem cells (hMSCs) can be derived from various adult and fetal tissues. However, the quality of tissues for the isolation of adult and fetal hMSCs is donor dependent with a nonreproducible yield. In addition, tissue engineering and cell therapy require large-scale production of a pure population of lineage-restricted stem cells that can be easily induced to differentiate into a specific cell type. Therefore, human embryonic stem cells (hESCs) can provide an alternative, plentiful source for generation of reproducible hMSCs. We have developed efficient differentiation protocols for derivation of hMSCs from hESCs, including coculture with murine OP9 stromal cells and feeder layer-free system. Our protocols have resulted in the generation of up to 49% of hMSCs, which expressed CD105, CD90, CD29, and CD44. The hMSCs exhibited high adipogenic, chondrocytic, and osteogenic differentiation in vitro. The latter correlated with osteocalcin secretion and vascular endothelial growth factor (VEGF) production by the differentiating hMSCs. hMSC-derived osteoblasts further differentiated and formed ectopic bone in vivo, and induced the formation of blood vessels in Matrigel implants. Our protocol enables generation of a purified population of hESC-derived MSCs, with the potential of differentiating into several mesodermal lineages, and particularly into vasculogenesis-inducing osteoblasts, which can contribute to the development of bone repair protocols.