gebhart/patrepeval huggingface dataset:
Plant peroxisomes: biochemistry, cell biology and biotechnological applications. (2002)

In the two decades since the last comprehensive work on plant peroxisomes appeared, the scientific approaches employed in the study of plant biology have changed beyond all recognition. The accelerating pace of plant research in the post-genomic era is leading us to appreciate that peroxisomes have many important roles in plant cells, including reserve mobilisation, nitrogen assimilation, defence against stress, and metabolism of plant hormones, which are vital for productivity and normal plant development. Many plant scientists are finding, and will no doubt continue to find, that their own area of research is connected in some way to peroxisomes. Written by the leading experts in the field, this book surveys peroxisomal metabolic pathways, protein targeting and biogenesis of the organelle and prospects for the manipulation of peroxisomal function for biotechnological purposes. It aims to draw together the current state of the art as a convenient starting point for anyone, student or researcher, who wishes to know about plant peroxisomes
Electronic and Geometric Structure of a Trinuclear Mixed-Valence Copper(II,II,III) Cluster (1998)

The four-electron reduction of dioxygen to water by trinuclear copper clusters is of great biological significance. Recently we reported the crystal structure of a trinuclear model complex in which the three coppers provide the four electrons necessary to fully reduce dioxygen, generating two μ3-oxo bridges. This complex is best described as a localized, mixed-valence Cu(II,II,III) system which has C2v effective symmetry. The magnetic properties of this trinuclear cluster have been investigated by MCD and SQUID magnetic susceptibility. The two Cu(II) ions are found to be ferromagnetically coupled with a triplet/singlet splitting of 14 cm-1. Density functional calculations reproduce these geometric, electronic, and magnetic properties of the trinuclear cluster and provide insight into their origin. Since the trinuclear copper complex has a 3+ charge, the Cu3O2 core is one electron too oxidized to permit each atom to be in a preferred oxidation state (2+ for Cu and 2− for O). The extra hole in this highly oxidized Cu3O2 cluster is found to be localized on one Cu, which is therefore a Cu(III) ion, rather than on an O ligand (which would then be an oxyl) due to the strong stabilization of the oxo valence orbitals which derives from bridging to the Cu(II) centers. The communication between the coppers is weak, as it involves superexchange through the oxo bridges which provide nearly orthogonal orbital pathways between the copper ions. This leads to a ferromagnetic interaction between the two Cu(II) ions and weak electronic coupling between the Cu(III) and the Cu(II) ions. In the idealized D3h high symmetry limit which would be the favored geometry in the case of complete electronic delocalization, the triplet ground state is orbitally degenerate and subject to a large Jahn−Teller distortion [E‘ ⊗ e‘] toward the observed C2v structure. This combination of a large Jahn−Teller distortion and weak electronic coupling leads to localization of the Cu(III) on one metal center.
Motion without movement (1991)

We describe a technique for displaying patterns that appear to move continuously without changing their positions. The method uses a quadrature pair of oriented filters to vary the local phase, giving the sensation of motion. We have used this technique in various computer graphic and scientific visualization applications.
New Explicit Conditions of Elliptic Curve Traces for FR-Reduction (2001)

Elliptic curve cryptosystems are based on the elliptic curve discrete logarithm problem (ECDLP). If elliptic curve cryptosystems avoid FR-reduction and anomalous elliptic curve over F_q, then with current knowledge we can construct elliptic curve cryptosystems over a smaller definition field. ECDLP has an interesting property that the security deeply depends on elliptic curve traces rather than definition fields, which does not occur in the case of the discrete logarithm problem (DLP). Therefore it is important to characterize elliptic curve traces explicitly from the security point of view. As for FR-reduction, supersingular elliptic curves or elliptic curve E/F_q with trace 2 have been reported to be vulnerable. However unfortunately these have been only results that characterize elliptic curve traces explicitly for FR- and MOV-reductions. More importantly, the secure trace against FR-reduction has not been reported at all. Elliptic curves with the secure trace means that the reduced extension degree is always higher than a certain level. In this paper, we aim at characterizing elliptic curve traces by FR-reduction and investigate explicit conditions of traces vulnerable or secure against FR-reduction. We show new explicit conditions of elliptic curve traces for FR-reduction. We also present algorithms to construct such elliptic curves, which have relation to famous number theory problems.
Digital video stabilization based on hybrid filtering (2014)

The algorithm based on SIFT feature matching and Kalman filter has been used for digital video stabilization, it is efficient in many applications. However, video obtained by the method is still not stable. An improved scheme in motion filtering is proposed in this paper. The scheme is that global motion vector estimated by Kalman filter is filtered by an ideal low-pass filter with the Hanning window, here the process is called hybrid filtering. For the jitter video, the global motion vector obtained by SIFT feature matching with RANSAC is filtered by the hybrid filtering, and then the video image is compensated, finally, the stable video image sequence is obtained. The experimental results show that the method can eliminate jitter component more effective than one that only use SIFT feature matching and Kalman filter. The stable video image sequence will be obtained.
Cation channel TRPC6 activation of TLR4 in endothelial cells mediates sepsis‐induced acute lung injury (2012)

Loss of lung vascular endothelial cell (EC) barrier integrity and inflammation are main pathogenic features of acute lung injury (ALI). Activation of transient receptor potential canonical channels (TRPC) induces intracellular Ca 2+ signaling, which promotes lung vascular permeability. In addition, it is known that LPS binding to TLR4 is crucial in mediating lung inflammation. However, the fundamental question whether TLR4 and Ca 2+ signaling converge to induce lung vascular leakiness and inflammation is unknown. Here we show that deficiency of the TRPC6 isoform prevented TLR4‐mediated signaling in endothelial cells rendering Trpc6 − / − mice resistant to endotoxin‐ and sepsis‐induced lung injury. We observed that LPS‐mediated diacylglycerol generation was responsible for inducing TRPC6 activity which in turn activated non‐muscle myosin light chain kinase (MYLK) in endothelial cells. Activated MYLK promoted MyD88 and IRAK4 interaction leading to activation of TLR4 signaling. Our findings therefore identified TRPC6 as an essential switch that “turns on” LPS‐induced increase in lung vascular hyper‐permeability and lung inflammation. Thus, strategies aimed at blocking the instigating TRPC6 activity may hold the key to preventing acute lung injury.
APPLICATION OF HMBC AND HMQC-TOCSY NMR METHODS TO ASSIGN THE STRUCTURES OF BICYCLIC-PEPTIDE MIMETICS (1994)

Abstract The structures of representative bicyclic peptides are confirmed through the NMR methods of HMBC and HMQC-TOCSY. Complete assignment of proton and carbon resonances is afforded by these two-dimensional NMR methods. HMQC-TOCSY is especially useful for assigning spectra in molecules having extensive proton spin systems and in establishing connectivities between protonated carbons. Long-range proton-carbon connectivities obtained by HMBC confirm structure in molecules containing heteroatoms or non-protonated carbons that interrupt proton spin systems. Key Words: NMRbicyclic peptidesHMBCHMQC-TOCSY
ChemInform Abstract: Platinum‐Catalyzed 1,4‐Diboration of α,β‐Unsaturated Ketones. (1998)

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.
Ultrasound contrast agent behavior near the fragmentation threshold (2002)

Understanding the fragmentation process of ultrasound contrast agents is important in therapeutic ultrasound applications (such as ultrasound-enhanced drug delivery), as well as in certain imaging applications (such as "flash echo" imaging. In the fragmentation of Optison/sup TM/ microbubbles, our observations suggest that there are two pressure thresholds, a threshold which leads to shell rupture and the production of smaller daughter bubbles, and another one leading to the onset of sustained inertial cavitation activity. Between the shell-disruption threshold and sustained IC threshold is a region where intermittent inertial cavitation activity was detected. The acoustic signature of the intermittent region, the pressure level for the various thresholds, and the strength of the subsequent cavitation activity are all highly dependent on the acoustic pulse parameters.
Fluorescence detection and quantitation of recombinant proteins containing oligohistidine tag sequences directly in sodium dodecyl sulfate‐polyacrylamide gels (2003)

Two fluorophore-nitrilotriacetic acid conjugates, Pro-Q Sapphire 365 and Pro-Q Sapphire 488 oligohistidine gel stains, have been developed for the fluorescence detection of fusion proteins containing oligohistidine tags directly in sodium dodecyl sulfate polyacrylamide gels, without the requirement for electroblotting, reporter enzymes or secondary detection reagents. Pro-Q Sapphire 365 oligohistidine gel stain exhibits bright-blue fluorescence (emission maximum = 450 nm) when illuminated with UV-A or UV-B light from a standard ultraviolet transilluminator. Pro-Q Sapphire 488 oligohistidine gel stain exhibits bright-green fluorescence (emission maximum = 515 nm) when illuminated with visible light from a laser-based gel scanner equipped with a 470 nm second-harmonic generation (SHG) or 488 nm argon-ion laser source. Typically, 25-65 ng of oligohistidine-tagged fusion protein in whole cell lysates is detectable using either stain. After documenting the fluorescence signal from the Pro-Q Sapphire dyes, gels may be post-stained with the red-fluorescent SYPRO Ruby protein gel stain in order to reveal the total protein pattern.
Phylogenetic characterization of two transovarially transmitted endosymbionts of the bedbug Cimex lectularius (Heteroptera: Cimicidae) (1997)

Two different inherited bacterial symbionts from ovary tissue of the bedbug Cimex lectularius were characterized by gene amplification and sequencing analysis of their 16S rDNA gene. The first bacterium belongs to the Wolbachia subgroup of the alpha-Proteobacteria, the second is a member of the gamma-subdivision, and is closely related to the bacterial parasite of the leafhopper Euscelidius variegatus (BEV) which was shown to be capable of transovarial transmission. The high similarity (> 97%) between the C. lectularius symbiont and BEV indicates that these two microorganisms belong to the same lineage and share the ability to invade distant insect hosts to fulfill their symbiotic functions and to establish transovarial transmission to future generations.
Swellable Packers for Well Fracturing and Stimulation (2007)

Abstract Reactive element packers (REPs), sometimes referred to as swelling packers or self-energizing packers, offer a simple solution for multiple-zone open-hole completions. These packers are run into the well and begin to swell when they come into contact with various wellbore fluids, with the typical fluids of choice being water- or oil-based fluids. As the packers swell, they seal off the annulus between the liner/casing and the open-hole wellbore to provide isolation between zones with different pressures, or to simply shut off flow in the annulus and prevent migration of fines along the wellbore. As REP technology makes its mark in zonal isolation, application of the technology for fracturing and well stimulation is beginning to be explored. REPs used for frac'ing and stimulation offer a simplified method of breaking the desired zone into smaller sections without adding the cost and complexity that may result from using the traditional cement and perforating methods. This paper will discuss this new application for REPs. Functionality will be discussed, as will possible advantages and disadvantages of using the REP for well stimulation and fracturing. Key packer parameters will be reviewed to help demystify a seemingly infinite number of sizing possibilities. Then, initial testing to verify and validate the packer for this application will be discussed. Finally, this extensive test data will then be shown to validate a complex mathematical prediction model used to determine the REP's capabilities.
Synthesis of Functionally and Stereochemically Diverse Polymers via Ring-Opening Metathesis Polymerization of Derivatives of the Biomass-Derived Platform Molecule Levoglucosenone Produced at Industrial Scale (2020)

The commercially available, abundant and homochiral cellulose pyrolysis product levoglucosenone (LGO) together with the readily derived isolevoglucosenone (isoLGO) form, in a stereoselective manner, Diels–Alder adducts with cyclopentadiene (CPD). These ring-fused norbornene systems, each of which incorporates six centers of chirality and is pseudoenantiomeric in nature, undergo ring-opening metathesis polymerization (ROMP) in the presence of a range of ruthenium-based catalysts to produce polymers embodying both carbo- and heterocyclic motifs. Under such conditions, controlled polymerizations take place with target molecular weights matching the theoretical ones and with low dispersities (from 1.1 to 1.4) normally being observed. Reduction of the carbonyl group in the Diels–Alder adduct derived from LGO provides the corresponding epimeric alcohols that can be etherified and the resulting ethers, including fluorine-containing ones, also yield well-controlled polymers via ROMP. This thus represents an efficient method for producing stereochemically and functionally diverse polymers from a renewable feedstock available at an industrial scale. These polymerizations are living ones as demonstrated by the facile preparation of block copolymers from the two Diels–Alder adducts.
Prostaglandin D2 contributes to cisplatin-induced neuropathic pain in rats via DP2 receptor in the spinal cord (2020)

The findings presented here indicate that enhanced PGD<sup>2</sup> signaling, <i>via</i> upregulation of L-PGDS in the spinal cord, contributes to mechanical allodynia <i>via</i> DP2 receptors in a cisplatin-induced neuropathic pain model in rats, and that a blockade of DP2 receptor activation may present a novel therapeutic target for managing CIPN.
Multi-layered topological insulator for THz detection (2016)

We report THz detection with GeTe/Sb2Te3 multi-layered topological insulator. Photoconductive-type detector device was fabricated and THz-induced change of the current was observed when the bias voltage was applied and THz pulse was irradiated.
SmartHear: A Smartphone-Based Remote Microphone Hearing Assistive System Using Wireless Technologies (2015)

In this paper, we propose a new smartphone-based hearing assistive system (SmartHear) using wireless technologies for individuals with mild-to-moderate hearing loss (HL). Our system is a stigma-free implementation of the personal frequency modulation (FM) system for people with HL, with enhanced accessibility, affordability, and customization and extension potentials. The SmartHear system consists of a smartphone running a mobile application and a Bluetooth handset coupled with the smartphone. The voice of the speaker is picked up by the smartphone placed near the speaker and transmitted wirelessly to the Bluetooth handset placed near the listener for listening. The transmission of the voice signals over radio waves overcomes the reverberation and ambient noise effects, and thus, the listener can listen from a distance with better clarity and ease. Speech intelligibility experiments demonstrate the efficacy of the proposed SmartHear system, showing an average improvement of 0.2 speech intelligibility score (on the scale of 0-1) across four typical audiograms for mild-to-moderate HL and in four signal-to-noise ratio conditions. A user survey reveals the favorable user experience with SmartHear in various dimensions, as compared to the conventional FM system.
Synthesis and In Vitro Cytotoxicity Studies of Novel L-Tryptophan–Polyamide Conjugates and L-Tryptophan Dimers Linked With Aliphatic Chains and Polyamides (2003)

The synthesis and biological evaluation of novel L-tryptophan pyrrole, imidazole polyamide conjugates (16-21), L-tryptophan-glycosylated pyrrole polyamide conjugates (28-30), L-tryptophan dimers (37-42) with straight carbon links of varying length, and L-tryptophan dimers (68-73) linked with pyrrole and imidazole polyamide from both sides by a flexible methylene chain of variable length are described. The compounds were prepared with varying numbers of pyrrole- and/or imidazole-containing polyamides and glycosylated pyrrole polyamides to determine the structural requirements for optimal in vitro antitumor activity. The compounds listed in Table 1 have been evaluated in a three cell line, one dose primary anticancer assay. The compounds listed in Table 2 have been evaluated against nine panels of 60 human cancer cell lines including leukemia, non-small cell lung cancer, colon cancer, CNS cancer, melanoma, ovarian cancer, renal cancer, prostate cancer, and breast cancer. It is observed from the initial cytotoxic data (Table 1) that compounds 16-19, 28-30, 68-69, and 71-73 have varying cytotoxic potencies against the three cancer cell lines. It is also observed, from the biological data from Table 2 for compounds 20-21, 37-42, and 70 against the 60 different tumor cells, that the L-tryptophan dimers 37-42 linked by a different number of carbon chains are more active than the L-tryptophan dimers linked by pyrrole or imidazole polyamides. The cytotoxic potency in tryptophan dimers, linked by a different number of carbon atoms increased the number of carbons between the two L-tryptophan rings.
Anthraquinone polymer catalysts for alkaline delignification of lignocellulosic matter. Part 1. Syntheses and characterizations (2012)

Abstract Syntheses of two new styrene monomers are described, which bear a C4 and C3 chain ending with an anthraquinone (AQ) unit, in para and meta positions of the benzene ring. Both monomers were submitted to radical polymerization, and three linear AQ polystyrene (PS) copolymers ( CP-A , CP-B , and CP-C ) were prepared. The first two differed by the nature of the link between the AQ and the PS network. An ether oxide group in CP-B gave better accessibility of AQ to the lignin polymer in lignocellulosics, and the incorporation of carboxylic acid functions in CP-C increased its hydrophilicity. The copolymers synthesized were characterized by 1 H nuclear magnetic resonance (NMR), 13 C NMR, ultraviolet, and Fourier Transform Infrared (FTIR) spectroscopies, such as by size exclusion chromatography (SEC) and thermogravimetry (TG). A cross-linked copolymer ( CP-3D ) bearing AQ units (11.3%) was prepared by emulsion polymerization in the presence of divinylbenzene. Contrary to linear copolymers, the latter was insoluble in aqueous and organic solutions, and displayed remarkable thermal stability.
Absolute near-infrared oximetry for urology: a quantitative study of the tissue hemoglobin saturation before and after testicular torsion in a rabbit model (2009)

We present an experimental study on four rabbits to demonstrate the feasibility of near-infrared spectroscopy in the noninvasive assessment of testicular torsion. We used a multi-distance frequency-domain method, based on a fixed detector position and a 9-mm linear scan of the illumination optical fibers, to measure absolute values of pre- and post-operative testicular oxygen saturation. Unilateral testicular torsions (by 0&deg;, 540&deg; or 720&deg;) on experimental testes and contralateral sham surgeries (no torsion) on control testes were performed and studied. Our results showed (a) a consistent baseline absolute tissue oxygen saturation value of 78% &plusmn; 5%; (b) a comparable absolute saturation of 77% &plusmn; 6% on the control side (testes after sham surgery); and (c) a significantly lower tissue oxygen saturation of 36% &plusmn; 2% on the experimental side (testes after 540&deg; or 720&deg; torsion surgery). These results demonstrate the capability of frequency domain nearinfrared spectroscopy in the assessment of absolute testicular hemoglobin desaturation caused by torsion, and show promise as a potential method to serve as a complement to conventional color and spectral Doppler ultrasonography.
Regulation of Macrophage Polarization and Wound Healing (2012)

Background: Macrophages (Mφs) participate in wound healing by coordinating inflammatory and angiogenic processes. Mφs respond to environmental cues by adopting either “classically” activated (M1) proinflammatory or “alternatively” activated (M2a, M2b, M2c, M2d) wound healing phenotypes. The Problem: Mφ polarization is essential for wound healing and aberrations in this process are linked to several pathologies. It is important to elucidate molecular mechanisms underlying Mφ polarization. Basic/Clinical Science Advances: Mφs are categorized as proinflammatory (M1) or anti-inflammatory/wound healing (M2). M1 Mφs are observed in initial tissue damage responses, are induced by exogenous pathogen-associated molecular patterns or endogenous damage-associated molecular patterns, and exhibit increased phagocytosis and pro-inflammatory cytokine production, facilitating innate immunity and wound debridement. M2 Mφs predominate later in repair, express vascular endothelial growth factor, transforming growth factor beta, and interleukin 10 (IL-10), are activated by varied stimuli, assist in the resolution of inflammation, and promote tissue formation and remodeling. Recent work has characterized a novel “M2d” phenotype resulting from adenosine-dependent “switching” of M1 Mφs that exhibits a pattern of marker expression that is distinct from canonical IL-4/IL-13–dependent M2a Mφs. Recent studies have demonstrated important roles for specific transcriptional elements in M1 and M2a Mφ polarization, notably members of the interferon regulatory factor family interferon regulatory factor 5 (IRF5) and IRF4, respectively. The role of these IRFs in M2d polarization and wound healing remains to be determined. Clinical Care Relevance: Knowledge of microenvironmental signals and molecular mechanisms that mediate Mφ polarization should permit their manipulation to regulate important physiological processes and resolve pathological conditions. Conclusion: Proper Mφ polarization is essential to effective wound healing, and distinct phenotypes, such as the angiogenic M2d Mφ, may be of critical importance to this process. The IRF5 transcription factor has been shown to play a key role in M1 Mφ activation and the Jumonji domain containing-3-IRF4 pathway has been implicated in M2 Mφ activation.