gebhart/patrepeval huggingface dataset:
Release of Proteins from Intact Chloroplasts Induced by Reactive Oxygen Species during Biotic and Abiotic Stress (2013)

Plastids sustain life on this planet by providing food, feed, essential biomolecules and oxygen. Such diverse metabolic and biosynthetic functions require efficient communication between plastids and the nucleus. However, specific factors, especially large molecules, released from plastids that regulate nuclear genes have not yet been fully elucidated. When tobacco and lettuce transplastomic plants expressing GFP within chloroplasts, were challenged with Erwinia carotovora (biotic stress) or paraquat (abiotic stress), GFP was released into the cytoplasm. During this process GFP moves gradually towards the envelope, creating a central red zone of chlorophyll fluorescence. GFP was then gradually released from intact chloroplasts into the cytoplasm with an intact vacuole and no other visible cellular damage. Different stages of GFP release were observed inside the same cell with a few chloroplasts completely releasing GFP with detection of only red chlorophyll fluorescence or with no reduction in GFP fluorescence or transitional steps between these two phases. Time lapse imaging by confocal microscopy clearly identified sequence of these events. Intactness of chloroplasts during this process was evident from chlorophyll fluorescence emanated from thylakoid membranes and in vivo Chla fluorescence measurements (maximum quantum yield of photosystem II) made before or after infection with pathogens to evaluate their photosynthetic competence. Hydrogen peroxide and superoxide anion serve as signal molecules for generation of reactive oxygen species and Tiron, scavenger of superoxide anion, blocked release of GFP from chloroplasts. Significant increase in ion leakage in the presence of paraquat and light suggests changes in the chloroplast envelope to facilitate protein release. Release of GFP-RC101 (an antimicrobial peptide), which was triggered by Erwinia infection, ceased after conferring protection, further confirming this export phenomenon. These results suggest a novel signaling mechanism, especially for participation of chloroplast proteins (e.g. transcription factors) in retrograde signaling, thereby offering new opportunities to regulate pathways outside chloroplasts.
Gamma gene promoter and enhancer structure in Seattle variant of hereditary persistence of fetal hemoglobin (1988)

A variant of hereditary persistence of fetal hemoglobin (HPFH), first described in a patient from Seattle, was studied by structural analysis of the gamma-globin genes. A family study suggested that the determinant for this form of HPFH, in which the HbF contains both G gamma- and A gamma-globin chains, segregated with the beta S gene. No deletions or other abnormalities were detected in the fetal to adult globin gene region by genomic mapping studies. All four gamma-globin genes were isolated from a cosmid library, and allelic pairs of gamma- globin genes were distinguished by linkage to either the beta S- or beta A-globin gene. Nucleotide sequence analysis of the four gamma- globin gene promoters revealed a total of three discrepancies compared with a reference sequence, but these were judged unlikely to be the underlying determinants. Sequence analysis of the enhancer region located 3′ to the A gamma-globin gene from the putative HPFH chromosome revealed three base substitutions, whereas this region was normal in the A gamma-globin gene linked to the beta A gene. These data raise the possibility that an alteration of enhancer function rather than promoter function could be the basis for this condition.
Structural and electronic property changes of single-walled carbon nanotubes under pressure (2001)

The mechanical and electronic properties of single-walled carbon nanotubes have been studied under hydrostatic pressure up to 2 GPa. A high volume compressibility of 0.024 GPa−1 was obtained. The carbon nanotubes are polygonized slightly when they form bundles of hexagonal close-packed structure and the inter-tubular gap is smaller by 0.25 Å than the equilibrium spacing of graphite (002). Under high pressure, further polygonization occurs to accommodate the extra amount of volume reduction. Accompanying the polygonization, the band gap of the nanotubes increases with increasing pressure. A discontinuous change in electrical resistivity was observed at 1.5 GPa pressure, suggesting a phase transition had occurred when the polygonized nanotubes became elliptical in cross-section.
Publisher's Note: “Loop-gap microwave resonator for hybrid quantum systems” [Appl. Phys. Lett. 112, 204102 (2018)] (2018)

First Page
ChemInform Abstract: Selective N‐Alkylation of Primary Amines with Chloroacetamides under pH‐Controlled Aqueous Conditions. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Visualizing and quantifying drug uptake in skin (2017)

Fluorescence, Raman, and nonlinear optical imaging techniques offer subcellular resolution, rapid real-time 3D image acquisition, and the ability to quantitatively analyze the uptake of drugs into skin.
Role of Fluxes in Optimizing the Optical Properties of Sr0.95Si2O2N2:0.05Eu2+ Green-Emitting Phosphor (2013)

Chlorides of NH₄Cl and SrCl₂ and fluorides of AlF₃ and SrF₂ were added to raw materials acting as the flux for preparing the SrSi₂O₂N₂:Eu<sup>2+</sup> phosphor. The effects of the fluxes on the phase formation, particle morphology, particle size, and photoluminescence properties were investigated. The results revealed that particle size, particle morphology and photoluminescence intensity were largely dominated by the type of the flux material and its adding amount. The chloride-based flux was found to favor the formation of the SrSi₂O₂N₂:Eu<sup>2+</sup> phase. Among the chloride-based fluxes, the sample added with the SrCl₂ flux presented the narrow particle distribution and cleaner surface, with enhanced emission intensity and an increased external quantum efficiency by 68% and 22%, respectively, compared with those of the sample without any flux adding.
Chip-based sequencing nucleic acids (2023)

A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.
Polarity inversion of N-face GaN using an aluminum oxide interlayer (2010)

The polarity of GaN grown by plasma-assisted molecular beam epitaxy was inverted from N-face to Ga-face by inserting a composite AlN/aluminum oxide (AlOx) interlayer structure at the inversion interface. The change in polarity was verified in situ by reflection high energy electron diffraction via intensity transients and postgrowth surface reconstructions, and ex situ by convergent beam electron diffraction and etch studies in an aqueous potassium hydroxide solution. The inverted materials showed smooth surfaces and good electrical properties. AlGaN/GaN high electron mobility transistors fabricated on the inverted epilayers showed good dc and high frequency performance. A current-gain cutoff frequency (fT) of 21 GHz and maximum oscillation frequency (fmax) of 61 GHz were measured in devices with a gate length of 0.7 μm. These data compare favorably to those of Ga-face AlGaN/GaN devices with a similar structure grown on Si-face SiC substrates.
A Novel Framework for Elastography and Modulus Estimation: Integration of Tissue Mechanics with Imaging (2006)

The feasibility of optical coherence elastography is examined and the steps necessary for registration of optical coherence tomography (OCT) images are developed. We address the drawbacks of conventional techniques for solving the "image registration problem and inverse elasticity problem (IEP)" and then propose a new scheme for simultaneous solution of both problems. We have previously exploited the kinematics of incompressible tissue as a side-constraint term in OCT registration, and we now assess how the integration of FEM-derived mechanics directly within the registration process, improves the overall quality. The new technique estimates fewer unknowns and still it generates more realistic strain/modulus maps with less sensitivity to local minima. It is composed of a series of computationally-efficient and robust algorithms to create elastograms and elastic modulus maps and it does not need to utilize a multi resolution grid. Finally, we apply our scheme to a porcine aorta and demonstrate its ability in recovering lipid pools both in the strain map and in the elastic modulus image.
Temperature calibration of an on-chip relaxation oscillator (2017)

This work investigates the calibration procedure of a conventional relaxation oscillator. First, the numerical analysis is performed in MATLAB in order to evaluate the sensitivity of the procedure to the noise generated inside the chip and measurement system. Next, the theory is experimentally verified by calibrating four test chip samples designed and manufactured in 0.35-μm CMOS technology. The test chips are calibrated with two different test methods: the first method measures the output frequency in the entire temperature range from -40 to 150°C during 12 hours; the second method measures the output frequency from 30 to 60°C during 30 seconds. The proposed calibration methods exhibit the reduction of the frequency error by 18× and 8×, having the total post-calibration precision of ±0.1 % and ±0.22 %, respectively.
Quantum Metropolis sampling: an algorithm to simulate thermal systems with a quantum computer (2016)

The original motivation to build a quantum computer came from Feynman who envisaged a machine capable of simulating generic quantum mechanical systems, a task that is intractable for classical computers. Such a machine would have tremendous applications in all physical sciences, including condensed matter physics, chemistry, and high energy physics. Part of Feynman's challenge was met by Lloyd who showed how to approximately decompose the time-evolution operator of interacting quantum particles into a short sequence of elementary gates, suitable for operation on a quantum computer. However, this left open the more fundamental problem of how to simulate the equilibrium and static properties of quantum systems. This requires the preparation of ground and Gibb's states on a quantum computer. For classical systems, this problem is solved by the ubiquitous Metropolis algorithm, a method that basically acquired a monopoly for the simulation of interacting particles. In this talk, I will demonstrate that the corresponding quantum problem can be solved by a quantum Metropolis algorithm. This validates the quantum computer as a universal simulator, and proves that the so-called sign ! problem occurring in quantum Monte Carlo methods can be resolved with a quantum computer.
Loss of the N-Linked Glycan at Residue 173 of Human Parainfluenza Virus Type 1 Hemagglutinin-Neuraminidase Exposes a Second Receptor-Binding Site (2008)

BCX 2798 (4-azido-5-isobutyrylamino-2,3-didehydro-2,3,4,5-tetradeoxy-d-glycero-d-galacto-2-nonulopyranosic acid) effectively inhibited the activities of the hemagglutinin-neuraminidase (HN) of human parainfluenza viruses (hPIV) in vitro and protected mice from lethal infection with a recombinant Sendai virus whose HN was replaced with that of hPIV-1 (rSeV[hPIV-1HN]) (I. V. Alymova, G. Taylor, T. Takimoto, T. H. Lin., P. Chand, Y. S. Babu, C. Li, X. Xiong, and A. Portner, Antimicrob. Agents Chemother. 48:1495-1502, 2004). The ability of BCX 2798 to select drug-resistant variants in vivo was examined. A variant with an Asn-to-Ser mutation at residue 173 (N173S) in HN was recovered from mice after a second passage of rSeV(hPIV-1HN) in the presence of BCX 2798 (10 mg/kg of body weight daily). The N173S mutant remained sensitive to BCX 2798 in neuraminidase inhibition assays but was more than 10,000-fold less sensitive to the compound in hemagglutination inhibition tests than rSeV(hPIV-1HN). Its susceptibility to BCX 2798 in plaque reduction assays was reduced fivefold and did not differ from that of rSeV(hPIV-1HN) in mice. The N173S mutant failed to be efficiently eluted from erythrocytes and released from cells. It demonstrated reduced growth in cell culture and superior growth in mice. The results for gel electrophoresis analysis were consistent with the loss of the N-linked glycan at residue 173 in the mutant. Sequence and structural comparisons revealed that residue 173 on hPIV-1 HN is located close to the region of the second receptor-binding site identified in Newcastle disease virus HN. Our study suggests that the N-linked glycan at residue 173 masks a second receptor-binding site on hPIV-1 HN.
The Role of Morphology in Optically Switchable Transistors Based on a Photochromic Molecule/p‐Type Polymer Semiconductor Blend (2019)

Abstract The correlation between morphology and optoelectronic performance in organic thin‐film transistors based on blends of photochromic diarylethenes (DAE) and poly(3‐hexylthiophene) (P3HT) is investigated by varying molecular weight ( M w = 20–100 kDa) and regioregularity of the conjugated polymer as well as the temperature of thermal annealing (rt‐160 °C) in thin films. Semicrystalline architectures of P3HT/DAE blends comprise crystalline domains, ensuring efficient charge transport, and less aggregated regions, where DAEs are located as a result of their spontaneous expulsion from the crystalline domains during the self‐assembly. The best compromise between field‐effect mobility ( μ ) and switching capabilities is observed in blends containing P3HT with M w = 50 kDa, exhibiting μ as high as 1 × 10 −3 cm 2 V −1 s −1 combined with a &gt;50% photoswitching ratio. Higher or lower M w than 50 kDa are found to be detrimental for field‐effect mobility and to lead to reduced device current switchability. The microstructure of the regioregular P3HT blend is found to be sensitive to the thermal annealing temperature, with an increase in μ and a decrease in current modulation being observed as a response to the light‐stimulus likely due to an increased P3HT‐DAE segregation, partially hindering DAE photoisomerization. The findings demonstrate the paramount importance of fine tuning the structure and morphology of bicomponent films for leveraging the multifunctional nature of optoelectronic devices.
Theoretical Investigation of Arsenic Desorption from GaAs(001) Surfaces under an Atmosphere of Hydrogen (2003)

We investigate the desorption of As from GaAs(001) surfaces under an atmosphere of hydrogen using the ab initio pseudopotential method. The GaAs surface is (2×4) reconstructed with arsenic-monohydrogen bonds, arsenic-dihydrogen bonds, and Ga–Ga dimer bonds. We propose a mechanism for As desorption from the (001) surface in the presence of ambient hydrogen. The calculated activation energy is close to the experimental value for the (1×1) to (2×4) transition according to an in situ gravimetric (GM) method.
Selective Etching of Ti3AlC2 MAX Phases Using Quaternary Ammonium Fluorides Directly Yields Ti3C2Tz MXene Nanosheets: Implications for Energy Storage (2023)

MXenes have been studied extensively for energy storage and other applications and are synthesized by selectively etching the A element from a MAX phase using concentrated etchants. However, the hazards associated with using toxic chemicals in their synthesis remain a roadblock in scaling up MXene production. To address this challenge, a safer process is demonstrated, consisting of simultaneous etching and exfoliation using a mixture of tetramethylammonium fluoride tetrahydrate (TMAF) and hydrochloric acid (HCl) at room temperature. The large size of the quaternary ammonium ion promoted simultaneous intercalation and exfoliation during the etching of Ti3AlC2, directly resulting in Ti3C2Tz MXene nanosheets without requiring additional delamination steps. The ratio of surface terminal groups on the Ti3C2Tz MXenes also changed with the etching duration and the molarity of the etchant. This method results in MXene yields exceeding 30 wt % of the starting mass of the parent MAX phase. Ti3C2Tz MXenes synthesized by this new method are particularly well-suited for applications in energy storage since these Ti3C2Tz-based electrodes exhibit stable and reversible pseudocapacitive behavior, with specific capacitance values comparable to those reported in the literature. Moreover, these MXenes also exhibit a slower degradation rate in aqueous dispersions as compared to MXenes etched with traditional methods.
Neurohormonal, Endocrine, and Immune Dysregulation and Inflammation in Cardiorenal Syndrome (2019)

"Organ crosstalk" is the complex physiological communication between different body systems, and it is necessary for the optimal equilibrium and functioning of the organism. In particular, heart and kidney function is tightly connected, and interplay between these two organs occurs through a vast array of dynamic and bidirectional mechanisms. The term cardiorenal syndrome (CRS) indicates an interaction between the heart and kidneys in acute and chronic disease settings. In all types of CRS, multiple pathophysiological processes are implicated in the initiation and progression of organ injury. In addition to hemodynamic parameters, endothelial injury, immunological imbalance, cell death, inflammatory cascades, oxidative stress, neutrophil migration, leukocyte trafficking, caspase-mediated apoptosis, extracellular vesicles, small noncoding RNAs, and epigenetics play pivotal roles in the development of CRS. In this review, we will focus on neurohormonal, endocrine, and immune dysregulation and inflammation as mechanisms involved in the pathogenesis of CRS.
Mechanistic Aspects of Cationic Polymerization of Alkenes (1996)

COLEEN PUGH The University of Michigan, Ann Arbor, MichiganI. INTRODUCTIONBecause a polymerization comprises several elementary reactions, the full mechanistic description of cationic polymerizations of alkenes must discuss the mechanisms of initiation, propagation, transfer, termination, and other reactions such as isomerization and rearrangements. These ele­ mentary reactions correspond to generation of active sites, monomer con­ sumption, transfer of activity from one chain end to a transfer agent such as monomer or counterion, and termination of the kinetic chain, respec­ tively. Carbenium ions are involved in nearly all of these reactions and therefore will be discussed first. This discussion supplements the general information provided in Chapter 2, which is devoted to reactions of carbe­ nium ions with various nucleophiles. The vast mechanistic information provided by living/controlled carbocationic polymerizations is covered in Chapter 4 and will not be discussed here. Our discussion focuses on sys­ tems which often do not provide well-defined polymers because of slow initiation, transfer and/or termination. Nevertheless, analysis of the chem­ istry and kinetics of these elementary reactions has elucidated the advan­ tages and disadvantages of various initiating systems, which has subse­ quently led to the development of new “living” systems for the synthesis of well-defined polymers.
Search for a Higgs Portal Scalar Decaying to Electron-Positron Pairs in the MicroBooNE Detector (2021)

We present a search for the decays of a neutral scalar boson produced by kaons decaying at rest, in the context of the Higgs portal model, using the MicroBooNE detector. We analyze data triggered in time with the Fermilab NuMI neutrino beam spill, with an exposure of 1.93×10^{20} protons on target. We look for monoenergetic scalars that come from the direction of the NuMI hadron absorber, at a distance of 100 m from the detector, and decay to electron-positron pairs. We observe one candidate event, with a standard model background prediction of 1.9±0.8. We set an upper limit on the scalar-Higgs mixing angle of θ<(3.3-4.6)×10^{-4} at the 95% confidence level for scalar boson masses in the range (100-200) MeV/c^{2}. We exclude, at the 95% confidence level, the remaining model parameters required to explain the central value of a possible excess of K_{L}^{0}→π^{0}νν[over ¯] decays reported by the KOTO collaboration. We also provide a model-independent limit on a new boson X produced in K→πX decays and decaying to e^{+}e^{-}.
New Scanning-Spot Beam Reflectarray Antenna Design (2021)

In this report, a new design for a reflectarray antenna using mirror configuration will be proposed. By adapting to the two characteristics of a reflectarray antenna that changes beam directions using frequency and polarization, it is possible to realize a multi-scanning beam whose performance is as good as a conventional multi-spot beam with one reflecting mirror. Herein, we examine a scanning-spot beam that changes the beam direction by using frequency in the elevation direction and polarization in the azimuth direction in the Ka band. As a result, the proposed design efficiently covered the desired service area.
P450 SUBFAMILY CYP2J AND THEIR ROLE IN THE BIOACTIVATION OF ARACHIDONIC ACID IN EXTRAHEPATIC TISSUES* (1999)

Historically, there has been intense interest in P450 metabolic oxidation, peroxidation, and reduction of xenobiotics. More recently, there has been a growing appreciation for the role of P450s in the oxidation of lipophilic endobiotics, such as bile acids, fat-soluble vitamins, and eicosanoids. This review details the emerging CYP2J subfamily of P450s and their role as catalysts of arachidonic acid metabolism.
Reflectance sharing: predicting appearance from a sparse set of images of a known shape (2006)

Three-dimensional appearance models consisting of spatially varying reflectance functions defined on a known shape can be used in analysis-by-synthesis approaches to a number of visual tasks. The construction of these models requires the measurement of reflectance, and the problem of recovering spatially varying reflectance from images of known shape has drawn considerable interest. To date, existing methods rely on either: (1) low-dimensional (e.g., parametric) reflectance models, or (2) large data sets involving thousands of images (or more) per object. Appearance models based on the former have limited accuracy and generality since they require the selection of a specific reflectance model a priori, and while approaches based on the latter may be suitable for certain applications, they are generally too costly and cumbersome to be used for image analysis. We present an alternative approach that seeks to combine the benefits of existing methods by enabling the estimation of a nonparametric spatially varying reflectance function from a small number of images. We frame the problem as scattered-data interpolation in a mixed spatial and angular domain, and we present a theory demonstrating that the angular accuracy of a recovered reflectance function can be increased in exchange for a decrease in its spatial resolution. We also present a practical solution to this interpolation problem using a new representation of reflectance based on radial basis functions. This representation is evaluated experimentally by testing its ability to predict appearance under novel view and lighting conditions. Our results suggest that since reflectance typically varies slowly from point to point over much of an object's surface, we can often obtain a nonparametric reflectance function from a sparse set of images. In fact, in some cases, we can obtain reasonable results in the limiting case of only a single input image.