gebhart/patrepeval huggingface dataset:
Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding (2008)

Understanding the underlying physics of the binding of small-molecule ligands to protein active sites is a key objective of computational chemistry and biology. It is widely believed that displacement of water molecules from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying molecular physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient descriptor of the contribution of the solvent to the binding free energy of a small molecule and its associated receptor that captures the effects of the ligand displacing the solvent from the protein active site with atomic detail. This descriptor quantitatively predicts (R(2) = 0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates physical properties of the active-site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity relationship of its inhibitors.
Method of making radio frequency ion source antenna and such antenna (1985)

In the method, the radio frequency (rf) antenna is made by providing a clean coil made of copper tubing or other metal conductor, which is coated with a tacky organic binder, and then with a powdered glass frit, as by sprinkling the frit uniformly over the binder. The coil is then heated internally in an inert gas atmosphere, preferably by passing an electrical heating current along the coil. Initially, the coil is internally heated to about 200/sup 0/C to boil off the water from the binder, and then to about 750 to 850/sup 0/C to melt the glass frit, while also burning off the organic binder. The melted frit forms a molten glass coating on the metal coil, which is then cooled to solidify the glass, so that the metal coil is covered with a thin continuous homogeneous impervious glass coating of substantially uniform thickness. The glass coating affords complete electrical insulation and complete dielectric protection for the metal coil of the rf antenna, to withstand voltage breakdown and to prevent sputtering, while also doubling the plasma generating efficiency of the rf antenna, when energized with RF power in the vacuum chamber of an ion source for a particle acceleratormore » or the like. The glass frit preferably contains approximately 45% lead oxide.« less
Introduction of artificial pinning centre in {open_quotes}Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8}{close_quotes} ceramics (1994)

Considering the phase equilibrium diagram of the system Bi{sub 2}O{sub 3}-SrO-CaO-CuO, single phase {open_quotes}Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8}{close_quotes} ceramics have been transformed by a simple annealing procedure into multi phase samples. The transformation results in the formation of second phases and in an increase of the intra grain critical current density at 1 T of five times. This increase is believed to express improved pinning properties of the superconducting crystals. The prepared pinning centres are believed to be e.g. coherent precipitates (Guinier-Preston-zones) within the superconducting crystals.
Seabed classification of multibeam sonar images (2002)

Seabed images, from multibeam hydrographic systems or from single or multibeam sidescans, convey a lot of information about seabed type. Statistical processing of portions of images can generate features adequate for seabed classification that agree with both large-scale interpretation and fine details. The authors describe Quester Tangent's QTC MULTIVIEW/sup TM/ system for statistical seabed classification, and present several results. This software uses many statistical algorithms to generate over 130 statistical features for each image patch. Principal components analysis extracts the linear combinations of features that best describe the variance in a data set of images. The selection of statistical features is thereby optimized for a particular sediment discrimination problem, rather than a set of features selected for general use. Data points are then assigned to classes by an established clustering process. Examples demonstrate the limitations imposed by sonar physics and by design details of multibeam systems. For accurate classification results, these limitations require respect, either through compensation steps in the processing or excluding pings acquired under non-standard conditions.
Low-power (mW) nonlinearities of polarization maintaining fibers (2019)

Polarization maintaining (PM) fibers are meant to maintain linear polarization along a preferred axis. A PM fiber can be seen as the fiber version of a very high order waveplate, designed with different refractive indices along two orthogonal axes. It is shown that monitoring the polarization of initially circularly polarized light sent through a PM fiber, leads not only to new sensing methods, but also to power control, saturable absorption, and optical path stabilization. Even at peak power levels not exceeding a few mW, nonlinear transmission is detected, with time constants in the microsecond range.
Quantitative magnetic resonance imaging of ultrasound fields (2002)

A Magnetic Resonance Imaging (MRI) technique is proposed that can be used to directly image an ultrasound (US) field in tissue in a non-invasive manner. Through the use of an oscillating magnetic field gradient, spin phase is modulated in proportion to the displacement amplitude arising from the ultrasound field. Based on MR measurements of spin displacement, pressure and intensity can also be obtained. A 5 cm diameter, focused US transducer (515 kHz) was used to direct an US field into a small MR imaging cavity surrounded by a resonant field gradient coil (0.4 Tesla/meter) while imaging with a spin-echo sequence. This allowed the clear visualization of US induced motions of less than 10 nm. Based on MR measures of these motions, measurements of US pressure, intensity and speed-of-sound can also be obtained in tissue.
Self-regenerating giant hyaluronan polymer brushes (2019)

Tailoring interfaces with polymer brushes is a commonly used strategy to create functional materials for numerous applications. Existing methods are limited in brush thickness, the ability to generate high-density brushes of biopolymers, and the potential for regeneration. Here we introduce a scheme to synthesize ultra-thick regenerating hyaluronan polymer brushes using hyaluronan synthase. The platform provides a dynamic interface with tunable brush heights that extend up to 20 microns - two orders of magnitude thicker than standard brushes. The brushes are easily sculpted into micropatterned landscapes by photo-deactivation of the enzyme. Further, they provide a continuous source of megadalton hyaluronan or they can be covalently-stabilized to the surface. Stabilized brushes exhibit superb resistance to biofilms, yet are locally digested by fibroblasts. This brush technology provides opportunities in a range of arenas including regenerating tailorable biointerfaces for implants, wound healing or lubrication as well as fundamental studies of the glycocalyx and polymer physics.
Detection and quantification of coronary calcium from dual energy chest x‐rays: Phantom feasibility study (2017)

Simulations indicate that proper DECC processing can faithfully recover coronary calcium signals. Beam hardening, errors in scatter estimation, cardiac motion, calcium residual misregistration etc., are all manageable. Simulations are valuable as we continue to optimize DE coronary calcium image processing and quantitative analysis.
Transmissive and reflective optical bandpass filters using guided-mode resonance effects (1994)

Novel filters based on the guided-mode resonance properties of planar, dielectric waveguide gratings have received some attention in the literature recently. 1–5 This type of diffractive optical element can couple externally propagating waves to waveguide modes resulting in complete energy exchange between forward and backward propagating lightwaves. This efficient interaction is achieved by using a waveguide grating with high spatial frequency such that only the zero orders propagate, with all higher diffraction order cut off. It is the purpose of this paper to present new optical filter designs that are based on guided-mode resonance effects in planar dielectric structures. With near-ideal reflection and transmission filters achievable, it is believed that these will find numerous applications in many fields such as laser design, optical sensing, and spectroscopy.
PixLabeler: User Interface for Pixel-Level Labeling of Elements in Document Images (2009)

We present a user interface design for labeling elements in document images at a pixel level. Labels are represented by overlay color, which might map to such terms as ldquohandwritingrdquo, ldquomachine printrdquo, ldquographicsrdquo, etc. The primary purpose is to streamline processes for manual production of ground truth data, which is necessary for training algorithms and evaluating performance. Unlike general paint-type programs, the UI design is targeted specifically toward selection of collections of foreground pixels that are likely to be meaningful elements in a document image analysis context. Our implementation, called PixLabeler, is available for download and allows customized plug-ins for bootstrapping according to the labeling task.
Direct Synthesis of 1,5‐Disubstituted‐4‐magnesio‐1,2,3‐triazoles, Revisited. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
50   Ω characteristic impedance low-pass metal powder filters (2007)

We have fabricated several 50 omega characteristic impedance low-pass metal powder filters. The filters are made with bronze or copper metal powder with varying amounts of metal powder in a metal powder/epoxy mixture. Our goal is to make a filter with a characteristic impedance Z = 50 omega at frequencies up to 10 GHz. Using a 78% bronze powder/epoxy mixture in a suitable geometry, we achieved an impedance Z = 54 omega at 4.2 K, with a cutoff frequency fc approximately/= 0.3 GHz and an attenuation A = Vout/Vin=0.0001 (-80 dB) at 10 GHz. We also made several non-50 omega low-pass bronze powder filters with fc = 1 MHz and A = 0.0001 at 10 MHz. Fabrication details and performance data will be presented for both types of filter.
Region-Based Discriminative Feature Pooling for Scene Text Recognition (2014)

We present a new feature representation method for scene text recognition problem, particularly focusing on improving scene character recognition. Many existing methods rely on Histogram of Oriented Gradient (HOG) or part-based models, which do not span the feature space well for characters in natural scene images, especially given large variation in fonts with cluttered backgrounds. In this work, we propose a discriminative feature pooling method that automatically learns the most informative sub-regions of each scene character within a multi-class classification framework, whereas each sub-region seamlessly integrates a set of low-level image features through integral images. The proposed feature representation is compact, computationally efficient, and able to effectively model distinctive spatial structures of each individual character class. Extensive experiments conducted on challenging datasets (Chars74K, ICDAR'03, ICDAR'11, SVT) show that our method significantly outperforms existing methods on scene character classification and scene text recognition tasks.
Discrete multitone echo cancelation (1996)

Multicarrier transmission methods have long been known to optimize the performance of data transceivers on bandlimited communication channels. One form of multicarrier transmission, known as discrete multitone modulation (DMT), is particularly attractive for its ability to be implemented using efficient digital signal processing techniques. Given a basic DMT system, it is possible to increase the aggregate data rate with full-duplex transmission using echo cancelation. However, DMT echo cancelation at first appears difficult because of the computational complexity required in a straightforward implementation to cancel the cross-echoes produced by each carrier into every carrier. This paper presents high-speed echo cancelation techniques for full-duplex data transmission using DMT systems. The techniques estimate the echo with a method of fast convolution that combines a complex multiply per tone with a short convolution in the time domain. In addition, the frequency-domain update of the echo parameters consists of one complex multiply per tap. As a result, these techniques can achieve much lower complexity than that required by traditional single-carrier technique, such as the least mean square (LMS) algorithm. This approach has been implemented for asymmetric digital subscriber line (ADSL) applications.
Digitally synthesized beat frequency-multiplexed fluorescence lifetime spectroscopy (2014)

Frequency domain fluorescence lifetime imaging is a powerful technique that enables the observation of subtle changes in the molecular environment of a fluorescent probe. This technique works by measuring the phase delay between the optical emission and excitation of fluorophores as a function of modulation frequency. However, high-resolution measurements are time consuming, as the excitation modulation frequency must be swept, and faster low-resolution measurements at a single frequency are prone to large errors. Here, we present a low cost optical system for applications in real-time confocal lifetime imaging, which measures the phase vs. frequency spectrum without sweeping. Deemed Lifetime Imaging using Frequency-multiplexed Excitation (LIFE), this technique uses a digitally-synthesized radio frequency comb to drive an acousto-optic deflector, operated in a cat's-eye configuration, to produce a single laser excitation beam modulated at multiple beat frequencies. We demonstrate simultaneous fluorescence lifetime measurements at 10 frequencies over a bandwidth of 48 MHz, enabling high speed frequency domain lifetime analysis of single- and multi-component sample mixtures.
Permutation Correction and Speech Extraction Based on Split Spectrum Through FastICA (2003)

A blind source deconvolution method without indeterminacy of permutation and scaling is proposed by using notable features of split spectrum and locational information on signal sources. A method for extracting human speech exclusively is also proposed by taking advantage of the rule, the property of FastICA separates sources in order of large non-Gaussianity from their mixtures and the fact that human speeches are usually larger in non-Gaussianity than noises. The proposed methods have been veried by several experiments in a real room.
A1 Ions: Peptide-Specific and Intensity-Enhanced Fragment Ions for Accurate and Multiplexed Proteome Quantitation (2022)

Accurate proteome quantitation is of great significance to deeply understand various cellular and physiological processes. Since a1 ions, generated from dimethyl-labeled peptides, exhibited high formation efficiency (up to 99%) and enhanced intensities (2.34-fold by average) in tandem mass spectra, herein, we proposed an a1 ion-based proteome quantitation (APQ) method, which showed high quantitation accuracy (relative errors < 7%) and precision (median coefficients of variation ≤ 11%) even in a 20-fold dynamic range. Notably, due to the mass differences of a1 ions from peptides with different N-terminal amino acids, APQ demonstrated interference-free capacity by distinguishing target peptides from the coisolated ones. By designing an isobaric dimethyl labeling strategy, we achieved simultaneous proteome-wide measurements across up to eight samples. Using APQ to quantify the time-resolved proteomic profiles during a TGF-β-induced epithelial-mesenchymal transition, we found many differentially expressed proteins associated with fatty acid degradation, indicating that fatty acid metabolism reprogramming occurred during the process. The APQ method combines high quantitation accuracy with multiplexing capacity, which is suitable for deep mining and understanding of dynamic biological processes.
The <i>C</i>‐terminal domain of the toxic fragment of a <i>Bacillus thuringiensis</i> crystal protein determines receptor binding (1991)

The insecticidal crystal proteins of Bacillus thuringiensis show a high degree of specificity. In vitro binding studies with several crystal proteins demonstrated a correlation between toxicity and binding to receptors of larval midgut epithelial cells. In order to study the domain-function relationships of the toxic fragment, hybrid crystal proteins based on CryIA(b) and CryIC were constructed. Two out of 11 hybrid proteins constructed exhibited insecticidal activity. Both dispalyed an insecticidal spectrum similar to that of the parental crystal protein from which the C-terminal part of the toxic fragment originated. In addition, in vitro binding studies directly demonstrated the involvement of the C-terminal part of the toxic fragment in receptor binding. These results demonstrate that the C-terminal part of the toxic fragment determines specific receptor binding, which in turn determines, to a large extent, the insect specificity.
A 1.5dB NF, 5.8GHz CMOS low-noise amplifier with on-chip matching (2007)

In this paper we describe the design of an integrated 5.8 GIU low noise amplifier in 90 nm CMOS technology. The design is a tuned cascode LNA with on-chip matching that has a sufficiently low noise figure and high gain to enable high receiver sensitivity. The measured performance is NF=l.SdB, gain=28 dB, IIP3= -5 dBm and Pd=15m\V; and NfW.SdB, gain=23 dB, HP3=-17 dBm and Pd=8 m\V.
Chemically Intractable No More: In Vivo Incorporation of “Click”-Ready Fatty Acids into Poly-[(<i>R</i>)-3-hydroxyalkanoates] in <i>Escherichia coli</i> (2016)

Poly-[(<i>R</i>)-3-hydroxyalkanoate] biopolymers, or PHAs, are biocompatible and biodegradable polyesters that can be produced by diverse microbial strains. PHA polymers have found widespread uses in applications ranging from sustainable replacements of nonbiodegradable bulk-commodity plastics to biomaterials. However, further expansion into other markets and industries has generally been limited by the inability to chemically modify these polymers. Recently, our lab engineered <i>E. coli</i> LSBJ, a microbial strain able to produce PHA copolymers with controlled unit compositions from simple and accessible fatty acid feedstocks. We envisioned meaningfully broadening the application spectrum of these materials via production of chemically tractable PHA biopolymers containing "click"-ready chemical functionalities. With a myriad of applications in mind, in this study we demonstrate the synthesis and biopolymerization of a panel of ω-azido fatty acids and take the first exploratory steps toward demonstrating their conjugation via a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. The convenience of accessing these materials will open the door to new applications for functionalized PHA polymers.
Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction (1992)

Oligonucleotide probes which match consensus sequences of the repetitive extragenic palindromic (REP) element hybridize to genomic DNA of diverse bacterial species. Primers based on the REP sequence generate complex band patterns with genomic DNA in the polymerase chain reaction (PCR), a technique named REP-PCR. We used REP-PCR with genomic DNA to fingerprint 47 isolates of Citrobacter diversus. Previously, 37 were assigned electrophoretic types (ETs) by multilocus enzyme electrophoresis and 35 were evaluated by using outer membrane protein profiles. Fingerprints were compared by visual inspection and by similarity coefficients (SimCs) based on the number of common bands versus total bands between two given isolates. DNA fingerprints were highly similar visually for patient pairs and outbreak-related sets. SimCs for these were > or = 0.952. Fingerprints of isolates with different ETs generally were distinctive. Among 21 unrelated isolates representing 15 ETs, only 6 of 210 comparisons had SimCs of > or = 0.952. REP-PCR rapidly generated DNA fingerprints which were highly similar for epidemiologically linked isolates of C. diversus and distinct for previously characterized strains within this species. The ability of this method to discriminate between C. diversus isolates with the same biotype was similar to that of multilocus enzyme electrophoresis and outer membrane protein profiles. REP-PCR may be useful in evaluation of apparent outbreaks of this or other bacterial species which possess these extragenic, repetitive elements.
Discovery and Structure of a Potent and Highly Specific Blocker of Insect Calcium Channels (2001)

We have isolated a novel family of insect-selective neurotoxins that appear to be the most potent blockers of insect voltage-gated calcium channels reported to date. These toxins display exceptional phylogenetic specificity, with at least a 10,000-fold preference for insect versus vertebrate calcium channels. The structure of one of the toxins reveals a highly structured, disulfide-rich core and a structurally disordered C-terminal extension that is essential for channel blocking activity. Weak structural/functional homology with omega-agatoxin-IVA/B, the prototypic inhibitor of vertebrate P-type calcium channels, suggests that these two toxin families might share a similar mechanism of action despite their vastly different phylogenetic specificities.
Non-mechanical beam steering in the mid-wave infrared (2017)

The mid-wave infrared (MWIR) portion of the electromagnetic spectrum is critically important for a variety of applications such as LIDAR and chemical sensing. Concerning the latter, the MWIR is often referred to as the “molecular fingerprint” region owing to the fact that many molecules display distinctive vibrational absorptions in this region, making it useful for gas detection. To date, steering MWIR radiation typically required the use of mechanical devices such as gimbals, which are bulky, slow, power-hungry, and subject to mechanical failure. We present the first non-mechanical beam steerer capable of continuous angular tuning in the MWIR. These devices, based on refractive, electro-optic waveguides, provide angular steering in two dimensions without relying on moving parts. Previous work has demonstrated non-mechanical beam steering (NMBS) in the short-wave infrared (SWIR) and near infrared (NIR) using a waveguide in which a portion of the propagating light is evanescently coupled to a liquid crystal (LC) layer in which the refractive index is voltage-tuned. We have extended this NMBS technology into the MWIR by employing chalcogenide glass waveguides and LC materials that exhibit high MWIR transparency. As a result, we have observed continuous, 2D MWIR steering for the first time with a magnitude of 2.74° in-plane and 0.3° out-of-plane.