gebhart/patrepeval huggingface dataset:
Cloning, nucleotide sequence, and expression of Achromobacter protease I gene (1989)

Achromobacter protease I (API) is a lysine-specific serine protease which hydrolyzes specifically the lysyl peptide bond. A gene coding for API was cloned from Achromobacter lyticus M497-1. Nucleotide sequence of the cloned DNA fragment revealed that the gene coded for a single polypeptide chain of 653 amino acids. The N-terminal 205 amino acids, including signal peptide and the threonine/serine-rich C-terminal 180 amino acids are flanking the 268 amino acid-mature protein which was identified by protein sequencing. Escherichia coli carrying a plasmid containing the cloned API gene overproduced and secreted a protein of Mr 50,000 (API') into the periplasm. This protein exhibited a distinct endopeptidase activity specific for lysyl bonds as well. The N-terminal amino acid sequence of API' was the same as mature API, suggesting that the enzyme retained the C-terminal extended peptide chain. The present experiments indicate that API, an extracellular protease produced by gram-negative bacteria, is synthesized in vivo as a precursor protein bearing long extended peptide chains at both N and C termini.
Efficacy of Experimental Animal and Vegetable Oil-Emulsion Vaccines for Newcastle Disease and Avian Influenza (1993)

Acceptable oil-emulsion vaccines were sought to replace mineral oil-emulsion vaccines that, by regulations, require a 42-day minimum holding period for poultry between injection and slaughter for consumption. Water-in-oil emulsions were prepared using animal or vegetable oils in a ratio of 4 parts oil to 1 part Newcastle disease or avian influenza aqueous antigen. Beeswax particles suspended in the oil at the 5% or 10% level (wt:vol) served as the oil-phase surfactant. Hemagglutination-inhibition titers induced by mineral-oil vaccines were not significantly different from those induced by the most efficacious formulations prepared from animal and vegetable oils. Tissue reaction from injection of animal- and vegetable-oil vaccines was less than that induced by mineral-oil vaccines. An inactivated avian influenza vaccine formulated from peanut oil induced protection against morbidity and death when vaccinated chickens were challenged with a virulent isolate of avian influenza virus.
A Simpler and More Generalizable Story Detector using Verb and Character Features (2017)

Story detection is the task of determining whether or not a unit of text contains a story. Prior approaches achieved a maximum performance of 0.66 F 1 , and did not generalize well across different corpora. We present a new state-of-the-art detector that achieves a maximum performance of 0.75 F 1 (a 14% improvement), with significantly greater generalizability than previous work. In particular, our detector achieves performance above 0.70 F 1 across a variety of combinations of lexically different corpora for training and testing, as well as dramatic improvements (up to 4,000%) in performance when trained on a small, disfluent data set. The new detector uses two basic types of features-ones related to events, and ones related to characters-totaling 283 specific features overall; previous detectors used tens of thousands of features, and so this detector represents a significant simplification along with increased performance.
Interaction of mitochondrial fission factor with dynamin related protein 1 governs physiological mitochondrial function in vivo (2018)

Mitochondria form a dynamic network governed by a balance between opposing fission and fusion processes. Because excessive mitochondrial fission correlates with numerous pathologies, including neurodegeneration, the mechanism governing fission has become an attractive therapeutic strategy. However, targeting fission is a double-edged sword as physiological fission is necessary for mitochondrial function. Fission is trigged by Drp1 anchoring to adaptors tethered to the outer mitochondrial membrane. We designed peptide P259 that distinguishes physiological from pathological fission by specifically inhibiting Drp1's interaction with the Mff adaptor. Treatment of cells with P259 elongated mitochondria and disrupted mitochondrial function and motility. Sustained in vivo treatment caused a decline in ATP levels and altered mitochondrial structure in the brain, resulting in behavioral deficits in wild-type mice and a shorter lifespan in a mouse model of Huntington's disease. Therefore, the Mff-Drp1 interaction is critical for physiological mitochondrial fission, motility, and function in vitro and in vivo. Tools, such as P259, that differentiate physiological from pathological fission will enable the examination of context-dependent roles of Drp1 and the suitability of mitochondrial fission as a target for drug development.
Studies of New Rechargeable Mg-Ion Battery Using Boron-Hydrogen Based Electrolytes (2016)

Mg-ion battery is one of the most promising candidates for a post Li-ion battery due to its high capacity, improved safety and potentially reduced cost. However, since the metallic Mg-anode is prone to passivation by electrolytes, we need to carefully use appropriate electrolytes which have high stability to the Mg metal. For example, common anions such as ClO 4 - , BF 4 - or TFSI - decompose on the Mg surface resulting in a highly resistive layer that partially or fully blocks Mg-ion transport. Although organo and chloride based reagents were found to be compatible with Mg metal, they still have severe issues such as highly corrosive nature and low Mg-ion transference number. 1) We have been pioneering the development of a new class of electrolytes based on a novel design strategy and offering halogen free and non-corrosive boron-hydrogen salts, which can also improve the transport and solubility properties. 2) Another serious challenge facing Mg battery technologies is the limited choice of cathode materials due to the difficulty to reversibly intercalate divalent Mg-ion in host structures analogues to those used in Li-ion batteries such as transition metal oxides. 3) Therefore, we have been studying alternative cathode chemistries beyond the intercalation types. The inertness and stability of the MMC electrolyte allow us to examine these new cathodes where fast and stable charge/discharge cycles can be performed with a relatively fine coulombic efficiency. In this presentation, we will unveil these new results and also show detailed mechanisms towards understanding the battery performance. [1] J. Wook Choi, D. Aurbach, doi:10.1038/natrevmats.2016.13, Nature Reviews Materials, 2016 [2] a) R. Mohtadi, M. Matsui, T. S. Arthur, S.-J. Hwang, Angew. Chem. Int. Ed. 2012 , 51, 9780 –9783; b) T. J. Carter, R. Mohtadi, T. S. Arthur, F. Mizuno, R. Zhang, S. Shirai, J. W. Kampf, Angew. Chem. Int. Ed. 2014 , 53, 3173-3177; c) O. Tutusaus, R. Mohtadi, ChemElectroChem. 2015 , 1, 51-57 d) O. Tutusaus, R. Mohtadi, T. Arthur. F. Mizuno, Angew. Chem. Int. Ed. 2015 , 27, 8011-8015 [3] a) H. D. Yoo, I. Shterenberg, Y. Gofer, G. Gershinsky, N. Pour, D. Aurbach, Energy Environ. Sci. 2013, 6, 2265-2279; b) R. Mohtadi, F. Mizuno Beilstein J. Nanotechnol. 2014, 5, 1291–1311
O4‐01‐02: STRUCTURE‐BASED INHIBITORS OF AMYLOID‐ BETA CORE SUGGEST A COMMON INTERFACE WITH TAU (2019)

Alzheimer's disease (AD) pathology is characterized by plaques of amyloid beta (Aβ) and neurofibrillary tangles of tau, but the molecular linkage of Aβ to tau remains unresolved. One proposed disease mechanism is through cross-seeding events, in which a compatible interface on aggregated Aβ induces tau to misfold. A crystal structure of the Aβ core (Aβ16-25D23N) determined by electron diffraction displaying characteristics of both fibrillar and oligomeric structure was used to design inhibitors. These inhibitors were validated for efficacy by testing for reduced aggregation and toxicity of monomeric Aβ, as well as toxicity of pre-formed Aβ aggregates in model N2a cells. Aβ fibrils treated with inhibitors reduced cross-seeding events in tau HEK293 biosensor cells. The inhibitors also reduced aggregation and homotypic seeding of tau. Mutations of amyloidogenic regions of tau were probed to identify key interfaces affected by our peptide inhibitor. Fibrils extracted from autopsied brains of patients with Alzheimer's disease were tested with the inhibitors for seeding in tau HEK293 biosensor cells to verify that these inhibitors target disease related conformations. Inhibitors targeting the Aβ core effectively block aggregation and toxicity of Aβ1-42, as well as reduced the seeded spread of tau aggregation from recombinant Aβ or tau fibrils, and AD derived fibrils. The ability of these inhibitors to interfere with both Aβ and tau seeds suggests that these aggregates share a common epitope, and supports the hypothesis that cross-seeding is one mechanism by which amyloid is linked to tau aggregation and could promote cognitive decline. Targeting this epitope could prove an effective strategy for targeting disease spread.
Introductions and early spread of SARS-CoV-2 in France, 24 January to 23 March 2020 (2020)

Following SARS-CoV-2 emergence in China, a specific surveillance was implemented in France. Phylogenetic analysis of sequences retrieved through this surveillance suggests that detected initial introductions, involving non-clade G viruses, did not seed local transmission. Nevertheless, identification of clade G variants subsequently circulating in the country, with the earliest from a patient who neither travelled to risk areas nor had contact with travellers, suggests that SARS-CoV-2 might have been present before the first recorded local cases.
Regular implementation algorithms of time domain aliasing cancellation (1996)

The authors propose two highly regular algorithms for realising the time domain aliasing cancellation (TDAC) technique. The first TDAC implementation, which is based on the fast discrete cosine transform, effectively adopts analysis and synthesis window functions in the transform structure. This implementation algorithm achieves the least computational complexity in TDAC processes. The second TDAC implementation, which extends Goertzel's concept, uses a simple selectable-fixed-coefficient second-order infinite impulse response (IIR) filter to recursively achieve multichannel encoding and decoding processes. With a properly selected coefficient, this recursive implementation achieves a lower round-off-error than the current fast implementations and the direct implementation in finite wordlength. In recently developed high quality consumer products, the first algorithm is suitable to be realised in digital signal processing chips and the second one will be a better choice for VLSI implementation.
Elastographic Dynamic Range Expansion Using Variable Applied Strains (1997)

In elastography, we want to image the entire range of stiffnesses of the elastic components found in inhomogeneous tissues. In order to achieve this, the elastographic dynamic range should equal the entire stiffness dynamic range in the target. Various sources of noise limit the dynamic range of elastography. The recently-defined strain filter concept offers an analytical and graphical way of observing these limitations. In this paper, we describe a method that achieves the expansion of the elastographic dynamic range. It involves the application of variable strains in combination with selective storage of strain data that have optimal elastographic signal-to-noise ratios. This expands the current dynamic range of elastography by orders of magnitude when compared to single compression elastography. The process is explained theoretically using the strain filter framework, and 1 D as well as 2D tissue simulations are used to corroborate the theory.
Binocular Stereo Techniques For The Direct Measurement Of Area Or Volume (1989)

We present a technique for measuring the area of mesa shaped features of constant height and irregular outline starting from a pair of stereo images captured above the feature. Our method is based on correlating the sign images of the Laplacian of Gaussian convolution of the two grey-level images'. We generalise this method to measure the volume of an irregularly shaped pile of material, such as a blob of sol-der paste which has been applied to a circuit board in preparation for reflow soldering.
Advanced mercuric iodide detectors for X-ray microanalysis. (1987)

We first present a brief tutorial on Mercuric Iodide (HgI2) detectors and the intimately related topic of near-room temperature ultralow noise preamplifiers. This provides both a physical basis and technological perspective for the topics to follow. We next describe recent advances in HgI2 applications to x-ray microanalysis, including a space probe Scanning Electron Microscope (SEM), Synchrotron x-ray detectors, and energy dispersive detector arrays. As a result of this work, individual detectors can now operate stably for long periods in vacuum, detect soft x-rays to the oxygen K edge at 523 eV, or count at rates exceeding 2x10(5)/sec. The detector packages are small, lightweight, and use low power. Preliminary HgI2 detector arrays of 10 elements with 500eV resolution have also been constructed and operate stably. Finally, we discuss expected advances in HgI2 array technology, including improved resolution, vacuum operation, and the development of soft x-ray transparent encapsulants. Array capabilities include: large active areas, high (parallel) count rate capability and spatial sensitivity. We then consider areas of x-ray microanalysis where the application of such arrays would be advantageous, particularly including elemental microanalysis, via x-ray fluorescence spectroscopy, in both SEMs and in scanning x-ray microscopes. The necessity of high count rate capability as spatial resolution increases is given particular attention in this connection. Finally, we consider the possibility of Extended X-ray Absorption Fine Structure (EXAFS) studies on square micron sized areas, using detector arrays.
Phase-matched second-harmonic generation in a polymer waveguide (1990)

Quasi-phase-matched second-harmonic generation has been observed in a periodically poled nonlinear optical polymer waveguide. Key elements in this demonstration include novel nonlinear optical polymers that can be spin coated, the design and fabrication of periodic electrodes for periodic poling and the optimization of waveguide parameters to obtain single-mode waveguides with a large overlap between fundamental and harmonic modes. Phase matching of the d33 nonlinear optical coefficient occurs over a distance L=230 μm.
Determination of epidural catheter placement using nerve stimulation in obstetric patients*1 (1999)

This study demonstrates that this test may have a role in improving the success rate of epidural anesthesia.
Synthesis and antiallergy activity of 4-oxo-4H-pyrido[1,2-a]thieno[2,3-d]pyrimidines (1981)

A series of 4-oxo-4H-pyrido[1,2-a]thieno[2,3-d]pyrimidines with substitutions in the 2, 3, and 7 positions was prepared. The compounds were evaluated in the rat passive cutaneous anaphylaxis test for antiallergy activity. Several compounds had potent oral activity and were found to be superior to disodium cromoglycate and doxantrazole. Structure-activity relationships are discussed.
HU-308: A specific agonist for CB <sub>2</sub> , a peripheral cannabinoid receptor (1999)

Two cannabinoid receptors have been identified: CB(1), present in the central nervous system (CNS) and to a lesser extent in other tissues, and CB(2), present outside the CNS, in peripheral organs. There is evidence for the presence of CB(2)-like receptors in peripheral nerve terminals. We report now that we have synthesized a CB(2)-specific agonist, code-named HU-308. This cannabinoid does not bind to CB(1) (K(i) > 10 microM), but does so efficiently to CB(2) (K(i) = 22.7 +/- 3.9 nM); it inhibits forskolin-stimulated cyclic AMP production in CB(2)-transfected cells, but does so much less in CB(1)-transfected cells. HU-308 shows no activity in mice in a tetrad of behavioral tests, which together have been shown to be specific for tetrahydrocannabinol (THC)-type activity in the CNS mediated by CB(1). However, HU-308 reduces blood pressure, blocks defecation, and elicits anti-inflammatory and peripheral analgesic activity. The hypotension, the inhibition of defecation, the anti-inflammatory and peripheral analgesic effects produced by HU-308 are blocked (or partially blocked) by the CB(2) antagonist SR-144528, but not by the CB(1) antagonist SR-141716A. These results demonstrate the feasibility of discovering novel nonpsychotropic cannabinoids that may lead to new therapies for hypertension, inflammation, and pain.
A high throughput CABAC algorithm using syntax element partitioning (2009)

Enabling parallel processing is becoming increasingly necessary for video decoding as performance requirements continue to rise due to growing resolution and frame rate demands. It is important to address known bottlenecks in the video decoder such as entropy decoding, specifically the highly serial Context-based Adaptive Binary Arithmetic Coding (CABAC) algorithm. Concurrency must be enabled with minimal cost to coding efficiency, power, area and delay. This work proposes a new CABAC algorithm for the next generation standard in which binary symbols are grouped by syntax elements and assigned to different partitions which can be decoded in parallel. Furthermore, since the distribution of binary symbols changes with quantization, an adaptive binary symbol allocation scheme is proposed to maximize throughput. Application of this next generation CABAC algorithm on five 720p sequences shows a throughput increase of up to 3x can be achieved with negligible impact on coding efficiency (0.06% to 0.37%), which is a 2 to 4x reduction in coding penalty compared with H.264/AVC and entropy slices. Area cost is also reduced by 2x. This increased throughput can be traded-off for low power consumption in mobile applications.
Analysis of Alpina officinarum Hance, chemically and biologically (2019)

<i>Alpinia officinarum</i> Hance is one of the most commonly used herbs belongs to Family Zingiberaceae. The current work deals with the qualitative and quantitative chemical study of this plant rhizomes in addition to the investigation of its anticancer activities. The results of the qualitative analysis showed a variation of phytochemical contents in this plant. While quantitative analysis showed a very promising percentage of active materials and Pharmacopeial constants. Analysis of elements like Cu, Zn & Mg were variable chromium was the lowest (0.680 ppm). The active constituents showed the highest percentage of carbohydrate (20.25 ± 1.11) and the lowest was of lipid (2.79 ± 1.03), other constituents percentage ranged from 5.11 ± 1.31 to 18.26 ± 1.24 for protein and flavonoids respectively. The pharmacopeial constant determinations reported the highest in moisture content (11.02 ± 1.05), Total ash, water-soluble ash, and acid insoluble ash were varied in values (5.64 ± 1.31 to 2.01 ± 1.12). The evaluation of the antitumor activities (<i>in vitro</i>) of the investigated plant rhizomes extract showed that; it exhibited a direct cytotoxic effect on the growth of some cell lines compared to the standard drug vinblastine sulphate. The activities were recorded against two cell lines; A-549 (Lung carcinoma) and CACO (colorectal carcinoma) with IC50 6.72 ± 0.5 and 7.6 ± 0.3 µg/ml respectively, these effects were better than the standard drug vinblastine sulphate (IC<sub>50</sub> were 24.6 ± 0.7& 30.3 ± 1.4 µg/ml). Moreover, the effect of the investigated extract was also promising on the other three cell lines (HCT-116 (Colon carcinoma, Hela (Cervical carcinoma) & Pc3 (prostate cancer) the best effect was on Hela with IC<sub>50</sub> of 24.5 ± 1.1 µg/ml better than vinblastine sulphate (59.7 ± 2.1 µg/ml).
Rapid diagnostics: the detection of neuraminidase activity as a technology for high-specificity targets (2001)

The accurate detection of influenza by clinical symptoms is challenging since multiple pathogenic viruses and bacteria mimic similar symptoms in a patient. With new and more effective influenza therapeutics available, there is a growing need for highly accurate and rapid diagnosis of influenza, particularly when the window of opportunity for proper treatment is measured in hours. A parallel technology, which is also used in the treatment of influenza, was developed for the rapid diagnosis of influenza by exploiting the enzymatic activity of influenza neuraminidase. This technology, which is called Pathozyme, offers the high specificity inherent from the conservation of the neuraminidase active site. The ZstatFlu test uses a small molecule derivative of sialic acid chemically coupled to a reporter group together with simple point-of-care reagents for directly detecting influenza from a patient specimen with high specificity. A second-generation platform technology using this neuraminidase detection system coupled with a more sensitive chemiluminescent reporter has been developed and formatted for reading on high-speed instant film. This modification resulted in a platform technology many-fold more sensitive than the former while maintaining its inherent high specificity. Preliminary data from a prototype tested during the mild 2000-2001 influenza season demonstrated that an optimized chemiluminescent test system could approach the accuracy of 14 day viral culture in a convenient 10-20 min test. This platform technology is currently being explored for the rapid detection of other pathogenic organisms where sensitivity, specificity and speed are essential in a point-of-care setting.
Imposing Fine-grain Next Generation Access Control over Database Queries (2017)

In this paper, we describe a system that leverages ANSI/INCITS Next Generation Access Control (NGAC) standard called Next-generation Database Access Control (NDAC) for accessing data in tables, rows, and columns in existing RDBMS products. NDAC imposes access control at the data level, eliminating the need for implementing and managing access control in applications and/or through the use of proprietary RDBMS mechanisms. Consequently, the same policies can protect multiple databases from queries sent from multiple applications. Furthermore, NDAC not only provides control down to the field level, but to varying fields of select rows. NDAC is unique in achieving this granularity of control without the use and coordination of multiple protection mechanisms. Operationally, users issue wide sweeping queries, and NDAC allows access to the optimal amount of data permissible for the user. The method includes an Access Manager for trapping and enforcing policy over SQL queries issued by applications as well as a Translator for converting SQL statements to NGAC inputs and converting NGAC authorization responses to either an access Deny or one or more permitted SQL statements.
Isolation of Hepatitis A Virus in Vitro in Cell Culture Directly from Human Specimens (1981)

Human hepatitis A virus (HAV) was isolated directly in cell culture from infected human fecal extracts using techniques developed for in vitro cultivation of the marmoset-adapted CR326 strain of human HAV. A very long incubation was required in first passage, but vigorous cell culture growth, with incubation periods and virus yields similar to those of the CR326 strain that was isolated originally in marmosets, was achieved on serial passage. As with the CR326 strain, there were no evident cytopathic effects. The isolates proved to be HAV virus based on specific activity in serologic tests and by tests for infectiousness in marmosets.