gebhart/patrepeval huggingface dataset:
Species-specific binding of sperm proteins to the extracellular matrix (zona pellucida) of the egg. (1994)

The zona pellucida is an extracellular matrix surrounding the mammalian egg where species-specific gamete recognition and signaling occur. Pig zona pellucida were isolated in large amounts and used as an affinity matrix for detergent-solubilized, biotinylated membrane proteins of pig spermatozoa. On non-reducing SDS-polyacrylamide gel electrophoresis, specifically bound sperm proteins migrated with M(r) 170,000, 150,000, 130,000, 56,000, and 50,000 (p50). Disulfide bond reduction separated each of the M(r) 130,000-170,000 proteins into M(r) 105,000 (p105) and M(r) 45,000 (p45) subunits, indicating that these high M(r) proteins are related. Based on two-dimensional electrophoresis, the M(r) 56,000 band was composed of three to four proteins that migrated with M(r) 56,000-62,000 (p56-62) in the second (reducing) dimension. p50 bound to heterologous zona pellucida (murine, bovine) and to Xenopus laevis oocyte envelopes, demonstrating a lack of species specificity to its binding and was identified as proacrosin/acrosin based on amino acid sequences of two tryptic peptides and its interaction with monospecific antibodies to proacrosin. In contrast, p105/p45 and one or more of the p56-62 proteins bound to pig zona pellucida but not to the egg extracellular matrices of the other species; these proteins therefore exhibited the species-specific binding to the zona pellucida expected for molecules involved in specific gamete adhesion. Amino acid sequences of nine tryptic peptides derived from p105/p45 did not match peptide sequences in existing databases, establishing it as a unique protein. These (p105/p45 and at least one p56-62 protein) are the first sperm membrane proteins to be identified that bind in a species-specific manner to the egg extracellular matrix.
Expression, purification and characterization of α-synuclein fibrillar specific scFv from inclusion bodies (2020)

<title>Abstract</title> Background: Aggregation of α-synuclein (α-syn) has been implicated in multiple neurodegenerative disorders including Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), collectively grouped as synucleinopathies. Recently, recombinant antibody fragments (Fab, scFvs and diabodies) against α-syn have emerged as an alternative to the traditional full-length antibody in immunotherapeutic approaches owing to their advantages including smaller size and higher stability, specificity and affinity. However, most of the recombinant antibody fragments tend to be expressed as inclusion bodies (IBs) making its purification extremely challenging. Results: In the current study, a single-chain variable fragment (scFv-F) antibody, targeting the pathogenic α-syn fibrils, was engineered and expressed in E.coli. Majority of the expressed scFv-F accumulated in insoluble aggregates as IBs. A variety of mild and harsh solubilizing conditions were tested to solubilize IBs containing scFv-F to obtain the active protein. To preserve secondary structure and bioactivity, a mild solubilizing protocol involving 100 mM Tris, pH 12.5 with 2 M urea was chosen to dissolve IBs. Slow on-column refolding method was employed to subsequently remove urea and obtain active scFv-F. A three-dimensional (3D) model was built using homology modeling and subjected to molecular docking with the known α-syn structure. Structural alignment was performed to delineate the potential binding pocket. Conclusion: The scFv-F thus purified demonstrated high specificity towards α-syn fibrils compared to monomers. Molecular modeling studies suggest that scFv-F shares the same structural topology with other known scFvs. We present evidence through structural docking and alignment that scFv-F binds to α-syn C-terminal region. In conclusion, mild solubilization followed by slow on-column refolding can be utilized as a generalized and efficient method for hard to purify disease relevant insoluble proteins and/or antibody molecules from IBs.
Development of Lean Alloyed Austenitic Stainless Steels with Reduced Tendency to Hydrogen Environment Embrittlement (2012)

Hydrogen gas is believed to play a more important role for energy supply in future instationary and mobile applications. In most cases, metallic materials are embrittled when hydrogen atoms are dissolved interstitially into their lattice. Concerning steels, in particular the ductility of ferritic grades is degraded in the presence of hydrogen. In contrast, austenitic steels usually show a lower tendency to hydrogen embrittlement. However, the so-called “metastable” austenitic steels are prone to hydrogen environmental embrittlement (HEE), too. Here, AISI 304 type austenitic steel was tensile tested in air at ambient pressure and in a 400 bar hydrogen gas atmosphere at room temperature. The screening of different alloys in the compositional range of the AISI 304 standard was performed with the ambition to optimize alloying for hydrogen applications. The results of the mechanical tests reveal the influence of the alloying elements Cr, Ni, Mn and Si on HEE. Besides nickel, a positive influence of silicon and chromium was found. Experimental results are supported by thermodynamic equilibrium calculations concerning austenite stability and stacking fault energy. All in all, the results of this work are useful for alloy design for hydrogen applications. A concept for a lean alloyed austenitic stainless steel is finally presented.
Pitfalls in Using Zernike Circle Polynomials Over Noncircular Pupils (2007)

We discuss the disadvantages of using Zernike circle polynomials for analyzing non-circular wavefronts, such as ocular wavefronts over elliptical pupils or annular wavefronts in astronomical telescopes. Numerical examples are considered to illustrate use of the orthonormal polynomials for noncircular pupils such as hexagonal, annular, elliptical, and square.
Oscillator With Low Phase Noise (1987)

Phase errors cancelled for high frequency stability. Radio-frequency oscillator achieves high stability of frequency through parallel, two-amplifier configuration in which effects cause phase noise tend to cancel each other. Circuit includes two amplifiers with resonating elements, each constitutes part of feedback loop of other. Generate same frequency because each circuit provides other with conditions necessary for oscillation.
Dancing with Giants: Wimpy Kernels for On-Demand I/O Isolation (2015)

To be trustworthy, security-sensitive applications must be small and simple--or wimpy. Because of their limited size and functions, they must securely compose with large, untrusted commodity systems--or giants--to survive. A security architecture based on a wimpy kernel can provide on-demand isolated I/O channels for wimp applications without bloating the underlying trusted computing base.
MuSK IgG4 autoantibodies cause myasthenia gravis by inhibiting binding between MuSK and Lrp4 (2013)

Myasthenia gravis (MG) is a severely debilitating autoimmune disease that is due to a decrease in the efficiency of synaptic transmission at neuromuscular synapses. MG is caused by antibodies against postsynaptic proteins, including (i) acetylcholine receptors, the neurotransmitter receptor, (ii) muscle-specific kinase (MuSK), a receptor tyrosine kinase essential for the formation and maintenance of neuromuscular synapses, and (iii) low-density lipoprotein receptor-related protein 4 (Lrp4), which responds to neural Agrin by binding and stimulating MuSK. Passive transfer studies in mice have shown that IgG4 antibodies from MuSK MG patients cause disease without requiring complement or other immune components, suggesting that these MuSK antibodies cause disease by directly interfering with MuSK function. Here we show that pathogenic IgG4 antibodies to MuSK bind to a structural epitope in the first Ig-like domain of MuSK, prevent binding between MuSK and Lrp4, and inhibit Agrin-stimulated MuSK phosphorylation. In contrast, these IgG4 antibodies have no direct effect on MuSK dimerization or MuSK internalization. These results provide insight into the unique pathogenesis of MuSK MG and provide clues toward development of specific treatment options.
Cardiac xenotransplantation (2012)

CXTx remains a promising technology for treating end-stage cardiac failure. Genetic modification of the donor and refinement of immunosuppressive regimens have extended heterotopic cardiac xenograft survival from minutes to in excess of 8 months.
An Efficient Application-Device Matching Method for the Mobile Software Ecosystem (2014)

In the mobile software ecosystem, a method that finds out the applications that are compatible with the device of an end user is called application-device matching. In the current mobile software environment, the device fragmentation causes substantial degree of inaccuracy in matching applications with devices as the traditional platform-centric method handles only the features of platform vendors without considering the unique feature set of a certain device, such as device-manufacturer's features, resulting in a low accuracy in matching applications and devices. This paper proposes a new matching method that is device-centric, which achieves high accuracy in application-device matching by grouping features of existing devices and then using it as criteria of application-device matching. To demonstrate the performance of our method, we conduct a case study with 22 devices and 10 applications in the Google Android mobile software ecosystem. The result of case study shows our proposed method shows a higher accuracy.
Synthesis and structure of carborane-substituted cyclic and polymeric phosphazenes (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and structure of carborane-substituted cyclic and polymeric phosphazenesH. R. Allcock, A. G. Scopelianos, J. P. O'Brien, and M. Y. BernheimCite this: J. Am. Chem. Soc. 1981, 103, 2, 350–357Publication Date (Print):January 1, 1981Publication History Published online1 May 2002Published inissue 1 January 1981https://pubs.acs.org/doi/10.1021/ja00392a019https://doi.org/10.1021/ja00392a019research-articleACS PublicationsRequest reuse permissionsArticle Views197Altmetric-Citations39LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Strategies for three-dimensional particle tracking with holographic video microscopy (2010)

The video stream captured by an in-line holographic microscope can be analyzed on a frame-by-frame basis to track individual colloidal particles' three-dimensional motions with nanometer resolution. In this work, we compare the performance of two complementary analysis techniques, one based on fitting to the exact Lorenz-Mie theory and the other based on phenomenological interpretation of the scattered light field reconstructed with Rayleigh-Sommerfeld back-propagation. Although Lorenz-Mie tracking provides more information and is inherently more precise, Rayleigh-Sommerfeld reconstruction is faster and more general. The two techniques agree quantitatively on colloidal spheres' in-plane positions. Their systematic differences in axial tracking can be explained in terms of the illuminated objects' light scattering properties.
Automated known problem diagnosis with event traces (2006)

Computer problem diagnosis remains a serious challenge to users and support professionals. Traditional troubleshooting methods relying heavily on human intervention make the process inefficient and the results inaccurate even for solved problems, which contribute significantly to user's dissatisfaction. We propose to use system behavior information such as system event traces to build correlations with solved problems, instead of using only vague text descriptions as in existing practices. The goal is to enable automatic identification of the root cause of a problem if it is a known one, which would further lead to its resolution. By applying statistical learning techniques to classifying system call sequences, we show our approach can achieve considerable accuracy of root cause recognition by studying four case examples.
Enabling resilient microgrid through programmable network (2017)

In this paper, we integrate programmable networks in microgrid to provide flexible and easy-to-manage communication solutions, thus enabling resilient microgrid operations in face of various cyber and physical disturbances. Specifically, two contributions have been made: (1) Establish a novel software defined networking (SDN) based communication architecture that abstracts the network infrastructure from the upper-level applications to significantly expedite the development of microgrid applications; (2) Create a hardware-in-the-loop cyberphysical platform for evaluating and validating the performance of the presented architecture, control techniques and SDN based functionalities. Test results have demonstrated that the new architecture can significantly enhance microgrid resilience, particularly for those that have high penetration of renewable energy sources.
Signaling and Functional Properties of lnterleukin-16 (1998)

Interleukin-16 is secreted from a variety of immune cells as a peptide of 17 kDa which aggregates into tetrameric form essential for IL-16s direct interaction with and cross linking of its receptor, the CD4 antigen. IL-16 stimulation of CD4+ cells results in the induction of cell motility, and in addition can function as a competence growth factor for CD4+ lymphocytes. These activities suggest that IL-16 could play a role in the accumulation and activation of CD4+ cells recruited to sites of inflammation. Along those lines, IL-16 has been identified at sites of inflammation associated with several different disease states. Its function as a competence growth factor specifically for CD4+ T cells may be useful for immune reconstitution in immunodeficiency diseases such as AIDS.
A new he core transmitter of a contactless power transfer system that is compatible with circular core receivers and H-shaped core receivers (2013)

Contactless power transfer systems for electric vehicles contain two types of transformers (a pair consisting of a transmitter and a receiver): a rectangular (H-shaped) core double-sided winding transformer and a circular core single-sided winding transformer. Since the magnetic field structures of these two transformers differ greatly, these two types of transformers have been incompatible in the past, although a number of compatible receivers have recently been proposed. This paper proposes a novel He core transmitter that is compatible with both types of receivers. The He core transmitter adds a central magnetic pole by dividing the winding coil of the H-shaped core transmitter. This transmitter can change the magnetic field structure by changing the connections of divided windings and can transfer power to both types of receivers. Compatibility tests at 3 kW are carried out, and the test results are presented.
Experimental and Theoretical Studies of a Low Power Cylindrical Hall Thruster (2005)

Summary form only given. Hall thruster is a mature electric propulsion device that holds considerable promise in terms of the propellant saving potential. The annular design of the conventional Hall thruster, however, does not naturally lend itself to scaling to low power. The efficiency tends to be lower, and the lifetime issues are more aggravated. Cylindrical geometry Hall thrusters have lower surface-to-volume ratio than conventional annular thrusters and, thus, seem to be more promising for scaling down. A miniaturized cylindrical Hall thruster (2.6 cm channel outer diameter, 50-300 W power range) exhibits performance comparable with conventional annular Hall thrusters of the similar size. The cylindrical thruster has discharge characteristics similar to those of the annular thrusters, but its propellant ionization efficiency is much higher than that of the annular thrusters. Significantly, a large fraction of multicharged xenon ions might be present in the outgoing ion flux generated by the cylindrical thruster. The operation of the cylindrical thruster is quieter than that of the annular thrusters. The characteristic peak in the discharge current fluctuation spectrum at 50-60 kHz appears to be due to ionization instabilities. Electron cross-field transport in a 2.6 cm cylindrical Hall thruster was studied through the analysis of experimental data and Monte Carlo simulations of electron dynamics in the thruster channel. Kinetic modeling of electron and ion dynamics in the thruster channel allows one to optimize the electron confinement and ion acceleration over a family of realizable magnetic field and plasma potential distributions
Confocal Scanning Laser Holography: A Tool for Non-Invasive Internal Measurement (2005)

Abstract Confocal Holography is a combination of two well known concepts: confocal microscopy and light (laser) holography. Confocal microscopy places an aperture at a conjugate focus to the specimen focus. This filters any rays that are not on the focus plane, allowing a 3-dimensional image of the specimen to be built up over a set of planes. Holography is the measurement of both the amplitude and phase characteristics of light. Typically most methods only measure the amplitude of the image. The phenomenon of interference allows the determination of the phase shift for a coherent source as well. The phase information is directly related to the index of refraction of a material, which in turn is a function of the temperature and composition.
Antibody BCF2 against scorpion toxin Cn2 from Centuroides noxius Hoffmann: primary structure and three-dimensional model as free Fv fragment and complexed with its antigen. (1999)

The antibody BCF2 generated against the mammal-specific toxin Cn2 of the scorpion Centuroides noxius Hoffmann neutralizes the effect of both the toxin and the venom. We cloned and sequenced the genes coding for the Fv fragment of BCF2. A three-dimensional (3D) model of the Fv fragment was generated using a knowledge-based approach. Furthermore, a 3D model of the complex Cn2-BCF2 was built using the nuclear magnetic resonance (NMR) structure of Cn2 and experimental results on a putative epitope region around the N and C termini. The initial complex conformations were submitted to a new refinement procedure of rigid-body energy minimization combined with flexible-side-chain molecular dynamics. The final complex, selected after an extensive evaluation, uses the loop 7-11 as the central part of the epitope. The generated complex allows the following conclusions: 1) the neutralizing capacity of BCF2 toward the venom of C. noxius might rather be caused by the high venom concentration and toxicity of Cn2 than by a broad specificity, 2) the region involved in the binding of Cn2 to the Na(+) channel, should overlap with the employed epitope region, and 3) contact residues SerL91, AsnL92, LeuH50, AspH56, TyrH95, and TyrH98 of BCF2 are candidates for mutations to broaden its specificity. Proteins 1999;37:130-143.
Synthesis of Biologically Active, Novel Monosaccharide Analogs of Lipid A (1984)

Journal Article Synthesis of Biologically Active, Novel Monosaccharide Analogs of Lipid A Get access Makoto Kiso, Makoto Kiso Department of Agricultural Chemistry, Gifu University, Gifu 501–11, Japan Search for other works by this author on: Oxford Academic Google Scholar Hideharu Ishida, Hideharu Ishida Department of Agricultural Chemistry, Gifu University, Gifu 501–11, Japan Search for other works by this author on: Oxford Academic Google Scholar Akira Hasegawa Akira Hasegawa Department of Agricultural Chemistry, Gifu University, Gifu 501–11, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 48, Issue 1, 1 January 1984, Pages 251–252, https://doi.org/10.1080/00021369.1984.10866131 Published: 01 January 1984 Article history Received: 29 August 1983 Published: 01 January 1984
Repurposing Decoder-Transformer Language Models for Abstractive Summarization (2019)

Neural network models have shown excellent fluency and performance when applied to abstractive summarization. Many approaches to neural abstractive summarization involve the introduction of significant inductive bias, exemplified through the use of components such as pointer-generator architectures, coverage, and partially extractive procedures, designed to mimic the process by which humans summarize documents. We show that it is possible to attain competitive performance by instead directly viewing summarization as a language modeling problem and effectively leveraging transfer learning. We introduce a simple procedure built upon decoder-transformers to obtain highly competitive ROUGE scores for summarization performance using a language modeling loss alone, with no beam-search or other decoding-time optimization, and instead relying on efficient nucleus sampling and greedy decoding.