gebhart/patrepeval huggingface dataset:
Highly Enantioselective Synthesis of 1,2,3‐Substituted Cyclopropanes by Using α‐Iodo‐ and α‐Chloromethylzinc Carbenoids (2012)

Herein, we report the enantio- and diastereoselective formation of trans-iodo- and trans-chlorocyclopropanes from α-iodo- and α-chlorozinc carbenoids by using a dioxaborolane-derived chiral ligand. The synthetically useful iodocyclopropane building blocks were derivatized by an electrophilic trapping of the corresponding cyclopropyl lithium species or a Negishi coupling to give access to a variety of enantioenriched 1,2,3-substituted cyclopropanes. The synthetic utility of this method was demonstrated by the formal synthesis of an HIV-1 protease inhibitor. In addition, the related stereoselective bromocyclopropanation was also investigated. New insights about the relative electrophilicity of haloiodomethylzinc carbenoids are also presented.
Supplementary Table 4 from <i>SETD2</i> Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma (2023)

&lt;p&gt;File contains genes that have focal somatic copy number amplifications&lt;/p&gt;
Optical Limiting Materials (1998)

Optical limiting materials. Methanofullerenes, fulleroids and/or other fullerenes chemically altered for enhanced solubility, in liquid solution, and in solid blends with transparent glass (SiO.sub.2) gels or polymers, or semiconducting (conjugated) polymers, are shown to be useful as optical limiters (optical surge protectors). The nonlinear absorption is tunable such that the energy transmitted through such blends saturates at high input energy per pulse over a wide range of wavelengths from 400-1100 nm by selecting the host material for its absorption wavelength and ability to transfer the absorbed energy into the optical limiting composition dissolved therein. This phenomenon should be generalizable to other compositions than substituted fullerenes.
Using interfaces to influence thermodynamic properties of metal hydrides (2018)

We report profound proximity effects on the enthalpy of solution and critical temperature ofnano-sized vanadium hydrides. We use single crystalline Cr/V and Fe/V (001) superlattices forthese studie ...
Successful online education - GeckoCIRCUITS as open-source simulation platform (2014)

Modern lectures in power electronics should be complemented by interactive content, e.g. computer assisted learning via web-based applets or exercises employing a circuit simulator. The online e-learning system “iPES” was established in 2001; since then the iPES Java applets are frequently used in academia and industry to teach the basics of power electronics. This paper introduces new features of the open-source power electronics circuit simulator GeckoCIRCUITS, which enable a more flexible way to generate online content in comparison to iPES. In particular, the animation of current paths in a circuit model as well as a new language translation and internationalization scheme will be presented in detail. Finally, the popular iPES platform will be enhanced or replaced with Java applets based on GeckoCIRCUITS.
Asymmetric Synthesis of Conformationally Constrained Fingolimod Analogues—Discovery of an Orally Active Sphingosine 1-Phosphate Receptor Type-1 Agonist and Receptor Type-3 Antagonist (2007)

Compound 1 (FTY720, Fingolimod) represents a new generation of immunosuppressant that modulates lymphocyte trafficking by interacting with the S1P(1) receptor. Compound 1 also provides a template molecule for studying the molecular biology of S1P receptors and related enzymes (kinases and phosphatases). In this study, two conformationally constrained analogues of 1 ( 3a and 3c) were asymmetrically synthesized in high optical purity. In vitro assessment documented that both analogues are Sphk2 substrates, their phosphorylated species are potent S1P(1) receptor agonists, and 3a-P is a potent S1P 3 antagonist. After oral administration in mice, both compounds evoked lymphopenia, but their duration of action differed markedly.
Towards practical biometric key generation with randomized biometric templates (2008)

Although biometrics have garnered significant interest as a source of entropy for cryptographic key generation, recent studies indicate that many biometric modalities may not actually offer enough uncertainty for this purpose. In this paper, we exploit a novel source of entropy that can be used with any biometric modality but that has yet to be utilized for key generation, namely associating uncertainty with the way in which the biometric input is measured. Our construction poses only a modest requirement on a user: the ability to remember a low-entropy password. We identify the technical challenges of this approach, and develop novel techniques to overcome these difficulties. Our analysis of this approach indicates that it may offer the potential to generate stronger keys: In our experiments, 40% of the users are able to generate keys that are at least 230 times stronger than passwords alone.
New 68Ga Glu-Urea-Lys(Ahx)-HBED-CC-bisphosponate as a dual-targeted imaging agent for PSMA and bone metastasis. (2016)

1395 Objectives Positron emission tomography (PET) imaging using 68Ga labeled Glu-Urea-Lys(Ahx)-HBED-CC-bisphosponate to target both PSMA and bone metastasis may be a valuable tool for diagnosis and monitoring therapeutic treatment of prostate cancer. Methods : 68Ga labeled N,N′-bis[2-hydroxy-5-(carboxyethyl)benzyl] ethylenediamine-N,N′-diacetic acid (HBED-CC) containing one bisphosphonate group and one Glu-Urea-Lys(Ahx) group, 1, was prepared and tested with hydroxyapatite binding assay, PSMA binding assay, biodistribution in mice, and animal PET imaging in LNCaP tumor-bearing mice (a tumor known to over express PSMA). Results The new ligand 1 reacted rapidly in a sodium acetate buffer with [68Ga]GaCl3 eluted from a commercial 68Ge/68Ga generator (pH 4, >98% labeling at room temperature in 10 min) to form [68Ga]1. Because labeling was nearly quantitative, the labeled product was used without further purification. This bisphosphonate, [68Ga]1, showed a strong binding to hydroxyapatite and it also retained high affinity to PSMA comparable to a known PSMA imaging agent, [68Ga]Glu-Urea-Lys(Ahx)-HBED-CC. The biodistribution of [68Ga]1 in normal mice showed excellent bone uptake and retention. In addition, a significant uptake in kidneys was observed, suggesting that [68Ga]1 also targeted PSMA sites in the kidneys. MicroPET imaging studies in mice with xenographed LNCaP tumor overexpressing PSMA showed high uptake in the tumor as well as in the bone. Conclusions The results suggest that [68Ga]1 may be suitable as a dual targeting imaging agent for PSMA and bone metastasis. Also, This dual-targeted imaging agents, [68Ga]1, may show improved sensitivity and specificity for detecting bone metastasis.
A Complex Containing HNRNPA2B1 and N 6 -methyladenosine Modified Transcripts Mediates Actions of Toxic Tau Oligomers (2020)

Summary The microtubule associated protein tau oligomerizes in response to stress and disease, but the function of oligomeric tau (oTau) and the ultimate mechanisms of toxicity are unknown. To gain insights, we have now used Cry2-based optogenetics to induce tau oligomers (oTau-c) in neuronal cultures. oTau-c can seed tau aggregation and biochemical fractionates in a manner similar to oTau. Optical induction of oTau elicits a translational stress response that includes cytoplasmic translocation of the TIA1, abundant stress granules (SGs) and reduced protein synthesis. Proteomic analysis identifies HNRNPA2B1 as a principle target of oTau. Imaging and immunoprecipitation verify the HNRNPA2B1 association with endogenous oTau in neurons, animal models and human Alzheimer brain tissue. Mechanistic studies demonstrate that HNRNPA2B1 functions as a linker, connecting oTau with N 6 -methyladenosine modified transcripts (m 6 A). Knockdown of HNRNPA2B1 prevents oTau from associating with m 6 A, prevents oTau-induced reductions in protein synthesis and reduces oTau-induced toxicity. Finally, we show striking increases in m 6 A-oTau and -HNRNPA2B1 complexes in brains of Alzheimer subjects and P301S tau mice. These results reveal a novel complex containing oTau, HNRNPA2B1 and m 6 A that contributes to the integrated stress response of oTau. Highlights Development of a powerful method combining optical induction of tau oligomerization with precision mass spectrometry to obtain time resolved evolution of protein interaction networks. Demonstration of a tripartite complex that links tau oligomers with HNRNPA2B1 and N 6 -methyladenosine modified RNA in cytoplasmic stress granules. Knockdown of HNRNPA2B 1 abrogates the interactions of oTau with N 6 -methyladenosine modified RNA, as well as inhibits oTau-mediated neurodegeneration. Discovery that N 6 -methyladenosine modified RNA is significantly increased in the brains of P301S tau transgenic mice and in patients with Alzheimer’s disease.
Metal-catalyzed uncaging of DNA-binding agents in living cells (2014)

Attachment of alloc protecting groups to the amidine units of fluorogenic DNA-binding bisbenzamidines or to the amino groups of ethidium bromide leads to a significant reduction of their DNA affinity. More importantly, the active DNA-binding species can be readily regenerated by treatment with ruthenium catalysts in aqueous conditions, even in cell cultures. The catalytic chemical uncaging can be easily monitored by fluorescence microscopy, because the protected products display both different emission properties and cell distribution to the parent compounds.
Cross-Resistance Patterns Among Lucilia cuprina (Diptera: Calliphoridae) Resistant to organophosphorus Insecticides (1998)

Strains of Lucilia cuprina (Wiedemann) have been characterized as having low, internlcdiate, or high levels of esterase-mediated hydrolysis of the organophosphorus insecticide, chlorfenvinphos. These levels correlate respectively with susceptibility to organophosphorus insecticides, malathion resistance, or diazinon resistance. Diazinon and chlorfenvinphos are diethyl organophosphorus insecticides having 2 methoxy groups attached to their central phosphorus atom, whereas malathion is a dimethyl organophosphorus insecticide having 2 methoxy groups attached to its phosphorus atom, and, unusually, malathion also has 2 carboxylester bonds in addition to the phosphoester bonds that define organophosphorus compounds. We tested larvae for resistance to diazinon and also assessed representative malathion-resistant and diazinon-resistant L. cuprina strains at the adult stage for resistance to 12 organophosphorus insecticides, including analog pairs differing only in respect to their dimethyl- diethyl status. Two malathion-resistant strains have low-level cross-resistance to diazinon (3 to 4-fold), 4 diazinon resistant strains have high-level diazinon resistance (11 to 16-fold), and 2 strains with a combined (malathion plus diazinon) resistance type also have high-level diazinon resistance (17 to 18-fold) relative to 3 organophosphorus insecticide-susceptible strains. One of the diazinon-resistant strains showed ≍ 2 times greater resistance factors toward diethyl organophosphorus insecticides than their dimethyl analogs while (leaving aside malathion to consider only the majority which have no carboxylester groups) a malathion-resistant strain showed 2-5 times greater resistance factors toward the dimethyl organophosphorus insectides than their diethyl analogs. The diazinon-resistant strain showed no resistance to 2 di-isopropyl organophosphorus compounds or to 2 organophosphorus insecticides which are asymmetric about the phosphorus atom (optically active). The malathion-resistant strain showed only slight resistance <3-fold) to either the di-isopropyl or optically active organophosphorus insecticides, including the di-isobropyl analog of malathion. These cross-resistance patterns parallel those of certain organophosphorus insecticide-resistant strains of Musca domestica L., in which diazinon and malathion resistances also are proposed to be esterase mediated, reinforcing other biochemical data suggesting a general mechanism among the higher Diptera
Frequency- and Duration-Dependent Effects of Cyclic Pressure on Select Bone Cell Functions (2001)

The present study demonstrated unique correlations between characteristic parameters of mechanical loading and osteoblast functions. Specifically, osteoblast proliferation was dependent on the frequency and on the duration of the applied cyclic pressure stimulus: decreased cell proliferation was only observed when these cells were exposed to cyclic pressure at 1.0-Hz (but not at 0.25-Hz) frequency for 1 h (but not for 20 min) daily for 5 days. In contrast, endothelial cells were not responsive to cyclic pressure, whereas fibroblast proliferation increased under similar test conditions. Most important, cyclic pressure affected various osteoblast genes differently: exposure of osteoblasts to cyclic pressure (at 1.0-Hz frequency for 1 h daily) resulted in enhanced transcription and translation of alkaline phosphatase after 5 days; the same mechanical stimulus, however, did not affect osteopontin mRNA expression during the same time periods. These findings provide cellular and molecular level information, which is not only important in elucidating the correlation between mechanical loading and bone homeostasis, but can be useful in development of new technology in skeletal tissue engineering.
Plane-by-Plane Inscription of Grating Structures in Optical Fibers (2017)

Plane-by-plane fabrication of fiber Bragg gratings in optical fibers using a short-pulse femtosecond IR laser is proposed and demonstrated.By incorporating a cylindrical lens in the fabrication setup, a plane of index modification can be directly inscribed in the fiber core by a single laser pulse.The planes of index modification are produced in the core of a free-standing fiber without an oil immersion objective.This plane-by-plane method simplifies the direct grating inscription process and allows for the fabrication of complicated grating structures.
Observation of Assembly of Fluorescent Si Nanoparticles Under the Influence of Electric Current (2002)

A silicon substrate patterned by an oxide is immersed in an alcohol solution of low-doped 1-nm Si nanoparticles. Reverse biasing draws particles to the substrate, mostly along the conducting current paths. Scanning electron and fluorescence microscopy show a tree-like network on the substrate. Avoidance of closed loops and preference for an angle of branching of 90 degrees-120 degrees are observed. The building block of the tree network is not individual particles but spherical particle aggregates approximately 150 nm in diameter.
Ethiodized Oil–Ethanol Capillary Embolization in Rabbit Kidneys: Temporal Histopathologic Findings (2004)

In the rabbit, selective renal arterial injection of EEM followed by administration of ethanol produces vascular endothelial damage initiating thrombosis that results in renal infarction and ablation within 24 hours.
Conformationally Tuned Large Two-Photon Absorption Cross Sections in Simple Molecular Chromophores (2001)

We investigate here the relationship between molecular architecture and two-photon absorption (TPA) processes in a class of alkyl-substituted 4-quinopyran chromophores. We find that TPA cross sections diverge as the one-photon gap energy nears one-half of the two-photon gap. The molecular strategy proposed here to tune these two-excitation gaps for maximizing TPA cross sections is to twist the molecule about the bond connecting the chromophore donor and acceptor phenylene fragments. Extremely large TPA cross sections, determined by the absorption bandwidth, can then be realized (imaginary part of the third-order polarizability approximately 2.6 x 10(5) x 10(-36) esu) for fundamental photon energies near 1.0 eV, when the torsional angle approaches 104 degrees. The required torsional angle is achieved by introduction of sterically encumbered 2,2',2' ',2' " tertiary alkyl substituents.
Visiting card understanding system (2003)

The authors present the visiting card understanding system, whose output is suitable for the input of a visiting-card database. The system consists of two modules. One is a document model which represents the hierarchical knowledge about the layout structure of visiting cards. The other is an understanding module which interprets the document model to general and test hierarchical hypotheses about the contents of a visiting card. Since the understanding module is fundamentally independent of document type, the system is applicable to many kinds of documents.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A prototype detector for a novel high-resolution PET system: BazookaPET (2012)

We have designed and are developing a novel proof-of-concept PET system called BazookaPET. In order to complete the PET configuration, at least two detector elements are required to detect positron-electron annihilation events. Each detector element of the BazookaPET has two independent data acquisition channels. One side of the scintillation crystal is optically coupled to a 4×4 silicon photomultiplier (SiPM) array and the other side is a CCD-based gamma camera. Using these two separate channels, we can obtain data with high energy, temporal and spatial resolution data by associating the data outputs via several maximum-likelihood estimation (MLE) steps. In this work, we present the concept of the system and the prototype detector element. We focus on characterizing individual detector channels, and initial experimental calibration results are shown along with preliminary performance-evaluation results. We measured energy resolution and the integrated traces of the slit-beam images from both detector channel outputs. A photo-peak energy resolution of ~5.3% FWHM was obtained from the SiPM and ~48% FWHM from the CCD at 662 keV. We assumed SiPM signals follow Gaussian statistics and estimated the 2D interaction position using MLE. Based on our the calibration experiments, we computed the Cramér-Rao bound (CRB) for the SiPM detector channel and found that the CRB resolution is better than 1 mm in the center of the crystal.
Deploying solid-phase synthesis to access thymine-containing nucleoside analogs that inhibit DNA repair nuclease SNM1A (2023)

Nucleoside analogs show useful bioactive properties. A versatile solid-phase synthesis that readily enables the diversification of thymine-containing nucleoside analogs is presented. The utility of the approach is demonstrated with the preparation of a library of compounds for analysis with SNM1A, a DNA damage repair enzyme that contributes to cytotoxicity. This exploration provided the most promising nucleoside-derived inhibitor of SNM1A to date with an IC<sub>50</sub> of 12.3 μM.
Transient Decrease in High Blood Pressure by In Vivo Transfer of Antisense Oligodeoxynucleotides Against Rat Angiotensinogen (1995)

The renin-angiotensin system plays an important role in blood pressure regulation. Angiotensinogen, which is mainly produced in the liver, is a unique component of the renin-angiotensin system, because angiotensinogen is only known as a substrate for angiotensin I generation. It is unclear whether circulating angiotensinogen is a rate-limiting step in blood pressure regulation. Recent findings of genetic studies and analyses suggest that the angiotensinogen gene may be a candidate as a determinant of hypertension. To test the hypothesis that angiotensinogen may modulate blood pressure, we transfected antisense oligonucleotides against rat angiotensinogen into the rat liver via the portal vein using liposomes that contain viral agglutinins to promote fusion with target cells, a technique that has been reported to be highly efficient. Transfection of antisense oligonucleotides resulted in a transient decrease in plasma angiotensinogen levels in spontaneously hypertensive rats from day 1 to day 7 after the injection, consistent with the reduction of hepatic angiotensinogen mRNA. Plasma angiotensin II concentration was also decreased in rats transfected with antisense oligonucleotides. Moreover, a transient decrease in blood pressure from day 1 to day 4 was observed, whereas transfection of sense and scrambled oligonucleotides did not result in any changes in plasma angiotensinogen level, blood pressure, or angiotensinogen mRNA level. Overall, our results demonstrate that transfection of antisense oligonucleotides against rat angiotensinogen resulted in a transient decrease in the high blood pressure of spontaneously hypertensive rats, accompanied by a decrease in angiotensinogen and angiotensin II levels.(ABSTRACT TRUNCATED AT 250 WORDS)
Immunoprotective Capacities of Human and Murine Monoclonal Antibodies Recognizing Serotype-Specific and Common Determinants of Gram-negative Bacteria (1990)

The value of passively transferred polyclonal antisera to lipopolysaccharides (LPS) for prevention or treatment of nosocomial infections caused by gram-negative bacilli has been demonstrated. Human monoclonal antibodies (human Mabs, or Humabs) may prove to be effective at replacing polyclonal antibodies and thereby circumventing many of the problems associated with polyclonal preparations such as heterogeneity of preparations and possible contamination with viral agents. To provide protection against the relevant gram-negative bacilli, the use of human Mabs that recognize conserved epitopes of LPS expressed by most, if not all, pathogenic gram-negative bacilli would be the simplest approach. However, considerable controversy still exists concerning the relative protective capacities, and therefore the therapeutic potential, of cross-reactive antibodies and antibodies that recognize serotype-specific epitopes of LPS.KeywordsMurine Monoclonal AntibodyProtective CapacityFisher TypeTherapeutic Monoclonal AntibodyChallenge StrainThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations* (2020)

The strategy of using DNA to program the assembly of nanoparticles into macroscopic materials emerged in the mid-1990s. In order to better understand the complex phenomena associated with nanoparticle assembly, analytical and numerical models have been proposed. A spherical nucleic-acid-gold nanoparticle conjugates will tend to avoid its neighbors that do not possess DNA strands by bending its DNA strands away from these neighboring particles to which it cannot hybridize. The small degree of flexibility allows for DNA strands to maximize hybridization interactions between particles, while the dynamic nature of the hybridization events allows the nanoparticle to sample several positions within a lattice and ultimately adopt a thermodynamically favored placement. The DNA coverage varied with the gold nanoparticle size, consistent with previously determined experimental values. The latter variable dictated the relative number of each type of DNA linkage per unit cell, which determined the maximum number of DNA connections that could be formed.