gebhart/patrepeval huggingface dataset:
A metasurface-based diamond frequency converter using plasmonic nanogap resonators (2021)

Diamond has attracted great interest as an appealing material for various applications ranging from classical to quantum optics. To date, Raman lasers, single photon sources, quantum sensing and quantum communication have been demonstrated with integrated diamond devices. However, studies of the nonlinear optical properties of diamond have been limited, especially at the nanoscale. Here, a metasurface consisting of plasmonic nanogap cavities is used to enhance both χ(2) and χ(3) nonlinear optical processes in a wedge-shaped diamond slab with a thickness down to 12 nm. Multiple nonlinear processes were enhanced simultaneously due to the relaxation of phase-matching conditions in subwavelength plasmonic structures by matching two excitation wavelengths with the fundamental and second-order modes of the nanogap cavities. Specifically, third-harmonic generation (THG) and second-harmonic generation (SHG) are both enhanced 1.6 × 107-fold, while four-wave mixing is enhanced 3.0 × 105-fold compared to diamond without the metasurface. Even though diamond lacks a bulk χ(2) due to centrosymmetry, the observed SHG arises from the surface χ(2) of the diamond slab and is enhanced by the metasurface elements. The efficient, deeply subwavelength diamond frequency converter demonstrated in this work suggests an approach for conversion of color center emission to telecom wavelengths directly in diamond.
Recherche des radicaux dans les réactions de O et C-phénylation par les composés pentavalents du bismuth (1986)

L'objet de cette these est l'etude du mecanisme des reactions d’O- et C-phenylation de differents substrats par les reactifs pentavalents du bismuth. La premiere partie est consacree a la detection du radical phenyle au moyen de la spectroscopie RPE et du piegeage de radicaux dans les reactions de phenylation par les reactifs du bismuth, du plomb, de l'iode, du soufre et de l'antimoine. Dans la seconde partie, une etude cinetique de certaines reactions de Q- et f-phenylation, suivies par HPLC et/ou spectroscopie UV-visible est decrite. Quelques conclusions generales sur le mecanisme de f-phenylation sont avancees. Dans la troisieme partie, differents mecanismes sont presentes, permettant d'expliquer la formation des produits de couplage lors de la reaction des phenols encombres avec les reactifs du bismuth V. Une nouvelle reaction, la para-C-phenylation des phenols encombres est mise en evidence.
Nuclear Microscopy: A Novel Technique for Quantitative Imaging of Gadolinium Distribution within Tissue Sections (2009)

All clinically-approved and many novel gadolinium (Gd)-based contrast agents used to enhance signal intensity in magnetic resonance imaging (MRI) are optically silent. To verify MRI results, a "gold standard" that can map and quantify Gd down to the parts per million (ppm) levels is required. Nuclear microscopy is a relatively new technique that has this capability and is composed of a combination of three ion beam techniques: scanning transmission ion microscopy, Rutherford backscattering spectrometry, and particle induced X-ray emission used in conjunction with a high energy proton microprobe. In this proof-of-concept study, we show that in diseased aortic vessel walls obtained at 2 and 4 h after intravenous injection of the myeloperoxidase-sensitive MRI agent, bis-5-hydroxytryptamide-diethylenetriamine-pentaacetate gadolinium, there was a time-dependant Gd clearance (2 h = 18.86 ppm, 4 h = 8.65 ppm). As expected, the control animal, injected with the clinically-approved conventional agent diethylenetriamine-pentaacetate gadolinium and sacrificed 1 week after injection, revealed no significant residual Gd in the tissue. Similar to known in vivo Gd pharmacokinetics, we found that Gd concentration dropped by a factor of 2 in vessel wall tissue in 1.64 h. Further high-resolution studies revealed that Gd was relatively uniformly distributed, consistent with random agent diffusion. We conclude that nuclear microscopy is potentially very useful for validation studies involving Gd-based magnetic resonance contrast agents.
The Sin3a repressor complex is a master regulator of STAT transcriptional activity (2012)

Tyrosine phosphorylation is a hallmark for activation of STAT proteins, but their transcriptional activity also depends on other secondary modifications. Type I IFNs can activate both the ISGF3 (STAT1:STAT2:IRF9) complex and STAT3, but with cell-specific, selective triggering of only the ISGF3 transcriptional program. Following a genome-wide RNAi screen, we identified the SIN3 transcription regulator homolog A (Sin3a) as an important mediator of this STAT3-targeted transcriptional repression. Sin3a directly interacts with STAT3 and promotes its deacetylation. SIN3A silencing results in a prolonged nuclear retention of activated STAT3 and enhances its recruitment to the SOCS3 promoter, concomitant with histone hyperacetylation and enhanced STAT3-dependent transcription. Conversely, Sin3a is required for ISGF3-dependent gene transcription and for an efficient IFN-mediated antiviral protection against influenza A and hepatitis C viruses. The Sin3a complex therefore acts as a context-dependent ISGF3/STAT3 transcriptional switch.
Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics (2023)

Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide’s biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M–1 and a buffer-independent association constant of ∼6 × 106 M–1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy–entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn–Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.
Challenging benchmark for location discovery in ad hoc networks (2008)

We have created the first comprehensive and challenging benchmark data set for the ad-hoc location discovery (LD). The benchmark is a collection of representative real-life distance measurement data that establishes a common basis for understanding, characterization, evaluation and comparison of the LD algorithms and solvers. It is constructed using a novel analysis methodology that systematically establishes the difficulty of discovering the locations. Presence of measurement noise renders the problem difficult even in dense networks. The noise impacts the continuous optimization underlying the LD calculations. We focus on the difficulty of node localization in dense networks. In such networks, the location calculation is viewed as a continuous optimization problem instance with an objective function and a set of constraints. We devise a number of new metrics that evaluate the difficulty of the continuous optimization based on the data set properties. For the LD optimization, a fast simulation methodology is devised for rapid analysis of the sensitivity of the goodness with respect to the data set properties. We present a number of applications for the benchmark data and use it for evaluation and comparison of six popular LD algorithms. The LD benchmarks are publicly available at: http://www.ece.rice.edu/~mm7/benchLD/.
Modular Multilevel Converters: Recent Achievements and Challenges (2021)

The modular multilevel converter (MMC) is currently one of the power converter topologies which has attracted more research and development worldwide. Its features, such as high quality of voltages and currents, high modularity and high voltage rating, have made the MMC a very good option for several applications including high-voltage dc (HVdc) transmission, static compensators (STATCOMs), and motor drives. However, its unique features such as the large number of submodules, floating capacitor voltages, and circulating currents require a dedicated control system able to manage the terminal variables, as well as the internal variables with high dynamical performance. In this paper, a review of the research and development achieved during the last years on MMCs is shown, focusing on the challenges and proposed solutions for this power converter still faces in terms of modeling, control, reliability, power topologies, and new applications.
High-power truncated-inverted-pyramid (AlxGa1−x)0.5In0.5P/GaP light-emitting diodes exhibiting &gt;50% external quantum efficiency (1999)

A truncated-inverted-pyramid (TIP) chip geometry provides substantial improvement in light extraction efficiency over conventional AlGaInP/GaP chips of the same active junction area (∼0.25 mm2). The TIP geometry decreases the mean photon path-length within the crystal, and thus reduces the effects of internal loss mechanisms. By combining this improved device geometry with high-efficiency multiwell active layers, record-level performance for visible-spectrum light-emitting diodes is achieved. Peak efficiencies exceeding 100 lm/W are demonstrated (100 mA dc, 300 K) for orange-emitting (λp∼610 nm) devices, with a peak luminous flux of 60 lumens (350 mA dc, 300 K). In the red wavelength regime (λp∼650 nm), peak external quantum efficiencies of 55% and 60.9% are measured under direct current and pulsed operation, respectively (100 mA, 300 K).
Differential connectivity of splicing activators and repressors to the human spliceosome (2015)

This study demonstrates that combining in-silico modeling with biochemistry can significantly advance the understanding of structure and function relationships in the human spliceosome.
5-hydroxymethylcytosine Marks Mammalian Origins Acting as a Barrier to Replication (2019)

In most mammalian cells, DNA replication occurs once, and only once between cell divisions. Replication initiation is a highly regulated process with redundant mechanisms that prevent errant initiation events. In lower eukaryotes, replication is initiated from a defined consensus sequence, whereas a consensus sequence delineating mammalian origin of replication has not been identified. Here we show that 5-hydroxymethylcytosine (5hmC) is present at mammalian replication origins. Our data support the hypothesis that 5hmC has a role in cell cycle regulation. We show that 5hmC level is inversely proportional to proliferation; indeed, 5hmC negatively influences cell division by increasing the time a cell resides in G1. Our data suggest that 5hmC recruits replication-licensing factors, then is removed prior to or during origin firing. Later we propose that TET2, the enzyme catalyzing 5mC to 5hmC conversion, acts as barrier to rereplication. In a broader context, our results significantly advance the understating of 5hmC involvement in cell proliferation and disease states.
ChemInform Abstract: A Theoretical Study on the Mechanism of the Superacid‐Catalyzed Unimolecular Isomerization of n‐Alkanes and n‐Alkenes. Comparison Between ab initio and Density Functional Results (1997)

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.
Cleavage specificity on synthetic peptide substrates of human rhinovirus 2 proteinase 2A. (1992)

Proteinase 2A of human rhinovirus serotype 2 (HRV2 2A) was expressed in Escherichia coli and partially purified; the preparation was used to study various enzymatic parameters. Using a 16-amino acid peptide representing the native cleavage region of HRV2 2A, an apparent Km value of 5.4 x 10(-4) mol/liter was determined. A minimum of 9 amino acids (comprising residues P8 to P1') was necessary for cleavage to occur. Proteolysis of substituted peptides was highly tolerant toward changes at P1, P2', and P3' but an absolute requirement for glycine P1' and a high preference for threonine P2 was found. Furthermore, HRV2 2A only cleaved peptide substrates derived from other rhinovirus serotypes and poliovirus that possessed P2 Thr and P1' Gly. Thus, the sequence Thr-X-Gly may form the basis of the cellular cleavage site processed by rhinoviral 2As during viral replication. Studies with various inhibitors support the hypothesis that HRV2 2A belongs to a new class of cysteine proteinases.
Selective N-Terminal Acylation of Peptides and Proteins with Tunable Phenol Esters (2022)

Selective modification of peptides and proteins is of foremost importance for the development of biopharmaceuticals and exploring biochemical pathways, as well as other applications. Here, we present a study on the development of a general and easily applicable selective method for <i>N</i>-terminal acylation of biomolecules, applying a new type of phenol esters. Key to the success was the development of highly tunable phenol activators bearing in the ortho-position, sulfonic acid or sulfonamide, acting as a steric shield for hydrolysis, and electron-withdrawing groups in the other ortho- and para-position for controlling the reactivity of the activated phenol esters. A library of heptapeptides, testing all 20 natural amino acids positioned at the <i>N</i>-terminal, were acylated in a selective manner at the <i>N</i>-terminus. The majority showed high conversion and excellent <i>N</i><sup>α</sup>-selectivity. Several biologically relevant biomolecules, including DesB30 insulin and human growth hormone, could also be modified at the <i>N</i>-terminal in a highly selective way, exemplified by either a fluorophore or a fatty acid sidechain. Finally, taking advantage of the possibility to accurately adjust the reactivity of the phenol esters, we present a potential strategy for the construction of dual active biopharmaceuticals through the employment of a bifunctional acylation linker and demonstrate its use in the creation of a GLP-1 insulin analogue, coupled through the lysine residue of GLP-1 and the <i>N</i>-terminal Phe<sup>B1</sup> amine of DesB30 insulin.
Towards nanoscale resonant gas sensors (2010)

In this paper, we present preliminary results in the field of resonant Nano- Electro-Mechanical Systems (NEMS), where the gas/bio detection is performed by the frequency shift due to mass loading of the adsorbed analyte. The sensitivity of the resonant NEMS chemical sensors based on SOI-CMOSFET technology platform and a given sensor geometry is theoretically proven to be equal to 1 Hz/zeptogram in mass loading for the case of a novel detector circuit based on MOSFET transistor. The minimum frequency shift of 1 ppm is designed for the case of an readout consisting of a MEMS/NEMS based oscillator. Piezoresistive detection circuits performed in SOI- CMOSFET technology are also investigated due to their attractiveness for integrated resonant NEMS sensors. Surface functionalization for NO 2 detection with CNT moieties is described, in accordance with the HSAB theory. Also, localized functionalization with NH 2 self-assembled monolayer followed by biotin attachment or Au nanoparticles decoration is experimentally proven within SOI-CMOS technology. Novel reliability challenges due to Wan Der Waals and Casimir forces acting in the nanometer gaps between different parts are identified. Finally, the noise limitations for the minimum detectable mass in resonant NEMS are shown. The adsorption-desorption noise on the functionalized surface appears to be the most important, and this may be in agreement with the kinetic theory of gases giving us a first indication of the number collisions per second per our sensing surface, in the range of 2·10 9 .
ChemInform Abstract: Geneserine Hydrochloride. (1994)

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.
Treatment of refractory open-angle glaucoma using ultrasonic circular cyclocoagulation: a prospective case series (2014)

UC(3) procedure seems to be an effective and well tolerated method to reduce intraocular pressure in patients with primary open-angle glaucoma. Studies directly comparing the efficacy and safety of the UC(3) procedure with that of trabeculectomy or diode laser are needed.
Electrospray mass spectrometry: application of ion evaporation theory to amino acids (1991)

We describe the result of applying the ion evaporation theory to a series of amino acids. The very good correlation (r = 0.98) of the natural logarithms of protonated molecule intensities observed by electrospray with the difference between the hydration free energies of molecules and the gas-phase binding free energies of molecules and protons in amino acids is consistent with the ion evaporation model. It seems that the difference in the protonated molecule intensities of amino acids obtained by electrospray can be explained by a scheme in which protonated molecules in the liquid phase are extracted into the gas phase after a charged droplet is formed.
Network formation during cocure of phenolic resins with vinyl‐ester and epoxy‐amine systems for use in multifunctional composites (2004)

Abstract Traditionally, multilayered composites have been manufactured in multiple steps that involve the fabrication of each layer separately and the bonding them together by using adhesives or secondary bonding. More recently, manufacturing techniques have been developed that enable the manufacture of multilayered hybrid composite parts in a single step. In one such technique known as coinjection resin transfer molding (CIRTM), two or more resins are simultaneously injected into a mold filled with a stationary fiber bed. This method not only cuts down manufacturing costs and time, but also offers the potential of cocure of the adjacent thermosetting resins inside the mold, which could aid in the formation of a tougher interphase between the layers and improve long‐term durability. The advantages offered by coinjection are, however, dependent on the successful cocure of the resins involved, and hence, there exists a need to determine compatible resin systems for coinjection. By compatible, it is meant that the resins must cure when in contact with each other, have compatible cure cycles (i.e., cure temperature, cure time, etc.), and result in acceptable physical and mechanical properties. The most commonly used matrix resins are vinyl‐ester resins. The cure of vinyl‐ester resin was found to be severely limited by contact with phenolic resin. This necessitates an impermeable separation layer between phenolic and vinyl‐ester resins in CIRTM manufacture. A possible candidate for this separation layer was epoxy‐amine‐based prepregs or adhesive layers. Thus, the cocure of mixtures of phenolic with epoxy‐amine was studied, and it was found that phenolic resin significantly affects the cure of epoxy‐amines. A model to quantify the effect of phenolic resin on the cure of epoxy‐amines has been proposed. By using this model, the fraction of primary amine consumed by the phenolic can be estimated. It was found that increasing the initial amine concentration in the cocure reaction mixture leads to an increase in the epoxy conversion as well as the T g of the material. Therefore, it is recommended that, in cocure of epoxy‐amine and phenolic resins, the initial concentration of amine must be greater than the stoichiometric amount to compensate for the loss of amine to the phenolic resin. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 91: 3107–3119, 2004
Motion compensated generalized reconstruction for free‐breathing dynamic contrast‐enhanced MRI (2010)

Abstract The analysis of abdominal and thoracic dynamic contrast‐enhanced MRI is often impaired by artifacts and misregistration caused by physiological motion. Breath‐hold is too short to cover long acquisitions. A novel multipurpose reconstruction technique, entitled dynamic contrast‐enhanced generalized reconstruction by inversion of coupled systems, is presented. It performs respiratory motion compensation in terms of both motion artefact correction and registration. It comprises motion modeling and contrast‐change modeling. The method feeds on physiological signals and x ‐ f space properties of dynamic series to invert a coupled system of linear equations. The unknowns solved for represent the parameters for a linear nonrigid motion model and the parameters for a linear contrast‐change model based on B‐splines. Performance is demonstrated on myocardial perfusion imaging, on six simulated data sets and six clinical exams. The main purpose consists in removing motion‐induced errors from time–intensity curves, thus improving curve analysis and postprocessing in general. This method alleviates postprocessing difficulties in dynamic contrast‐enhanced MRI and opens new possibilities for dynamic contrast‐enhanced MRI analysis. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
Indium 111-labeled J591 anti-PSMA antibody for vascular targeted imaging in progressive solid tumors (2015)

J591 is a monoclonal antibody that targets the external domain of the prostate-specific membrane antigen (PSMA). Besides prostate cancer cells, it also targets the neovasculature of non-prostate solid tumors. We provide an analysis of the antibody mass-dose dependency of lesion uptake and normal tissue retention, together with an assessment of lesion detectability using 111In-J591 imaging, compared with conventional imaging in patients with a variety of solid tumors. Twenty patients in six cohorts received fixed amounts (5, 10, 20, 40, 60, and 100 mg) of J591 in a phase I trial. A maximum of four administrations per patient was given, with each administration separated by 3 weeks. All antibody administrations included 370 MBq (10 mCi) of 111In labeled to 2 mg of J591 via the chelating agent DOTA. Three whole body (WB) gamma camera scans with at least one SPECT scan, along with multiple WB count-rate measurements and blood samples, were obtained for all patients. The effect of escalating antibody mass on lesion uptake and normal tissue retention was evaluated using lesion, liver, serum, and WB residence times and ratios thereof for each treatment cycle. Lesion detectability using 111In-J591 imaging was compared to the standard imaging on a lesion-by-lesion basis. A total of 170 lesions in 20 patients were detected by standard or 111In-J591 imaging. 111In-J591 targeted both skeletal and soft tissue diseases in all tumor types. 111In-J591 imaging identified 74% (20/27) of skeletal lesions, 53% (18/34) of nodes, and 64% (70/109) of other soft tissue/organ lesions. There was increasing 111In-J591 uptake in lesions with increasing antibody mass-dose, coupled with decreasing retention in the liver for increments up to 20 mg, and no significant change at higher antibody mass. Radiolabeled J591 antibody has potential as a targeting agent for solid tumor vasculature and lesion detection. Bone and soft tissue lesions arising from tumors of diverse origin were targeted by the anti-PSMA antibody J591. For the detection of lesions in these tumors by J591 antibody scans, an antibody mass of 20 mg is adequate. The optimal time of imaging is 5 to 7 days post-injection.