gebhart/patrepeval huggingface dataset:
General One-Step Synthesis of Free Hexofuranosyl 1-Phosphates Using Unprotected 1-Thioimidoyl Hexofuranosides (2005)

A general one-step strategy is developed for the synthesis of hexofuranosyl 1-phosphates starting from new unprotected glycofuranosyl donors. It required first the preparation of new 1-thiohexofuranosides bearing a thioimidoyl heterocycle as a leaving group. The presence of sulfur and/or nitrogen atom(s) on the aglycon allowed remote activation of these thioglycofuranosides by anhydrous phosphoric acid and led to the target phosphates 9, 27, 29, and 30 in good to excellent selectivities and, more importantly, with very limited or no ring expansion. Moreover, this one-step phosphorylation reaction could be significantly improved by avoiding any tedious protecting group manipulations on negatively charged compounds and by focusing on a simple but general procedure of purification. This approach was applied to the diastereocontrolled synthesis of d-galacto- and d-glucofuranosyl 1-phosphates and also to the preparation of rare epimer and/or deoxy counterparts, that is, d-manno- and d-fucofuranosyl derivatives.
Data from AZD8055 Is a Potent, Selective, and Orally Bioavailable ATP-Competitive Mammalian Target of Rapamycin Kinase Inhibitor with <i>In vitro</i> and <i>In vivo</i> Antitumor Activity (2023)

&lt;div&gt;Abstract&lt;p&gt;The mammalian target of rapamycin (mTOR) kinase forms two multiprotein complexes, mTORC1 and mTORC2, which regulate cell growth, cell survival, and autophagy. Allosteric inhibitors of mTORC1, such as rapamycin, have been extensively used to study tumor cell growth, proliferation, and autophagy but have shown only limited clinical utility. Here, we describe AZD8055, a novel ATP-competitive inhibitor of mTOR kinase activity, with an IC&lt;sub&gt;50&lt;/sub&gt; of 0.8 nmol/L. AZD8055 showed excellent selectivity (∼1,000-fold) against all class I phosphatidylinositol 3-kinase (PI3K) isoforms and other members of the PI3K-like kinase family. Furthermore, there was no significant activity against a panel of 260 kinases at concentrations up to 10 μmol/L. AZD8055 inhibits the phosphorylation of mTORC1 substrates p70S6K and 4E-BP1 as well as phosphorylation of the mTORC2 substrate AKT and downstream proteins. The rapamycin-resistant T37/46 phosphorylation sites on 4E-BP1 were fully inhibited by AZD8055, resulting in significant inhibition of cap-dependent translation. &lt;i&gt;In vitro&lt;/i&gt;, AZD8055 potently inhibits proliferation and induces autophagy in H838 and A549 cells. &lt;i&gt;In vivo&lt;/i&gt;, AZD8055 induces a dose-dependent pharmacodynamic effect on phosphorylated S6 and phosphorylated AKT at plasma concentrations leading to tumor growth inhibition. Notably, AZD8055 results in significant growth inhibition and/or regression in xenografts, representing a broad range of human tumor types. AZD8055 is currently in phase I clinical trials. Cancer Res; 70(1); 288–98&lt;/p&gt;&lt;/div&gt;
Active-Pixel Image Sensors With Programmable Resolution (1996)

Active-pixel image sensors with programmable resolution proposed for use in applications in which speed and efficiency of processing of image data enhanced by providing those data at varying resolutions. Such applications include modeling of biological vision, stereoscopic range-finding, recognition of patterns, tracking targets, and progressive transmission of compressed images. In target-tracking application, sensor initially forms low-resolution image from which area of interest identified, then sensor set at high resolution for examination of identified area. Outputs of contiguous pixels combined. Sensor of this type made to act as though it comprised fewer and larger pixels.
Identification of CD163 as an antiinflammatory receptor for HMGB1-haptoglobin complexes (2016)

Secreted by activated cells or passively released by damaged cells, extracellular HMGB1 is a prototypical damage-associated molecular pattern (DAMP) inflammatory mediator. During the course of developing extracorporeal approaches to treating injury and infection, we inadvertently discovered that haptoglobin, the acute phase protein that binds extracellular hemoglobin and targets cellular uptake through CD163, also binds HMGB1. Haptoglobin-HMGB1 complexes elicit the production of antiinflammatory enzymes (heme oxygenase-1) and cytokines (e.g., IL-10) in WT but not in CD163-deficient macrophages. Genetic disruption of haptoglobin or CD163 expression significantly enhances mortality rates in standardized models of intra-abdominal sepsis in mice. Administration of haptoglobin to WT and to haptoglobin gene-deficient animals confers significant protection. These findings reveal a mechanism for haptoglobin modulation of the inflammatory action of HMGB1, with significant implications for developing experimental strategies targeting HMGB1-dependent inflammatory diseases.
Autoimmunity-Associated LYP-W620 Does Not Impair Thymic Negative Selection of Autoreactive T Cells (2014)

A C1858T (R620W) variation in the PTPN22 gene encoding the tyrosine phosphatase LYP is a major risk factor for human autoimmunity. LYP is a known negative regulator of signaling through the T cell receptor (TCR), and murine Ptpn22 plays a role in thymic selection. However, the mechanism of action of the R620W variant in autoimmunity remains unclear. One model holds that LYP-W620 is a gain-of-function phosphatase that causes alterations in thymic negative selection and/or thymic output of regulatory T cells (Treg) through inhibition of thymic TCR signaling. To test this model, we generated mice in which the human LYP-W620 variant or its phosphatase-inactive mutant are expressed in developing thymocytes under control of the proximal Lck promoter. We found that LYP-W620 expression results in diminished thymocyte TCR signaling, thus modeling a "gain-of-function" of LYP at the signaling level. However, LYP-W620 transgenic mice display no alterations of thymic negative selection and no anomalies in thymic output of CD4(+)Foxp3(+) Treg were detected in these mice. Lck promoter-directed expression of the human transgene also causes no alteration in thymic repertoire or increase in disease severity in a model of rheumatoid arthritis, which depends on skewed thymic selection of CD4(+) T cells. Our data suggest that a gain-of-function of LYP is unlikely to increase risk of autoimmunity through alterations of thymic selection and that LYP likely acts in the periphery perhaps selectively in regulatory T cells or in another cell type to increase risk of autoimmunity.
Idaho Explosives Detection System (2004)

This is a preprint of a paper intended for publication in a journal or proceedings. Since changes may be made before publication, this preprint should not be cited or reproduced without permission of the author. This document was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, or any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or responsibility for any third party&amp;apos;s use, or the results of such use, of any information, apparatus, product or process disclosed in this report, or represents that its use by such third party would not infringe privately owned rights. The views expressed in this paper are not necessarily those of the U.S. Government or the sponsoring agency.
Antileukemia T-cell responses in CLL – We don't need no aberration (2015)

Effective antigen-specific cancer immunotherapy requires exact knowledge of tumor-associated epitopes that can act as rejection antigens. Although the current paradigm views mutation-derived neoantigens as the most promising targets, we have recently demonstrated that leukemia-specific T-cell responses associated with survival benefit in CLL patients target a panel of non-mutated tumor-associated antigens.
Characterization of Glucose Sensor Prepared with the Electropolymerized Pyrrole Containing a Saccharide Unit (2000)

Amperometric glucose sensors were prepared by electropolymerization of a pyrrole derivative having a saccharide unit, 1-(3-D-gluconamidopropyl)pyrrole, in the presence of glucose oxidase (GOD). The response current of the GOD-immobilized electrode was approximately stable for 50 days after an initial loss of signal over the first few days. However, the interference of electroactive compounds such as ascorbic acid, uric acid and acetaminophen to the glucose response was large. Such an interference of electroactive compounds was largely lowered by using the GOD-immobilized electrode with Nafion and PPD films as inner film, but the influence of uric acid still remained. The use of Nafion film as the inner film, was more effective in reducing the interference of electroactive compounds on glucose response than that of poly (o-phenylenediamine), which the use of both film produced the best results in the interference study.
ChemInform Abstract: NUCLEOPHILER CHARAKTER VON ACYLRADIKALEN, SUBSTITUENTENEFFEKTE BEI DER HOMOLYTISCHEN ACYLIERUNG VON PROTONIERTEN HETEROAROMATISCHEN BASEN (1972)

Abstract Die Chinoline (I) werden durch die Benzoylradikale (II), die aus den entsprechenden Benzaldehyden mit Brenztraubensäure erzeugt werden, in schwefelsaurer Lösung zu den Ketonen (III) acyliert.
Design and Fabrication of a Planar Coupling Structure for Photonic Band Gap Devices (2002)

In this paper we present the design and fabrication of a planar coupling structure for photonic band gap devices. Calculations predict a coupling efficiency of greater than 90% from a multimode silicion waveguide to a singlemode photonic crystal channel. Experimental results are presented.
Development of biocompatible NaGdF4: Er3+, Yb3+ upconversion nanoparticles used as contrast agents for bio‐imaging (2019)

Upconversion nanoparticles with special fluorescence and magnetic properties have been considered an alternative contrast agent for multiple bio ‐ imaging techniques. It is important to understand the effects of the surface properties and dosage of upconversion nanoparticles on both the magnetic resonance (MRI) image and the photoluminescence spectrum. Here, NaGdF 4 : Er 3+ , Yb 3+ upconversion nanoparticles (UCNPs) modified with amine functional group were produced through a one‐pot thermal decomposition. The average length of the cubic UCNPs is estimated at 53 ±13 nm. The effect of the dosage of amine modified UCNPs on the MRI image is investigated. The T 1 and T 2 relaxivities of the amine modified UCNPs in agarose gel at 3 T are r 1 = 6.79 ±0.14 and r 2 = 17.0 ±0.18 (mmol/L) −1 s −1 , which are comparable to the relaxivities of commercially available MRI contrast agents. In addition, the photoluminescence of the amine modified UCNPs at low concentrations &lt; 150 µg/mL are further investigated with the excitation wavelength (λ ex ) at 980 nm. The internalization of the amine modified UCNPs cultured with human umbilical vascular endothelial cells (HUVEC) is observed by the fluorescence imaging. Meanwhile, T 1 ‐weighted MRI imaging of HUVEC cells treated with amine modified UCNPs at 10 µg/mL can be obtained. No significant toxic effect on cells is found when the concentration of the amine modified UCNPs is &lt; 300 µg/mL. This study indicates that a low concentration of amine‐modified NaGdF 4 : Er 3+ , Yb 3+ UCNPs can be used as the contrast agent for both fluorescence imaging and magnetic resonance imaging.
0608 Detached Eddy Simulation of Rotating Stall in a Transonic Centrifugal Compressor with Single Splitter Blades (2010)

In order to improve the performance and operating range of centrifugal compressors, it is indispensable to understand unsteady behavior of vortical flows. In this paper, the flow fields in a centrifugal compressor with single splitter blades have been investigated by Detached Eddy Simulation(DES). The simulation showed that the vortex breakdown occurred in the tip leakage vortex of full blade and discharged a part of the leakage vortex interacting with a horseshoe vortex around the leading edge of splitter blade. Moreover, the horseshoe vortex interacted with the leading edge of adjacent full blade periodically. It means that such unsteadiness of flow fields inside the impellers affects total performance characteristics.
Helix–Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth (2020)

A detailed understanding of forces guiding the rapid folding of a polypeptide from an apparently random coil state to an ordered α-helical structure following the rate-limiting preorganization of the initial three residue backbones into helical conformation is imperative to comprehending and regulating protein folding and for the rational design of biological mimetics. However, several details of this process are still unknown. First, although the helix-coil transition was proposed to originate at the residue level (<i>J. Chem. Phys.</i> <b>1959,</b> <i>31</i>, 526-535; <i>J. Chem. Phys.</i> <b>1961,</b> <i>34</i>, 1963-1974), all helix-folding studies have only established it between time-averaged bulk states of a long-lived helix and several transiently populated random coils, along the whole helix model sequence. Second, the predominant thermodynamic forces driving either this two-state transition or the faster helix growth following helix nucleation are still unclear. Third, the conformational space of the random coil state is not well-defined unlike its corresponding α-helix. Here we investigate the restrictions placed on the conformational space of a Gly residue backbone, as a result of it immediately succeeding a nascent α-helical turn. Analyses of the temperature-dependent 1D-, 2D-NMR, FT-IR, and CD spectra and GROMACS MD simulation trajectory of a Gly residue backbone following a model α-helical turn, which is artificially rigidified by a covalent hydrogen bond surrogate, reveal that: (i) the α-helical turn guides the ϕ torsion of the Gly exclusively into either a predominantly populated entropically favored α-helical (α-ϕ) state or a scarcely populated random coil (RC-ϕ) state; (ii) the α-ϕ state of Gly in turn favors the stability of the preceding α-helical turn, while the RC-ϕ state disrupts it, revealing an entropy-driven synergetic guidance for helix growth in the residue following helix nucleation. The applicability of a current synergetic guidance mechanism to explain rapid helix growth in folded and unfolded states of proteins and helical peptides is discussed.
A novel synthetic DNA vaccine elicits protective immune responses against Powassan virus (2020)

Powassan virus (POWV) infection is a tick-borne emerging infectious disease in the United States and North America. Like Zika virus, POWV is a member of the family Flaviviridae. POWV causes severe neurological sequalae, meningitis, encephalitis, and can cause death. Although the risk of human POWV infection is low, its incidence in the U.S. in the past 16 years has increased over 300%, urging immediate attention. Despite the disease severity and its growing potential for threatening larger populations, currently there are no licensed vaccines which provide protection against POWV. We developed a novel synthetic DNA vaccine termed POWV-SEV by focusing on the conserved portions of POWV pre-membrane and envelope (prMEnv) genes. A single immunization of POWV-SEV elicited broad T and B cell immunity in mice with minimal cross-reactivity against other flaviviruses. Antibody epitope mapping demonstrated a similarity between POWV-SEV-induced immune responses and those elicited naturally in POWV-infected patients. Finally, POWV-SEV induced immunity provided protection against POWV disease in lethal challenge experiments.
In vivo Patterns of Tau Pathology, Amyloid-β Burden, and Neuronal Dysfunction in Clinical Variants of Alzheimer’s Disease (2016)

The clinical heterogeneity of Alzheimer's disease is not reflected in the rather diffuse cortical deposition of amyloid-β. We assessed the relationship between clinical symptoms, in vivo tau pathology, amyloid distribution, and hypometabolism in variants of Alzheimer's disease using novel multimodal PET imaging techniques. Tau pathology was primarily observed in brain regions related to clinical symptoms and overlapped with areas of hypometabolism. In contrast, amyloid-β deposition was diffusely distributed over the entire cortex. Tau PET imaging may thus serve as a valuable biomarker for the localization of neuronal injury in vivo and may help to validate atypical subtypes of Alzheimer's disease.
SPC12-5: Relay Selection in Multi-Node Cooperative Communications: When to Cooperate and Whom to Cooperate with? (2006)

In this paper, we propose a new cooperative communication protocol, which achieves high bandwidth efficiency while guaranteeing full diversity order. The proposed scheme considers relay selection via the available partial channel state information (CSI) at the source and the relays. More precisely, the source determines when it needs to cooperate with one relay only among arbitrary N relays and which relay to cooperate with in case of cooperation, i.e., "When to cooperate?" and "Whom to cooperate with?". In case of cooperation, the source employs the optimal relay, which has the maximum instantaneous scaled harmonic mean function of its source-relay and relay-destination channels' gains. For the symmetric scenario, we prove that full diversity is guaranteed and that a significant increase of the bandwidth efficiency is achieved. Furthermore, we show the tradeoff between the achievable bandwidth efficiency and the corresponding error rate. Finally, the obtained analytical results are verified through computer simulations.
Rigorous comparison of the spectral SNR of FTIR and EC-QCL spectroscopy(Conference Presentation) (2016)

FTIR spectroscopy using a thermal light source has been the dominant method for obtaining infrared spectra since the 1950’s. Unfortunately the limited surface brightness and low spatial coherence of black-body radiators limits the spectral SNR in microspectroscopy and stand-off detection. Two recent innovations are addressing this problem a) FTIR instruments illuminated by high-spatial coherence broad-band supercontinuum sources and b) high spatial coherence narrow-band EC-QCL’s. Here we ask whether these two approaches offer equivalent sensitivity. By noting an analogy with near-infrared optical coherence tomography we rigorously show that the high temporal coherence of the EC-QCL brings an additional, very large SNR advantage over an FTIR instrument illuminated by a supercontinuum source under otherwise matched conditions. Specifically if a spectrum containing N points is recorded by both instruments using the same illumination intensity and the same detector noise level, then the EC-QCL can deliver a given spectral SNR in a time xN shorter than the FTIR instrument. This factor can reach x100, potentially even x1000, in realistic applications. We exploit the analogy with OCT further by developing a mid-infrared “swept laser”, using commercially available components, in which the tuning rate is much higher than in commercial EC-QCL devices. We use this swept laser to demonstrate the SNR advantage experimentally, using a custom-made EC-QCL spectrometer and PDMS polymer samples. We explore the potential upper limits on spectral acquisition rates, both from the fundamental kinetics of gain build-up in the external cavity and from likely mechanical limits on cavity tuning rates.
Simple and cost effective fabrication of 3D porous core–shell Ni nanochains@NiFe layered double hydroxide nanosheet bifunctional electrocatalysts for overall water splitting (2019)

Meticulously designed 3D porous core–shell Ni nanochains@NiFe LDH nanosheets bifunctional electrocatalysts outperform the state-of-the-art IrO<sub>2</sub> (+)//Pt/C (−) electrodes and most of the reported LDH electrocatalysts for overall water splitting.
<title>Development of critical dimension measurement scanning electron microscope for ULSI (S-8000 series)</title> (1996)

The semiconductor industry is moving from half-micron to quarter-micron design rules. To support this evolution, Hitachi has developed a new critical dimension measurement scanning electron microscope (CD-SEM), the model S-8800 series, for quality control of quarter- micron process lines. The new CD-SEM provides detailed examination of process conditions with 5 nm resolution and 5 nm repeatability (3 sigma) at accelerating voltage 800 V using secondary electron imaging. In addition, a newly developed load-lock system has a capability of achieving a high sample throughput of 20 wafers/hour (5 point measurements per wafer) under continuous operation. To support user friendliness, the system incorporates a graphical user interface (GUI), an automated pattern recognition system which helps locating measurement points, both manual and semi-automated operation, and user-programmable operating parameters.
FIZZ1 and Ym as Tools to Discriminate between Differentially Activated Macrophages (2002)

Although it is well-established that macrophages can occur in distinct activation states, the molecular characteristics of differentially activated macrophages, and particularly those of alternatively activated macrophages (aaMphi), are still poorly unraveled. Recently, we demonstrated that the expression of FIZZ1 and Ym is induced in aaMphi as compared with classically activated macrophages (caMphi), elicited in vitro or developed in vivo during infection with Trypanosoma brucei brucei. In the present study, we analyzed the expression of FIZZ1 and Ym in caMphi and aaMphi elicited during Trypanosoma congolense infection and show that the use of FIZZ1 and Ym for the identification of aaMphi is not limited to T. b. brucei infection and is independent of the organ sources from which macrophages are obtained. We also demonstrate that FIZZ1 can be used to discriminate between different populations of aaMphi. Furthermore, we studied the effects of various stimuli, and combinations thereof, on the expression of FIZZ1 and Ym in macrophages from different mouse strains and demonstrate that regulation of the expression of FIZZ1 and Ym in macrophages is not dependent on the mouse strain. Finally, we show that these genes can be used to monitor the macrophage activation status without the need to obtain pure macrophage populations.
Diagnosis of bronchiectasis and airway wall thickening in children with cystic fibrosis: Objective airway-artery quantification (2017)

• More peripheral airways are visible in CF patients compared to controls. • Structural lung changes in CF patients are greater with each airway generation. • Number of airways visualized on CT could quantify CF lung disease. • For objective airway disease quantification on CT, lung volume standardization is required.
Plasma Fibronectin in Patients with Brain Tumors (1985)

Fibronectin, a large molecular weight glycoprotein normally found on the surface of many cells, was measured in the plasma of 15 normal volunteers and 75 patients with various kinds of brain tumors or other kinds of neurological disorders. The mean plasma fibronectin in the control group was 253 micrograms/ml. Statistically significant elevations in fibronectin levels were found in patients with progressive high grade astrocytomas (mean = 413 micrograms/ml). The majority of patients with high grade astrocytomas in remission had normal levels of fibronectin (mean = 273 micrograms/ml). Elevations were noted in patients with low grade astrocytomas, meningiomas, and benign nonneoplastic neurological disorders. Plasma fibronectin may be useful diagnostically and therapeutically in identifying and managing some patients with high grade gliomas. However, of greater importance is the observation that fibronectin elevation is the result of a tumor-host interaction.