gebhart/patrepeval huggingface dataset:
Synthesis and Biological Studies of O3‐Aryl Galactosides as Galectin Inhibitors (2020)

Abstract β‐Galactose derivatives have recently been reported to selectively inhibit galectin‐3, and a library of O3‐arylated galactosides with varying substitution patterns was designed to study such inhibitions further. The O3‐arylated galactosides were synthesized using diaryliodonium salts under mild and transition metal free conditions, providing the target products in moderate to good yields. An O3‐trifluoroethylated galactoside was also synthesized using iodonium salt chemistry. Azido‐substituted products were subsequently transformed into the corresponding triazoles. After deprotection, a selection of galactoside derivatives were evaluated for inhibitory potencies against galectins‐1, 3, 4 N (N‐terminal domain), 4 C (C‐terminal domain), 7, 8 N, 8 C, 9 N, and 9 C and one compound with promising affinity and selectivity for both the N‐ and C‐terminal domain of galectin‐9 was discovered.
Immunochemical Studies of Infectious Mononucleosis (1977)

The major sialoglycopeptide released from bovine erythrocytes by papain has been purified and characterized. The glycopeptide contains 82% by weight carbohydrate in molar ratios of galactose - 5.5:N-acetylglucosamine - 3.6:sialic acid - 2.6:N-acetylgalactosamine - 1.0. The carbohydrate and amino acid composition is quite different from the glycoprotein extracted from bovine erythrocyte stroma with hot 75% ethanol. The glycopeptide is devoid of reactivity with Paul-Bunnell heterophile antibody of infectious mononucleosis - an activity expressed to high degree on the bovine erythrocyte and associated with glycoprotein. The glycopeptide does react, however, with another antibody found in infectious mononucleosis as well as most normal human sera tested.
Multiplexed Ion Mobility Spectrometry-Orthogonal Time-of-Flight Mass Spectrometry (2007)

Ion mobility spectrometry (IMS) coupled to orthogonal time-of-flight mass spectrometry (TOF) has shown significant promise for the characterization of complex biological mixtures. The enormous complexity of biological samples (e.g., from proteomics) and the need for both biological and technical analysis replicates imposes major challenges for multidimensional separation platforms with regard to both sensitivity and sample throughput. A major potential attraction of the IMS-TOF MS platform is separation speeds exceeding that of conventional condensed-phase separations by orders of magnitude. Known limitations of the IMS-TOF MS platforms that presently mitigate this attraction include the need for extensive signal averaging due to factors that include significant ion losses in the IMS-TOF interface and an ion utilization efficiency of less than approximately 1% with continuous ion sources (e.g., ESI). We have developed a new multiplexed ESI-IMS-TOF mass spectrometer that enables lossless ion transmission through the IMS-TOF as well as a utilization efficiency of >50% for ions from the ESI source. Initial results with a mixture of peptides show a approximately 10-fold increase in signal-to-noise ratio with the multiplexed approach compared to a signal averaging approach, with no reduction in either IMS or TOF MS resolution.
Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer (2018)

Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan shield. Here, we show that a cleavage-independent, stabilized, soluble Env trimer mimic (BG505 NFL.664) exhibits a "closed-form", native-like, prefusion conformation akin to furin-cleaved Env trimers. The crystal structure of BG505 NFL.664 at 3.39 Å resolution with two potent bNAbs also identifies the full epitopes of PGV19 and PGT122 that target the receptor binding site and N332 supersite, respectively. Quantitative site-specific analysis of the glycan shield reveals that native-like glycan processing is maintained despite furin-independent maturation in the secretory pathway. Thus, cleavage-independent NFL Env trimers exhibit quaternary protein and carbohydrate structures similar to the native viral spike that further validate their potential as vaccine immunogen candidates.
Endovascular treatment of multiple aneurysms involving the posterior intracranial circulation. (1996)

The results of surgery on multiple intracranial aneurysms tha involve the vertebrobasilar circulation are poor, and associated patient mortality remains high. We describe the endovascular treatment of four patients with mutiple aneurysms that involved the posterior intracrancial circulation. Satisfactory occlusion of all aneurysms was achieved by using electrolytically detachable coils, and all patients had a good clinical recovery. Our early experience suggests that endovascular coil occlusion may be a particularly suitable method for treating this high-risk condition.
Supporting hierarchical robot programming in integrated development environment (IDE) of Open Platform for Robotic Services (OPRoS) (2011)

There are many platforms for robot S/W applications. To reduce the complexity of robot programming, components, the units of robot software for building and recycling source, are employed, and there are several component-based platforms. As components are the lowest units of robot S/W, there are several levels above them to convey the user's intentions to a robot. There are the application level, task level, and content/service level. This paper introduces robot programming levels which are interchangeable and recyclable. Also integrated development environments are presented to support the robot programming levels in Open Platform for Robotic Services.
Well-balanced immune response and protective efficacy induced by a single dose of live attenuated tetravalent dengue vaccine (KD-382) in monkeys (2020)

One of the challenges developing a live attenuated tetravalent dengue vaccine (TDV) is to overcome the presumed viral interference that may be preventing the induction of a balanced immune response to all 4 serotypes of the dengue virus (DENV1-4). Our live attenuated TDV candidate was developed from wild-type (wt) parental strains (DENV1/03135, DENV2/99345, DENV3/16562, and DENV4/1036, respectively) using a classical host range mutation strategy: the same strategy used for the approved live attenuated smallpox, polio, and MMR vaccines. Our vaccine candidate is expected to mimic natural dengue virus infection, as it provides all the components of dengue virus, including both structural and nonstructural proteins. Therefore, induction of more solid and comprehensive immune responses against pathogenic dengue viruses is also expected. In this study, we evaluated the neutralizing antibody responses for each serotype induced by a single subcutaneous administration of 6 formulations, which were composed of different combinations of vaccine strains and were all of different dosages. These formulations were tested in dengue-naïve cynomolgus macaques. As a result, regardless of the TDV formulation, all the monkeys immunized with TDVs seroconverted to all the 4 serotypes at day 30. Next, we evaluated protection ability of the selected formulations of TDV candidate, no RNAemia was detected from any of the immunized monkeys upon s.c. challenge with wtDENV. The findings of this non-human primate study indicate that our vaccine candidate is very promising; it can be further evaluated for safety and efficacy in human clinical studies.
Low temperature polymerization of novel, monotropic liquid crystalline benzoxazines (2009)

Abstract Cationic ring opening polymerization at a lower temperature range/faster polymerization than ordinary benzoxazine resins has been achieved without added initiators or catalysts via liquid crystalline (LC) benzoxazine resins. Faster polymerization is observed even above the liquid crystal forming temperature. The FTIR spectra show that opening of the oxazine ring occurs even at 110 °C generating phenolic groups that auto‐catalyzed the cationic polymerization of the monomer increasing the rate of polymerization. The newly formed H‐bonds inhibit the formation of LC phases after polymerization. Some of the monomers show nematic LC transitions upon cooling. None of them showed LC transitions during the heating cycle, exhibiting monotropic LC phases. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5871–5881, 2009
Mechanism and kinetics of dithiobenzoate-mediated RAFT polymerization. I. The current situation (2006)

Investigations into the kinetics and mechanism of dithiobenzoate-mediated Reversible Addition-Fragmentation Chain Transfer (RAFT) polymerizations, which exhibit nonideal kinetic behavior, such as induction periods and rate retardation, are comprehensively reviewed. The appreciable uncertainty in the rate coefficients associated with the RAFT equilibrium is discussed and methods for obtaining RAFT-specific rate coefficients are detailed. In addition, mechanistic studies are presented, which target the elucidation of the fundamental cause of rate retarding effects. The experimental and theoretical data existing in the literature are critically evaluated and apparent discrepancies between the results of different studies into the kinetics of RAFT polymerizations are discussed. Finally, recommendations for further work are given. (c) 2006 Wiley Periodicals, Inc.
A linearly dispersive magnetostatic delay line at X-band (1979)

Experimentally verified calculations which have been performed show that the group delay versus frequency characteristic for magnetostatic forward volume waves in a YIG film of thickness t spaced an equal distance t from a ground plane can be essentially linear over a substantial frequency range. In particular, results are reported on an experimental YIG magnetostatic delay line which showed a linear delay ranging from 50 to 230 nS/cm (linearity ±3 nS/cm) over a 1 GHz bandwidth at X-band frequencies. The 20 μm thick YIG film, grown epitaxially on GGG, was spaced 20 μm above a ground plane using an alumina dielectric. The alumina was fabricated by: (a) thinning a conventional substrate by grinding and polishing; or (b) depositing Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> by rf sputtering. Input and output transducers were simple 5 mm long by 50 μm wide gold microstrip lines defined in 5 μm thick gold and open circuited at one end. Results obtained using a network analyzer were in close agreement with the theoretical calculation. The characteristic observed represents a potential pulse-compression factor of 230.
Segmentation of the left ventricle in cardiac MR images (2002)

This paper describes a segmentation technique to automatically extract the myocardium in 4D cardiac MR images for quantitative cardiac analysis and the diagnosis of patients. Three different modules are presented. The automatic localization algorithm is able to approximately locate the left ventricle in an image using a maximum discrimination technique. Then, the local deformation algorithm can deform active contours so that they align to the edges in the image to produce the desired outlining of the myocardium. Finally, the global localization algorithm is able to propagate segmented contours from one image in the data set to all the others. We have experimented with the proposed method on a large number of patients and present some examples to show the strengths and pitfalls of our algorithm.
Chemical Tools for Studying Biological Hydrogen Sulfide (2013)

Although hydrogen sulfide (H2S) has historically been recognized as a toxic gas, recent studies have established H2S as an important, endogenously-produced signaling molecule active in a wide array of (patho)physiological roles in biological systems. As the multifaceted biological roles of H2S continue to emerge, tools to modulate, measure, and detect biological H2S are needed. Here we highlight recent biocompatible advances in reaction-based H2S detection methods and their associated benefits and pitfalls.
LaF 3 :Ce nanocomposite scintillator for gamma-ray detection (2007)

Nanophosphor LaF<sub>3</sub>:Ce has been synthesized and incorporated into a matrix to form a nanocomposite scintillator suitable for application to γ-ray detection. Owing to the small nanocrystallite size (sub-10 nm), optical emission from the γ / nanophosphor interaction is only weakly Rayleigh scattered (optical attenuation length exceeds 1 cm for 5-nm crystallites), thus yielding a transparent scintillator. The measured energy resolution is <i>ca.</i> 16% for <sup>137</sup>Cs γ rays, which may be improved by utilizing brighter nanophosphors. Synthesis of the nanophosphor is achieved via a solution-precipitation method that is inexpensive, amenable to routine processing, and readily scalable to large volumes. These results demonstrate nanocomposite scintillator proof-of- principle and provide a framework for further research in this nascent field of scintillator research.
Chromis-1, a Ratiometric Fluorescent Probe Optimized for Two-Photon Microscopy Reveals Dynamic Changes in Labile Zn(II) in Differentiating Oligodendrocytes (2018)

Despite the significant advantages of two-photon excitation microscopy (TPEM) over traditional confocal fluorescence microscopy in live-cell imaging applications, including reduced phototoxicity and photobleaching, increased depth penetration, and minimized autofluorescence, only a few metal ion-selective fluorescent probes have been designed and optimized specifically for this technique. Building upon a donor-acceptor fluorophore architecture, we developed a membrane-permeant, Zn(II)-selective fluorescent probe, chromis-1, that exhibits a balanced two-photon cross section between its free and Zn(II)-bound form and responds with a large spectral shift suitable for emission-ratiometric imaging. With a K<sub>d</sub> of 1.5 nM and wide dynamic range, the probe is well suited for visualizing temporal changes in buffered Zn(II) levels in live cells as demonstrated with mouse fibroblast cell cultures. Moreover, given the importance of zinc in the physiology and pathophysiology of the brain, we employed chromis-1 to monitor cytoplasmic concentrations of labile Zn(II) in oligodendrocytes, an important cellular constituent of the brain, at different stages of development in cell culture. These studies revealed a decrease in probe saturation upon differentiation to mature oligodendrocytes, implying significant changes to cellular zinc homeostasis during maturation with an overall reduction in cellular zinc availability. Optimized for TPEM, chromis-1 is especially well-suited for exploring the role of labile zinc pools in live cells under a broad range of physiological and pathological conditions.
A neutralizing antibody that blocks delivery of the enzymatic cargo of Clostridium difficile toxin TcdB into host cells (2017)

<i>Clostridium difficile</i> infection is the leading cause of hospital-acquired diarrhea and is mediated by the actions of two toxins, TcdA and TcdB. The toxins perturb host cell function through a multistep process of receptor binding, endocytosis, low pH-induced pore formation, and the translocation and delivery of an N-terminal glucosyltransferase domain that inactivates host GTPases. Infection studies with isogenic strains having defined toxin deletions have established TcdB as an important target for therapeutic development. Monoclonal antibodies that neutralize TcdB function have been shown to protect against <i>C. difficile</i> infection in animal models and reduce recurrence in humans. Here, we report the mechanism of TcdB neutralization by PA41, a humanized monoclonal antibody capable of neutralizing TcdB from a diverse array of <i>C. difficile</i> strains. Through a combination of structural, biochemical, and cell functional studies, involving X-ray crystallography and EM, we show that PA41 recognizes a single, highly conserved epitope on the TcdB glucosyltransferase domain and blocks productive translocation and delivery of the enzymatic cargo into the host cell. Our study reveals a unique mechanism of <i>C. difficile</i> toxin neutralization by a monoclonal antibody, which involves targeting a process that is conserved across the large clostridial glucosylating toxins. The PA41 antibody described here provides a valuable tool for dissecting the mechanism of toxin pore formation and translocation across the endosomal membrane.
IMS Instrumentation I: Isolated data acquisition for ion mobility spectrometers with grounded ion sources (2020)

Abstract The drift voltage required for operating ion mobility spectrometers implies high voltage isolation of either the ion source or the detector. Typically, the detector is grounded due to the sensitivity of the small ion currents to interferences and thus higher requirements for signal integrity than the ion source. However, for certain ion sources, such as non-radioactive electron emitters or electrospray ionization sources, or for coupling with other instruments, such as gas or liquid chromatographs, a grounded ion source is beneficial. In this paper, we present an isolated data acquisition interface using a 16 bit, 250 kilosamples per second analog to digital converter and fiber optic transmitters and receivers. All spectra recorded via this new data acquisition interface and with a grounded ion source show the same peak shapes and noise when compared with a grounded detector, allowing additional freedom in design.
Cloning, nucleotide sequence determination and expression of the genes encoding cytochrome P‐450<sub>soy</sub> (<i>soyC</i>) and ferredoxin<sub>soy</sub> (<i>soyB</i>) from <i>Streptomyces griseus</i> (1993)

Xenobiotic transformation by Streptomyces griseus (ATCC13273) is catalysed by a cytochrome P-450, designated cytochrome P-450soy. A DNA segment carrying the structural gene encoding P-450soy (soyC) was cloned using an oligonucleotide probe constructed from the protein sequence of a tryptic peptide. Following DNA sequencing the deduced amino acid sequence of P-450soy was compared with that for P-450cam, revealing conservation of important structural components including the haem pocket. Expression of the cloned soyC gene product was demonstrated in Streptomyces lividans by reduced CO:difference spectral analysis and Western blotting. Downstream of soyC, a gene encoding a putative [3Fe-4S] ferredoxin (soyB), named ferredoxinsoy, was identified.
Novel 5-substituted 3-(2-naphthalenyl)-3-(1H-imidazol-l-ylmethy)-2-methylisoxazolidine derivatives. (1989)

The synthesis and antifungal activity of a series of novel 5-substituted 3-(2-naphthalenyl)-3-(1H-imidazol-1-ylmethyl)-2- methylisoxazolidine derivatives are described. When tested in vitro in solid agar assays, some of the compounds demonstrated moderate to potent activity against Trichophyton rubrum and Candida albicans.
A NEW CHART FOR ANALYZING MULTIPROCESS PERFORMANCE (1990)

This article describes a new chart which can be used for determining the performance of a group of processes relative to specification limits. This chart has three primary purposes. It illustrates, on one chart, the overall status of a group of processe..
Rapid High Temperature Solar Thermal Biomass Gasification in a Prototype Cavity Reactor (2010)

High temperature biomass gasification has been performed in a prototype concentrated solar reactor. Gasification of biomass at high temperatures has many advantages compared with historical methods of producing fuels. Enhancements in overall conversion, product composition ratios, and tar reduction are achievable at temperatures greater than 1000°C. Furthermore, the utilization of concentrated solar energy to drive these reactions eliminates the need to consume a portion of the product stream for heating and some of the solar energy is stored as chemical energy in the product stream. Experiments to determine the effects of temperature, gas flow rate, and feed type were conducted at the high flux solar furnace at the National Renewable Energy Laboratory, Golden, CO. These experiments were conducted in a reflective cavity multitube prototype reactor. Biomass type was found to be the only significant factor within a 95% confidence interval. Biomass conversion as high as 68% was achieved on sun. Construction and design considerations of the prototype reactor are discussed as well as initial performance results.
Discrete Frequency Infrared Vibrational Circular Dichroism Spectroscopy & Imaging (2021)

Vibrational Circular Dichroism (VCD) arises from chiroptical phenomena in biological samples. We demonstrate VCD imaging, a novel microscopy technique that can provide molecular- and spatially-specific chirality mapping of biological tissues by measuring optical activity.
Heat immunotherapy with heat shock protein expression by hyperthermia using magnetite nanoparticles (2007)

Hyperthermia is a possible approach for cancer therapy. However, a major technical problem associated with the use of hyperthermia is the difficulty of heating the local tumor region to the intended temperature without damaging normal tissue. Accordingly, in hyperthermia treatment, the expression of heat shock proteins (HSPs) has been considered a complicating factor because the expression of HSPs protects cells from apoptotic cell death. In cancer immunity, on the other hand, HSPs, including HSP70, have been shown to play an important role in immune reactions. If HSP expression induced by hyperthermia is involved in tumor immunity, novel cancer immunotherapy based on hyperthermia treatment can be developed. In such a strategy, a tumor-specific hyperthermia system that can induce necrotic cell death via HSP expression without damaging non-cancerous tissues would be highly advantageous. An intracellular hyperthermia system using functionalized magnetite nanoparticles, including magnetite cationic liposomes and antibody-conjugated magnetoliposomes, facilitates tumor-specific hyperthermia; this can induce necrotic cell death via HSP expression, which in turn induces antitumor immunity. We term this novel cancer therapy as “heat immunotherapy.” This review discusses recent progress in cancer immunology via HSP expression and novel immunotherapy based on hyperthermia.
Investigation of Mode Interaction in Optical Microresonators for Kerr Frequency Comb Generation (2014)

Mode interaction in silicon nitride micro-resonators is investigated. We provide clear experimental evidence of mode interaction between two family modes and mode interaction is demonstrated to be the cause of the comb generation in resonators with normal dispersion.
Room Temperature Continuous Wave Lasing in Nanopillar Photonic Crystal Cavities (2012)

We demonstrate room temperature continuous wave lasing in bottom-up photonic crystal cavities formed by patterned III-V nanopillars. Single-cell high-Q photonic crystal cavities are formed with nanopillars by selective-area epitaxy. Control of the nanopillar geometry and heterostructures allows for high-Q and large confinement factor, resulting in a low threshold power density of 75 W/cm2 at 1040 nm emission wavelength.
Semaphorin 3E and Plexin-D1 Control Vascular Pattern Independently of Neuropilins (2004)

The development of a patterned vasculature is essential for normal organogenesis. We found that signaling by semaphorin 3E (Sema3E) and its receptor plexin-D1 controls endothelial cell positioning and the patterning of the developing vasculature in the mouse. Sema3E is highly expressed in developing somites, where it acts as a repulsive cue for plexin-D1-expressing endothelial cells of adjacent intersomitic vessels. Sema3E-plexin-D1 signaling did not require neuropilins, which were previously presumed to be obligate Sema3 coreceptors. Moreover, genetic ablation of Sema3E or plexin-D1 but not neuropilin-mediated Sema3 signaling disrupted vascular patterning. These findings reveal an unexpected semaphorin signaling pathway and define a mechanism for controlling vascular patterning.