gebhart/patrepeval huggingface dataset:
Fluorosomes: a convenient new reagent to detect and block multivalent and complex receptor‐ligand interactions (2010)

We describe for the first time fluorescent virus-like particles decorated with biologically active mono- and multisubunit immune receptors of choice and the basic application of such fluorosomes (FSs) to visualize and target immune receptor-ligand interactions. For that purpose, human embryonic kidney (HEK)-293 cells were stably transfected with Moloney murine leukemia virus (MoMLV) matrix protein (MA) GFP fusion constructs. To produce FSs, interleukins (ILs), IL-receptors (IL-Rs), and costimulatory molecules were fused to the glycosyl phosphatidyl inositol anchor acceptor sequence of CD16b and coexpressed along with MoMLV group-specific antigen-polymerase (gag-pol) in MA::GFP(+) HEK-293 cells. We show that IL-2 decorated but not control-decorated FSs specifically identify normal and malignant IL-2 receptor-positive (IL-2R(+)) lymphocytes by flow cytometry. In addition to cytokines and costimulatory molecules, FSs were also successfully decorated with the heterotrimeric IL-2Rs, allowing identification of IL-2(+) target cells. Specificity of binding was proven by complete inhibition with nonlabeled, soluble ligands. Moreover, IL-2R FSs efficiently neutralized soluble IL-2 and thus induced unresponsiveness of T cells receiving full activation stimuli via T-cell antigen receptor and CD28. FSs are technically simple, multivalent tools for assessing and blocking mono- and multisubunit immune receptor-ligand interactions with natural constituents in a plasma membrane context.
Training and Meta-Training Binary Neural Networks with Quantum Computing (2019)

Quantum computers promise significant advantages over classical computers for a number of different applications. We show that the complete loss function landscape of a neural network can be represented as the quantum state output by a quantum computer. We demonstrate this explicitly for a binary neural network and, further, show how a quantum computer can train the network by manipulating this state using a well-known algorithm known as quantum amplitude amplification. We further show that with minor adaptation, this method can also represent the meta-loss landscape of a number of neural network architectures simultaneously. We search this meta-loss landscape with the same method to simultaneously train and design a binary neural network.
Ku‐band GaN HPA MMIC with high‐power and high‐PAE performances (2014)

A Ku‐band high‐power and high‐power‐added efficiency (PAE) high‐power amplifier (HPA) monolithic microwave‐integrated circuit (MMIC) is demonstrated with a 0.25 μm gallium nitride (GaN) high electron mobility transistor technology on a silicon carbide substrate. Measured continuous‐wave performances for the two‐stage HPA in‐fixture exhibit 17.5–18.3 W of output power ( P OUT ) and 36.4–39.5% of PAE over the frequency range of 13.5–14.5 GHz. The fabricated two‐stage HPA MMIC with all matching networks is as small as 3.3 × 3.5 mm, generating an output power density of 1522 mW/mm 2 .
Renal Artery Stenosis Evaluation: Diagnostic Performance of Gadobenate Dimeglumine–enhanced MR Angiography—Comparison with DSA (2008)

CE MR angiography performed with 0.1 mmol/kg gadobenate dimeglumine, compared with DSA, is safe and provides good sensitivity, specificity, and accuracy for detection of significant renal artery steno-occlusive disease.
Ion beam switching magnet employing HTS coils (1998)

This paper describes the design, construction, and testing of an ion beam switching high-temperature superconducting (HTS) magnet installed at Institute of Geological and Nuclear Science (IGNS) in New Zealand. It was designed by a consortium comprising American Superconductor Corporation (ASC), ISYS, Applied Engineering Technologies (AET), the New Zealand Institute for Industrial Research and Development (IRL), and Alphatech. The work was also supported in part by New Zealand Foundation for Research and Technology-Technology for Business Growth Programme. The magnet generates 0.72 T in the airgap between two 410/spl times/700 mm warm iron poles. The Bi-2223 HTS coils are conduction-cooled with a single stage Gifford-McMahon (G-M) type cryocooler for steady-state operation. The magnet was fully tested at ASC during the fall of 1996. This represents the first large-scale fully operational HTS physics magnet announced so far. The successful operation of this magnet has verified maturation of HTS magnet technology employing conduction cooling techniques with G-M type cryocoolers. Long term operation of this magnet in continuous use will prove the reliability of HTS magnet systems in critical applications and is expected to open future opportunities for HTS in other related areas.
2D-NMR Studies of Polyvinylidene Fluoride (2012)

This study employs a variety of solution 2D-NMR techniques to characterize the microstructure of polyvinylidene fluoride (PVDF). The microstructural characterization of PVDF is of great interest as it provides useful information to understand the polymerization process. It also provides insight into the relationship between the chemical structure of polymers and their physical and chemical properties. Through a combination of 1D-NMR experiments such as 19F{1H} 1D-NMR and 2D-NMR experiments such as 1) 19F{13C} heteronuclear single quantum coherence (HSQC) with continuous 1H decoupling, 2) 19F-19F gradient double quantum filtered correlation spectroscopy (gDQCOSY) with continuous 1H decoupling, and 3) 19F-19F selective correlation spectroscopy (COSY) with continuous 1H decoupling, the microstructures and resonance assignments of PVDF have been identified. Very weak resonances, which have been reported in the literature but have not been previously assigned, are assigned in this work. In addition to the resonances of main chain sequences, the resonance assignments of end groups in PVDF are presented.
Stereoselective Synthesis of β-2-Deoxyribonucleosides from 1-O-Acetyl-3-O-[2-(methylsulfinyl)ethyl]-2-deoxyribose (1989)

Abstract β-2-Deoxyribonucleosides are prepared stereoselectively from 1-O-acetyl-5-O-benzyl-3-O-[2-(methylsulfinyl)ethyl]-2-deoxy-D-erythro-pentofuranose by the reaction with the silyl or zinc derivatives of nucleoside bases in the presence of trimethylsilyl trifluoromethanesulfonate.
Lithography process control using scatterometry metrology and semi-physical modeling (2007)

In this paper, results and analysis are presented from Advanced Micro Devices' (AMD) efforts at calculating lithography dose and focus parameters using scatterometry metrology and semi-physical CD models. The system takes advantage of the accurate and precise top and bottom CD data produced by scatterometry to differentiate dose and focus variation. To build the lithography process model, scatterometry data is generated for each field of a focus-exposure matrix (FEM) wafer, and the resulting top and bottom CD data is used to fit the parameters of series expansions relating CD to dose and focus. When new CD data is generated, the models can be inverted to solve for dose and focus independently. Our methodology employs a flexible modeling and inversion approach in an attempt to make the technique applicable to any production film stack and any line spacing regime. The quality of the inversion results are highly correlated to the degree of focus observability present in the system. Our results will show how a series of litho process with varied film stacks and line/space ratios respond to this technique, and we will report some best practices for a variety of use cases ranging from equipment characterization to focus monitoring on product.
Analysis of Breath Specimens for Biomarkers ofPlasmodium falciparumInfection (2015)

Currently, the majority of diagnoses of malaria rely on a combination of the patient's clinical presentation and the visualization of parasites on a stained blood film. Breath offers an attractive alternative to blood as the basis for simple, noninvasive diagnosis of infectious diseases. In this study, breath samples were collected from individuals during controlled malaria to determine whether specific malaria-associated volatiles could be detected in breath. We identified 9 compounds whose concentrations varied significantly over the course of malaria: carbon dioxide, isoprene, acetone, benzene, cyclohexanone, and 4 thioethers. The latter group, consisting of allyl methyl sulfide, 1-methylthio-propane, (Z)-1-methylthio-1-propene, and (E)-1-methylthio-1-propene, had not previously been associated with any disease or condition. Before the availability of antimalarial drug treatment, there was evidence of concurrent 48-hour cyclical changes in the levels of both thioethers and parasitemia. When thioether concentrations were subjected to a phase shift of 24 hours, a direct correlation between the parasitemia and volatile levels was revealed. Volatile levels declined monotonically approximately 6.5 hours after initial drug treatment, correlating with clearance of parasitemia. No thioethers were detected in in vitro cultures of Plasmodium falciparum. The metabolic origin of the thioethers is not known, but results suggest that interplay between host and parasite metabolic pathways is involved in the production of these thioethers.
Control of pattern-recognition receptors by an ER protein complex in plant immunity (2009)

Perception of pathogen-associated molecular patterns (PAMPs)by patternrecognition receptors (PRRs) plays an important rolein plant innate immunity. In Arabidopsis, the leucine-richrepeat receptor kinases (LRR-RKs) EFR and FLS2 mediaterecognition of the bacterial PAMPs EF-Tu and flagellin,respectively. Only limited knowledge exists on how EFR andFLS2 function at the molecular level. Here, we identify byforward genetics the Arabidopsis stromalderived factor 2(SDF2) as being required for responses mediated by EFR andFLS2. Sdf2-2 mutants are more susceptible to bacteria fungi,indicating that other, yet unknown PRRs also require SDF2.SDF2 resides in the endoplasmic reticulum (ER) in a complexwith ERdj3B and the luminal binding protein (BiP). ERdj3Band BiP are components of the ER-quality control (ER-QC),and EFR accumulation is impaired in the sdf2 mutant. Erdj3bmutants were independently identified in our screen, and lossof ERdj3B function leads to compromised EFR and FLS2responses. Additionally, sdf2 and erdj3b mutants wereimpaired in the unfolded protein response induced by the drugtunicamycin. Our results demonstrate that severalsurface-exposed PRRs require the ER complex SDF2-ERdj3B-BiP for their function, and provide the firstdemonstration of a physiological requirement for ER qualitycontrol in trans-membrane receptor function in plants.
IOL with Square-Edged Optic and Reduced Dysphotopsia (2011)

Edge undulation of the square-edged optic is an effective addition to intraocular lens designs that reduces the potential for dysphotopsia caused by the optic edge internal reflection of light.
Vav in natural killer cells is tyrosine phosphorylated upon cross-linking of Fcγ RIIIA and is constitutively associated with a serine/threonine kinase (1996)

Cross-linking of Fc gamma RIIIA (CD16) receptor on natural killer (NK) cells induces receptor-associated tyrosine kinase activation and tyrosine phosphorylation of numerous intracellular proteins, including phospholipase C (PLC)-gamma 1, PLC-gamma 2 and the associated zeta chain. Here we report that Vav, a proto-oncogene, also became tyrosine phosphorylated upon stimulation of CD16 in interleukin 2-activated NK cells (LAK-NK) as well as in an NK cell line, NK3.3. In addition, we observed that in LAK-NK cells, Vav was associated with a 70 kDa protein that also became tyrosine phosphorylated upon CD16 cross-linking. The association of this 70 kDa protein with Vav was disrupted by ionic detergent treatment. Tyrosine phosphorylation of Vav was inhibited by herbimycin A, a specific tyrosine kinase inhibitor. In vitro kinase assays with Vav immunoprecipitates derived from NK3.3 cells or LAK-NK cells resulted in the appearance of a phosphorylated 58 kDa protein, suggesting the presence of a kinase within the Vav immunoprecipitates. Cross-linking of CD16 did not enhance this Vav-associated kinase activity. Phosphoamino acid analysis of the 58 kDa protein revealed that it was phosphorylated only on serine and threonine residues, indicating that an unidentified serine/threonine kinase is constitutively associated with Vav. These observations suggest that the downstream signalling events regulated by Vav and its associated proteins are complex involving both tyrosine kinases as well as the yet unidentified serine/threonine kinase in NK cells.
ChemInform Abstract: THE SYNTHESIS OF α,α‐DIFLUOROALDEHYDES AND KETONES VIA CLAISEN REARRANGEMENTS (1985)

Abstract Aus dem Alkohol (Ia) erhält man über den Ether (Ib) mit LDA die Li‐Verbindung (Ilc), die zum Hydrolyseprodukt (IIa) bzw. dem Silyl‐Derivat (IIb) führt.
Zeolite-Like Boron Imidazolate Frameworks (BIFs): Synthesis and Application (2020)

This review is devoted to discussion of the latest advances in design and applications of boron imidazolate frameworks (BIFs) that are a particular sub-family of zeolite-like metal–organic frameworks family. A special emphasis is made on nanostructured hybrid materials based on BIF matrices and their modern applications, especially in environment remediation and energy conversion.
Mapping quantitative trait loci for freezing tolerance in a recombinant inbred line population of Arabidopsis thaliana accessions Tenela and C24 reveals REVEILLE1 as negative regulator of cold acclimation (2012)

The ability to increase freezing tolerance when exposed to low temperatures is a property of many plant species from temperate climates and involves a wide array of metabolic adjustments and changes in gene expression. In Arabidopsis thaliana, natural accessions show high variation in their acclimation capacity, and freezing tolerance correlates with natural habitat temperatures. To investigate the genetic basis of this variation, a recombinant inbred line population from reciprocal crosses between the accessions C24 and Tenela (Te), showing large variation in tolerance, was established. Over 250 recombinant inbred lines were genotyped for 69 single nucleotide polymorphism markers in a linkage map with 391.9 centimorgans (cM) and phenotyped for their freezing tolerance using the electrolyte leakage method that reports cell damage after a freeze-thaw cycle. Mapping of quantitative trait loci (QTL) for acclimated plants revealed three QTL regions on chromosomes 2, 4 and 5. Based on gene expression data, QTL regions were screened for genes differentially responding to low temperature in C24 and Te. Among the candidate genes, the Myb family transcription factor REVEILLE1 (At5g17300) on chromosome 5 was identified as a novel negative regulator of freezing tolerance in Arabidopsis.
Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry (2019)

At the onset of a drug discovery program, the goal is to identify novel compounds with appropriate chemical features that can be taken forward as lead series. Here, we describe three prospective case studies, Bruton Tyrosine Kinase (BTK), RAR-Related Orphan Receptor γ t (RORγt), and Human Leukocyte Antigen DR isotype (HLA-DR) to illustrate the positive impact of high throughput virtual screening (HTVS) on the successful identification of novel chemical series. Each case represents a project with a varying degree of difficulty due to the amount of structural and ligand information available internally or in the public domain to utilize in the virtual screens. We show that HTVS can be effectively employed to identify a diverse set of potent hits for each protein system even when the gold standard, high resolution structural data or ligand binding data for benchmarking, is not available.
IL-1β Promotes Antimicrobial Immunity in Macrophages by Regulating TNFR Signaling and Caspase-3 Activation (2013)

In vivo control of Mycobacterium tuberculosis reflects the balance between host immunity and bacterial evasion strategies. Effector Th1 cells that mediate protective immunity by depriving the bacterium of its intracellular niche are regulated to prevent overexuberant inflammation. One key immunoregulatory molecule is Tim3. Although Tim3 is generally recognized to downregulate Th1 responses, we recently described that its interaction with Galectin-9 expressed by M. tuberculosis-infected macrophages stimulates IL-1β secretion, which is essential for survival in the mouse model. Why IL-1β is required for host resistance to M. tuberculosis infection is unknown. In this article, we show that IL-1β directly kills M. tuberculosis in murine and human macrophages and does so through the recruitment of other antimicrobial effector molecules. IL-1β directly augments TNF signaling in macrophages through the upregulation of TNF secretion and TNFR1 cell surface expression, and results in activation of caspase-3. Thus, IL-1β and downstream TNF production lead to caspase-dependent restriction of intracellular M. tuberculosis growth.
Perturbation of Hydrogen Bonding Networks over Supported Lipid Bilayers by Poly (Allylamine Hydrochloride) (2019)

&lt;div&gt;&lt;div&gt;&lt;div&gt;&lt;p&gt;Water is vital to many biochemical processes and is necessary for driving many fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation (SFG) spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine, PC) and anionic (phosphatidylglycerol, PG, and phosphatidylserine, PS) lipids as they are exposed to the common polycation poly (allylamine hydrochloride) (PAH) in 100 mM NaCl. We show that as the concentration of PAH is increased, the interfacial water molecules are irreversibly displaced and find that it requires 10 times more PAH to displace interfacial water molecules from membranes formed from purely zwitterionic lipids when compared to membranes that contain the anionic PG and PS lipids. This outcome is likely due to difference in (1) the energy with which water molecules are bound to the lipid headgroups, (2) the number of water molecules bound to the headgroups, which is related to the headgroup area, and (3) the electrostatic interactions between the PAH molecules and the negatively charged lipids that are favored when compared to the zwitterionic lipid headgroups. The findings presented here contribute to establishing causal relationships in nanotoxicology and to understanding, controlling, and predicting the initial steps that lead to the lysis of cells exposed to membrane disrupting polycations, or to transfection.&lt;/p&gt;&lt;/div&gt;&lt;/div&gt;&lt;/div&gt;
Optimization of 1.8V I/O circuits for performance, reliability at the 100 nm technology node (2003)

We describe the methodology and challenges in designing robust receiver and driver buffers in a state-of-the-art sub-100 nm CMOS technology. Issues addressed are the gate voltage limitations due to very thin gate oxides, channel hot carriers, process variability and design margins. The bi-directional buffer is 90 /spl mu/m/spl times/114 /spl mu/m in size and has a maximum speed of 150 MHz with a 50 ohm termination.
<title>Micromachining of optically transparent materials by laser ablation of a solution containing pyrene</title> (2001)

Optically transparent materials such as fused silica, quartz crystal, calcium fluoride, and fluorocarbon polymer were etched upon irradiation of organic solution containing pyrene with a conventional KrF or XeCl excimer laser. Threshold fluences for etching were 240 mJ/cm<SUP>2</SUP> for fused silica, 330 mJ/cm<SUP>2</SUP> for quartz crystal, 740 mJ/cm<SUP>2</SUP> for calcium fluoride, and 45 mJ/cm<SUP>2</SUP> for fluorocarbon polymer. These threshold values were remarkably low compared with those of direct ablation by using conventional lasers. Their etch rates remarkably depended on a concentration of pyrene: the etch rate became higher as the pyrene concentration increased. It means that pyrene molecules play an important role in this process. The mechanisms for this process is discussed by cyclic multiphotonic absorption of pyrene in the excited states, thermal relaxation, and formation of super-heated solution. As the results suggest, the process is based on the combination of two physical processes in the interface between the transparent materials and the liquid: one is a heating process by a super-heated liquid and the other is an attacking process by a high temperature and pressure vapor. The mechanism is also referred to thermal properties of materials.
Computer-controlled Raman spectrometer for time-resolved measurements in low-pressure gaseous samples (1986)

A spectrometer for measuring spontaneous Raman scattering in gaseous samples at pressures below 100 Pa (0.75 Torr) with nanosecond time resolution is presented. The apparatus was developed for studying intramolecular vibrational energy distributions in infrared multiphoton excited molecules and makes it possible to study the anti-Stokes Raman scattering from isolated molecules at pressures down to 14 Pa (110 mTorr). To achieve high sensitivity and time resolution simultaneously, spectral resolution (1 nm) is sacrificed. Because of the low level of the signals, the measurements are completely computer controlled. A detailed description of the apparatus, including the multichannel data-acquisition hardware and computer interface, is given.
Using Tsypkin's Approach for the Study of a Class of Mixed-Signal Nonlinear Systems (2006)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> An extension of Tsypkin's approach is proposed, in order to determine the values of the oscillation frequencies of mixed-signal nonlinear systems consisting of one possibly nonideal relay, one discrete-time block with a zeroth-order hold, and one continuous-time block. Several methods for determining the shape of the complex oscillations in some situations are then proposed and discussed. </para>
Folding Lennard-Jones proteins by a contact potential (1999)

We studied the possibility to approximate a Lennard-Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native) conformations were then identified by molecular dynamics. Then we turned to investigate whether one can find a pairwise contact potential, whose ground states are the contact maps associated with these native conformations. We show that such a requirement cannot be satisfied exactly, i.e., no such contact parameters exist. Nevertheless, we found that one can find contact energy parameters for which an energy minimization procedure, acting in the space of contact maps, yields maps whose corresponding structures are close to the native ones. Finally, we show that when these structures are used as the initial point of a molecular dynamics energy minimization process, the correct native folds are recovered with high probability.
m-Plane GaN-Based Blue Superluminescent Diodes Fabricated Using Selective Chemical Wet Etching (2009)

An m-plane-GaN based blue superluminescent diode was demonstrated utilizing the asymmetric chemical properties of the ±c facets. The non-reflecting -c plane facet, intended to prevent optical feedback along the c-axis waveguide, was fabricated by KOH wet etching. KOH selectively etched the cleaved -c facet leading to the formation of hexagonal pyramids without etching the +c facet. The peak wavelength and full width at half max were 439 and 9 nm at 315 mA, respectively, with an output power of 5 mW measured out of the +c facet.