gebhart/patrepeval huggingface dataset:
Systematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae (2018)

The pentose phosphate pathway (PPP) plays an important role in the synthesis of ribonucleotides and aromatic amino acids. During bioethanol production from cellulosic biomass composed mainly of D-glucose and D-xylose, the PPP is also involved in xylose metabolism by engineered Saccharomyces cerevisiae. Although the activities and thermostabilities of the four PPP enzymes (transaldolase: TAL1, transketolase: TKL1, ribose-5-phosphate ketol-isomerase: RKI1 and D-ribulose-5-phosphate 3-epimerase: RPE1) can affect the efficiency of cellulosic ethanol production at high temperatures, little is known about the suitable expression levels of these PPP genes. Here, we overexpressed PPP genes from S. cerevisiae and the thermotolerant yeast Kluyveromyces marxianus either singly or in combination in recombinant yeast strains harboring a mutant of xylose isomerase (XI) and evaluated xylose consumption and ethanol production of these yeast transformants in glucose/xylose mixed media at 36 °C. Among the PPP genes examined, we found that: (1) strains that overexpressed S. cerevisiae TKL1 exhibited the highest rate of xylose consumption relative to strains that overexpressed other PPP genes alone; (2) overexpression of RKI1 and TAL1 derived from K. marxianus with S. cerevisiae TKL1 increased the xylose consumption rate by 1.87-fold at 24 h relative to the control strain (from 0.55 to 1.03 g/L/h); (3) the strains with XI showed higher ethanol yield than strains with xylose reductase and xylitol dehydrogenase and (4) PHO13 disruption did not improve xylose assimilation under the experimental conditions. Together these results indicated that optimization of PPP activity improves xylose metabolism in genetically engineered yeast strains, which could be useful for commercial production of ethanol from cellulosic material.
Effect of Low‐Energy Accelerated Ion Bombardment on the Properties of Metal‐Organic Decomposition Derived SrBi 2 (Ta,Nb) 2 O 9 Thin Films Processed at Low Temperature (2004)

Ferroelectric SrBi 2 (Ta,Nb) 2 O 9 (SBTN) thin films were deposited on Pt (200 nm)/TiO x (40 nm)/SiO 2 (100 nm)/Si substrates by metal‐organic decomposition. The effects of bombardment from accelerated argon and oxygen ions on the properties of SBTN thin films were investigated. It was found that the argon ion bombardment could decrease the crystallization temperature owing to the increase of internal energy of the films. Also, the oxygen vacancies at the interface between the SBTN film and platinum bottom electrode or at grain boundaries in the film were passivated through the oxygen ion treatment, resulting in the improved electrical properties. By optimizing the process parameters and using bombardment of accelerated argon and oxygen ions, SBTN films with good ferroelectric and electrical properties could be obtained, at a temperature as low as 650°C.
Flavors and Fragrances, 3. Aromatic and Heterocyclic Compounds (2016)

The article contains sections titled: 1. Aromatic Compounds 1.1. Hydrocarbons 1.2. Alcohols and Ethers 1.3. Aldehydes and Acetals 1.4. Ketones 1.5. Esters of Araliphatic Alcohols and Aliphatic Acids 1.6. Aromatic Acids 1.7. Esters Derived from Aromatic and Araliphatic Acids 1.7.1. Benzoates 1.7.2. Phenylacetates 1.7.3. Cinnamates 1.8. Miscellaneous Compounds 2. Phenols and Phenol Derivatives 2.1. Phenols, Phenyl Esters, and Phenyl Ethers 2.2. Phenol Alcohols and their Esters 2.3. Phenol Aldehydes 2.4. Phenol Ketones 2.5. Phenolcarboxylates 2.5.1. Salicylates 2.5.2. Resorcyclic Acid Esters 2.6. O, O,S, and S,S Heterocycles 2.6.1. Cyclic Ethers 2.6.2. Lactones 2.6.3. Glycidates 2.6.4. Miscellaneous Compounds 3. N and N,S Heterocycles
Hot Test in Mixer Settlers of Alpha Barrier with AHA in PUREX Process (2012)

In the PUREX process, the first U-Pu purification cycle (1CUPu) is not efficient enough for the decontamination of uranium flow out of neptunium. In this context, molecules known for their strong complexing power for actinides(IV) in aqueous phase, such as acetohydroxamic acid (AHA) have been tested in batch experiments to strip Np and Pu from TBP solvent loaded with U. A phenomenological model was developed and with the help of this model, a flowsheet of a counter-current alpha barrier process was designed and tested in C17 glove boxes in ATALANTE facility. A decontamination factor DFU/Np of 480 was obtained, higher than DFU/Np required by UNIREP standards.
Transient alterations in granule cell proliferation, apoptosis and migration in postnatal developing cerebellum of CRMP1−/– mice (2006)

Collapsin response mediator proteins (CRMPs) consist of five homologous cytosolic proteins that participate in signal transduction involved in a variety of physiological events. CRMP1 is highly expressed during brain development; however, its functions remains unclear. To gain insight into its function, we generated CRMP1(-/-) mice with a knock-in LacZ gene. No gross anatomical changes or behavioral alterations were observed. Expression of CRMP1 was examined by the expression of the knocked-in LacZ gene, in situ hybridization with riboprobes and by imunohistochemistry. CRMP1 was found to be highly expressed in the developing the cerebellum, olfactory bulbs, hypothalamus and retina. In adults, expression level was high in the olfactory bulbs and hippocampus but very low in the retina and cerebellum and undetectable in hypothalamus. To study potential roles of CRMP1, we focused on cerebellum development. CRMP1(-/-) mice showed a decrease in the number of granule cells migrating out of explants of developing cerebellum, as did treatment of the explants from normal mice with anti-CRMP1 specific antibodies. CRMP1(-/-) mice showed a decrease in granule cell proliferation and apoptosis in external granule cell layers in vivo. Adult cerebellum of CRMP1(-/-) did not show any abnormalities.
Rapid Screening of Wood Chemical Component Variations Using Transmittance Near-Infrared Spectroscopy (2005)

A rapid transmittance near-infrared (NIR) spectroscopy method was developed to predict the variation in chemical composition of solid wood. The effect of sample preparation, sample quantity (single versus stacked multiple wood wafers), and NIR acquisition time on the quantification of alpha-cellulose and lignin content was investigated. Strong correlations were obtained between laboratory wet chemistry values and the NIR-predicted values. In addition to the experimental protocol and method development, improvements in calibration error associated with utilizing stacked multiple wood wafers as opposed to single wood wafers are also discussed.
ChemInform Abstract: UEBERGANGSMETALL‐SUBSTITUIERTE VB ELEMENTSYSTEME 7. MITT. UEBERGANGSMETALL‐ANTIMON(III)BROMIDE (1975)

Abstract Die Metallate (I) reagieren in Cyclohexan mit Antimonbromid zu den Derivaten (II), die mit äquivalenten Mengen des Na‐metallats bei Raumtemperatur in 2‐3 Tagen zu den stabilen Zweikernkomplexen (IIIa) und (IIIb) umgesetzt werden.
ABCA4 Gene Sequence Variations in Patients With Autosomal Recessive Cone-Rod Dystrophy (2003)

Our findings confirm that a substantial percentage of patients with autosomal recessive cone-rod dystrophy are likely to harbor a mutation in the ABCA4 gene as the cause of their disease. The fundus phenotype observed in such patients is quite variable, and certain fundus phenotypes may be more associated with certain genotypes. Clinical Relevance Identification of the molecular genetic basis for various inherited human retinal dystrophies, such as cone-rod dystrophy, facilitates a potentially better understanding of the mechanisms by which photoreceptor cells degenerate. This in turn provides guidance as to how to better proceed in identifying the most optimal future therapeutic strategies.
Measurement of ψ(2S) meson production in pp collisions at $\sqrt{s}=7\ \mbox{TeV}$ (2012)

The differential cross-section for the inclusive production of <i>ψ</i>(2<i>S</i>) mesons in <i>pp</i> collisions at [Formula: see text] has been measured with the LHCb detector. The data sample corresponds to an integrated luminosity of 36 pb<sup>-1</sup>. The <i>ψ</i>(2<i>S</i>) mesons are reconstructed in the decay channels <i>ψ</i>(2<i>S</i>)→<i>μ</i><sup>+</sup><i>μ</i><sup>-</sup> and <i>ψ</i>(2<i>S</i>)→<i>J</i>/<i>ψπ</i><sup>+</sup><i>π</i><sup>-</sup>, with the <i>J</i>/<i>ψ</i> meson decaying into two muons. Results are presented both for promptly produced <i>ψ</i>(2<i>S</i>) mesons and for those originating from <i>b</i>-hadron decays. In the kinematic range <i>p</i><sub>T</sub>(<i>ψ</i>(2<i>S</i>))≤16 GeV/<i>c</i> and 2<<i>y</i>(<i>ψ</i>(2<i>S</i>))≤4.5 we measure [Formula: see text] where the last uncertainty on the prompt cross-section is due to the unknown <i>ψ</i>(2<i>S</i>) polarization. Recent QCD calculations are found to be in good agreement with our measurements. Combining the present result with the LHCb <i>J</i>/<i>ψ</i> measurements we determine the inclusive branching fraction [Formula: see text] where the last uncertainty is due to the [Formula: see text], [Formula: see text] and [Formula: see text] branching fraction uncertainties.
Minimal packing duration in close reduction for nasal bone fracture treatment (2015)

The present study demonstrated that 1-day packing had comparable postoperative outcome with reducing the patients' discomfort. As such, a longer packing duration was not needed to achieve stable results one day is a reasonable packing time for most nasal bone fractures.
Cartilage tissue engineering using differentiated and purified induced pluripotent stem cells (2012)

The development of regenerative therapies for cartilage injury has been greatly aided by recent advances in stem cell biology. Induced pluripotent stem cells (iPSCs) have the potential to provide an abundant cell source for tissue engineering, as well as generating patient-matched in vitro models to study genetic and environmental factors in cartilage repair and osteoarthritis. However, both cell therapy and modeling approaches require a purified and uniformly differentiated cell population to predictably recapitulate the physiological characteristics of cartilage. Here, iPSCs derived from adult mouse fibroblasts were chondrogenically differentiated and purified by type II collagen (Col2)-driven green fluorescent protein (GFP) expression. Col2 and aggrecan gene expression levels were significantly up-regulated in GFP+ cells compared with GFP- cells and decreased with monolayer expansion. An in vitro cartilage defect model was used to demonstrate integrative repair by GFP+ cells seeded in agarose, supporting their potential use in cartilage therapies. In chondrogenic pellet culture, cells synthesized cartilage-specific matrix as indicated by high levels of glycosaminoglycans and type II collagen and low levels of type I and type X collagen. The feasibility of cell expansion after initial differentiation was illustrated by homogenous matrix deposition in pellets from twice-passaged GFP+ cells. Finally, atomic force microscopy analysis showed increased microscale elastic moduli associated with collagen alignment at the periphery of pellets, mimicking zonal variation in native cartilage. This study demonstrates the potential use of iPSCs for cartilage defect repair and for creating tissue models of cartilage that can be matched to specific genetic backgrounds.
Soluble CD40 Ligand Stimulates CD40-Dependent Activation of the β2 Integrin Mac-1 and Protein Kinase C Zeda (PKCζ) in Neutrophils: Implications for Neutrophil-Platelet Interactions and Neutrophil Oxidative Burst (2013)

Recent work has revealed an essential involvement of soluble CD40L (sCD40L) in inflammation and vascular disease. Activated platelets are the major source of sCD40L, which has been implicated in platelet and leukocyte activation, although its exact functional impact on leukocyte-platelet interactions and the underlying mechanisms remain undefined. We aimed to determine the impact and the mechanisms of sCD40L on neutrophils. We studied neutrophil interactions with activated, surface-adherent platelets as a model for leukocyte recruitment to the sites of injury. Our data show that CD40L contributes to neutrophil firm adhesion to and transmigration across activated surface-adherent platelets, possibly through two potential mechanisms. One involves the direct interaction of ligand-receptor (CD40L-CD40), i.e., platelet surface CD40L interaction with neutrophil CD40; another involves an indirect mechanism, i.e. soluble CD40L stimulates activation of the leukocyte-specific β2 integrin Mac-1 in neutrophils and thereby further promotes neutrophil adhesion and migration. Activation of the integrin Mac-1 is known to be critical for mediating neutrophil adhesion and migration. sCD40L activated Mac-1 in neutrophils and enhanced neutrophil-platelet interactions in wild-type neutrophils, but failed to elicit such responses in CD40-deficient neutrophils. Furthermore, our data show that the protein kinase C zeta (PKCζ) is critically required for sCD40L-induced Mac-1 activation and neutrophil adhesive function. sCD40L strongly stimulated the focal clustering of Mac-1 (CD11b) and the colocalization of Mac-1 with PKCζ in wild-type neutrophils, but had minimal effect in CD40-deficient neutrophils. Blocking PKCζ completely inhibited sCD40L-induced neutrophil firm adhesion. Moreover, sCD40L strongly stimulates neutrophil oxidative burst via CD40-dependent activation of PI3K/NF-KB, but independent of Mac-1 and PKCζ. These findings may contribute to a better understanding of the underlying mechanisms by which sCD40L/CD40 pathway contributes to inflammation and vascular diseases.
Photoelectron Spectroscopic Study of C12A7:e- and Alq3 Interface:  The Formation of a Low Electron-Injection Barrier (2007)

12CaO·7Al2O3 electride (C12A7:e-) is a promising material for the cathode of organic light-emitting diodes (OLEDs), because it has a low work function (φWF = 2.4 eV), comparable to metal potassium, and good chemical/thermal stability in an ambient atmosphere. This study examines interfacial electronic structures between C12A7:e- and tris-8-hydroxyquinoline aluminum (Alq3) by ultraviolet photoelectron spectroscopy, finding that a low electron-injection barrier of 0.6 eV, which is approximately half of the value for the Al/LiF/Alq3 interface with the lowest injection barrier, is achieved when the interface is formed on the C12A7:e- film surface obtained by using vacuum annealing and subsequent He plasma treatment. This treatment yields little change in the surface chemical composition and retains a low φWF value (3.1 eV) of C12A7:e-. These results suggest that C12A7:e- has high potential as an efficient electron-injection electrode for OLEDs.
Permeability of Chemical Delivery Systems Across Rabbit Corneal (SIRC) Cell Line and Isolated Corneas: A Comparative Study (2000)

The purpose of this study was to investigate the corneal permeability of phenylephrone chemical delivery systems (CDS) across isolated cornea and to evaluate the utility of the SIRC cell line (epithelial cells originating from rabbit cornea) as an in vitro model for predicting the ocular permeability. The effect of benzalkonium chloride (BAC) on the drug permeability through SIRC cell layers was also studied. The transport of phenylephrone CDS across the isolated cornea of the albino rabbit was measured at various pH values using a two-chamber glass diffusion cell, and the results were compared with the reported permeability values across SIRC cells of rabbit origin. Corneal membranes showed lower flux values for compounds, especially for hydrophilic compounds, than the SIRC cell line. A significant correlation was observed between the permeability coefficients through corneal membranes and SIRC cells. When the pH of the transport medium was increased, the permeability coefficients increased and lag times decreased in both in vitro models. Furthermore, both in vitro models showed significant correlation between permeability coefficients and lipophilicities of the drugs. The three esters, having higher lipophilic characteristics, showed higher permeability than phenylephrine HCl. The phenylacetyl ester of phenylephrone showed a three-fold increase in penetration across SIRC cell layers in the presence of 0.01% BAC. These results suggest that the use of SIRC cell layers can reasonably predict the permeability of ophthalmic drugs across corneal membranes.
Computer Simulation of the Mechanical Properties of Amorphous Polymer Nanostructures (2003)

The mechanical properties of polymeric nanostructures have been investigated by means of Monte Carlo and molecular dynamics simulations. A continuum mechanics model was applied to determine an apparent modulus for such structures from results of virtual deformation simulations. A recently proposed method based on strain fluctuations was also used to calculate the elasticity tensor for the structures. The effect of size on the apparent modulus of ultra-small structures was explored. Our results indicate that, for a given system at a specified temperature, the modulus of a small structure can be significantly smaller than that of the bulk material. Furthermore, in small systems the elastic constants are shown to become anisotropic.
A Software to Visualize, Edit, Model and Mesh Vascular Networks (2022)

Computational fluid dynamics (CFD) is a key tool for a wide range of research areas, beyond the computer science community. In particular, CFD is used in medicine to measure blood flow from patient specific models of arteries. In this field, the creation of accurate meshes remains the most challenging step, as it is based on the segmentation of medical images, a time-consuming task which often requires manual intervention by medical doctors. In this context, user-friendly, interactive softwares are valuable. They enable to spread the new advances in numerical treatment to the medical community and enrich them with the expert knowledge (e.g anatomical knowledge) of clinicians. In this work, we present a user interface dedicated to the meshing of vascular networks from centerlines. It allows for the 3D visualization and edition of input centerlines, which constitute a simplified, easy-to-manipulate representation of vascular networks. The surface of the artery can be reconstructed from the modified centerlines by an editable parametric model and then meshed with high quality hexahedral elements. At every step of the process, the network can be confronted with medical images with enhanced visualization. The software will be released publicly. Clinical relevance- This tool facilitates the manual extraction and editing of vascular networks by medical doctors. It opens the generation of hexahedral meshes for computational fluid dynamics studies to non-expert users.
Synthesis and photoinitiated polymerization of new ionic liquid methacrylates (2022)

Abstract Synthesis of new ionic liquid methacrylates and dimethacrylates is described comprising ammonium structures and various anions (bis(trifluoromethylsulfonyl)imide (NTf 2 ), tris(pentafluoroethyl)trifluorophosphate (FAP), triflate (TFl), and trifluoroacetate (TFAc)). The structure of the anion has a stronger effect on both melting behavior and photopolymerization kinetics compared to the cation pattern. Photo‐differential scanning calorimetry investigation shows significant differences in the polymerization rate and final conversion depending on both the polymerization technique (bulk or solution polymerization using an ionic liquid as solvent) and the ionic liquid monomer under consideration. The results show that NTf 2 or FAP should be preferred as anion over TFl and TFAc in the crosslinking photoinitiated polymerization because NTf 2 and FAP result in both faster polymerization and higher final conversion. Interestingly, the presence of an ionic liquid methacrylate comprising the same anion as the ionic liquid dimethacrylate during the photoinitiated polymerization of the ionic liquid dimethacrylates results in an increase in final conversion that may be caused by lower crosslink density of the network formed, and therefore, higher mobility during the crosslinking process.
Suppression of vacuum breakdown using thin-film coatings (1994)

Thin-film metal and metal oxide coatings ion sputter deposited onto the cathode electrode of a parallel-plate high-voltage gap were found to suppress electron emission in high vacuum. Electric fields as high as 60 kV/mm have been sustained across a 1 mm gap for pulse durations of 10 μs. Lesser electric fields were sustained for pulse durations exceeding 10 ms. The behavior of 500 nm thick coatings was independent of the type of coating used, whereas the breakdown voltage for thinner coatings depended upon the material and the deposition conditions. The breakdown properties of various coatings, as well as a discussion of the suppression of electron emission is presented.
Poster Session 4 (2011)

spectively), (p<0.0001 for RX versus NL, p<0.001 for PN versus NL and p<0.0005 for RF versus NL). IVRP was significantly different in NL (79.3±8.3 msec) compared to RX (93.0±23.8, p<0.05) and compared to RF (46.0±9.9, p<0.0001), but was not significantly different from normal in PN (70.0 ± 25.5, p=NS). The ratio of TD/IVRP showed significant progressive increase with progression of the pattern of dias- tolic function from NL (0.74±0.13) to RX (1.16±0.74, p<0.05), to PN (1.57±0.44, p<0.005), with the higher value in RF (2.67±1.28, p<0.0001). Conclusion: TD, IVRP and TD/IVRP are easily obtainable and reliable measures for identification of left ventricular systolic and diastolic dysfunction.
Exponential TD Learning: A Risk-Sensitive Actor-Critic Reinforcement Learning Algorithm (2023)

Incorporating risk in the decision-making process has been shown to lead to significant performance improvement in optimal control and reinforcement learning algorithms. We construct a temporal-difference risk-sensitive reinforcement learning algorithm using the exponential criteria commonly used in risk-sensitive control. The proposed method resembles an actor-critic architecture with the ‘actor’ implementing a policy gradient algorithm based on the exponential of the reward-to-go, which is estimated by the ‘critic’. The novelty of the update rule of the ‘critic’ lies in the use of a modified objective function that corresponds to the underlying multiplicative Bellman’s equation. Our results suggest that the use of the exponential criteria accelerates the learning process and reduces its variance, i.e., risk-sensitiveness can be utilized by actor-critic methods and can lead to improved performance.
A Partial Characterization of a Class of Matrices Defined by Solutions to the Linear Complementarity Problem (1982)

In this paper we analyze the class of matrices, Q 0 , characterized as all n × n matrices, M, for which the linear complementarity problem, w = Mz + q, w, z ≥ 0, w′z = 0, has a solution whenever q is feasible. The method is to analyze the faces of the linear cone. Cone[I, −M] where I is the n × n identity. Essentially, a labelling requirement for the faces is shown necessary for M to be in Q 0 . With proper restrictions and nondegenerate assumptions sufficiency is also shown. These results arc related to the signs of the minors of M and some conjectures in this area are also discussed.
A Computational Investigation of the Interaction of Pulses in Two-Pulse Jets (2008)

Large-eddy simulations (LES) and Reynolds-averaged Navier-Stokes (RANS) simulations of the interaction of the second pulse with the first pulse in a double-injection event are presented in this study. The opposing effects of the turbulence generated by the first pulse to accelerate mixing of the second pulse, and the residual bulk velocity from the first pulse to accelerate penetration of the second pulse are analyzed. The LES results show greater influence of the turbulence whereas the RANS results show greater influence of the bulk velocity.