gebhart/patrepeval huggingface dataset:
Immunofluorescent localization of a Ca2+-dependent neutral protease in hamster muscle (1981)

A Ca2+-dependent neutral thiol protease is widely distributed in mammalian tissues and has been implicated in muscle protein turnover. As a first step to understanding the physiological function of this enzyme, its cellular and subcellular localization has been studied in hamster cardiac and skeletal muscle by means of indirect immunofluorescence. The results showed that the Ca2+-dependent protease is located either at the plasma membrane or in the connective tissue matrix that surrounds the muscle cels. The uniform distribution along membranes and around capillaries indicated that the protease is not confined to connective tissue cells. This evidence, together with the Ca2+-dependence of the enzyme, suggests a distribution throughout the extracellular connective tissue of the muscle. In this position, it would seem unlikely that the enzyme could participate in protein turnover within muscle cells in normal tissue.
Determining the Internal Quantum Efficiency of PbSe Nanocrystal Solar Cells with the Aid of an Optical Model (2008)

We determine the internal quantum efficiency (IQE) of the active layer of PbSe nanocrystal (NC) back-contact Schottky solar cells by combining external quantum efficiency (EQE) and total reflectance measurements with an optical model of the device stack. The model is parametrized with the complex index of refraction of each layer in the stack as calculated from ellipsometry data. Good agreement between the experimental and modeled reflectance spectra permits a quantitative estimate of the fraction of incident light absorbed by the NC films at each wavelength, thereby yielding well-constrained QE spectra for photons absorbed only by the NCs. Using a series of devices fabricated from 5.1+/-0.4 nm diameter PbSe NCs, we show that thin NC cells achieve an EQE and an active layer IQE as high as 60+/-5% and 80+/-7%, respectively, while the QE of devices with NC layers thicker than about 150 nm falls, particularly in the blue, because of progressively greater light absorption in the field-free region of the films and enhanced recombination overall. Our results demonstrate that interference effects must be taken into account in order to calculate accurate optical generation profiles and IQE spectra for these thin film solar cells. The mixed modeling/experimental approach described here is a rigorous and powerful way to determine if multiple exciton generation (MEG) photocurrent is collected by devices with EQE<100%. On the basis of the magnitudes and shapes of the IQE spectra, we conclude that the 1,2-ethanedithiol treated NC devices studied here do not produce appreciable MEG photocurrent.
Plant Extracts of the Family Lauraceae: A Potential Resource for Chemopreventive Agents that Activate the Nuclear Factor-Erythroid 2-Related Factor 2/Antioxidant Response Element Pathway (2014)

Cells and tissues counteract insults from exogenous or endogenous carcinogens through the expression of genes encoding antioxidants and phase II detoxifying enzymes regulated by antioxidant response element promoter regions. Nuclear factor-erythroid 2-related factor 2 plays a key role in regulating the antioxidant response elements-target gene expression. Hence, the Nrf2/ARE pathway represents a vital cellular defense mechanism against damage caused by oxidative stress and xenobiotics, and is recognized as a potential molecular target for discovering chemopreventive agents. Using a stable antioxidant response element luciferase reporter cell line derived from human breast cancer MDA-MB-231 cells combined with a 96-well high-throughput screening system, we have identified a series of plant extracts from the family Lauraceae that harbor Nrf2-inducing effects. These extracts, including Litsea garrettii (ZK-08), Cinnamomum chartophyllum (ZK-02), C. mollifolium (ZK-04), C. camphora var. linaloolifera (ZK-05), and C. burmannii (ZK-10), promoted nuclear translocation of Nrf2, enhanced protein expression of Nrf2 and its target genes, and augmented intracellular glutathione levels. Cytoprotective activity of these extracts against two electrophilic toxicants, sodium arsenite and H2O2, was investigated. Treatment of human bronchial epithelial cells with extracts of ZK-02, ZK-05, and ZK-10 significantly improved cell survival in response to sodium arsenite and H2O2, while ZK-08 showed a protective effect against only H2O2. Importantly, their protective effects against insults from both sodium arsenite and H2O2 were Nrf2-dependent. Therefore, our data provide evidence that the selected plants from the family Lauraceae are potential sources for chemopreventive agents targeting the Nrf2/ARE pathway.
Hard Acid and Soft Nucleophile Systems. Part 13. Aluminum Chloride-Sodium Iodide-Acetonitrile System : A Very Mild Reagent for Selective Dealkylation (Commemoration Issue Dedicated to Professor Shigeo Tanimoto On the Occation of His Retirement) (1992)

A new combination reagent system (A1C13-NaI-CH3CN) was devised for selective demethylation of aliphatic methyl ether in the presence of aromatic methyl ether under mild conditions.This reagent system cleaved the methyl ether of primary alcohol faster than that of secondary alcohol.The order of reactivity of ethers is aliphatic benzyl ether>aromatic benzyl ether, aliphatic methyl ether (primary >secondary)>>aromatic methyl ether.Benzyl ester and ethylene acetal were deprotected but methyl ester, acetate, lactone, and a,$-unsaturated ketone remained intact.KEY WORDS : Aluminum chloride / Sodium iodide / Acetonitrile / Selective dealkylation / Methyl ether / Benzyl ether / Ethylene acetal / Benzyl ester / Hard acid / Soft nucleophileThe concept of "Hard" and "Soft" was introduced in chemistry in 1963 by Pearson and used to classify the various acids and bases3).The HSAB principle is an expression on reactivity that a hard acid combines with a hard base and a soft acid does with a soft base preferentially.Although the use of this principle had been limited only in inorganic chemistry in the early stage, this was also well recognized in the organic chemistry after the expansion into organic chemistry in 19674).A chemical bond has the hard-soft dissymmetry as well as the charge dissymmetry.Thus, a combination system of a hard acid and a soft nucleophile may cleave the bond which consists of a hard base and a soft acid).Previously we have developed various combination systems') of a hard Lewis acid and a thiol or a sulfide as a soft nucleophile for C-O bond cleavage reactions') of methyl ethers, benzyl ethers, esters, and lactones, according to the general concept as shown in Fig. 1.To avoid foul smell of a thiol or a sulfide, we have devised a new combination system (A1C13-NaI-acetonitrile), where a thiol or a suifide is replaced by iodide ion * ,'f',
Epigenetic remodeling during monolayer cell expansion reduces therapeutic potential (2021)

ABSTRACT Understanding how cells remember previous mechanical environments to influence their fate, or mechanical memory, informs the design of biomaterials and therapies in medicine. Current regeneration therapies require two-dimensional (2D) cell expansion processes to achieve large cell populations critical for the repair of damaged (e.g. connective and musculoskeletal) tissues. However, the influence of mechanical memory on cell fate following expansion is unknown, and mechanisms defining how physical environments influence the therapeutic potential of cells remain poorly understood. Here, we show that the organization of histone H3 trimethylated at lysine 9 (H3K9me3) and expression of tissue-identifying genes in primary cartilage cells (chondrocytes) transferred to three-dimensional (3D) hydrogels depends on the number of previous population doublings on tissue culture plastic during 2D cell expansion. Decreased levels of H3K9me3 occupying promoters of dedifferentiation genes after the 2D culture were also retained in 3D culture. Suppression of H3K9me3 during expansion of cells isolated from a murine model similarly resulted in the loss of the chondrocyte phenotype and global remodeling of nuclear architecture. In contrast, increasing levels of H3K9me3 through inhibiting H3K9 demethylases partially rescued the chondrogenic nuclear architecture and gene expression, which has important implications for tissue repair therapies, where expansion of large numbers of phenotypically-suitable cells is required. Overall, our findings indicate mechanical memory in primary cells is encoded in the chromatin architecture, which impacts cell fate and the phenotype of expanded cells. SIGNIFICANCE STATEMENT Tissue regeneration procedures, such as cartilage defect repair (e.g. Matrix-induced Autologous Chondrocyte Implantation) often require cell expansion processes to achieve sufficient cells to transplant into an in vivo environment. However, the chondrocyte cell expansion on 2D stiff substrates induces epigenetic changes that persist even when the chondrocytes are transferred to a different (e.g. 3D) or in vivo environment. Treatments to alter epigenetic gene regulation may be a viable strategy to improve existing cartilage defect repair procedures and other tissue engineering procedures that involve cell expansion.
RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach (2002)

To physically characterize the web of interactions connecting the Saccharomyces cerevisiae proteins suspected to be RNA polymerase II (RNAPII) elongation factors, subunits of Spt4/Spt5 and Spt16/Pob3 (corresponding to human DSIF and FACT), Spt6, TFIIF (Tfg1, -2, and -3), TFIIS, Rtf1, and Elongator (Elp1, -2, -3, -4, -5, and -6) were affinity purified under conditions designed to minimize loss of associated polypeptides and then identified by mass spectrometry. Spt16/Pob3 was discovered to associate with three distinct complexes: histones; Chd1/casein kinase II (CKII); and Rtf1, Paf1, Ctr9, Cdc73, and a previously uncharacterized protein, Leo1. Rtf1 and Chd1 have previously been implicated in the control of elongation, and the sensitivity to 6-azauracil of strains lacking Paf1, Cdc73, or Leo1 suggested that these proteins are involved in elongation by RNAPII as well. Confirmation came from chromatin immunoprecipitation (ChIP) assays demonstrating that all components of this complex, including Leo1, cross-linked to the promoter, coding region, and 3' end of the ADH1 gene. In contrast, the three subunits of TFIIF cross-linked only to the promoter-containing fragment of ADH1. Spt6 interacted with the uncharacterized, essential protein Iws1 (interacts with Spt6), and Spt5 interacted either with Spt4 or with a truncated form of Spt6. ChIP on Spt6 and the novel protein Iws1 resulted in the cross-linking of both proteins to all three regions of the ADH1 gene, suggesting that Iws1 is likely an Spt6-interacting elongation factor. Spt5, Spt6, and Iws1 are phosphorylated on consensus CKII sites in vivo, conceivably by the Chd1/CKII associated with Spt16/Pob3. All the elongation factors but Elongator copurified with RNAPII.
PWM Switching Frequency Effects on Eddy Current Sensors for Magnetically Suspended Flywheel Systems (2003)

A flywheel magnetic bearing (MB) pulse width modulated power amplifier (PWM) configuration is selected to minimize noise generated by the PWMs in the flywheel position sensor system. Two types of noise are addressed: beat frequency noise caused by variations in PWM switching frequencies, and demodulation noise caused by demodulation of high order harmonics of the switching voltage into the MB control band. Beat frequency noise is eliminated by synchronizing the PWM switch frequencies, and demodulation noise is minimized by selection of a switching frequency which does not have harmonics at the carrier frequency of the sensor. The recommended MB PWM system has five synchronized PWMs switching at a non-integer harmonic of the sensor carrier.
Parkinsonism-inducing neurotoxin, tetrahydropyridine: Uptake of the i phenylpyridine by dopamine neuro) (substantia nigra/caudate-putamen/nucleus accumbens/locus cerul (2016)

N- Methyl - 4 - phenyl - 1,2,3,6 - tetrahydropy- ridine (MPTP) produces neuropathological and clinical ab- normalities in humans, monkeys, and mice that closely re- semble idiopathic parkinsonism. N-Methyl-4-phenylpyridine (MPP+), a metabolite of MPTP formed by monoamine oxidase B, is accumulated into striatal and cerebral cortical synapto- somes by the dopamine and norepinephrine uptake systems, respectively, whereas MPTP itself is not accumulated. The potencies of drugs in inhibiting (3H)MPP+ or (3H)dopamine uptake into striatal synaptosomes are very similar, as are potencies in inhibiting (3H)MPP+ or (3H)norepinephrine up- take into cortical synaptosomes. The Km values for (3H)MPP+ uptake are 170 and 65 nM and the Vmax values are 2 and 0.1 nmol/g of tissue per min in rat striatum and cortex, respec- tively, similar to values for (3H)dopamine uptake. Autoradi- ography of accumulated (3H)MPP+ in slices of rat brain shows high densities in the caudate-putamen and nucleus ac- cumbens. Furthermore, blockade of dopamine uptake by mazindol prevents MPTP-induced damage to nigrostriatal dopamine neurons, indicating that MPP+ concentration into dopamine neurons explains their selective destruction by
Pyridazines. VIII. Syntheses and Nuclear Magnetic Resonance Spectra of Cinnoline N-Oxides. (1963)

Cinnoline 1-oxide (II), cinnoline 2-oxide (III), 4-methylcinnoline 1-oxide (V), 4-methylcinnoline 2-oxide (VI), 3-chlorocinnoline 1-oxide (VIII), and 3-methoxycinnoline 1-oxide (XXI) were synthesized. For confirmation of the structure of these compounds, cinnoline 1-oxide (II) and 3-chlorocinnoline 1-oxide (VIII) were prepared from their corresponding 5, 6, 7, 8-tetrahydro derivatives (XI and XIII) by bromination with N-bromosuccimide followed by dehydrobromination with sodium methoxide. The structures of isomeric 4-methylcinnoline N-oxides were determined by the application of ultraviolet and nuclear magnetic resonance spectroscopies. The nuclear magnetic resonance spectra of the cinnoline N-oxides synthesized were examined. The interpretation of the spectra was made in connection with those of pyridazine N-oxides and of quinoline N-oxides. The proton H8 shows its signal peak at a lower field than do the other protons, owing to the magnetic anisotropy effect of the N-O group.
A New Approach to Load Balance for Parallel/Compositional Simulation Based on Reservoir-Model Overdecomposition (2013)

Summary The quest for efficient and scalable parallel reservoir simulators has been evolving with the advancement of high-performance computing architectures. Among the various challenges of efficiency and scalability, load imbalance is a major obstacle that has not been fully addressed and solved. The causes of load imbalance in parallel reservoir simulation are both static and dynamic. Robust graph-partitioning algorithms are capable of handling static load imbalance by decomposing the underlying reservoir geometry to distribute a roughly equal load to each processor. However, these loads that are determined by a static load balancer seldom remain unchanged as the simulation proceeds in time. This so-called dynamic imbalance can be exacerbated further in parallel compositional simulations. The flash calculations for equations of state (EOSs) in complex compositional simulations not only can consume more than half of the total execution time but also are difficult to balance merely by a static load balancer. The computational cost of flash calculations in each gridblock heavily depends on the dynamic data such as pressure, temperature, and hydrocarbon composition. Thus, any static assignment of gridblocks may lead to dynamic load imbalance in unpredictable manners. A dynamic load balancer can often provide solutions for this difficulty. However, traditional techniques are inflexible and tedious to implement in legacy reservoir simulators. In this paper, we present a new approach to address dynamic load imbalance in parallel compositional simulation. It overdecomposes the reservoir model to assign each processor a bundle of subdomains. Processors treat these bundles of subdomains as virtual processes or user-level migratable threads that can be dynamically migrated across processors in the run-time system. This technique is shown to be capable of achieving better overlap between computation and communication for cache efficiency. We use this approach in a legacy reservoir simulator and demonstrate a reduction in the execution time of parallel compositional simulations while requiring minimal changes to the source code. Finally, it is shown that domain overdecomposition, together with a load balancer, can improve speedup from 29.27 to 62.38 on 64 physical processors for a realistic simulation problem.
Surface Functionalization and Patterning Techniques to Design Interfaces for Biomedical and Biosensor Applications (2006)

Abstract Summary: In this paper, we present a review of our research activity related to the use of plasma deposition and etching technologies for the production of functional polymers (protein affinity and anti‐fouling) and their application to the fabrication chemical contrasts at micro and sub micron scale. Plasma deposition processes of acrylic acid (ppAA) and PEO‐like films to obtain functionalized surfaces are illustrated, together with optical lithography and colloidal lithography techniques used for micro and nanoscale patterning. In particular, microstructure based upon a combination of pulsed plasma polymerized acrylic acid (with carboxyl retention up to 15%) and cell repulsive PEO‐like character (CO content higher than 70%) have been realized and characterized by XPS and TOF‐SIMS. Furthermore, colloidal lithography is used for fabrication of sub‐micron (100 nm diameter) ppAA functionalized nanostructures and protein adsorption and cell growth experiments are described, demonstrating the reliability of plasma polymers for micro and nanobiotechnology applications. L929 cells growth on micropatterned PEO‐like surfaces (left), PPAA nanostructures after O 2 plasma etching (right). magnified image L929 cells growth on micropatterned PEO‐like surfaces (left), PPAA nanostructures after O 2 plasma etching (right).
Numerical and Experimental Flame Stabilization Analysis in the New Spinning Combustion Technology Framework (2020)

Abstract Global warming, climate change and pollution are burning environmental issues. To reduce the carbon footprint of the aviation sector, aeronautical companies have been striving to lower engine emissions via the development of reliable lean combustors. In this context, effort has been devoted to the better understanding of various flame dynamics with emphasis on thermoacoustic instabilities, lean blow-off and extinctions. In line with this effort, Safran Helicopter Engines has recently developed and patented the revolutionary spinning combustion technology (SCT) for its next generation of combustors. This technology has indeed great flexibility when it comes to ignition and blow-off capabilities. To better understand the various physical mechanisms occurring in a SCT combustor, a joint numerical and experimental analysis of the flame stabilization in this spinning combustion technology framework has been devised. On the experimental side, the NTNU atmospheric annular combustor has been modified to introduce a relevant azimuthal component of velocity while operating under premixed fuel conditions, following the SCT concept. Note that to reduce temperature at the backplane of the chamber, film cooling is incorporated to avoid fuel injector damage. On the numerical side, high fidelity Large Eddy Simulations of the test bench have been carried out with the AVBP code developed at CERFACS, providing insights on the flame stabilization in this unique SCT geometry. In particular, it is noted that there is a strong interaction between the cooling film and the highly swirled flames exiting from the fuel injector bend. In that respect, changing the injector or global equivalence ratios while operating the SCT is shown to affect the combustion of this design.
One-Pot Synthesis ofS-Acetamidomethyl-N-fluorenylmethoxy-carbonyl-L-cysteine (Fmoc-Cys(Acm)-OH) (1987)

A new strategy for the preparation of S-acetamidomethyl-N-fluorenyl-methoxycarbonyl-L-cysteine is reported. Inexpensive, readily available reagents are used, and no special equipment is required. A very homogeneous product is obtained after a simple crystallization at the end of the process, without purification of intermediates.
Graph-Inceptor: Towards Extreme Data Ingestion, Massive Graph Creation and Storage (2023)

Graph processing is increasingly popular given the wide range of phenomena represented as graphs (e.g., social media networks, pharmaceutical drug compounds, or fraud networks, among others). The increasing amount of data available requires new approaches to efficiently ingest and process such data. In this research, we describe a solution at a conceptual level in the context of the Graph-Massivizer architecture. Graph-Inceptor aims to bridge the void among ETL tools enabling data transformations required for graph creation and enrichment and supporting connectors to multiple graph storages at a massive scale. Furthermore, it aims to enhance ETL operations by learning from data content and load and making decisions based on machine-learning-based predictive analytics.
Rhodium-Catalyzed Intermolecular Oxidative Cross-Coupling of (Hetero)Arenes with Chalcogenophenes (2013)

A straightforward and efficient method for the rhodium-catalyzed intermolecular oxidative cross-coupling of arenes and heteroarenes with thio- and selenophene derivatives (chalcogenophenes) via double C-H bond cleavage has been developed by using Cu(OAc)2/AgSbF6 as an oxidant. The reaction is applicable to a wide range of (hetero)arenes carrying a directing group and chalcogenophenes to yield substituted biaryl heterocyclic derivatives and oligothiophene derivatives in moderate to high yields.
ChemInform Abstract: SINGLET OXYGENATION OF 7‐ARYL‐ AND 7‐ALKYL‐1,3,5‐CYCLOHEPTATRIENES. SUBSTITUENT EFFECTS ON THE PRODUCT DISTRIBUTION OF TROPYLIDENE‐ AND NORCARADIENE‐DERIVED ENDOPEROXIDES (1983)

Abstract Bei der Singlett‐Sauerstoff‐Addition an 7‐Aryl bzw. 7‐Alkyl‐l ,3 ,5‐cy‐ cloheptatriene (II) entstehen die Tropiliden‐endoperoxide (I) sowie die Norcaradienendoperoxide (IV).
Decay of correlations in low density parity check codes: Low noise regime (2009)

Consider transmission over a binary additive white gaussian noise channel using a fixed low-density parity check code. We consider the posterior measure over the code bits and the corresponding correlation between two codebits, averaged over the noise realizations. We show that for low enough noise variance this average correlation decays exponentially fast with the graph distance between the code bits. One consequence of this result is that for low enough noise variance the GEXIT functions (further averaged over a standard code ensemble) of the belief propagation and optimal decoders are the same.