gebhart/patrepeval huggingface dataset:
Temporal changes in respiratory adenovirus serotypes circulating in the greater Toronto area, Ontario, during December 2008 to April 2010 (2013)

Abstract Background Certain adenovirus serotypes cause severe infections, especially in children. It is important to monitor temporal changes in serotypes causing clinical disease. The objective of this study was to document circulating respiratory adenovirus serotypes by sequencing adenovirus culture isolates from the Greater Toronto Area, Ontario, during December 2008 to April 2010. Methods Nucleic acid extraction was performed on 90 respiratory tract adenovirus culture isolates. PCR amplification was conducted with primers targeting the adenovirus hexon gene hypervariable region 7. Sanger sequencing and phylogenetic analyses were performed to determine serotype identities. Results Among 90 clinical respiratory isolates sequenced, eight different serotypes were identified. Serotype 3 (34, 38%), serotype 2 (30, 30%), and serotype 1 (14, 16%) isolates were most common; serotypes 5, 6, 11, 17 and 21 were also observed. Seventeen (50%) of the 34 HAdV-3 isolates were identified between December 2008 and February 2009, while none were identified from December 2009 to February 2010. Between December 2008 and April 2009, the two most common serotypes were HAdV-3 and HAdV-2, detected in 18 (53%) and 8 (24%) of the 34 cultures isolates, respectively. However, from December 2009 to April 2010, there was an increase in HAdV-2, which became the most prevalent serotype, detected in 10 (50%) of the 20 isolates identified (p = 0.05). Conclusions There was a gradual shift in prevailing adenovirus serotypes during the 17 month study period, from predominantly HAdV-3 to HAdV-2. If an adenovirus vaccine were to be broadly implemented, multiple serotypes should be included.
Trend Tests for Case-Control Studies of Genetic Markers: Power, Sample Size and Robustness (2002)

The Cochran-Armitage trend test is commonly used as a genotype-based test for candidate gene association. Corresponding to each underlying genetic model there is a particular set of scores assigned to the genotypes that maximizes its power. When the variance of the test statistic is known, the formulas for approximate power and associated sample size are readily obtained. In practice, however, the variance of the test statistic needs to be estimated. We present formulas for the required sample size to achieve a prespecified power that account for the need to estimate the variance of the test statistic. When the underlying genetic model is unknown one can incur a substantial loss of power when a test suitable for one mode of inheritance is used where another mode is the true one. Thus, tests having good power properties relative to the optimal tests for each model are useful. These tests are called efficiency robust and we study two of them: the maximin efficiency robust test is a linear combination of the standardized optimal tests that has high efficiency and the MAX test, the maximum of the standardized optimal tests. Simulation results of the robustness of these two tests indicate that the more computationally involved MAX test is preferable.
Surface-simulation synthesis of the substrate-binding site of an enzyme. Demonstration with trypsin (1985)

From the X-ray co-ordinates of bovine trypsin and its complexes with substrate analogues (benzamidine) and with soya-bean trypsin inhibitor, a peptide (TP) was designed and synthesized by surface-simulation synthesis, a concept previously introduced by this laboratory, to mimic the binding site of trypsin. Also, a control peptide (CTP) was synthesized that contained all the amino acids present in the TP peptide, except that their order was randomized. The radioiodinated TP peptide bound specifically to adsorbents of benzamidine, whereas the control CTP peptide exhibited no binding activity. Conjugates to succinyl (3-carboxypropionyl)-lysozyme of the TP peptide, control CTP peptide and other unrelated peptides were examined by a radiometric binding assay for the ability to bind soya-bean trypsin inhibitor and human alpha 1-antitrypsin. Conjugates of the TP peptide exhibited considerable binding activity to adsorbents of soya-bean trypsin inhibitor or alpha 1-antitrypsin. None of the other peptide conjugates possessed any binding activity. Action of the active-site-directed reagents phenylmethanesulphonyl fluoride and di-isopropyl phosphorofluoridate on free TP and CTP peptides resulted in the modification of a serine residue in the TP peptide whereas the CTP peptide remained unaltered. The TP peptide, either in the free form or as a conjugate on succinyl-lysozyme, had no enzymic activity on protein substrates or on tosylarginine methyl ester. These findings indicated that the binding activity of an enzyme was well mimicked by the surface-stimulation peptide but that reproduction of the catalytic activity was not obtained.
Discovery of Novel and Highly Selective Inhibitors of Calpain for the Treatment of Alzheimer’s Disease: 2-(3-Phenyl-1<i>H</i>-pyrazol-1-yl)-nicotinamides (2017)

Calpain overactivation has been implicated in a variety of pathological disorders including ischemia/reperfusion injury, cataract formation, and neurodegenerative diseases such as Alzheimer's disease (AD). Herein we describe our efforts leading to the identification of ketoamide-based 2-(3-phenyl-1H-pyrazol-1-yl)nicotinamides as potent and reversible inhibitors of calpain with high selectivity versus related cysteine protease cathepsins, other proteases, and receptors. Broad efficacy in a set of preclinical models relevant to AD suggests that inhibition of calpain represents an attractive approach with potential benefit for the treatment of AD.
An opamp with 375V µ s slew rate, ± 100mA output current (1985)

A report on a bipolar opamp which exhibits a 375V/μs slew rate, a 60MHz gain bandwidth product, and a voltage gain of 25K will be presented. The output circuit can drive ±100mA.
The Concept of the Acid Mantle of the Skin: Its Relevance for the Choice of Skin Cleansers (1995)

Whereas soap has long been the only cleansing agent, a new generation of cleansers, the so-called synthetic detergents or syndets, has been developed during the last decades. They offer a wide variety of formulations and are therefore becoming more and more important for cleansing of diseased and healthy skin. Among the syndets, especially those with a pH of about 5.5 seem to be relevant. In contrast to alkaline soap, they do not interfere with the cutaneous microflora, whose composition is linked to the skin surface pH. As their irritancy potential might be even lower than that of soap, the benefit-to-risk ratio of syndets appears favorable.
A Novel Method to Incorporate Bioactive Cytokines as Adjuvants on the Surface of Virus Particles (2008)

Cytokines have been used extensively as adjuvants in vaccines. However, practical considerations limit their use; diffusion from antigen, short half-lives and additional production costs. To address these problems we have developed a technology that efficiently produces inactivated, whole-virus influenza vaccine bearing membrane-bound cytokines. To provide “proof of principle,” we chose chicken interleukin-2 (IL-2) and chicken granulocyte–macrophage colony-stimulating factor. Fusion constructs were generated in which their coding regions were linked to the influenza virus transmembrane encoding domains of the neuraminidase and hemagglutinin genes, respectively. These fusion constructs were used to establish stable Madin–Darby Canine Kidney cell lines, constitutively expressing membrane-bound cytokine. Cell surface expression was verified by immunofluorescence and cytokine-specific bioassays. Influenza virus harvested from infected cytokine-bearing cells was purified, inactivated, and confirmed to include membrane-bound cytokine by immunofluorescence, Western blotting and bioassay. Cytokine bioactivity was preserved using several standard virus inactivation protocols. Both cytokine-bearing influenza vaccines are now being tested for immunogenicity in vivo. Initial experiments indicate that chickens injected with IL-2-bearing influenza have elevated antiviral antibody levels, compared to chickens given conventional vaccine. In conclusion, this technology offers a novel method to utilize cytokines and other immunostimulatory molecules as adjuvants for viral vaccines.
Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp (2013)

A new emerging disease in shrimp, first reported in 2009, was initially named early mortality syndrome (EMS). In 2011, a more descriptive name for the acute phase of the disease was proposed as acute hepatopancreatic necrosis syndrome (AHPNS). Affecting both Pacific white shrimp Penaeus vannamei and black tiger shrimp P. monodon, the disease has caused significant losses in Southeast Asian shrimp farms. AHPNS was first classified as idiopathic because no specific causative agent had been identified. However, in early 2013, the Aquaculture Pathology Laboratory at the University of Arizona was able to isolate the causative agent of AHPNS in pure culture. Immersion challenge tests were employed for infectivity studies, which induced 100% mortality with typical AHPNS pathology to experimental shrimp exposed to the pathogenic agent. Subsequent histological analyses showed that AHPNS lesions were experimentally induced in the laboratory and were identical to those found in AHPNS-infected shrimp samples collected from the endemic areas. Bacterial isolation from the experimentally infected shrimp enabled recovery of the same bacterial colony type found in field samples. In 3 separate immersion tests, using the recovered isolate from the AHPNS-positive shrimp, the same AHPNS pathology was reproduced in experimental shrimp with consistent results. Hence, AHPNS has a bacterial etiology and Koch's Postulates have been satisfied in laboratory challenge studies with the isolate, which has been identified as a member of the Vibrio harveyi clade, most closely related to V. parahemolyticus.
Circulating interleukin-8 concentrations in patients with multiple organ failure of septic and nonseptic origin (1994)

In septic patients, high amounts of circulating IL-8 concentrations correlate with fatal outcome, whereas only low plasma concentrations of IL-8 are present in patients with nonseptic, multiple organ failure. This finding suggests that the signals involved in the exacerbation of IL-8 production are different, depending on infectious or noninfectious etiology.
Time-frequency analysis of VHF wave form for precise location of partial discharge in small-scale high voltage apparatuses (2004)

This study is aimed to develop the technique for locating partial discharges in small-scale high voltage apparatuses like rotating machines and transformers. Conventionally for such a purpose, discharge signals detected at different points are compared in time domain to determine the time lag. However, for small-scale apparatuses, a high precision of the location is required. In addition, as the inspection is usually performed in a small room, the waveform may be highly interfered by reflected waves. In the experiment, radio frequency signals in VHF range radiated from the discharge point were carefully acquired the time lag between these signals was determined by more than two whip antennas. Direct comparison in time domain was not suitable since the signals were not completely the same. Time-frequency analysis was then applied to the waveform. Specific part of the waveform was extracted by using a proper window function and subjected to phase analysis. Location of the discharge point was performed using the phase spectrum. It was proved that the technique was suitable to avoid the influence of the interference by the reflected waveform. The precision of location was as good as several centimeters.
An engineering‐driven approach for separating pressure and saturation using 4D seismic: application to a Jurassic reservoir in the UK North Sea (2005)

A technique is shown for estimating pressure and saturation changes from 4D seismic without the need for rock and fluid physics. This is a further refinement and development of a previously published method. Here, a multi‐attribute approach is taken, in which a cycle of calibration, training, and principal component analysis produces an optimal combination of attributes. The methodology is applied to a Jurassic reservoir in the UK North Sea with encouraging results. It has highlighted saturation changes previously hidden by the effect of pore pressure on the rock frame, even where AVO methods have failed, and can be validated against flow rates for water production.
Hybrid ARQ for robust video streaming over wireless LANs (2002)

The authors address the problem of transmission of multimedia data over a wireless local area network (LAN). The wireless LAN is modeled as a packet erasure channel. We present a solution that efficiently combines Automatic Repeat Request (ARQ) and Forward Error Correction (FEC) coding for sending compressed video and audio over a packet network.
Real-Time Traffic Measurement from Single Loop Inductive Signatures (2002)

Accurate traffic data acquisition is essential for effective traffic surveillance, which is the backbone of advanced transportation management and information systems (ATMIS). Inductive loop detectors (ILDs) are still widely used for traffic data collection in the United States and many other countries. Three fundamental traffic parameters—speed, volume, and occupancy—are obtainable via single or double (speed-trap) ILDs. Real-time knowledge of such traffic parameters typically is required for use in ATMIS from a single loop detector station, which is the most commonly used. However, vehicle speeds cannot be obtained directly. Hence, the ability to estimate vehicle speeds accurately from single loop detectors is of considerable interest. In addition, operating agencies report that conventional loop detectors are unable to achieve volume count accuracies of more than 90% to 95%. The improved derivation of fundamental real-time traffic parameters, such as speed, volume, occupancy, and vehicle class, from single loop detectors and inductive signatures is demonstrated.
Curvature-constrained motion within a limited workspace (2002)

We pose the following questions: Given two points within a closed area W/spl sub/R/sup 2/, each with a prescribed direction of motion in it, (i) what is the shortest path of bounded curvature that joins them and lies completely in W? (ii) what is the minimum number of cusps one needs to design a path in W? These kind of questions appear in various applications, such as robot motion planning. The proposed approach makes use of a tool dubbed the reflective unfolding operator which has a clear geometric interpretation and provides an interesting means for solving other trajectory design problems. In this text, the approach is applied to the following problem: for a car moving with bounded curvature and possible reversals, given the starting and target directions of motion at the center of a disc D of some radius R, design the shortest possible path fully lying in D. The path produced by the algorithm turns out to also be of the lowest complexity (the minimum number of cusps).
Internally quenched peptides for the study of lysostaphin: an antimicrobial protease that kills Staphylococcus aureus (2006)

Lysostaphin (EC. 3.4.24.75) is a protein secreted by Staphylococcus simulans biovar staphylolyticus and has been shown to be active against methicillin resistant S. aureus (MRSA). The design and synthesis of three internally quenched substrates for lysostaphin based on the peptidoglycan crossbridges of S. aureus, and their use in fluorescence resonance energy transfer (FRET) assays is reported. These substrates enabled the gathering of information about the endopeptidase activity of lysostaphin and the effect that mutations have on its enzymatic ability. Significant problems with the inner filter effect and substrate aggregation were encountered; their minimisation and the subsequent estimation of the kinetic parameters for the interaction of lysostaphin with the substrates is described, as well as a comparison of substrates incorporating two FRET pairs: Abz-EDDnp and DABCYL-EDANS. In addition to this, the points of cleavage caused by lysostaphin in Abz-pentaglycine-EDDnp have been determined by HPLC and mass spectrometry analysis to be between glycines 2 and 3(approximately 60%) and glycines 3 and 4 (approximately 40%).
Collection of scintillation light from small BGO crystals (1995)

We propose to develop a high resolution positron emission tomography (PET) detector designed for animal imaging. The detector consists of a 2-D array of small bismuth germanate (BGO) crystals coupled via optical fibers to a multi-channel photomultiplier tube (MC-PMT). Though this approach offers several advantages over the conventional BGO block design, it does require that a sufficient number of scintillation photons be transported from the crystal, down the fiber and into the PMT. In this study we use simulations and experimental data to determine how to maximize the signal reaching the PMT. This involves investigating factors such as crystal geometry, crystal surface treatment, the use of reflectors, choice of optical fiber, coupling of crystal to the optical fiber and optical fiber properties. Our results indicate that using 2/spl times/2/spl times/10 mm BGO crystals coupled to 30 cm of clad optical fiber, roughly 50 photoelectrons are produced at the PMT photocathode for a 511 keV interaction. This is sufficient to clearly visualize the photopeak and provide adequate timing resolution for PET. Based on these encouraging results, a prototype detector will now be constructed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Glycoprotein 330, a member of the low density lipoprotein receptor family, binds lipoprotein lipase in vitro (1993)

Glycoprotein 330 (gp330), a cell-surface protein that is localized in clathrin-coated pits, is structurally related to both the low density lipoprotein receptor (LDLR) and the LDLR-related protein/alpha 2-macroglobulin receptor (LRP). We recently demonstrated that gp330 and LRP may be functionally related as well; both bind the 39-kDa polypeptide referred to as receptor-associated protein (Kounnas, M. Z., Argraves, W. S., and Strickland, D. K. (1992) J. Biol. Chem. 267, 21162-21166). In this report, we tested several other LRP ligands for their ability to interact with human and rat gp330 in vitro. Gp330 did not exhibit detectable binding to the LRP ligands, alpha 2-macroglobulin protease complex or Pseudomonas aeruginosa exotoxin A. However, we found that gp330 (purified from human or rat) bound the lipolytic enzyme lipoprotein lipase (LPL) with high affinity (Kd = 6.1 and 2.7 nM, respectively). The binding was saturable, divalent cation dependent, and inhibited by heparin or receptor-associated protein. Because LRP has also been shown to bind LPL, the present findings further extend the functional similarities between gp330 and LRP. By analogy to the postulated role of the LRP-LPL interaction in facilitating hepatic clearance of LPL-associated lipoproteins from the blood (Beisiegel, U., Weber, W., and Bengtsson-Olivercrona, G. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 8342-8346; Chappell, D. A., Fry, G. L., Waknitz, M. A., Iverius, P. H., Williams, S. E., and Strickland, D. K. (1992) J. Biol. Chem. 267, 25764-25767), we speculate that the gp330-LPL interaction described herein may contribute to the uptake of LPL-associated lipoproteins in tissues expressing gp330. Consistent with this possibility, we found that LPL promoted in vitro binding of 125I-lipoproteins to gp330.
Tampered Image Detection Using Image Matching (2008)

With the development of image processing software, such as Photoshop, scientific analysis for detecting tampered images becomes a critical research issue. A hybrid image matching algorithm for image analysis is proposed and evaluated. Features are extracted using blob detectors and interest point detectors. This combination ensures sufficient correspondences in small image patches while maintaining high accuracy. Nearest neighbors are searched using hybrid spill tree in order to reduce the computational load. Applying the algorithm to tampered image detection, a novel solution is proposed utilizing the scale space information and gradient orientation information from the corresponding features. Furthermore, an order regularity of scale space between the corresponding patches and a description for object rotation are also proposed. In addition, we conducted experiments on tampered images, proving the method to be powerful.
Liquid Marbles Supported by Monodisperse Poly(methylsilsesquioxane) Particles (2014)

The preparation of model, well-controlled colloidal assemblies has been a central approach to understanding and optimizing the characteristics and functionality of complex colloidal dispersion systems. This approach, which has created a significant literature and rather deep understanding for emulsions and foams, has yet to be established for the liquid marble (water-in-air) motif. In this article we report the preparation of well-controlled liquid marbles using monodisperse micron-size particles of poly(methylsilsesquioxane) (PMSQ). The low cohesive nature of the stabilizing particles, their narrow size distribution, and their hydrophobicity permit the formation of liquid marbles containing a particulate monolayer with a hexagonally close-packed (HCP) structure. The "cleaning process" by rolling of liquid marbles under a flow of air on a hydrophobic substrate was useful to obtain the monolayer structure. Moreover, the monolayer structure was only obtained from liquids with high surface energy, whereas the others were not useful even though multilayered structure was formed from liquids that have intermediate surface energy.
The Clinical Study on Huanglianjiedu Decoction on for patients with Senile Dementia,the Type of Hyperactivity of Heart-Fire and Liver Fire in TCM (2007)

Objective:To obsrve the effect of Huanglianjiedu Decoction(HD,黄连解毒汤) on intelligence and capacity for daily activities of patients with senile dementia,the Type of Hyperactivity of Heart-Fire and Liver Fire in TCM. Methods:Patients taking HD for 3 months'later,the MMSE,HDS and activities of daily living(ADL)were selected to access the intelligence and capacity for daily activities. Furthermore,levels of superoxidase(SOD) and lactoperoxidase (LPO) were tested.Results: Scores of MMSE,HDS and ADL were significant different before and after the treatment,and the levels of SOD and LPO were also.Conclusion: HD could improve intelligence and capacity for daily activities of the patients.The mechanism was possible related to antioxidation.
Information Theory and Reliable Communication. (1970)

Communication Systems and Information Theory. A Measure of Information. Coding for Discrete Sources. Discrete Memoryless Channels and Capacity. The Noisy-Channel Coding Theorem. Techniques for Coding and Decoding. Memoryless Channels with Discrete Time. Waveform Channels. Source Coding with a Fidelity Criterion. Index.