gebhart/patrepeval huggingface dataset:
Selective Identification of α-Galactosyl Epitopes inN-Glycoproteins Using Characteristic Fragment Ions from Higher-Energy Collisional Dissociation (2020)

The α-galactosyl epitope is a terminal <i>N</i>-glycan moiety of glycoproteins found in mammals except in humans, and thus, it is recognized as an antigen that provokes an immunogenic response in humans. Accordingly, it is necessary to analyze the α-galactosyl structure in biopharmaceuticals or organ transplants. Due to an identical glycan composition and molecular mass between α-galactosyl <i>N</i>-glycans and hybrid/high-mannose-type <i>N</i>-glycans, it is challenging to characterize α-galactosyl epitopes in <i>N</i>-glycoproteins using mass spectrometry. Here, we describe a method to identify α-galactosyl <i>N</i>-glycopeptides in mice glycoproteins using liquid chromatography with tandem mass spectrometry with higher-energy collisional dissociation (HCD). The first measure was an absence of [Y<sub>HM</sub>] ion peaks in the HCD spectra, which was exclusively observed in hybrid and/or high-mannose-type <i>N</i>-glycopeptides. The second complementary criterion was the ratio of an <i>m</i>/<i>z</i> 528.19 (Hex<sub>2</sub>HexNAc<sub>1</sub>) ion to <i>m</i>/<i>z</i> 366.14 (Hex<sub>1</sub>HexNAc<sub>1</sub>) ion (<i>I</i><sub><i>m</i>/<i>z</i>528</sub>/<i>I</i><sub><i>m</i>/<i>z</i>366</sub>). The measure of [<i>I</i><sub><i>m</i>/<i>z</i>528</sub>/<i>I</i><sub><i>m</i>/<i>z</i>366</sub> > 0.3] enabled a clear-cut determination of α-galactosyl <i>N</i>-glycopeptides with high accuracy. In Ggta1 knockout mice, we could not find any α-galactosyl <i>N</i>-glycoproteins identified in WT mice plasma. Using this method, we could screen for α-galactosyl <i>N</i>-glycoproteins from mice spleen, lungs, and plasma samples in a highly sensitive and specific manner. Conclusively, we suggest that this method will provide a robust analytical tool for determination of α-galactosyl epitopes in pharmaceuticals and complex biological samples.
Numerical analysis of thermal impact on hydro-mechanical properties of clay (2014)

As is known, high-level radioactive waste (HLW) is commonly heat-emitting. Heat output from HLW will dissipate through the surrounding rocks and induce complex thermo-hydro-mechanical-chemical (THMC) processes. In highly consolidated clayey rocks, thermal effects are particularly significant because of their very low permeability and water-saturated state. Thermal impact on the integrity of the geological barriers is of most importance with regard to the long-term safety of repositories. This study focuses on numerical analysis of thermal effects on hydro-mechanical properties of clayey rock using a coupled thermo-mechanical multiphase flow (TH2M) model which is implemented in the finite element programme OpenGeoSys (OGS). The material properties of the numerical model are characterised by a transversal isotropic elastic model based on Hooke's law, a non-isothermal multiphase flow model based on van Genuchten function and Darcy's law, and a transversal isotropic heat transport model based on Fourier's law. In the numerical approaches, special attention has been paid to the thermal expansion of three different phases: gas, fluid and solid, which could induce changes in pore pressure and porosity. Furthermore, the strong swelling and shrinkage behaviours of clayey material are also considered in the present model. The model has been applied to simulate a laboratory heating experiment on claystone. The numerical model gives a satisfactory representation of the observed material behaviour in the laboratory experiment. The comparison of the calculated results with the laboratory findings verifies that the simulation with the present numerical model could provide a deeper understanding of the observed effects.
[Preclinical studies of live intranasal H5N1 influenza vaccine with the deleted HS1 gene]. (2012)

The paper gives the results of evaluating the efficiency of deINS1 pandemic H5N1 vaccine candidate VN1203delNS1 which was constructed by reverse genetics on the basis of influenza virus strain A/Vietnam/1203/04. The safety, immunogenicity and cross-protection of the vaccine strain against different H5N1 virus clades were demonstrated in mouse and macaque models. The results showed the possibility of designing a new-generation replication-deficient intranasal influenza vaccine, by applying an approach to deleting the NS1 pathogenicity factor, an antagonist of the interferon system.
Novel Diamino Derivatives of [1,2,4]Triazolo[1,5-a][1,3,5]triazine as Potent and Selective Adenosine A2aReceptor Antagonists (2004)

Piperazine derivatives of 2-furanyl[1,2,4]triazolo[1,5-a][1,3,5]triazine have recently been demonstrated to be potent and selective adenosine A(2a) receptor antagonists with oral activity in rodent models of Parkinson's disease. We have replaced the piperazinyl group with a variety of linear, monocyclic, and bicyclic diamines. Of these diamines, (R)-2-(aminomethyl)pyrrolidine is a particularly potent and selective replacement for the piperazinyl group. With this diamine component, we have been able to prepare numerous analogues with low nanomolar affinity toward the A(2a) receptor and good selectivity with respect to the A(1) receptor (>200-fold in some cases). Selected analogues from this series of [1,2,4]triazolo[1,5-a][1,3,5]triazine have now been shown to be orally active in the mouse catalepsy model.
INTERNET REACTOR LABORATORY: A NUCLEAR REACTOR PHYSICS AND ENGINEERING EDUCATION MODALITY FOR THE 21st CENTURY (2021)

The “second generation” Internet Reactor Laboratory (IRL) has been installed and is currently functional at the PULSTAR reactor of the Nuclear Reactor Program (NRP) at North Carolina State University (NCSU). The NRP has offered IRL based reactor physics experiments and training to external academic institutions and organizations since 2004. In 2016, the United States and the Republic of Vietnam entered into an Administrative Arrangement under Section 123 of the Atomic Energy Act, with a goal of enhancing nuclear training and education for Vietnamese engineering students. Funding was provided by the DOE to upgrade the PULSTAR IRL infrastructure to state-of-the-art remote data acquisition and video teleconferencing capabilities supporting content sharing across multiple remote user platforms. Subsequently, a Cisco Telepresence and LabView reactor data acquisition system were installed and commissioned at the PULSTAR facility. Using this “second generation” system, and during IRL sessions, up to 100 remote students may interact with the control room staff via the Telepresence system using their mobile device or PC, and view 130 channels of live reactor telemetry via the remote client LabView application while recording the data for subsequent review and analysis. LabView graphical user interfaces (GUI) are provided for each IRL module, and incorporate embedded supporting documents such as schematics and diagrams that aid in illustrating associated technical details and concepts. Consequently, the educational experience offered to remote students and trainees is enhanced and assured to be of the same quality as offered to onsite students/trainees at NCSU.
High Density Ink Jet Printing of Bio-molecules for Photonic Crystal-based Microarray Applications (2011)

High density inkjet printing of protein solutions was investigated for photonic crystal based microarray applications. Spacing of 60um has been demonstrated between unique inkjet-printed spots on a silicon substrate.
Quantum Electronic Phenomena and Structures (invited talk). (2015)

Abstract not provided.
Fluid-filled microstructured optical fibers and switching applications (2009)

We filled a refractive index matching liquid into the air holes of a Ge-doped solid-core microstructured optical fiber (MOF) with a fiber Bragg grating (FBG) to investigate its switching functions. A type of thermo-optic in-fiber switch based on the tunable bandgap effect was demonstrated in the fluid-filled FBG at the Bragg wavelength of 830nm, and its extinction ratio depends strongly on the reflectivity of the FBG. Another type of optical switch with an extinction ratio of 30 dB was developed in the fluid-filled MOF at a long wavelength of 1200 or 1400nm, attributing to the absorption of the filled liquid. Such two types of switches can turn on/off the light transmission via a small temperature adjustment of ±5 or ±10ºC, respectively, and will find useful applications in all-fiber optical communication systems.
Applications of Ionic Liquids in Electrolyte Systems (2010)

Abstract The sections in this article are Introduction Electrolyte Properties of Ionic Liquids Electrochemical Stability Dye‐sensitized Solar Cells
A tropane-based ibogaine analog rescues folding-deficient SERT and DAT (2020)

Abstract Missense mutations that give rise to protein misfolding are rare, but collectively, defective protein folding diseases are consequential. Folding deficiencies are amenable to pharmacological correction (pharmacochaperoning), but the underlying mechanisms remain enigmatic. Ibogaine and its active metabolite noribogaine correct folding defects in the dopamine transporter (DAT), but they rescue only a very limited number of folding-deficient DAT mutants, which give rise to infantile Parkinsonism and dystonia. Herein, a series of analogs was generated by reconfiguring the complex ibogaine ring system and exploring the structural requirements for binding to wild type transporters, and for rescuing two equivalent synthetic folding-deficient mutants, SERT-PG 601,602 AA and DAT-PG 584,585 AA. The most active tropane-based analog ( 9b ) was also an effective pharmacochaperone in vivo , in Drosophila harboring DAT-PG 584,585 AA and rescued six out of 13 disease-associated human DAT mutants in vitro. Hence, a novel lead pharmacochaperone has been identified that demonstrates medication development potential for patients harboring DAT mutants.
Halogen and Hydrogen Bonding in Povidone-Iodine and Related Co-Phases (2017)

Povidone-iodine is a widely used antiseptic and on the World Health Organization’s List of Essential Medicines. We report the X-ray crystal structure of a two-monomer unit model compound showing that the structure of povidone-iodine comprises protonated pyrrolidone units linked by intermolecular hydrogen bonds along with triiodide anions. We also report an unusual example of a system exhibiting both a cocrystal and coamorphous form in a halogen bonded lactam model compound with diiodotetrafluorobenzene.
High Performance Front Camera ADAS Applications on TI's TDA3X Platform (2015)

Advanced driver assistance systems (ADAS) are designed to increase driver's situational awareness and road safety by providing essential information, warning and automatic intervention to reduce the possibility/severity of an accident. Of the various types of ADAS modalities available, camera based ADAS are being widely adopted for their usefulness in varied applications, overall reliability and adaptability to new requirements. But camera based ADAS also represents a complex, high-performance, and low-power compute problem, requiring specialized solutions. This paper introduces a high performance front camera ADAS based on a small area, low power System-on-Chip (SoC) solution from Texas Instruments called Texas Instruments Driver Assist 3x (TDA3x). The paper illustrates compute capabilities of the device in implementation of a typical front camera ADAS. The paper also introduces key programming concepts related to heterogeneous programmable compute cores in the SoC and the software framework to use those cores in order to develop the front camera solutions. These aspects will be of interest not only to the ADAS developers but for computer vision and compute intensive embedded system development.
Large-scale optical characterization of solid-state quantum emitters (2022)

Solid-state quantum emitters have emerged as a leading quantum memory for quantum networking applications. However, standard optical characterization techniques are neither efficient nor repeatable at scale. In this work, we introduce and demonstrate spectroscopic techniques that enable large-scale, automated characterization of color centers. We first demonstrate the ability to track color centers by registering them to a fabricated machine-readable global coordinate system, enabling systematic comparison of the same color center sites over many experiments. We then implement resonant photoluminescence excitation in a widefield cryogenic microscope to parallelize resonant spectroscopy, achieving two orders of magnitude speed-up over confocal microscopy. Finally, we demonstrate automated chip-scale characterization of color centers and devices at room temperature, imaging thousands of microscope fields of view. These tools will enable accelerated identification of useful quantum emitters at chip-scale, enabling advances in scaling up color center platforms for quantum information applications, materials science, and device design and characterization.
Enhanced thermal stability and mechanical properties of nitrogen deficient titanium aluminum nitride (Ti0.54Al0.46Ny) thin films by tuning the applied negative bias voltage (2017)

Aspects on the phase stability and mechanical properties of nitrogen deficient (Ti0.54Al0.46)Ny alloys were investigated. Solid solution alloys of (Ti,Al)N were grown by cathodic arc deposition. The kinetic energy of the impinging ions was altered by varying the substrate bias voltage from −30 V to −80 V. Films deposited with a high bias value of −80 V showed larger lattice parameter, finer columnar structure, and higher compressive residual stress resulting in higher hardness than films biased at −30 V when comparing their as-deposited states. At elevated temperatures, the presence of nitrogen vacancies and point defects (anti-sites and self-interstitials generated by the ion-bombardment during coating deposition) in (Ti0.54Al0.46)N0.87 influence the driving force for phase separation. Highly biased nitrogen deficient films have point defects with higher stability during annealing, which cause a delay of the release of the stored lattice strain energy and then accelerates the decomposition tendencies to thermodynamically stable c-TiN and w-AlN. Low biased nitrogen deficient films have retarded phase transformation to w-AlN, which results in the prolongment of age hardening effect up to 1100 °C, i.e., the highest reported temperature for Ti-Al-N material system. Our study points out the role of vacancies and point defects in engineering thin films with enhanced thermal stability and mechanical properties for high temperature hard coating applications.
Production of Polyclonal Antisera (2006)

Abstract Although the advances offered by the development of monoclonal antibody techniques have revolutionized the specificity, uniformity, and quantity of antibodies, there remain many circumstances in which polyclonal antibodies are more desirable than monoclonal antibodies. Production of polyclonal antisera takes less time and effort than production of monoclonal antibodies, requires relatively simple and readily available equipment, and produces reagents that can be used for immunoprecipitation, immunoblotting, and enzyme‐linked immunosorbent assays (ELISAs). The and in this unit describe the production of polyclonal antisera specific for protein antigens in rabbits, rats, mice, and hamsters. The presents a method for preparing serum from blood.
Mid IR applications of Si photonics (2016)

A review of passive and active photonic devices in three mid-IR silicon photonics material platforms suitable for communications and sensing, silicon on insulator (SOI), suspended silicon and germanium on silicon, is presented.
Umami taste perception and preferences of the domestic cat (Felis catus), an obligate carnivore (2023)

The domestic cat (Felis catus) is an obligate carnivore, and as such has a meat-based diet. Several studies on the taste perception of cats have been reported, indicating that their sense of taste has evolved based on their carnivorous diet. Here, we propose that umami (mediated by Tas1r1-Tas1r3) is the main appetitive taste modality for the domestic cat by characterizing the umami taste of a range of nucleotides, amino acids, and their mixtures for cats obtained using complementary methods. We show for the first time that cats express Tas1r1 in taste papillae. The cat umami receptor responds to a range of nucleotides as agonists, with the purine nucleotides having the highest activity. Their umami receptor does not respond to any amino acids alone; however, 11 l-amino acids with a range of chemical characteristics act as enhancers in combination with a nucleotide. l-Glutamic acid and l-Aspartic acid are not active as either agonists or enhancers of the cat umami receptor due to changes in key binding residues at positions 170 and 302. Overall, cats have an appetitive behavioral response for nucleotides, l-amino acids, and their mixtures. We postulate that the renowned palatability of tuna for cats may be due, at least in part, to its specific combination of high levels of inosine monophosphate and free l-Histidine that produces a strong synergistic umami taste enhancement. These results demonstrate the critical role that the umami receptor plays in enabling cats to detect key taste compounds present in meat.
Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings (2009)

Biophysically detailed models of single cells are difficult to fit to real data. Recent advances in imaging techniques allow simultaneous access to various intracellular variables, and these data can be used to significantly facilitate the modelling task. These data, however, are noisy, and current approaches to building biophysically detailed models are not designed to deal with this. We extend previous techniques to take the noisy nature of the measurements into account. Sequential Monte Carlo ("particle filtering") methods, in combination with a detailed biophysical description of a cell, are used for principled, model-based smoothing of noisy recording data. We also provide an alternative formulation of smoothing where the neural nonlinearities are estimated in a non-parametric manner. Biophysically important parameters of detailed models (such as channel densities, intercompartmental conductances, input resistances, and observation noise) are inferred automatically from noisy data via expectation-maximization. Overall, we find that model-based smoothing is a powerful, robust technique for smoothing of noisy biophysical data and for inference of biophysical parameters in the face of recording noise.
Colloidal Chemistry in Molten Salts: Synthesis of Luminescent In1–xGaxP and In1–xGaxAs Quantum Dots (2018)

Control of composition, stoichiometry, and defects in colloidal quantum dots (QDs) of III-V semiconductors has proven to be difficult due to their covalent character. Whereas the synthesis of colloidal indium pnictides such as InP, InAs, and InSb has made significant progress, gallium-containing colloidal III-V QDs still remain largely elusive. Gallium pnictides represent an important class of semiconductors due to their excellent optoelectronic properties in the bulk; however, the difficulty with the synthesis of gallium-containing colloidal III-V QDs has largely prohibited their exploration as solution-processed semiconductors. Here we introduce molten inorganic salts as high-temperature solvents for the synthesis and manipulation of III-V QDs. We demonstrate cation exchange reactions on presynthesized InP and InAs QDs to form In<sub>1- x</sub>Ga <sub>x</sub>P and In<sub>1- x</sub>Ga <sub>x</sub>As QDs at temperatures above 380 °C. This approach produces novel ternary alloy QDs with controllable compositions that show size- and composition-dependent absorption and emission features. Emission quantum yields of up to ∼50% can be obtained for In<sub>1- x</sub>Ga <sub>x</sub>P/ZnS core-shell QDs. A comparison of the optical properties of InP/ZnS core-shells with In<sub>1- x</sub>Ga <sub>x</sub>P/ZnS core-shells reveals that Ga incorporation leads to significant improvement in the optical properties of III-V/II-VI core-shell emitters which is of great importance for quantum dot-based lighting and display applications. This work also demonstrates the potential of molten inorganic salts as versatile solvents for the synthesis and processing of colloidal nanomaterials at temperatures inaccessible for traditional solvents.
Supplementary Table 2 from CCT244747 Is a Novel Potent and Selective CHK1 Inhibitor with Oral Efficacy Alone and in Combination with Genotoxic Anticancer Drugs (2023)

&lt;p&gt;PDF file, 118K, Supplementary Table 2 Summary of Effects of Irinotecan, Gemcitabine and CCT244747 alone or in combination on human tumor xenografts growth delay.&lt;/p&gt;
Enhanced In Vitro Biocompatibility and Water Dispersibility of Magnetite and Cobalt Ferrite Nanoparticles Employed as ROS Formation Enhancer in Radiation Cancer Therapy (2018)

Abstract Efficient magnetic reactive oxygen species (ROS) formation enhancing agents after X‐ray treatment are realized by functionalizing superparamagnetic magnetite (Fe 3 O 4 ) and Co‐ferrite (CoFe 2 O 4 ) nanoparticles with self‐assembled monolayers (SAMs). The Fe 3 O 4 and CoFe 2 O 4 nanoparticles are synthesized using Massart's coprecipitation technique. Successful surface modification with the SAM forming compounds 1‐methyl‐3‐(dodecylphosphonic acid) imidazolium bromide, or (2‐{2‐[2‐hydroxy‐ethoxy]‐ethoxy}‐ethyl phosphonic acid provides biocompatibility and long‐term stability of the Fe 3 O 4 and CoFe 2 O 4 nanoparticles in cell media. The SAM‐stabilized ferrite nanoparticles are characterized with dynamic light scattering, X‐ray powder diffraction, a superconducting quantum interference device, Fourier transform infrared attenuated total reflectance spectroscopy, zeta potential measurements, and thermogravimetric analysis. The impact of the SAM‐stabilized nanoparticles on the viability of the MCF‐7 cells and healthy human umbilical vein endothelial cells (HUVECs) is assessed using the neutral red assay. Under X‐ray exposure with a single dosage of 1 Gy the intracellular SAM stabilized Fe 3 O 4 and CoFe 2 O 4 nanoparticles are observed to increase the level of ROS in MCF‐7 breast cancer cells but not in healthy HUVECs. The drastic ROS enhancement is associated with very low dose modifying factors for a survival fraction of 50%. This significant ROS enhancement effect by SAM‐stabilized Fe 3 O 4 and CoFe 2 O 4 nanoparticles constitutes their excellent applicability in radiation therapy.
The Nucleophilic Substitution of Various Substituted Fluoroarenetricarbonylchromium Complexes with Methoxide (1986)

Abstract The tricarbonylchromium complexes of a variety of di- and trisubstituted fluoro- and difluoroarenes have been reacted in refluxing methoxide/methanol to yield SNAr-type substitution products. The reaction mixtures were analyzed by glpc and nmr. Methoxide substitution of each fluoride in the complexes occurred rapidly. These are the first examples of the substitution of two fluorides in a tricarbonylchromium complex by a nucleophile. Fluoride was displaced from arenes containing alkyl, methoxy, amino, and alkylamino substituents.