gebhart/patrepeval huggingface dataset:
Entrapment of Carbon Dioxide in the Active Site of Carbonic Anhydrase II (2008)

The visualization at near atomic resolution of transient substrates in the active site of enzymes is fundamental to fully understanding their mechanism of action. Here we show the application of using CO(2)-pressurized, cryo-cooled crystals to capture the first step of CO(2) hydration catalyzed by the zinc-metalloenzyme human carbonic anhydrase II, the binding of substrate CO(2), for both the holo and the apo (without zinc) enzyme to 1.1A resolution. Until now, the feasibility of such a study was thought to be technically too challenging because of the low solubility of CO(2) and the fast turnover to bicarbonate by the enzyme (Liang, J. Y., and Lipscomb, W. N. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 3675-3679). These structures provide insight into the long hypothesized binding of CO(2) in a hydrophobic pocket at the active site and demonstrate that the zinc does not play a critical role in the binding or orientation of CO(2). This method may also have a much broader implication for the study of other enzymes for which CO(2) is a substrate or product and for the capturing of transient substrates and revealing hydrophobic pockets in proteins.
Luminance independent chromaticity preprocessing for HDR video coding (2016)

We introduce a constant luminance HDR video coding pipeline, which converts the source video to linear Y u'v' color space and applies a dedicated chromaticity transformation before encoding. This reduces perceivable color artifacts without modifying the core codec itself. We validate our approach by a user study that shows a significant improvement in perceived color quality at high compression rates without sacrificing luminance quality compared to current standard coding pipelines.
Adenophostins A and B: Potent agonists of inositol-1,4,5-trisphosphate receptor produced by Penicillium brevicompactum. Taxonomy, fermentation, isolation, physico-chemical and biological properties. (1993)

New inositol-1,4,5-trisphosphate (InsP3) agonists, adenophostins A(1) and B(2), were isolated from the culture broth of Penicillium brevicompactum SANK 11991 and SANK 12177. Its structures were related to adenine nucleotides. The agonistic activity of adenophostins A or B for binding to the InsP3 receptor was higher than InsP3 itself.
Service Flow Identifier in Proxy Mobile IPv6 (2010)

This document proposes extensions to Proxy Mobile IPv6 that allows
service flow identification and binding, and PMIP tunnels will be set
up based on the service flow granularity. Therefore, multiple service
flows of the mobile node can be separately controlled, e.g. QoS,
charging, traffic control, and provides the precondition of flow
mobility among multiple interfaces of the mobile node.
Inverse geometry for grating-based x-ray phase-contrast imaging (2009)

Phase-contrast imaging using conventional polychromatic x-ray sources and grating interferometers has been developed and demonstrated for x-ray energies up to 60 keV. Here, we conduct an analysis of possible grating configurations for this technique and present further geometrical arrangements not considered so far. An inverse interferometer geometry is investigated that offers significant advantages for grating fabrication and for the application of the method in computed tomography (CT) scanners. We derive and measure the interferometer’s angular sensitivity for both the inverse and the conventional configuration as a function of the sample position. Thereby, we show that both arrangements are equally sensitive and that the highest sensitivity is obtained, when the investigated object is close to the interferometer’s phase grating. We also discuss the question whether the sample should be placed in front of or behind the phase grating. For CT applications, we propose an inverse geometry with the sample position behind the phase grating.
IHOSR/extractive distillation for ethanol separation. [Distillation with intermediate heat pumps and sidestream return] (1984)

Separation of ethanol-water mixtures is difficult because: 1) fermentation-derived feeds are dilute (less than 10wt.% ethanol); 2) ethanol and water form a low-boiling azeotrope at approximately 95 wt.% ethanol; and 3) the internal reflux ratio is limited to relatively high values (approximately 0.86) by the tangential pinch at high ethanol concentrations. Work reviewed by Furter and Cook demonstrate that the vapor-liquid equilibrium (VLE) relationship can be altered by adding a variety of salts to eliminate both the azeotrope and the tangential pinch. However, extractive distillation with salt addition is not widely used for separating ethanol-water mixtures at present, partly because other methods can break the azeotrope. In addition elimination of the constraint of the internal reflux ratio by the tangential pinch offers little advantage when the ratio is constrained by the dilute character of the feed. This article discusses the technique which combines extractive distillation with an innovative approach to using heat pumps in distillation ''distillation with intermediate heat pumps and optimal sidestream return'' (IHOSR distillation). A particular embodiment of the IHOSR concept, described here, is useful for separating dilute feeds such as ethanol water mixtures. The combination of IHOSR distillation with extractive distillation appears to make it possible to more » take advantage of the relaxation of the tangential pinch accompanying salt addition while producing anhydrous ethanol. A system composed of a column with an IHOSR heat pump, an extractive distillation column, an evaporator, and a spray drier is proposed which includes extensive heat integration. Potential advantages of this system include the capability to produce anhydrous ethanol, and columns with fewer stages and smaller diameters than conventional systems for separating ethanol and water. « less
High-Speed Plasmonic-Silicon Modulator Driven by Epsilon-Near-zero Conductive Oxide (2020)

Transparent conductive oxides (TCOs) such as indium-tin oxide (ITO) have attracted increasing interests in integrated photonics and silicon photonics, owing to their large plasma dispersion and epsilon-near-zero (ENZ) effect. The nonlinear change of refractive index induced by free carrier modulation leads to a large electro-optic modulation with ultra-compact device footprint and unprecedented energy efficiency. However, high-speed modulation result is rare, mainly due to the lack of high-speed device design and fabrication quality. In this article, we characterize the fundamental electro-optic modulation structure consisting of Au/ITO/oxide/p-Si capacitor, showing that the property of ITO is greatly affected by the process condition. We also report an 8-μm-long hybrid plasmonic-silicon modulator driven by an ENZ ITO capacitor, achieving 100fJ/bit energy efficiency, 3.5 GHz modulation bandwidth, and 4.5 Gb/s data rate. The electro-absorption modulator covers a broad optical bandwidth from 1515 to 1580 nm wavelength. For future development of such modulators, we point out that by replacing ITO with higher mobility TCO materials, we can achieve 40 GHz modulation bandwidth and 0.4 fJ/bit energy efficiency using a 3-μm-long device.
Single-carrier space-time block-coded transmissions over frequency-selective fading channels (2003)

We study space-time block coding for single-carrier block transmissions over frequency-selective multipath fading channels. We propose novel transmission schemes that achieve a maximum diversity of order N/sub t/N/sub r/(L+1) in rich scattering environments, where N/sub t/ (N/sub r/) is the number of transmit (receive) antennas, and L is the order of the finite impulse response (FIR) channels. We show that linear receiver processing collects full antenna diversity, while the overall complexity remains comparable to that of single-antenna transmissions over frequency-selective channels. We develop transmissions enabling maximum-likelihood optimal decoding based on Viterbi's ( 1998) algorithm, as well as turbo decoding. With single receive and two transmit antennas, the proposed transmission format is capacity achieving. Simulation results demonstrate that joint exploitation of space-multipath diversity leads to significantly improved performance in the presence of frequency-selective fading channels.
A novel therapeutic approach combining human plasma‐derived Factors VIIa and X for haemophiliacs with inhibitors: evidence of a higher thrombin generation rate <i>in vitro</i> and more sustained haemostatic activity <i>in vivo</i> than obtained with Factor VIIa alone (2003)

The present study demonstrated that the combination of FVIIa and FX appeared to have a higher and more sustainable haemostatic potential than FVIIa alone, and less thrombogenicity than FEIBA. A therapeutic approach combining FVIIa and FX could be a promising and novel approach to compensate for the disadvantages of rFVIIa and FEIBA for haemophiliacs with inhibitors.
iPSC-Based Compound Screening and In Vitro Trials Identify a Synergistic Anti-amyloid β Combination for Alzheimer’s Disease (2017)

In the process of drug development, in vitro studies do not always adequately predict human-specific drug responsiveness in clinical trials. Here, we applied the advantage of human iPSC-derived neurons, which offer human-specific drug responsiveness, to screen and evaluate therapeutic candidates for Alzheimer's disease (AD). Using AD patient neurons with nearly 100% purity from iPSCs, we established a robust and reproducible assay for amyloid β peptide (Aβ), a pathogenic molecule in AD, and screened a pharmaceutical compound library. We acquired 27 Aβ-lowering screen hits, prioritized hits by chemical structure-based clustering, and selected 6 leading compounds. Next, to maximize the anti-Aβ effect, we selected a synergistic combination of bromocriptine, cromolyn, and topiramate as an anti-Aβ cocktail. Finally, using neurons from familial and sporadic AD patients, we found that the cocktail showed a significant and potent anti-Aβ effect on patient cells. This human iPSC-based platform promises to be useful for AD drug development.
Fast diffuse correlation spectroscopy (DCS) for non-invasive measurement of intracranial pressure (ICP) (Conference Presentation) (2017)

Intracranial pressure (ICP) monitoring has a key role in the management of neurosurgical and neurological injuries. Currently, the standard clinical monitoring of ICP requires an invasive transducer into the parenchymal tissue or the brain ventricle, with possibility of complications such as hemorrhage and infection. A non-invasive method for measuring ICP, would be highly preferable, as it would allow clinicians to promptly monitor ICP during transport and allow for monitoring in a larger number of patients. We have introduced diffuse correlation spectroscopy (DCS) as a non-invasive ICP monitor by fast measurement of pulsatile cerebral blood flow (CBF). The method is similar to Transcranial Doppler ultrasound (TCD), which derives ICP from the amplitude of the pulsatile cerebral blood flow velocity, with respect to the amplitude of the pulsatile arterial blood pressure. We believe DCS measurement is superior indicator of ICP than TCD estimation because DCS directly measures blood flow, not blood flow velocity, and the small cortical vessels measured by DCS are more susceptible to transmural pressure changes than the large vessels. For fast DCS measurements to recover pulsatile CBF we have developed a custom high-power long-coherent laser and a strategy for delivering it to the tissue within ANSI standards. We have also developed a custom FPGA-based correlator board, which facilitates DCS data acquisitions at 50-100 Hz. We have tested the feasibility of measuring pulsatile CBF and deriving ICP in two challenging scenarios: humans and rats. SNR is low in human adults due to large optode distances. It is similarly low in rats because the fast heart rate in this setting requires a high repetition rate.
Defectivity reduction in area selective atomic layer deposition by monolayer design (Conference Presentation) (2019)

Lithography faces an increasing number of challenges as errors in pattern overlay and placement become increasingly significant as scaling continues. The flexibility of removing a lithography step offers a significant advantage in fabrication as it has the potential to mitigate these errors. Furthermore, this strategy also relaxes design rules in semiconductor fabrication enabling concepts like self-alignment. The use of selective area atomic layer deposition with self-assembled monolayers that incorporate different side group functionalities was evaluated in the deposition of a sacrificial etch mask. Monolayers with weak supramolecular interactions between components (e.g. Van der Waals) were found to exhibit significant defectivity when depositing this material at and below 100nm feature sizes. The incorporation stronger supramolecular interacting groups in the monolayer design, such as hydrogen bonding units or pi-pi interactions, did not produce an added benefit over the weaker interacting components. However, incorporation of reactive moieties in the monolayer component enabled the subsequent reaction of a SAM surface generating a polymer at the surface and providing a more effective barrier, greatly reducing the number and types of defects observed in the selectively deposited ALD film. These reactive monolayers enabled the selective deposition of a film with critical dimensions as low as 15nm. The deposited film was then used as an effective barrier for standard isotropic etch chemistries, allowing the selective removal of a metal without degradation to the surrounding surface. This work enables selective area ALD as a technology by (1) the development of a material that dramatically reduces defectivity and (2) the demonstrated use of the selectively deposited film as an etch mask and its subsequent removal under mild conditions.
An <sup>18</sup>F-Labeled PSMA Ligand for PET/CT of Prostate Cancer: First-in-Humans Observational Study and Clinical Experience with <sup>18</sup>F-JK-PSMA-7 During the First Year of Application (2019)

In preclinical trials, the recently developed tracer 2-methoxy-<sup>18</sup>F-DCFPyL (<sup>18</sup>F-JK-prostate-specific membrane antigen [PSMA]-7) has shown favorable properties regarding clinical performance and radiochemical accessibility. The aim of this study was to evaluate the clinical utility of <sup>18</sup>F-JK-PSMA-7 for PET/CT imaging of patients with prostate cancer. <b>Methods:</b> In an Institutional Review Board-approved pilot study, the initial clinical utility of PET/CT imaging with <sup>18</sup>F-JK-PSMA-7 was directly compared with <sup>68</sup>Ga-PSMA-11 PET/CT in a group of 10 patients with prostate cancer. The 2 PSMA tracers were administered to each patient less than 3 wk apart. Next, we analyzed the data of 75 consecutive patients who had undergone clinical <sup>18</sup>F-JK-PSMA-7 PET/CT imaging for tumor localization of biochemical recurrence (BCR). <b>Results:</b> The pilot study in 10 patients who were examined with both PSMA tracers demonstrated that <sup>18</sup>F-JK-PSMA-7 was at least equivalent to <sup>68</sup>Ga-PSMA-11. All unequivocally <sup>68</sup>Ga-PSMA-11-positive lesions could be also detected using <sup>18</sup>F-JK-PSMA-7, and in 4 patients additional suspected PSMA-positive lesions were identified (1 patient changed from PSMA-negative to PSMA-positive). In patients with BCR (after prostatectomy or radiotherapy), the capacity of <sup>18</sup>F-JK-PSMA-7 PET/CT to detect at least one PSMA-positive lesion was 84.8%. The prostate-specific antigen (PSA)-stratified detection rate of <sup>18</sup>F-JK-PSMA-7 after prostatectomy varied among 54.5% (6/11 patients; PSA < 0.5 μg/L), 87.5% (14/16 patients; PSA 0.5-2 μg/L), and 90.9% (20/22 patients; PSA > 2 μg/L). <b>Conclusion:</b> The tracer <sup>18</sup>F-JK-PSMA-7 was found to be safe and clinically useful. We demonstrated that <sup>18</sup>F-JK-PSMA-7 was not inferior when directly compared with <sup>68</sup>Ga-PSMA-11 in a pilot study but indeed identified additional PSMA-avid suspected lesions in oligometastasized patients with BCR. In a subsequent analysis of a clinical cohort of BCR patients, <sup>18</sup>F-JK-PSMA-7 was useful in tumor localization. <sup>18</sup>F-JK-PSMA-7 is recommended for future prospective trials.
LignoForce System for the Recovery of Lignin from Black Liquor: Feedstock Options, Odor Profile, and Product Characterization (2016)

Lignin can be precipitated from kraft black liquor (BL) through the addition of an acidifying agent such as carbon dioxide or sulfuric acid. In most of the existing lignin precipitation processes that are using acid addition, sufficient acid is added to drop the pH of the black liquor from about 13–14 to about 9–10, followed by lignin particle coagulation, lignin slurry filtration, and lignin cake washing with sulfuric acid and water. At pH values of less than 11, the potential exists for the generation of significant quantities of totally reduced sulfur (TRS) compounds and other volatile sulfur species. Such compounds which include hydrogen sulfide, methyl mercaptan, dimethyl sulfide, and dimethyl disulfide are strongly odorous compounds with well-known negative effects on human health and other forms of life. To address this problem, as well as other problems associated with existing lignin recovery processes, FPInnovations and Noram recently developed a new process called the LignoForce System. This process employs a black liquor oxidation step to convert TRS compounds present in kraft black liquor to nonvolatile species. This paper discusses the applicability of the LignoForce System to several feedstock black liquors (e.g., softwood, hardwood, and eucalyptus) as well as the sulfur compound outgassing potential from various stages of this process compared to a reference case in which the black liquor was not oxidized. In addition, the emission of volatile sulfur and organic compounds from the two lignin products at different temperatures is discussed and compared.
An Experimental Testbed for Multi-Robot Tracking of Manifolds and Coherent Structures in Flows (2013)

In this paper, we describe the development of an experimental testbed capable of producing controllable ocean-like flows in a laboratory setting. The objective is to develop a testbed to evaluate multi-robot strategies for tracking manifolds and Lagrangian coherent structures (LCS) in the ocean. Recent theoretical results have shown that LCS coincide with minimum energy and minimum time optimal paths for autonomous vehicles in the ocean. Furthermore, knowledge of these structures enables the prediction and estimation of the underlying fluid dynamics. The testbed is a scaled flow tank capable of generating complex and controlled quasi-2D flow fields that exhibit wind-driven double-gyre flows. Particle image velocimetry (PIV) is used to extract the 2D surface velocities and the data is then processed to verify the existence of manifolds and Lagrangian coherent structures in the flow. The velocity data is then used to evaluate our previously proposed multi-robot LCS tracking strategy in simulation.
Analysis K-SVD: A Dictionary-Learning Algorithm for the Analysis Sparse Model (2012)

The synthesis-based sparse representation model for signals has drawn considerable interest in the past decade. Such a model assumes that the signal of interest can be decomposed as a linear combination of a few atoms from a given dictionary. In this paper we concentrate on an alternative, analysis-based model, where an analysis operator-hereafter referred to as the analysis dictionary-multiplies the signal, leading to a sparse outcome. Our goal is to learn the analysis dictionary from a set of examples. The approach taken is parallel and similar to the one adopted by the K-SVD algorithm that serves the corresponding problem in the synthesis model. We present the development of the algorithm steps: This includes tailored pursuit algorithms-the Backward Greedy and the Optimized Backward Greedy algorithms, and a penalty function that defines the objective for the dictionary update stage. We demonstrate the effectiveness of the proposed dictionary learning in several experiments, treating synthetic data and real images, and showing a successful and meaningful recovery of the analysis dictionary.
Conformational defects in high-strain, electrostrictive polymers (2003)

Alternative methodologies are sought whereby high-strain electrostrictive polymer can be generated without the need of electron-beam irradiation, which is expensive and difficult to reproduce. One of these alternative approaches has been the use of chlorinated P(VDF-TrFE) copolymers, which in the present paper are subsequently referred to as "terpolymers". To be converted into high-strain electrostrictive films, terpolymers do not need to be irradiated, a significant advantage. Like P(VDF-TrFE), the terpolymers retain considerable polarization due to the existence of polar crystalline regions, but these ferroelectric regions are short-range due to the presence of the chlorine atoms, which disrupt the long-range ferroelectric regions. In this paper, we present Fourier transform infrared spectroscopic evidence and computational results that strongly indicate that the chlorine atom does indeed favor formation of disordered crystalline regions.
Iridium‐Catalyzed C—H Coupling Reaction of Heteroaromatic Compounds with Bis(pinacolato)diboron: Regioselective Synthesis of Heteroarylboronates. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Development of a 1 kW PEM fuel cell power source (2001)

This article reports on the development of key components, specifications, configuration and operating characteristics of a hydrogen-fueled portable power source with a polymer electrolyte (membrane) fuel cell (PEFC or PEMFC). A 1 kW class fuel cell module operating on an exclusive method of internal humidification was developed for the power source. A DC/AC inverter, in which a general-purpose integrated power module (IPM) was used as a switching device for microprocessor-based power conversion control, was developed to save the cost of generating DC power output from the cell module. The power source supplies full power within 2 min from start-up, and is capable of generating rated 1 kW power for about 3 h, and even longer if the cylinders are replaced. This power source has been confirmed to offer a high power generation efficiency of 30% or higher in overall output range, yielding good-quality power with little noise.
Implementation and experiment of dual-mass vibratory gyroscope with high quality factor (2012)

The implementation of the dual-mass MEMS vibratory gyroscope in device-level vacuum packing was presented. The electrostatic actuation and capacitive sensing methods were adopted in electrical design of gyroscope. The self-resonance drive circuit with automatic gain control was employed in the drive closed-loop, and the open loop detect circuit was used. In order to reduce environment impact on the performances of gyroscope, real-time temperature compensation system was designed using Platinum resistor as temperature sensor. Experiment results show that the MEMS gyroscope can achieve the performances as follows: mechanical quality factor is above 100 000, the operating range is ±500°/s with scaling factor 21.453mV/°/s, nonlinearity and asymmetry error are better than 200ppm, and the 1σ bias stability <; 8°/h with the bandwidth over 100Hz. The complete MEMS gyroscope draws about 11mA under power supply ±12V, and the whole system volume is 31mm*31mm*12mm.