gebhart/patrepeval huggingface dataset:
Mitochondrial Proteomic Analysis of a Cell Line Model of Familial Amyotrophic Lateral Sclerosis (2004)

Mutations in copper-zinc superoxide dismutase (SOD1) have been linked to a subset of familial amytrophic lateral sclerosis (fALS), a fatal neurodegenerative disease characterized by progressive motor neuron death. An increasing amount of evidence supports that mitochondrial dysfunction and apoptosis activation play a critical role in the fALS etiology, but little is known about the mechanisms by which SOD1 mutants cause the mitochondrial dysfunction and apoptosis. In this study, we use proteomic approaches to identify the mitochondrial proteins that are altered in the presence of a fALS-causing mutant G93A-SOD1. A comprehensive characterization of mitochondrial proteins from NSC34 cells, a motor neuron-like cell line, was achieved by two independent proteomic approaches. Four hundred seventy unique proteins were identified in the mitochondrial fraction collectively, 75 of which are newly discovered proteins that previously had only been reported at the cDNA level. Two-dimensional gel electrophoresis was subsequently used to analyze the differences between the mitochondrial proteomes of NSC34 cells expressing wild-type and G93A-SOD1. Nine and 36 protein spots displayed elevated and suppressed abundance respectively in G93A-SOD1-expressing cells. The 45 spots were identified by MS, and they include proteins involved in mitochondrial membrane transport, apoptosis, the respiratory chain, and molecular chaperones. In particular, alterations in the post-translational modifications of voltage-dependent anion channel 2 (VDAC2) were found, and its relevance to regulating mitochondrial membrane permeability and activation of apoptotic pathways is discussed. The potential role of other proteins in the mutant SOD1-mediated fALS is also discussed. This study has produced a short list of mitochondrial proteins that may hold the key to the mechanisms by which SOD1 mutants cause mitochondrial dysfunction and neuronal death. It has laid the foundation for further detailed functional studies to elucidate the role of particular mitochondrial proteins, such as VDAC2, in the pathogenesis of familial ALS.
Abstract 3756: Prediction of xenograft response to MM-121, an anti-ErbB3 inhibitor, using computational modeling and measurements of five biomarkers (2010)

Abstract One of the challenges faced by targeted therapeutics currently in the clinic is the relatively small population of patients who derive significant benefit from their use. We report the development of a preclinical classifier which can correctly predict xenograft response to MM-121, an anti-ErbB3 antibody, based on the measurement of a few key biomarkers in cell lysates. Deregulation of the ErbB family receptors is common in many cancers. Using a combination of computational modeling and quantitative experiments we identified ErbB3 as a key mediator of mitogenic signaling downstream of the ErbB receptors. Based on these results, we developed MM-121, a first in class anti-ErbB3 monoclonal antibody that blocks heregulin-induced signaling and inhibits tumor growth in multiple xenograft models of human cancer. Here we present our efforts to derive a predictive biomarker signature that identifies tumors that are responsive to MM-121. Using our computational model of the ErbB signaling pathway we identified the five most critical proteins for predicting activation of phospho-AKT - a key mediator of cell survival and apoptosis. These proteins include MM-121's target, ErbB3, and its ligand, heregulin. We profiled these biomarkers in a large panel of cancer cell lines, and using the measured effect of MM-121 on inhibiting tumor growth in eight xenograft tumor models, we determined a classification rule for predicting xenograft response. We subsequently used this classification rule to correctly predict a priori MM-121 response in 11 xenograft models. These results suggest that our computationally-derived biomarker signature is sufficient for predicting response to MM-121 in xenografts, and could offer significant clinical benefit by helping select patients for MM-121 treatment. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3756.
Parallel phase-shifting digital holography and its applications to high-speed 3D imaging and microscopy (2017)

1,000,000 FPS quantitative phase and 3D imaging of a high-speed and transparent object have been achieved by parallel phase-shifting digital holography. Also, 3D imaging and tracking of a dynamic and micro object has been demonstrated.
The<i>Schizosaccharomyces pombe</i>Aurora–related Kinase Ark1 Interacts with the Inner Centromere Protein Pic1 and Mediates Chromosome Segregation and Cytokinesis (2002)

The chromosomal passenger proteins aurora-B, survivin, and inner centromere protein (INCENP) have been implicated in coordinating chromosome segregation with cell division. This work describes the interplay between aurora, survivin, and INCENP orthologs in the fission yeast Schizosaccharomyces pombe and defines their roles in regulating chromosome segregation and cytokinesis. We describe the cloning and characterization of the aurora-related kinase gene ark1(+), demonstrating that it is an essential gene required for sister chromatid segregation. Cells lacking Ark1p exhibit the cut phenotype, DNA fragmentation, and other defects in chromosome segregation. Overexpression of a kinase-defective version of Ark1, Ark1-K147R, inhibits cytokinesis, with cells exhibiting an elongated, multiseptate phenotype. Ark1p interacts physically and/or genetically with the survivin and INCENP orthologs Bir1p and Pic1p. We identified Pic1p in a two-hybrid screen for Ark1-K147R interacting partners and went on to map domains in both proteins that mediate their binding. Pic1p residues 925-972 are necessary and sufficient for Ark1p binding, which occurs through the kinase domain. As with Ark1-K147R, overexpression of Ark1p-binding fragments of Pic1p leads to multiseptate phenotypes. We also provide evidence that the dominant-negative effect of Ark1-K147R requires Pic1p binding, indicating that the formation of Ark1p-Pic1p complexes is required for the execution of cytokinesis.
Clinical and immunologic responses of vaccinated and unvaccinated calves to infection with a virulent type-II isolate of bovine viral diarrhea virus (1998)

A single dose of a modified-live type-I isolate of BVDV vaccine protects young calves from clinical signs of disease associated with type-II isolates.
Electronic Structure of Unoccupied States of Fluorinated Fullerenes C<sub>60</sub>F<sub>18</sub>and C<sub>60</sub>F<sub>36</sub> (2008)

Comparative study of near edge X‐ray absorption fine structure spectra (NEXAFS) of fluorinated fullerenes C60Fx (x = 0, 18, 36) has been implemented. Local density of unoccupied states was obtained and an accurate boundary between π* and (π+σ)* states was determined. The experimental evidence was found that unoccupied π*‐ states of C60Fx are delocalized ones and form cluster shells that sequentially disappear in fluorination starting from the highest state. As a result, the density of the lowest π* ‐ state (LUMO) was revealed to remain being constant in fluorination despite the π ‐electron subsystem exhaustion.
Mathematical and Physical Modelling of Transient Multi-Phase Flows in a Ladle Shroud during Start-Up (2023)

The Ladle Shroud has become an important part of secondary steelmaking, with its role in reducing liquid steel contamination and process improvements. Due to the inherent negative pressure at the lower nozzle–Ladle Shroud joint, it is well known that Ladle Shrouds, protecting steel flows between a Ladle and a tundish below, can suffer from inadvertent ingress of air. Therefore, there is a need to apply inert gas injection at the joint. In the present paper, 3D transient multi-phase simulations of flows occurring for a Reverse Tapered Ladle Shroud during start-up were studied using CFD software ANSYS Fluent 19.1. This allowed us to study the initial multi-phase flow developed during the start-up and potential steel reoxidation, based on a first principles approach. Time-dependent phase fields as well as attendant velocity and turbulence fields were obtained, resulting in the prediction of a turbulent multi-phase flow during start-up and filling. Additionally, some transient phenomena like steel splashing and air suction were observed mathematically. A full-scale water model of the Ladle Shroud was used to qualitatively validate the initial multi-phase turbulent flow inside the Ladle Shroud, in the absence of inert gas injection.
Core–shell metal fluoride nanoparticles via fluorolytic sol–gel synthesis – a fast and efficient construction kit (2017)

An efficient, fast and easy construction kit using the fluorolytic sol–gel synthesis of rare-earth-doped alkaline earth fluoride core–shell nanoparticles at room temperature is presented, capable of synthesizing several hundred grams to kilograms of core–shell particles in one batch.
Current and Emerging Microfluidic-Based Integrated Solutions for Free Hemoglobin and Hemolysis Detection and Measurement (2021)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTCurrent and Emerging Microfluidic-Based Integrated Solutions for Free Hemoglobin and Hemolysis Detection and MeasurementNoman NaeemNoman NaeemInstitute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.More by Noman NaeemView Biography, Klaus-Stefan DreseKlaus-Stefan DreseThe Institute of Sensor and Actuator Technology (ISAT), 96450 Coburg, GermanyMore by Klaus-Stefan DreseView Biography, Lynn PatersonLynn PatersonInstitute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.More by Lynn PatersonView Biography, and Maïwenn Kersaudy-Kerhoas*Maïwenn Kersaudy-KerhoasInstitute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.Infection Medicine, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH8 9YL, U.K.*Email: [email protected]More by Maïwenn Kersaudy-KerhoasView Biographyhttps://orcid.org/0000-0002-8185-8230Cite this: Anal. Chem. 2022, 94, 1, 75–85Publication Date (Web):December 3, 2021Publication History Published online3 December 2021Published inissue 11 January 2022https://pubs.acs.org/doi/10.1021/acs.analchem.1c04567https://doi.org/10.1021/acs.analchem.1c04567review-articleACS PublicationsCopyright © 2021 American Chemical SocietyRequest reuse permissionsArticle Views1228Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Absorption,Anatomy,Electromagnetic radiation,Peptides and proteins,Quantum mechanics Get e-Alerts
Best Dioctahedral Smectite for Nitrogen Heterocyclics AdsorptionA Reactivity Index Study (2001)

The activity of nitrogen heterocyclics present in biomacromolecules and its suitable sorbent from the dioctahedral smectite family is investigated using a range of reactivity index using density functional theory (DFT). For the first time, a novel function λ has been defined for quantitative description of weak adsorption cases, which was so far qualitative inside the domain of DFT. From the values of the local softness, it is concluded that the local acidities of the inorganic material systems are dependent on several characteristics, which are of importance within the framework of the hard and soft acids and bases (HSAB) principle. We first rationalized an understanding of the electronic structures of a range of nitrogen heterocyclics ranging from indole, imidazole, pyrrole, and pyridine, followed by the local softness calculation to locate its active site. We compared its activity with that of the OH group of isomorphously substituted (Fe3+, Mg2+, Fe2+, and Li+) dioctahedral smectite family. Two types of interactions were identified between heterocyclics and smectite. The ordering for best sorption follows the order Mg2+ > Fe2+ > Fe3+ > Li+, whereas the order for best sorbent is imidazole > pyridine > pyrrole > indole. The results rationalize the experimental observation.
A 64-Kb 0.37V 28nm 10T-SRAM with mixed-Vth read-port and boosted WL scheme for IoT applications (2016)

In low voltage SRAM for IoT application, although static noise margin (SNM) and write margin (WM) decide VMIN, Icell / Ioff ratio and Icell are also important in order to keep performance and achieve better operating efficiency. We propose a new mixed Vth RP design which can achieve better Icell and Icell / Ioff ratio. Furthermore, combination of the proposed mixed Vth and boosted read wordline (RWL) scheme improves the worst case bitline delay time by 72.3% at 0.45V. In the measurement results, we confirmed a minimum operating voltage (VMIN) for the 64 Kb SRAM of 0.370 V with 99% yield at room temperature.
ChemInform Abstract: Synthesis of the Thiazolone Analogue of the Acetylcholinesterase Inhibitor, Huperzine A. (1994)

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.
Acoustooptic processor for real-time synthetic aperture radar Image formation (1986)

A real-time optical processor has been built to investigate the applicability of optical processing to synthetic aperture radar image formation. By taking advantage of the high processing speed and large time-bandwidth product of acoustooptic devices (AODs) combined with the multichannel correlation capability of CCD detectors used in the time delay and integrate (TDI) mode, a small real-time SAR processor can be built. The required 2-D matched filtering operation is first performed in range using the AOD and then the azimuthal matched filtering is performed using either a fixed or alterable mask in a TDI correlator configuration. 1 A processor has been built to investigate the effect of system architecture on image quality and system complexity. The system is described and experimentally obtained PSF and image data are shown. The potential for system miniaturization and ruggedization is also discussed.
Pharmacological repression of RORγ is therapeutic in the collagen-induced arthritis experimental model (P5214) (2013)

Abstract The nuclear receptor RORγ has been shown to play an essential role in the development of Th17 cells. Previously, it was reported that the potent and selective RORγ inverse agonist SR2211 was effective at modulating RORγ activity in cell culture. More recently we demonstrated that the RORγ inverse agonist SR2211 can repress expression and production inflammatory cytokines in Th17 cells and LPS stimulated RAW264.7 cells. Here we present in vivo efficacy of SR2211 in an experimental model of arthritis, the murine collagen induced arthritis or CIA model. Significantly reduced Joint CIA scores were observed in SR2211 treated mice as compared with vehicle in the acute phase of the model. CIA represents an autoimmune environment characterized by the accumulation of inflammatory cells into the synovium leading to the destruction of joints. In this model cytokines have been shown to be important regulators of synovial inflammation. Administration of SR2211 in CIA mice led to an increase in IFNγ in ex vivo stimulated draining lymph nodes. As IFNγ has been shown to be beneficial for the treatment of rheumatoid arthritis. In previous work, patients treated with IFNγ showed significant therapeutic potential of RA the data presented suggest the potential of targeting RORγ to repress inflammatory T cell function and macrophage activation in arthritis. Thus, SR2211 has potential utility in the treatment of inflammatory disease.
Non-link switching issue for broadcasting visible light communication (2015)

Visible light communication (VLC) which offers the possibility of using light sources for simultaneous illumination and data communications will be a promising incorporation technique with lighting application. In this paper, we will suggest one resource allocation for VLC broadcasting system which based on broadcasting visible light communication and diversity technology. The proposed protocol can solve the limitation coverage issue, intensity modulation in VLC and link switching issue of exhibition service scenario. Visitors can download data stream of interesting target from supported and neighbor LED without collision and link switching extra process.
Asynchronous current‐mode multiple‐valued VLSI system based on two‐color two‐rail coding (2001)

Abstract In deep submicron VLSI, the asynchronous data protocol is a known technique to solve the performance degradation and increase in power dissipation problems arising from wiring such as cross queues. In this paper, we propose a new asynchronous multiple‐valued data communication scheme without rest phases in multiple‐valued data transfers. This scheme uses two‐rail R ‐value complementary signal pairs, and the sum of the two‐rail signal pair is always a constant for “valid data.” Along with defining a two‐rail signal pair with each signal having an odd phase or an even phase, each signal level in the even phase is set to always be larger than in the odd phase. The sum of a two‐rail signal pair becomes the minimum and the maximum, respectively, of the odd phase and the even phase. Consequently, if the sum of the two‐rail signal pair is examined, the monotonicity can be maintained in data transitions in two phases, and valid data can be detected by a simple threshold calculation. Furthermore, an asynchronous control circuit layout based on the linear sum of a two‐rail signal pair focuses on “the ability to implement the linear addition of current only at the connections” and clearly shows the ability to implement a more compact system than current‐mode multiple‐valued circuit systems. © 2001 Scripta Technica, Electron Comm Jpn Pt 2, 84(11): 60–67, 2001
Frontispiece: How to Build Prussian Blue Based Water Oxidation Catalytic Assemblies: Common Trends and Strategies (2021)

The reaction of cyanoferrate ions (yellow solution) with cobalt ions (pink solution) affords CoFe Prussian blue assemblies with cubic structures. As soon as the liquids are mixed (and this can be done even in a simple glassware), the solution turns orange-brown, and precipitation occurs. Such assemblies have been acknowledged as efficient, robust, and precious-metal free heterogeneous water oxidation catalysts. The Minireview by F. Karadas and co-workers on page 3638 highlights the common strategies to design and prepare cyanide-based electrocatalytic, photocatalytic, and photoelectrochemical assemblies and explores the role of structural units in cobalt-based Prussian blue analogues for the establishment of structure–catalytic-activity relationship.
A novel Sudoku solving technique using column based permutation (2015)

“Sudoku” is the Japanese abbreviation of “Suuji wa dokushin ni kagiru”, which means “the numbers must occur only once”. It is a challenging and interesting puzzle that trains our mind logically. In recent years, solving Sudoku puzzles has become a widespread phenomenon. The problem of solving a given Sudoku puzzle finds numerous applications in the domain of Steganography, Visual Cryptography, DNA Computing, Watermarking, etc. Thus, solving the Sudoku puzzle in efficient manner is very important. However, incidentally all the existing Sudoku solving techniques are primarily either guess based heuristics or computation intensive soft computing methodologies. They also solve the puzzle by traversing on each and every individual cell. In this paper, a novel Sudoku solving technique is proposed which solves Sudoku puzzles without guessing a cell and by generating only the desired permutations among columns, which consist of only groups of cells.
Aircraft Electrical Power Systems and Nonlinear Dynamic Loads (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Aircraft utilize electrical power for many functions ranging from simple devices such as resistive heaters to highly advanced and complex systems responsible for communications, situational awareness, electronic warfare and fly-by-wire flight controls. The operational states of these electronic systems affect safety, mission success and the overall economic expense of operation and maintenance. These electronic systems rely on electrical power within established limits of power quality.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;In recent years, electrical power quality is becoming excessively degraded due to increased usage of nonlinear and dynamic loads coupled to aircraft power systems that were neither designed nor tested for these loads.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Legacy power generation systems were designed for electrical loads with resistive and inductive properties, which previously represented the majority of actual aircraft electrical loads. As more complex and advanced electronic systems were invented, mostly due to developments in semiconductors, the characteristics of electrical load signatures evolved and transitioned from mostly linear to a dominant nonlinear and randomly dynamic composition. This transition to predominantly nonlinear loads is primarily due to the fundamental processing techniques of electrical power from its original state (i.e. AC/DC source) to the various required intermediate and final states of power in order to accomplish the tasks required of the electronic systems.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Switch Mode Power Supplies (SMPSs) and other rectifying circuits using SCRs and diodes, are commonly used on the inputs to avionics equipment, creating the nonlinear loads that adversely affect the power system's power quality. The adverse effects can reduce reliability and degrade the electronic systems resulting in various degrees of faults.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Understanding cause and effect relationships of the dominant nonlinear and dynamic loads on aircraft electrical power systems is the purposes of this paper. Actual test data of military aircraft power systems exhibiting these conditions is presented here to make the reader aware of the problem and provide a relative basis for comparison. An analytical model is used to replicate the issues and show how simulations can aid engineers with determining the effects on their systems without performing costly and possibly destructive tests on actual equipment. These efforts support future activities such as revision of standards for aircraft electrical power systems and ultimately how they are designed, tested and utilized in a more severe and complex environment.&lt;/div&gt;&lt;/div&gt;