gebhart/patrepeval huggingface dataset:
Experimental and Computational Investigation of Au<sub>25</sub> Clusters and CO<sub>2</sub>: A Unique Interaction and Enhanced Electrocatalytic Activity (2012)

Atomically precise, inherently charged Au(25) clusters are an exciting prospect for promoting catalytically challenging reactions, and we have studied the interaction between CO(2) and Au(25). Experimental results indicate a reversible Au(25)-CO(2) interaction that produced spectroscopic and electrochemical changes similar to those seen with cluster oxidation. Density functional theory (DFT) modeling indicates these changes stem from a CO(2)-induced redistribution of charge within the cluster. Identification of this spontaneous coupling led to the application of Au(25) as a catalyst for the electrochemical reduction of CO(2) in aqueous media. Au(25) promoted the CO(2) → CO reaction within 90 mV of the formal potential (thermodynamic limit), representing an approximate 200-300 mV improvement over larger Au nanoparticles and bulk Au. Peak CO(2) conversion occurred at -1 V (vs RHE) with approximately 100% efficiency and a rate 7-700 times higher than that for larger Au catalysts and 10-100 times higher than those for current state-of-the-art processes.
Single-Particle Fluorescence Spectrometer for Ambient Aerosols (2003)

A fluorescence particle spectrometer (FPS) for real-time measurement of the fluorescence spectra of aerosol particles in the size range 1-10 w m diameter is reported. The prototype FPS has a sufficiently high sample rate (from 5 to 28 l/min for 3.5 w m to 11 w m diameter particles) to measure aerosol within buildings at practical rates (from 1 up to 600 particle fluorescence spectra per minute). Previously reported bioaerosol prototype detectors for measurement of single particle spectra (Pan et al., Opt. Lett ., 24, 116-118 (1999); Hill et al., Field Anal. Chem. Tech ., 3, 221-239 (1999)) were unable to sample the ambient environment; air containing particles had to be forced under pressure into a sample cell. In addition, sample rates were so small (less than 0.01 l/min) as to be impractical for most applications. The present design overcomes these deficiencies by the use of an airtight cell that highly concentrates micrometer-sized particles. A virtual impactor first concentrates aerosol particles, which are then drawn under negative pressure through an aerodynamic focusing nozzle in the inlet of the instrument, through the sample region, providing further concentration. The rate of particle spectra measured by the FPS increases significantly when the particle inlet is within a few meters of some common sources of indoor biological particles, e.g., a person coughing, sneezing, or rubbing his skin, or the presence of a dog. The spectra obtained have a variety of spectral shapes. The FPS may be useful in a variety of areas, e.g., in studying and monitoring airborne particles that cause diseases or allergies.
Optimization and Control of Dynamic Bioprocesses (2001)

For many applications, such as commodity chemical production, ore leaching, waste treatment, and environmental remediation, bioprocesses can be less expensive, more energy-efficient, and more environmentally friendly than conventional processes. The key to effective implementation of bioprocesses is rational design, optimization, and process control. We are applying the tools of intelligent systems to develop supervisory systems for the optimization and control of continuous, dynamic, and uncharacterized bioprocesses. We have designed, built, and evaluated hierarchical hardware and software systems for the control of microbial oxidation of soluble iron in a continuous stirred tank reactor. The supervisory control module uses stochastic learning to determine what system parameters (i.e., pH, dilution rate, and temperature) should be, based on the state of the system. An expert-based flow-rate controller optimizes reactor performance for each set of system parameters. Theoretically, high reactor conversion can be obtained much faster by varying these multiple parameters simultaneously as opposed to the traditional method of varying a single parameter at any given instance.
A new algorithm for bi-directional link self healing for arbitrary redundant networks (1998)

We present a new algorithm for automatic protection switching (APS) which permits loopback recovery from edge and node failures for arbitrary redundant networks. Loopback based APS recovery is desirable because it generally requires less spare bandwidth capacity than path based APS recovery. Our algorithm allows more flexible network design than algorithms which depend on specific topologies such as rings or interconnected rings.
Directed Molecular Evolution Reveals Gaussia Luciferase Variants with Enhanced Light Output Stability (2013)

Gaussia Luciferase (Gluc) has proven to be a powerful mammalian cell reporter for monitoring numerous biological processes in immunology, virology, oncology, and neuroscience. Current limitations of Gluc as a reporter include its emission of blue light, which is absorbed by mammalian tissues, limiting its use in vivo, and a flash-type bioluminescence reaction, making it unsuited for high-throughput applications. To overcome these limitations, a library of Gluc variants was generated using directed molecular evolution and screened for relative light output, a shift in emission spectrum, and glow-type light emission kinetics. Several variants with a 10-15 nm shift in their light emission peak were found. Further, a Gluc variant that catalyzes a glow-type bioluminescence reaction, suited for high-throughput applications, was also identified. These results indicate that molecular evolution could be used to modulate Gluc bioluminescence reaction characteristics.
A novel self-aligned highly reliable sidewall split-gate flash memory (2006)

A self-aligned sidewall split-gate Flash memory cell is fabricated with overerase immunity. Particularly, the sidewall corner of the floating-gate is deliberately rounded to release the electric field lines encountered in the poly-to-poly erase. The unit cell size of 12.7 F/sup 2/ (F is the feature size), formed in a 32-Mb NOR architecture, and the acceptable erase speed of 20 ms for block erase (512 K bits, 16 pages) are quite competitive. Endurance cycles up to 10/sup 5/ confirm the novel cell to be highly reliable as compared with the conventional source-side erase scheme. The bake experiment at 250/spl deg/C before and after program/erase cycles indicates the cell not only free of extrinsic defects in the manufacturing process but also experiencing excellent retention characteristics. Disturb effects during the programming and read-out operations are examined in detail and the operating conditions for disturbs inhibition are readily determined. We eventually elaborate on the differences between the proposed cell structure and existing ones, as well as on the NAND architecture application.
High temperature stability of transparent silica aerogels for solar thermal applications (2019)

Solar thermal energy systems combined with low-cost thermal storage provide a sustainable, dispatchable source of renewable energy. One approach to increase the attractiveness of these systems is to use high-performing solar transparent, thermally insulating silica aerogel to significantly increase efficiency. Several past works have proposed using these ultra-nanoporous materials to reduce thermal losses in the receiver, but only recently have aerogels reached the high solar transparency necessary to be considered for concentrated solar applications (&gt;97%). However, the durability and stability of optically transparent silica aerogels at the operating conditions of solar-thermal receivers has not been examined. Here, we investigate the high temperature stability of transparent silica aerogel for use in concentrated solar thermal energy applications. Transparent samples (visible transmission &gt;95% at 4 mm thickness) were annealed for several months at 400, 600, and 800 °C to investigate the relative change in nanostructure, solar transparency, and effective thermal conductivity. Results showed that at 400 and 600 °C, the temperature-dependent changes reach a plateau within 30 days of continuous annealing, but at 800 °C, samples are structurally unstable. A simple receiver efficiency model was used to show stable performance at 400 and 600 °C temperatures, even after months of exposure. This work validates that transparent silica aerogels can be used in solar thermal receivers below 800 °C, yielding appreciable increases in efficiency for solar energy harvesting operation.
Robustness of a Derivative-Free Adaptive Control Law (2014)

Although adaptive control theory offers mathematical tools to achieve required system performance without excessive dependence on modeling, its application to safety-critical systems can be limited by the presence of unmodeled dynamics. This paper examines the robustness to unmodeled dynamics of a recently developed derivative-free adaptive control law. In contrast to derivative-based adaptive laws, it is shown, using a Lyapunov–Krasovskii functional, that robustness to unmodeled dynamics is improved by increasing the adaptation gain. This is accomplished by including a bias term in the set of basis functions employed by the adaptive control law. It is shown that derivative-based adaptive laws do not offer the same advantage. Examples are presented that compare these two forms of adaptation in the context of sensitivity to unmodeled dynamics.
Plastic distributed feedback laser biosensor (2008)

A wide variety of optical resonator structures have been used for label-free detection of chemical compounds, biomolecules, and cells, and several approaches have been developed commercially for application in life science research, environmental monitoring, quality control testing, and diagnostic testing. Label-free resonant optical sensors generally detect shifts in resonant wavelength or coupling angle caused by the interaction between the target molecule and the evanescent portion of resonant modes. Active resonator sensors, such as the distributed feedback laser (DFB) biosensor demonstrated in this work, have been drawing special interest because they generate their own narrow linewidth stimulated emission, while retaining simple light coupling instrumentation. Altering the refractive index (RI) of the media exposed to the DFB laser surface or surface adsorption of biomolecules changes the effective RI associated with the resonant mode, and results in modulation of the stimulated emission wavelength. The DFB laser sensor biosensor was fabricated with organic material on a flexible plastic substrate using a large surface-area nanoreplica molding process.
<title>Two methods for increasing the depth of focus of imaging systems</title> (2003)

In this paper we describe two approaches for extending the depth of field in incoherent imaging system. The first one, a hybrid opto-digital incoherent imaging system, relies on an optical setup whereby the image is deliberately distorted, followed by a digital restoration stage. The second, an all-optical incoherent imaging system is based on a spatially code multiplexed multiple Fresnel lens mask, poisitioned in the lens aperture. Both provide a relatively high optical throughput and small contrast reduction, for an extremely wide range misfocus positions. For both cases, design considerations for an extended depth of field will be described. It is important to mention that both approaches are able to provide results in real time, thus enabling their usage in practical systems; yet the all-optical system presents a remarkable simplification.
High Resolution Light Microscopic Evaluation of Boar Semen Quality Sperm Cytoplasmic Droplet Retention in Relationship with Boar Fertility Parameters (2007)

The purpose of this study was to investigate the relationship between fertility and quantitative measures of boar semen quality, including various patterns of sperm cytoplasmic droplet (CD) retention, as determined by high power differential interference contrast (DIC) microscopy. A total of 116 ejaculates were collected from a nucleus herd of 18 Large White boars over an eight month period. Semen quality parameters were analyzed for each ejaculate by calculating the percentage of normal spermatozoa, spermatozoa possessing a CD in the proximal, distal, or distal midpiece reflex position, total spermatozoa with an attached cytoplasmic droplet, spermatozoa with non-CD related aberrations and total spermatozoa with abnormalities. Of the 116 ejaculates received, 71 ejaculates from 13 boars had corresponding fertility data from single-sire inseminations of multiparous sows. The fertility data included farrowing rate (FR) and total number born (TNB). The monthly FR encompassed one month before and one month after the date of semen collection. Detection of differences for fertility and semen quality parameters was performed by separating the boars into either an above-average or below-average group based on the mean FR (74.01 +/- 1.43%) or TNB (12.34 +/- 0.17) for the study. For FR, the boars in the below-average group had a significantly lower percentage of normal spermatozoa and significantly higher percentage of spermatozoa possessing distal CDs, total attached CDs and total abnormalities compared to the boars in the above-average group. Conversely, for TNB there were no significant differences between the above- and below-average groups for the semen quality parameters. These data suggest that the attached CD may negatively affect FR, but not TNB. The detection of relationships between the boar fertility parameters and the retention of the sperm CD after ejaculation, document the advantage of high power DIC microscopy in conventional semen evaluation.
Global incorporation of norleucine in place of methionine in cytochrome P450 BM‐3 heme domain increases peroxygenase activity (2003)

In this study we have replaced all 13 methionine residues in the cytochrome P450 BM-3 heme domain (463 amino acids) with the isosteric methionine analog norleucine. This experiment has provided a means of testing the functional limits of globally incorporating into an enzyme an unnatural amino acid in place of its natural analog, and also an efficient way to test whether inactivation during peroxide-driven P450 catalysis involves methionine oxidation. Although there was no increase in the stability of the P450 under standard reaction conditions (in 10 mM hydrogen peroxide), complete substitution with norleucine resulted in nearly two-fold-increased peroxygenase activity. Thermostability was significantly reduced. The fact that the enzyme can tolerate such extensive amino acid replacement suggests that we can engineer enzymes with unique chemical properties via incorporation of unnatural amino acids while retaining or improving catalytic properties. This system also provides a platform for directing enzyme evolution using an extended set of protein building blocks.
Orally Bioavailable Small Molecule Ketoamide‐Based Inhibitors of Cathepsin K (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
A newly developed anesthetic based on a unique chemical core (2019)

Intravenous anesthetic agents are associated with cardiovascular instability and poorly tolerated in patients with cardiovascular disease, trauma, or acute systemic illness. We hypothesized that a new class of intravenous (IV) anesthetic molecules that is highly selective for the slow type of γ-aminobutyric acid type A receptor (GABA<sub>A</sub>R) could have potent anesthetic efficacy with limited cardiovascular effects. Through in silico screening using our GABA<sub>A</sub>R model, we identified a class of lead compounds that are <i>N</i>-arylpyrrole derivatives. Electrophysiological analyses using both an in vitro expression system and intact rodent hippocampal brain slice recordings demonstrate a GABA<sub>A</sub>R-mediated mechanism. In vivo experiments also demonstrate overt anesthetic activity in both tadpoles and rats with a potency slightly greater than that of propofol. Unlike the clinically approved GABAergic anesthetic etomidate, the chemical structure of our <i>N</i>-arylpyrrole derivative is devoid of the chemical moieties producing adrenal suppression. Our class of compounds also shows minimal to no suppression of blood pressure, in marked contrast to the hemodynamic effects of propofol. These compounds are derived from chemical structures not previously associated with anesthesia and demonstrate that selective targeting of GABA<sub>A</sub>R-slow subtypes may eliminate the hemodynamic side effects associated with conventional IV anesthetics.
DSP-based transcoding of digital video signals with MPEG-2 format (2000)

MPEG-2 video coding is widely used in broadcasting and increasingly in studio applications. For reasons of limited storage and/or transmission capacity, it may be necessary to reduce the bit rate of MPEG-2 video bitstreams. We present an implementation of a frequency domain transcoder (FDTC) on a media processor which reduces the bit rate of an incoming video bitstream in real time. The FDTC has a low complexity and low memory requirements. A rate control with low delay provides a bitstream with constant bit rate (CBR) at the output, independent whether the input bit rate is variable (VBR) or constant (CBR). The FDTC achieves a better or same peak signal-to-noise ratio (PSNR) than a bulky cascade of a complete MPEG-2 video decoder and encoder.
Total Synthesis and Evaluation of [Ψ[CH<sub>2</sub>NH]Tpg<sup>4</sup>]Vancomycin Aglycon:  Reengineering Vancomycin for Dual <scp>d</scp>-Ala-<scp>d</scp>-Ala and <scp>d</scp>-Ala-<scp>d</scp>-Lac Binding (2006)

An effective synthesis of [Psi[CH(2)NH]Tpg(4)]vancomycin aglycon (5) is detailed in which the residue 4 amide carbonyl of vancomycin aglycon has been replaced with a methylene. This removal of a single atom was conducted to enhance binding to D-Ala-D-Lac, countering resistance endowed to bacteria that remodel their D-Ala-D-Ala peptidoglycan cell wall precursor by a similar single atom change (ester O for amide NH). Key elements of the approach include a synthesis of the modified vancomycin ABCD ring system featuring a reductive amination coupling of residues 4 and 5 for installation of the deep-seated amide modification, the first of two diaryl ether closures for formation of the modified CD ring system (76%, 2.5-3:1 kinetic atropodiastereoselectivity), a Suzuki coupling for installation of the hindered AB biaryl bond (90%) on which the atropisomer stereochemistry could be thermally adjusted, and a macrolactamization closure of the AB ring system (70%). Subsequent DE ring system introduction enlisted a room-temperature aromatic nucleophilic substitution reaction for formation of the remaining diaryl ether (86%, 6-7:1 kinetic atropodiastereoselectivity), completing the carbon skeleton of 5. Consistent with expectations and relative to the vancomycin aglycon, 5 exhibited a 40-fold increase in affinity for D-Ala-D-Lac (K(a) = 5.2 x 10(3) M(-1)) and a 35-fold reduction in affinity for D-Ala-D-Ala (K(a) = 4.8 x 10(3) M(-1)), providing a glycopeptide analogue with balanced, dual binding characteristics. Beautifully, 5 exhibited antimicrobial activity (MIC = 31 microg/mL) against a VanA-resistant organism that remodels its D-Ala-D-Ala cell wall precursor to d-Ala-d-Lac upon glycopeptide antibiotic challenge, displaying a potency that reflects these binding characteristics.
Wireless Performance Evaluation of Building Layouts: Closed-Form Computation of Figures of Merit (2021)

This paper presents a part of our ground-breaking work on evaluation of buildings in terms of wireless friendliness at the building-design stage. The main goal is to devise building design practices that provide for a good performance of wireless networks deployed in buildings. In this paper, the interference gain (IG) and power gain (PG) are defined as two figures of merit (FoM) of the wireless performance of buildings. The FoMs bridge the gap between building design and wireless communications industries. An approach to derive exact closed-form equations for these FoMs is proposed for the first time. The derived analytic expressions facilitate straightforward and more computationally efficient numerical evaluation of the proposed FoMs as compared to Monte Carlo simulations for well-known indoor propagation models. It is shown that the derived closed-form expression can be readily employed to evaluate the impact of building properties, such as the sizes and the aspect ratios (ARs) of rooms, on the wireless performance. The proposed approach sheds light to architects on evaluation and design of wireless-friendly building layouts.
On beyond hidden source estimates—Improving the output of blind source separation algorithms (2015)

In the presence of multiple simultaneously active acoustic sources, microphone response signals are typically additive mixtures of “acoustic images”—that is, filtered and delayed versions of hypothetical yet intangible “source signals.” Under certain conditions, Blind Source Separation (BSS) algorithms can “demix” sets of such microphone responses into output signals often called “Hidden Source Estimates” and characterized as estimates of those inaccessible source signals. However, despite the name of these algorithms and the characterization of their outputs, BSS algorithms generally do not actually reconstruct the original source signals. Indeed, it is not even clear that the notion of “source signal” is always well-defined. We argue that a valid BSS output can best be understood as an estimate of some unknown member of an entire equivalence class of related signals, and that certain members of these classes are much more useful and ontologically well-grounded than others. Notably, acoustic images are particularly interesting members of these equivalence classes. We present a method for converting arbitrary hidden source estimates into acoustic images, and explore the utility of enhancing BSS algorithms so that they output specific acoustic images rather than generic hidden source estimates.
A candidate serum biomarker for bladder pain syndrome/interstitial cystitis (2009)

Reliable diagnostic markers for Bladder Pain Syndrome/Interstitial Cystitis (IC) currently are not available. This study evaluated the feasibility of diagnosing IC in humans and domestic cats from the spectra of dried serum films (DSFs) using infrared microspectroscopy. Spectra were obtained from films from 29 humans and 34 domestic cats to create classification models using Soft Independent Modeling by Class Analogy (SIMCA). Ultrafiltration of serum improved discrimination capability. The classification models for both species successfully classified spectra based on condition (healthy/sick), and a different set of masked spectra correctly predicted the condition of 100% of the subjects. Classification required information from the 1500-1800 cm(-1) spectral region to discriminate between subjects with IC, other disorders, and healthy subjects. Analysis of cat samples using liquid chromatography-mass spectroscopy revealed differences in the concentration of tryptophan and its metabolites between healthy and affected cats. These results demonstrate the potential utility of infrared microspectroscopy to diagnose IC in both humans and cats.