gebhart/patrepeval huggingface dataset:
Characterization of the p.L145F and p.S135N Mutations in SOD1: Impact on the Metabolism of Fibroblasts Derived from Amyotrophic Lateral Sclerosis Patients (2022)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of the upper and lower motor neurons (MNs). About 10% of patients have a family history (familial, fALS); however, most patients seem to develop the sporadic form of the disease (sALS). <i>SOD1</i> (Cu/Zn superoxide dismutase-1) is the first studied gene among the ones related to ALS. Mutant SOD1 can adopt multiple misfolded conformation, lose the correct coordination of metal binding, decrease structural stability, and form aggregates. For all these reasons, it is complicated to characterize the conformational alterations of the ALS-associated mutant SOD1, and how they relate to toxicity. In this work, we performed a multilayered study on fibroblasts derived from two ALS patients, namely SOD1<sup>L145F</sup> and SOD1<sup>S135N</sup>, carrying the p.L145F and the p.S135N missense variants, respectively. The patients showed diverse symptoms and disease progression in accordance with our bioinformatic analysis, which predicted the different effects of the two mutations in terms of protein structure. Interestingly, both mutations had an effect on the fibroblast energy metabolisms. However, while the SOD1<sup>L145F</sup> fibroblasts still relied more on oxidative phosphorylation, the SOD1<sup>S135N</sup> fibroblasts showed a metabolic shift toward glycolysis. Our study suggests that SOD1 mutations might lead to alterations in the energy metabolism.
ChemInform Abstract: Novel Anthraquinone Derivatives with Redox‐Active Functional Groups Capable of Producing Free Radicals by Metabolism: Are Free Radicals Essential for Cytotoxicity? (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ESD Power Grid Design (2011)

The Electrostatic Discharge ESD power grid and metal interconnects have a significant impact on the (ESD) robustness of the semiconductor chip. In the ESD design synthesis of interconnects, there are two primary issues. With the design synthesis of the interconnects, the failure of the interconnect is critical to the determination of the interconnect minimum requirements. In ESD design synthesis, guidelines and ground rules are needed to identify the proper wire width and via number based on the ESD objective. The power grid resistance is critical to the ability of the semiconductor current to discharge the current to the power rail bond pads. This chapter highlights some of the power grid considerations for Charged Device Model (CDM), IEC 61000-4-2, and Human Metal Model (HMM) specifications. ESD design rule checking (DRC) and verification methodologies can be used to avoid ESD failures. Controlled Vocabulary Terms electrostatic discharge; power grids; semiconductor devices; wires (electric)
Characteristic pH and electrolyte concentration dependences of 2‐aminopyridine‐derivatized oligosaccharides (N‐glycans) in sonic‐spray ionization mass spectrometry (2005)

The intensities of ion signals from neutral oligosaccharides (N-glycans) derivatized with 2-aminopyridine (PA) were analyzed by ion trap mass spectrometry with a sonic-spray ionization (SSI) source, in both positive- and negative-ion modes, while varying the pH and concentration of ammonium acetate buffer solution. Two characteristic results are reported and discussed. The first characteristic is the pH dependence of the ion intensities; on increasing the solution pH from 4.3 to 8.6, positive ion intensities increase and negative ion intensities decrease. The second characteristic concerns the dependence of ion intensities on electrolyte concentration; on increasing the electrolyte concentration, the SSI efficiency for the PA N-glycans first increases and then decreases. Assuming that the SSI mechanism essentially conforms to the statistical charging model and the charge residue model, a new model that focuses a great deal of attention on the counter (electrolyte) ion distribution surrounding the solvated analyte (PA N-glycan) is proposed, in particular to rationalize the characteristic pH dependence.
The effect of unsaturated fatty acid and triglyceride oil addition on the mechanical and antibacterial properties of acrylic bone cements (2015)

Acrylic bone cements have an elastic modulus several times higher than the surrounding trabecular bone. This has been hypothesized to contribute to certain clinical complications. There are indications that the addition of specific fatty acids and triglyceride oils may reduce the elastic modulus of these types of cements. Some of these additives also appear to have inherent antibiotic properties, although this has never been evaluated in bone cements. In this study, several types of fatty acids and triglyceride oils were evaluated for use in acrylic bone cements. Their mechanical properties were evaluated under uniaxial compression testing and selected cements were then further characterized in terms of microstructure, handling and antibacterial properties using scanning electron microscopy, polymerization temperature measurements, agar diffusion tests and bactericidal activity assays of cement extracts. It was found that any of the evaluated fatty acids or triglyceride oils could be used to tailor the stiffness of acrylic bone cements, although at varying concentrations, which also depended on the type of commercial base cement used. In particular, the addition of very small amounts of linoleic acid (<2.0 wt%) resulted in Young's moduli and compressive strengths in the range of human trabecular bone, while maintaining a similar setting time. Further, the addition of 12.6 wt% ricinoleic acid to Osteopal V cement was found to have a significant antibacterial effect, inhibiting growth of Staphylococcus aureus in an agar diffusion test as well as demonstrating 100% bactericidal activity against the same strain.
Hybrid integrated metro ring node subsystem on a chip (2003)

We report on a hybrid integrated metro ring node subsystem on a chip that consists of an array of four independent reconfigurable optical add-drop circuits, each with power monitoring and automatic load balancing, and supporting shared and dedicated protection protocols in two-fiber metro ring optical networks. The four-channel metro ring node chip has polymeric optical waveguiding circuitry, thermally actuated with heaters consisting of resistive strips of metal. Photodiode arrays are flip-chip mounted on top of 45° mirrors cut in the waveguides of optical power taps. The mirrors are fabricated by Excimer laser ablation of the polymer followed by smoothing and metalization. The non-integrated implementation of a metro ring node uses 48 discrete elements, namely 8 1×2 switches, 8 2×2 switches, 8 VOAs, 12 taps, and 12 photodiodes. The proposed integrated solution is an exemplary embodiment of the benefits of optoelectronic integration as it provides, when compared to the discrete solution, significant cost reduction, space savings, lower electrical power consumption, higher reliability (fewer devices, runs cooler), and fewer board-level fiber interconnects.
总血红蛋白、碳氧血红蛋白、高铁血红蛋白浓度无创连续监测的现状 (2013)

术中及时发现贫血，确定一氧化碳中毒者碳氧血红蛋白的浓度，调整药物剂量以防止高铁血红蛋白浓度超过中毒水平都很重要。脉搏氧饱和度仪的工作原理是发射光到组织并测定被组织吸收的光量。实验室氧血红蛋白计也利用同样的原理检测血红蛋白浓度。这两种仪器的工作原理相同，脉搏氧饱和度仪经过改造也可用于监测血红蛋白浓度。目前市场上有两种脉搏氧饱和度仪，MasimoRainbowSETandOrSenseNBM-200MP，都可以同时检测总血红蛋白浓度，Masimo还能检测高铁血红蛋白和碳氧血红蛋白。本文旨在就有关同行对这些仪器准确性的评议文献进行综述。
Knoevenagel Condensation Reaction in a Membrane Microreactor. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Poster Sessions (2007)

Previously, we have shown that indole-3-carbinol (I3C), a compound derived from cruciferous vegetable, inhibits different inflammatory mediators in lipopolysaccharide (LPS)-activated macrophages and suppresses angiogenic markers in vascular endothelial cells. Because the activated macrophages may release angiogenic factors to induce angiogenesis, the aim of this study was to investigate the effects I3C on activated macrophage-induced angiogenesis. In cocultivated macrophages and vascular endothelial cells, LPS significantly enhanced nitric oxide (NO) production and tube formation, whereas cotreatment with I3C inhibited such enhancement. To clarify the roles of I3C on macrophages, the macrophages were treated with LPS as well as I3C or NO synthase inhibitor, Nitro-L-arginine methyl ester (L-NAME), and the treated condition medium (CM) was used to cultivate vascular endothelial cells. The results indicated that I3C or L-NAME containing CM significantly inhibited CM-stimulated tube formation, vascular endothelial growth factor (VEGF) secretion, and matrix metalloproteinase-9 (MMP-9) activity. To understand the effects of I3C or L-NAME on vascular endothelial cells, the LPSactivated macrophage CM was used to cultivate vascular endothelial cells in the presence of I3C or L-NAME. The results showed that I3C and L-NAME inhibited CM-induced NO production, tube formation, VEGF secretion and, MMP-9 activity in vascular endothelial cells. In summary, we demonstrate that the cruciferous vegetable derivative, I3C, not only inhibits LPS stimulated macrophage activation but also affects vascular endothelial cells to inhibit macrophage-induced angiogenesis, and such effect is dependent upon NO production.
Amino acid residues involved in cholinesterase inhibition with metaproterenol and its bisdimethylcarbamate (2012)

Introduction: Selectivity of cholinesterases and their interaction with various compounds, especially drugs, is a subject of many studies in the field of biochemistry and pharmacology, due to important roles of cholinesterases in organism and their involvement in metabolism of many drugs. Metaproterenol is a bronchodilator used in the treatment of asthma. Metacarb (bisdimethylcarbamate of metaproterenol) is structurally related to bambuterol. Bambuterol, a prodrug of bronchodilator terbutaline and one of the most selective butyrylcholinesterase (BChE) inhibitor. Metacarb, like bambuterol, carbamylates the active site serine and progressively inhibits cholinesterases. Metaproterenol, a final product of decarbamylation, is reversible cholinesterase inhibitor. The aim of the work was to identify amino acids that govern the inhibition with metaproterenol and metacarb by determining dissociation (KI) and inhibition rate (ki) constants, respectively. Results and discussion: Metaproterenol and metacarb were studied as inhibitors of mouse recombinant acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and six AChE mutants. Mutations in the choline-binding site (Y337A) combined with those in the acyl pocket (F295L/Y337A, F297I/Y337A, and F295L/F297I/Y337A) or those in the peripheral site (Y124Q and Y72N/Y124Q/W286R) were employed to mimic BChE active site residues. Competitive inhibition was observed for AChE w.t., BChE w.t., choline binding site and acyl pocket mutants, while non-competitive inhibition was noticed in case of peripheral site mutants. All studied cholinesterases displayed poor affinity (1/KI) for metaproterenol binding (KI=0.32 – 13 mM). However, even than 3 times higher affinity of BChE than AChE was observed. Although mutations in choline binding site and acyl pocket mimics BChE, affinities of these mutants were up to 4 times higher than that of BChE. Peripheral site mutants had the same or a 3 times lower affinity than AChE w.t. The inhibition rate constant of BChE inhibition by metacarb was 280 times higher than that of AChE. All mutations employed, except those including F297I, increased inhibition rates comparing to AChE w.t. (up to 30-times for F295L/Y337A and Y124Q) and therefore decreased selectivity seen for the wild type enzymes. Conclusions: Cholinesterase selectivity for metaproterenol reversible binding and carbamylation selectivity of metacarb is dictated with amino residues in choline-binding site and peripheral site residues.
8.1: Invited Paper : Achieving Near‐Correct Focus Cues in a 3D Display using Multiple Image Planes (2006)

Abstract Focus cues specify inappropriate 3d scene parameters in conventional displays because the light comes from a single surface, independent of the depth relations in the portrayed scene. We examine the efficacy of a stereo‐display prototype designed to minimize these problems by using multiple image planes to present near‐correct focus cues. Each eye's view is the sum of several images presented at different focal distances. Variation in focal distance is provided by either multiple beam splitters or by use of a switchable lens. The stimulus to accommodation is more consistent with the portrayed depth than with conventional displays. Compared to a normal, fixed‐distance display, observers show improved stereoscopic performance in different psychophysical tasks including speed of fusing stereoscopic images. The multiple image‐planes approach provides a practical solution for some shortcomings of conventional displays.
Towards Practical and Robust DNA-Based Data Archiving Using ‘Yin-Yang Codec’ System (2019)

ABSTRACT DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense however of introducing biocompatibility challenges or at the risk of decoding failure. Here, we propose a robust transcoding algorithm named the “Yin-Yang Codec” (YYC), using two rules to encode two binary bits into one nucleotide, to generate DNA sequences highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200-nt oligo pools and in vivo as an ~54-kb DNA fragment in yeast cells. Sequencing results show that YYC exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.94% at 10 4 molecule copies and an achieved recovery rate of 87.53% at 100 copies. In addition, the in vivo storage demonstration achieved for the first time an experimentally measured physical information density of 198.8 EB per gram of DNA (44% of the theoretical maximum for DNA).
Genomics and Emerging Drug Discovery Technologies (2007)

As in other areas of the biological sciences, a decisive move into the genomics era is underway for the study of helminths. As sequencing technologies improve and costs continue to drop, genomes are becoming available and will eventually be taken for granted by parasitologists and drug discovery researchers as being core knowledge for any organism of interest. Within a decade, it is plausible to envision the availability of draft or complete genomes from 100 nematode and platyhelminth species. Helminth genome sequencing offers substantial challenges to assembly and annotation because of size, repeat and gene structure and sequence polymorphisms. Research programmes in parasitology will need to adapt to effectively make use of these genomes and to identify the most promising opportunities for the application of genomic information to the development of control strategies, including anthelmintics. Immediate avenues for the use of genomes include superior description of gene and protein expression and function through microarrays, proteomics and RNA interference.
Identification of a subunit of NADH-dehydrogenase as a p49/STRAP-binding protein (2008)

These data suggest that p49/STRAP plays a role in the regulation of intracellular processes such as cardiac cellular metabolism, gene expression, and possibly aging.
The Fermi gamma-ray spectrum of the inner galaxy: Implications for annihilating dark matter (2009)

Recently, a preliminary spectrum from the Fermi Gamma-ray Space Telescope has been presented for the inner galaxy (-30 &lt; l &lt; 30, -5 &lt; b &lt; 5), as well as the galactic center (-1 &lt; l &lt; 1, -1&lt; b &lt; 1). We consider the implications of these data for dark matter annihilation models, especially models capable of producing the cosmic-ray excesses previously observed by PAMELA and Fermi. These local cosmic-ray excesses, when extrapolated to the inner galaxy, imply inverse Compton scattering (ICS) gamma-ray signals largely consistent with the preliminary Fermi gamma-ray spectrum. For specific halos and models, particularly those with prompt photons, the data have begun to constrain the allowed parameter space. Although significant modeling and background uncertainties remain, we explore how large a signal is permitted by the current data. Based upon this, we make predictions for what signal could be present in other regions of the sky where dark matter signals may be easier to isolate from the astrophysical backgrounds.
Determination of the Radical Reactivity Ratios of 2-(N-Ethylperfluorooctanesulfonamido)ethyl Acrylate and Methacrylate in Copolymerizations with N,N-Dimethylacrylamide by in Situ 1H NMR Analysis As Established for Styrene–Methyl Methacrylate Copolymerizations (2018)

A model system of styrene (St) and methyl methacrylate (MMA) was copolymerized in an NMR tube at 60 °C using 2,2′-azobis(isobutyronitrile) as the initiator and pyridazine as an internal standard to optimize an in situ 1H NMR spectroscopic method for determining reactivity ratios by generating data at hundreds of instantaneous comonomer compositions (244 data points from 8 to 91 mol % St) starting with only nine initial comonomer compositions. The radical reactivity ratios of styrene (rSt = 0.697 ± 0.010) and methyl methacrylate (rMMA = 0.491 ± 0.007) were determined by nonlinear least-squares fitting of a Mayo–Lewis plot of the instantaneous copolymer composition as a function of the comonomer feed composition using the terminal model and MINITAB statistical software, in which the copolymer composition was calculated by assuming that all comonomer consumed was converted to copolymer without side reactions; the results were similar to accepted literature values for the terminal and implicit penultimate models. After correcting for changes in the "lock" value at the initial stages of the copolymerization (because of solids formed in the sealed NMR tube), the same technique was used to determine the reactivity ratios of 2-(N-ethylperfluorooctanesulfonamido)ethyl acrylate (FOSA; rFOSA = 1.624 ± 0.048) and 2-(N-ethylperfluorooctanesulfonamido)ethyl methacrylate (FOSM; rFOSM = 2.876 ± 0.083) in their radical copolymerizations with N,N-dimethylacrylamide (DMA; rDMA = 1.126 ± 0.031 with FOSA; rDMA = 0.859 ± 0.026 with FOSM).
On some Latin morphological (ir)regularities (2012)

Two Latin irregular case-endings are well-attested in epigraphic sources: the 2nd-declension nominative plural in -eis and the 3rd-declension genitive singular in -us. Although inconsistent with Latin productive inflectional patterns, these two forms can nevertheless be regarded as prototypically-structured morphological classes that are defined by 'schemas'. Both the synchronic structure and the diachronic development of these classes provide evidence for the existence of an organized storage that is midway between rote-learning and rule processing, thus supporting a scalar view of morphological (ir)regularity.
Zeolite‐Assisted Lignin‐First Fractionation of Lignocellulose: Overcoming Lignin Recondensation through Shape‐Selective Catalysis (2020)

Organosolv pulping releases reactive monomers from both lignin and hemicellulose by the cleavage of weak C-O bonds. These monomers recombine to form undesired polymers through the formation of recalcitrant C-C bonds. Different strategies have been developed to prevent this process by stabilizing the reactive monomers (i.e., lignin-first approaches). To date, all reported approaches rely on the addition of capping agents or metal-catalyzed stabilization reactions, which usually require high pressures of hydrogen gas. Herein, a metal- and additive-free approach is reported that uses zeolites as acid catalysts to convert the reactive monomers into more stable derivatives under organosolv pulping conditions. Experiments with model lignin compounds showed that the recondensation of aldehydes and allylic alcohols produced by the cleavage of β-O-4' bonds was efficiently inhibited by the use of protonic β zeolite. By applying a zeolite with a preferred pore size, the bimolecular reactions of reactive monomers were effectively inhibited, resulting in stable and valuable monophenolics. The developed methodology was further extended to birch wood to yield monophenolic compounds and value-added products from carbohydrates.
Selective ETAAntagonists. 5. Discovery and Structure−Activity Relationships of Phenoxyphenylacetic Acid Derivatives (2000)

The fifth paper in this series describes the culmination of our investigations into the development of a potent and selective ET(A) receptor antagonist for the treatment of diseases mediated by ET-1. Receptor site mapping of several ET(A) antagonists prepared previously identified a common cationic binding site which prompted synthesis of phenoxyphenylacetic acid derivative 13a, which showed good in vitro activity (IC(50) 59 nM, rat aortic ET(A)). Optimization of 13a led to the identification of 27b, which exhibited an IC(50) of 4 nM. Although this did not translate into the expected in vivo potency, a compound of comparable in vitro activity, 27a (RPR118031A), showed a far better pharmacokinetic profile and in vivo potency (75 micromol/kg) and was duly proposed and accepted as a development candidate.
Rotationally resolved photoelectron spectra from vibrational autoionization of NO Rydberg levels (1997)

Rotationally resolved photoelectron spectra from vibrational autoionization of individual rotational levels of the nlR (v=1, 11⩽n⩽15, 0⩽lR⩽3) Rydberg states of NO are measured by combining two-color double-resonance excitation via the NO A 2∑+ (vi=1, Ni=19) state with time-of-flight photoelectron spectroscopy. The photoelectron spectra show that both even-l and odd-l continuum partial waves are generated by the autoionization events, and thus provide evidence for angular momentum exchange between the outgoing electron and the molecular-ion core. We interpret these observations as caused by the multipolar interactions between the outgoing electron and the vibrating nuclear core, which appear to be brought about both by the dependence on internuclear distance of the electron-ion-core electronic interaction and by Rydberg-valence state couplings.
Surgical Labyrinthectomy of the Rat to Study the Vestibular System (2018)

To study the vestibular system or the vestibular compensation process, a number of methods have been developed to cause vestibular damage, including surgical or chemical labyrinthectomy and vestibular neurectomy. Surgical labyrinthectomy is a relatively simple, reliable, and rapid method. Here, we describe the surgical technique for rat labyrinthectomy. A postauricular incision is made under general anesthesia to expose the external auditory canal and the tympanic membrane, after which the tympanic membrane and the ossicles are removed without the stapes. The stapes artery, which is located between the stapes and the oval window, is a vulnerable structure and must be preserved to obtain a clear surgical field. A hole to fenestrate the vestibule is made with a 2.1-mm drill bur superior to the stapes. Then, 100% ethanol is injected through this hole and aspirated several times. Meticulous dissection under a microscope and careful bleeding control are essential to obtain reliable results. Symptoms of vestibular loss, such as nystagmus, head tilting, and a rolling motion, are seen immediately after surgery. The rotarod or rotation chair test can be used to objectively and quantitatively evaluate the vestibular function.