gebhart/patrepeval huggingface dataset:
Development of Sorbents for Extraction and Stabilization of Nucleic Acids (2016)

This effort focused on development of a combined storage and delivery system intended to offer much-needed stability to biomolecules, especially DNA and RNA. The goal was to provide stabilization methods for reagents and targets in order to allow for a wider range of applications through utilization of organized porous materials as scaffolds for their encapsulation. This report details the synthesis of solid support materials, selection of stabilization components, and development of methods for their application. Design considerations focused on control of interactions with the nucleic acids that result in degradation. Over the course of the effort, the potential for adsorption of RNA, DNA, and ssDNA onto porous organosilicate sorbents with and without additional stabilizing reagents was demonstrated. Improved binding capacities were achieved with sorbents using chemical functionalities rather than proteins and sugars. These sorbents were found to provide similar improvements in stability to the traditional stabilization compounds. The materials were further shown to provide capture and subsequent stabilization of targets from a complex solution.
All-optical regeneration of differential phase-shift keyed signals based on phase-sensitive amplification (2005)

All-optical regeneration of differential phase-shift keyed signals based on phase-sensitive amplification in a nonlinear fiber Sagnac interferometer is described. Nearly ideal phase regeneration can be achieved in the undepleted pump regime, with output differential phase noise limited only by fast fluctuations of the pump phase relative to the DPSK signal. Operating in the depleted pump regime offers the possibility of simultaneously regenerating both phase and amplitude information of DPSK signals while providing low noise, phase-sensitive gain.
Insights in Behavior of Variably Formulated Alginate-Based Microcapsules for Cell Transplantation (2015)

Alginate-based microencapsulation of live cells may offer the opportunity to treat chronic and degenerative disorders. So far, a thorough assessment of physical-chemical behavior of alginate-based microbeads remains cloudy. A disputed issue is which divalent cation to choose for a high performing alginate gelling process. Having selected, in our system, high mannuronic (M) enriched alginates, we studied different gelling cations and their combinations to determine their eventual influence on physical-chemical properties of the final microcapsules preparation, in vitro and in vivo. We have shown that used of ultrapure alginate allows for high biocompatibility of the formed microcapsules, regardless of gelation agents, while use of different gelling cations is associated with corresponding variable effects on the capsules' basic architecture, as originally reported in this work. However, only the final application which the capsules are destined to will ultimately guide the selection of the ideal, specific gelling divalent cations, since in principle there are no capsules that are better than others.
Metabolic Pathway for 2-Keto-<scp>l</scp>-gulonic Acid Formation in<i>Gluconohacter melanogenus</i>IFO 3293 (1990)

Journal Article Metabolic Pathway for 2-Keto-l-gulonic Acid Formation in Gluconohacter melanogenus IFO 3293 Get access Tatsuo Hoshino, Tatsuo Hoshino Department of Applied Microbiology, Nippon Roche Research Center, 200, Kajiwara, Kamakura, Kanagawa 247, Japan Search for other works by this author on: Oxford Academic Google Scholar Teruhide Sugisawa, Teruhide Sugisawa Department of Applied Microbiology, Nippon Roche Research Center, 200, Kajiwara, Kamakura, Kanagawa 247, Japan Search for other works by this author on: Oxford Academic Google Scholar Masaaki Tazoe, Masaaki Tazoe Department of Applied Microbiology, Nippon Roche Research Center, 200, Kajiwara, Kamakura, Kanagawa 247, Japan Search for other works by this author on: Oxford Academic Google Scholar Masako Shinjoh, Masako Shinjoh Department of Applied Microbiology, Nippon Roche Research Center, 200, Kajiwara, Kamakura, Kanagawa 247, Japan Search for other works by this author on: Oxford Academic Google Scholar Akiko Fujiwara Akiko Fujiwara Department of Applied Microbiology, Nippon Roche Research Center, 200, Kajiwara, Kamakura, Kanagawa 247, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 54, Issue 5, 1 May 1990, Pages 1211–1218, https://doi.org/10.1080/00021369.1990.10870126 Published: 01 May 1990 Article history Received: 20 November 1989 Published: 01 May 1990
Bismuth Perfluoroalkylphosphinates: New Catalysts for Application in Organic Syntheses (2016)

Commercially available BiPh<sub>3</sub> was treated with perfluoroalkylphosphinic acids [for example, (C<sub>2</sub> F<sub>5</sub> )<sub>2</sub> P(O)OH] to generate novel, highly Lewis acidic bismuth(III) perfluoroalkylphosphinates of the type Ph<sub>x</sub> Bi[R<sup>F</sup><sub>2</sub> PO<sub>2</sub> ]<sub>3-x</sub> (x=0, 1, 2) (R<sup>F</sup> =-C<sub>2</sub> F<sub>5</sub> , -C<sub>4</sub> F<sub>9</sub> ). The first bismuth(V) perfluoroalkylphosphinate, Ph<sub>3</sub> Bi[(C<sub>2</sub> F<sub>5</sub> )<sub>2</sub> PO<sub>2</sub> ]<sub>2</sub> , was synthesized from Ph<sub>3</sub> BiCl<sub>2</sub> and Ag[(C<sub>2</sub> F<sub>5</sub> )<sub>2</sub> PO<sub>2</sub> ]. Examples for the successful application of the catalytically active bismuth(III) and bismuth(V) phosphinates in carbon-carbon bond forming reactions, such as Friedel-Crafts acylation and alkylation, Diels-Alder, Strecker and Mannich reaction, are presented.
Commercial packaging of an optical microelectromechanical systems microphone. (2010)

A microelectromechanical systems (MEMS) optical microphone has been presented that measures the interference of light resulting from its passage through a diffraction grating and reflection from a vibrating diaphragm. [J. Acoust. Soc. Am. 122, (2007).] In this embodiment, both the diffractive optical element and the sensing diaphragm are micromachined on silicon. Additional system components include a semiconductor laser, photodiodes, and required readout electronics. In our efforts to commercialize this technology for hearing-aids and other applications, a goal has been set to achieve a microphone contained in a small surface mount package (occupying 2 × 2 × 1 mm3 volume), with ultra-low noise (15 dBA) and broad frequency response (20 Hz–20 kHz). Such a microphone would be consistent in size with the smallest MEMS microphones available today, but would have the noise performance characteristics of professional-audio microphones at least 10× larger in size and 10× more expensive to produce. This paper will present several unique challenges in our effort to develop the first surface mount packaged optical MEMS microphone, including the optical and acoustic design of the package. Dynamic models used for simulating frequency response and noise spectra of complete capsules will be presented and compared with measurements performed on recent prototypes.
Influence of Gas Feed Composition and Pressure on the Catalytic Conversion of CO<sub>2</sub>to Hydrocarbons Using a Traditional Cobalt-Based Fischer−Tropsch Catalyst (2009)

The hydrogenation of CO2 using a traditional Fischer−Tropsch Co−Pt/Al2O3 catalyst for the production of valuable hydrocarbon materials is investigated. The ability to direct product distribution was measured as a function of different feed gas ratios of H2 and CO2 (3:1, 2:1, and 1:1) as well as operating pressures (ranging from 450 to 150 psig). As the feed gas ratio was changed from 3:1 to 2:1 and 1:1, the production distribution shifted from methane toward higher chain hydrocarbons. This change in feed gas ratio is believed to lower the methanation ability of Co in favor of chain growth, with possibly two different active sites for methane and C2−C4 products. Furthermore, with decreasing pressure, the methane conversion drops slightly in favor of C2−C4 paraffins. Even though under certain reaction conditions product distribution can be shifted slightly away from the formation of methane, the catalyst studied behaves like a methanation catalyst in the hydrogenation of CO2.
Polymerization of Microtubule-associated Protein Tau under Near-physiological Conditions (1995)

Neurofibrillary tangles, which form in certain degenerating neurons in the brains of patients with Alzheimer's disease, are amassed from filaments having a straight or paired helical morphology. Solubilization of these filaments reveals that they are composed of the microtubule-associated protein tau. It has not previously been shown, however, that tau will assemble to form filaments of similar morphology under conditions representative of the intracellular environment. We have succeeded in forming such filaments using tau purified from porcine or rat microtubules. The filaments are relatively straight with narrowing at irregular intervals, and are about 10 nm wide, a morphology similar to that of straight filaments seen in Alzheimer's disease neurofibrillary tangles. At tau concentrations of 1-10 microM, in vitro assembly occurs at physiological pH, ionic strength, temperature, and reducing potential, and each one of these factors modulates the reaction. Assembly is judged to be only slowly reversible by the exponential rather than normal distribution of filament lengths, and by the limited disassembly observed under conditions which inhibit polymerization. Tau purified directly from whole brain tissue rather than from microtubules does not polymerize under conditions described in this report.
A Quantum Dot Swept Laser Source Based upon a Multisection Laser Device (2008)

An all semiconductor swept laser source relying on state filling in quantum dot lasers is discussed. The use of a multi-contact laser operating at the saturated gain of the ground state allows a new type of swept laser source to be realised. Analysis of the prototype device is made and design rules for optimised operation are discussed.
Broad-Spectrum Resistance to Different Geographic Strains of<i>Papaya ringspot virus</i>in Coat Protein Gene Transgenic Papaya (2003)

ABSTRACT Papaya ringspot virus (PRSV) is a major limiting factor for cultivation of papaya (Carica papaya) in tropical and subtropical areas throughout the world. Although the coat protein (CP) gene of PRSV has been transferred into papaya by particle bombardment and transgenic lines with high resistance to Hawaii strains have been obtained, they are susceptible to PRSV isolates outside of Hawaii. This strain-specific resistance limits the application of the transgenic lines in other areas of the world. In this investigation, the CP gene of a local strain isolated from Taiwan, designated PRSV YK, was transferred into papaya via Agrobacterium-mediated transformation. A total of 45 putative transgenic lines were obtained and the presence of the transgene in papaya was confirmed by polymerase chain reaction amplification. When the plants of transgenic lines were challenged with PRSV YK by mechanical inoculation, they showed different levels of resistance ranging from delay of symptom development to complete immunity. Molecular analysis of nine selected lines that exhibited different levels of resistance revealed that the expression level of the transgene is negatively correlated with the degree of resistance, suggesting that the resistance is manifested by a RNA-mediated mechanism. The segregation analysis showed that the transgene in the immune line 18-0-9 has an inheritance of two dominant loci and the other four highly resistant lines have a single dominant locus. Seven selected lines were tested further for resistance to three PRSV heterologous strains that originated in Hawaii, Thailand, and Mexico. Six of the seven lines showed varying degrees of resistance to the heterologous strains, and one line, 19-0-1, was immune not only to the homologous YK strain but also to the three heterologous strains. Thus, these CP-transgenic papaya lines with broad-spectrum resistance have great potential for use in Taiwan and other geographic areas to control PRSV.
Monoclonal Antibodies Targeting the Alpha-Exosite of Botulinum Neurotoxin Serotype/A Inhibit Catalytic Activity (2015)

The paralytic disease botulism is caused by botulinum neurotoxins (BoNT), multi-domain proteins containing a zinc endopeptidase that cleaves the cognate SNARE protein, thereby blocking acetylcholine neurotransmitter release. Antitoxins currently used to treat botulism neutralize circulating BoNT but cannot enter, bind to or neutralize BoNT that has already entered the neuron. The light chain endopeptidase domain (LC) of BoNT serotype A (BoNT/A) was targeted for generation of monoclonal antibodies (mAbs) that could reverse paralysis resulting from intoxication by BoNT/A. Single-chain variable fragment (scFv) libraries from immunized humans and mice were displayed on the surface of yeast, and 19 BoNT/A LC-specific mAbs were isolated by using fluorescence-activated cell sorting (FACS). Affinities of the mAbs for BoNT/A LC ranged from a KD value of 9.0×10-11 M to 3.53×10-8 M (mean KD 5.38×10-9 M and median KD 1.53×10-9 M), as determined by flow cytometry analysis. Eleven mAbs inhibited BoNT/A LC catalytic activity with IC50 values ranging from 8.3 ~73×10-9 M. The fine epitopes of selected mAbs were also mapped by alanine-scanning mutagenesis, revealing that the inhibitory mAbs bound the α-exosite region remote from the BoNT/A LC catalytic center. The results provide mAbs that could prove useful for intracellular reversal of paralysis post-intoxication and further define epitopes that could be targeted by small molecule inhibitors.
SLIDE: subspace-based line detection (1994)

An analogy is made between each straight line in an image and a planar propagating wavefront impinging on an array of sensors so as to obtain a mathematical model exploited in recent high resolution methods for direction-of-arrival estimation in sensor array processing. The new so-called SLIDE (subspace-based line detection) algorithm then exploits the spatial coherence between the contributions of each line in different rows of the image to enhance and distinguish a signal subspace that is defined by the desired line parameters. SLIDE yields closed-form and high resolution estimates for line parameters, and its computational complexity and storage requirements are far less than those of the standard method of the Hough transform. If unknown a priori, the number of lines is also estimated in the proposed technique. The signal representation employed in this formulation is also generalized to handle grey-scale images as well. The technique has also been generalized to fitting planes in 3-D images. Some practical issues of the proposed technique are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
5‐HT<sub>2B</sub> receptors play a key role in mediating the excitatory effects of 5‐HT in human colon <i>in vitro</i> (2002)

1. 5-Hydroxytryptamine (5-HT) is known to produce a number of different effects in the gastrointestinal tract of various species, and has been proposed to play a key role in a number of intestinal disorders in man, including irritable bowel syndrome (IBS), although the receptors involved have yet to be established. The aim of the present study was to investigate the distribution and function of 5-HT(2B) receptors in human colon, and to establish their possible role in the aetiology of IBS. 2. The distribution of 5-HT(2B) receptor mRNA and protein were investigated by quantitative RT - PCR, Western analysis and immunocytochemistry. High levels of both mRNA and protein for 5-HT(2B) receptors were found throughout the human gastrointestinal tract, and in particular in colon, where 5-HT(2B) receptors were found predominantly in the longitudinal and circular smooth muscle layers within the muscularis externa, and in the myenteric nerve plexus lying between these two layers. 3. Electrical field stimulation of longitudinal muscle preparations of human colon mounted in organ baths resulted in neuronally-mediated contractile responses, that were significantly potentiated by application of 5-HT (up to 10(-7) M), with a pEC(50) of 8.2 +/- 0.1 (n=49 donors). The response to 5-HT was inhibited by a number of selective 5-HT(2B) receptor antagonists. 4. This study has shown for the first time that, in contrast to animal studies, the excitatory effects of 5-HT in human colon are mediated by 5-HT(2B) receptors. It is proposed that these receptors contribute to the putative 5-HT-induced colonic smooth muscle hypersensitivity associated with IBS.
Numerical Simulation of Static and Dynamic Characteristics of Dual-Gate Metal Oxide Semiconductor Thyristor (1995)

Static and dynamic characteristics of a newly proposed vertical metal oxide semiconductor (MOS)-gated thyristor structure called the dual-gate MOS thyristor (DGMOT) are reported for the first time. The feature of this device is that IGBT mode turn-off is achieved due to a novel integration of a lateral n-metal oxide semiconductor field effect transistor (MOSFET) with the thyristor structure while the thyristor mode operation is achieved in the on state. It is possible to obtain a lower on-state voltage drop in the DGMOT while preserving its fast turn-off speed. It has been numerically demonstrated using 600 V forward blocking devices that the on-state voltage drop of 1.04 V and the turn-off time of 0.40 µ s are achieved. This result suggests that the DGMOT could be a superior alternative to the power bipolar junction transistor and may expand the application fields of the MOS-gated devices to the low-frequency operation circuit.
Advanced Geometric-Based Inter Prediction for Versatile Video Coding (2020)

Block-based partitioning is one of the fundamental techniques in video coding. Geometric-based block partitioning is a well-studied method to enable better spatial adaptation to the signal properties. This paper introduces the most recent proposal of advanced geometric-based inter prediction (GIP) made to the state-of-the-art are video coding standard - Versatile Video Coding (VVC). Implemented in the latest test model VTM-6.0 to generalize the existing triangle partition mode (TPM) and evaluated with the Joint Video Experts Team (JVET) Common Test Conditions (CTC) sequences, the proposed advanced GIP scheme provides luma BD-rate reduction of 0.56% for random access (RA) and 1.37% for low-delay (LB) test cases with 2% encoder runtime increase and negligible decoder runtime increase. Furthermore, BD-rate reductions up to 2.92% and 3.49% for RA and LB test cases can be achieved in the absence of multiple related VVC inter prediction tools.
Flexible reconfigurable multiplier blocks suitable for enhancing the architecture of FPGAs (2003)

A new architecture is proposed for configurable blocks which can be used to dynamically construct multipliers. An array of these blocks is capable of being configured to perform any 8m by 8n bits signed/unsigned binary multiplication. The new design is based on the radix-4 overlapped multiple-bit scanning algorithm. This yields excellent multiplication times, at the same time allowing multiply accumulate (MAC) operations, without modification. The new design is compared to our previous scheme, and shown to be both faster and require fewer transistors.
Towards a neurophysiological signature for fibromyalgia (2016)

Abstract Patients with fibromyalgia (FM) show characteristically enhanced unpleasantness to painful and nonpainful sensations accompanied by altered neural responses. The diagnostic potential of such neural alterations, including their sensitivity and specificity to FM (vs healthy controls) is unknown. We identify a brain signature that characterizes FM central pathophysiology at the neural systems level. We included 37 patients with FM and 35 matched healthy controls, and analyzed functional magnetic resonance imaging responses to (1) painful pressure and (2) nonpainful multisensory (visual–auditory–tactile) stimulation. We used machine-learning techniques to identify a brain-based FM signature. When exposed to the same painful stimuli, patients with FM showed greater neurologic pain signature (NPS; Wager et al., 2013. An fMRI-based neurologic signature of physical pain. N Engl J Med 2013;368:1388–97) responses. In addition, a new pain-related classifier (“FM-pain”) revealed augmented responses in sensory integration (insula/operculum) and self-referential (eg, medial prefrontal) regions in FM and reduced responses in the lateral frontal cortex. A “multisensory” classifier trained on nonpainful sensory stimulation revealed augmented responses in the insula/operculum, posterior cingulate, and medial prefrontal regions and reduced responses in the primary/secondary sensory cortices, basal ganglia, and cerebellum. Combined activity in the NPS, FM pain, and multisensory patterns classified patients vs controls with 92% sensitivity and 94% specificity in out-of-sample individuals. Enhanced NPS responses partly mediated mechanical hypersensitivity and correlated with depression and disability ( P uncorrected < 0.05); FM-pain and multisensory responses correlated with clinical pain ( P uncorrected < 0.05). The study provides initial characterization of individual patients with FM based on pathophysiological, symptom-related brain features. If replicated, these brain features may constitute objective neural targets for therapeutic interventions. The results establish a framework for assessing therapeutic mechanisms and predicting treatment response at the individual level.
Regulation of an <i>ATG7</i> - <i>beclin 1</i> Program of Autophagic Cell Death by Caspase-8 (2004)

Caspases play a central role in apoptosis, a well-studied pathway of programmed cell death. Other programs of death potentially involving necrosis and autophagy may exist, but their relation to apoptosis and mechanisms of regulation remains unclear. We define a new molecular pathway in which activation of the receptor-interacting protein (a serine-threonine kinase) and Jun amino-terminal kinase induced cell death with the morphology of autophagy. Autophagic death required the genes ATG7 and beclin 1 and was induced by caspase-8 inhibition. Clinical therapies involving caspase inhibitors may arrest apoptosis but also have the unanticipated effect of promoting autophagic cell death.