gebhart/patrepeval huggingface dataset:
Novel fluorescence-based integrated sensor for chemical and biological agent detection (2004)

There is a renewed interest in the development of chemical and biological agent sensors due to the increased threat of weapons deployment by terrorist organizations and rogue states. Optically based sensors address the needs of military and homeland security forces in that they are reliable, rapidly deployed, and can provide continuous monitoring with little to no operator involvement. Nomadics has developed optically based chemical weapons sensors that utilize reactive fluorescent chromophores initially developed by Professor Tim Swager at MIT. The chromophores provide unprecedented sensitivity and selectivity toward toxic industrial chemicals and certain chemical weapon agents. The selectivity is based upon the reactivity of the G-class nerve agents (phosphorylation of acetylcholinesterase enzyme) that makes them toxic. Because the sensor recognizes the reactivity of strong electrophiles and not molecular weight, chemical affinity or ionizability, our system detects a specific class of reactive agents and will be able to detect newly developed or modified agents that are not currently known. We have recently extended this work to pursue a combined chemical/biological agent sensor system incorporating technologies based upon novel deep ultraviolet (UV) light emitting diodes (LEDs) developed out of the DARPA Semiconductor UV Optical Sources (SUVOS) program.
Effect of pentoxifylline on cerebral edema in cats (1974)

Pentoxifylline, a methylxanthine derivative, was given intravenously to cats, starting 24 hours before or immediately after cerebral edema was induced in one hemisphere by a standard freezing lesion. Pentoxifylline caused a reduction of the cerebral edema, with preferential involvement of the gray matter. Treatment given during 72 or 96 hours after the lesion was made reduced the increase in water and sodium content and also reduced the decrease in potassium content in the injured hemisphere. It is suggested that the reduction of the edematous changes caused by pentoxifylline is mainly due to the inhibition of 39,59-AMP-phosphodiesterase, to the enhanced cerebral blood flow, and to the inhibition of alpha-adrenergic effects.
<title>De-noising and contrast enhancement via wavelet shrinkage and nonlinear adaptive gain</title> (1996)

This paper presents an approach which addresses both de-noising and contrast enhancement. In a multiscale wavelet analysis framework, we take advantage of both soft thresholding and hard thresholding wavelet shrinkage techniques to reduce noise. In addition, we carry out nonlinear processing to enhance contrast within structures and along boundaries. Feature restoration and enhancement are accomplished by modifying the gain of a signal's variational energy. The multiscale discrete dyadic wavelet transform adapted in this paper is treated as a process for the diffusion of variational energy from a signal stored as the power (scaled variational energy) of wavelet coefficients. We show that a discrete dyadic wavelet transform has the capability to separate feature variational energy from noise variational energy. De- noising and feature enhancement are achieved by simultaneously lowering noise variational energy and raising feature variational energy in the transform domain. We present methods for achieving this objective, including regulated soft thresholding and adaptive nonlinear processing combined with hard thresholding. We have applied this algorithm to synthetic and real signals as well as images with additive Gaussian white noise. Experimental results show that de-noised as well as enhanced signals and images are free from artifacts. Sample analysis and experimental results are presented.
Occupational cancer burden in Great Britain (2012)

A sound knowledge base is required to target resources to reduce workplace exposure to carcinogens. This project aimed to provide an objective estimate of the burden of cancer in Britain due to occupation. This volume presents extensive analyses for all carcinogens and occupational circumstances defined as definite or probable human occupational carcinogens by the International Agency for Research on Cancer. This article outlines the structure of the supplement - two methodological papers (statistical approach and exposure assessment), eight papers presenting the cancer-specific results grouped by broad anatomical site, a paper giving industry sector results and one discussing work-related cancer-prevention strategies. A brief summary of the methods and an overview of the updated overall results are given in this introductory paper. A general discussion of the overall strengths and limitations of the study is also presented. Overall, 8010 (5.3%) total cancer deaths in Britain and 13,598 cancer registrations were attributable to occupation in 2005 and 2004, respectively. The importance of cancer sites such as mesothelioma, sinonasal, lung, nasopharynx, breast, non-melanoma skin cancer, bladder, oesophagus, soft tissue sarcoma and stomach cancers are highlighted, as are carcinogens such as asbestos, mineral oils, solar radiation, silica, diesel engine exhaust, coal tars and pitches, dioxins, environmental tobacco smoke, radon, tetrachloroethylene, arsenic and strong inorganic mists, as well as occupational circumstances such as shift work and occupation as a painter or welder. The methods developed for this project are being adapted by other countries and extended to include social and economic impact evaluation.
Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase. (1993)

Adenylosuccinate adenosine 5'-monophosphate lyase (EC 4.3.2.2; ASL) catalyzes two distinct reactions in adenosine 5'-monophosphate (AMP) biosynthesis. A S413P mutation in ASL segregates with mental retardation in an affected family (Stone, R. L., Aimi, J., Barshop, B. A., Jaeken, J., Van den Berghe, G., Zalkin, H., and Dixon, J. E. (1992) Nature Genet. 1, 59-63). ASL and S413P ASL have been expressed, purified, and kinetically characterized. Lowering the Escherichia coli growth temperature to 25 degrees C and the concentration of inducer, isopropyl-1-thio-beta,D-galactopyranoside, to 40 microM was necessary for synthesis of soluble, tetrameric enzymes. The recombinant enzymes were purified to homogeneity using anion exchange chromatography followed by chromatography on Blue 2A Sepharose. At pH 7.0 and 25 degrees C, the kcat for cleavage of 5-amino-4-imidazole-N-succinocarboxamide ribotide (SAI-CAR) by ASL was 90 s-1 with a Km of 2.35 microM. The kcat for adenylosuccinate (SAMP) cleavage was 97 s-1 with a Km of 1.79 microM. The catalytic mechanism involved one general base catalyst (pK alpha = 6.4) and one general acid catalyst (pK alpha = 7.5). ASL follows an ordered uni-bi reaction mechanism with fumarate released first. 5-Amino-4-imidazolecarboxamide ribotide (AICAR) and AMP were competitive with SAICAR and SAMP (Ki[AICAR] = 11.3 microM; Ki[AMP] = 9.2 microM), whereas fumarate inhibited noncompetitively (Kii = 2.3 mM, Kis = 2.8 mM). The competitive inhibition by AICAR and AMP suggests a single active site that binds both SAICAR and SAMP. The kinetic constants at pH 7.0, 25 degrees C and the kcat/Km versus pH profiles for ASL and S413P ASL were very similar. These results are consistent with S413P being a structural rather than a catalytic defect.
High Level Transcription of the Complement Regulatory Protein CD59 Requires an Enhancer Located in Intron 1 (1999)

CD59 is a complement regulatory protein and may also act as a signal-transducing molecule. CD59 transgenic mice have been generated using a CD59 minigene (CD59 minigene-1). Although this minigene contained a 4.6-kilobase pair 5'-flanking region from the human CD59 gene as a promoter, the expression levels of the CD59 mRNA were substantially lower than those observed in humans, suggesting that CD59 gene expression might also require other transcriptional regulatory elements such as an enhancer. To investigate the transcriptional regulation of the CD59 gene, we used three cell lines that express CD59 at different levels. We have identified DNase I-hypersensitive sites in intron 1 in HeLa cells, which express CD59 at high levels, but not in Jurkat (intermediate level) or Raji cells (low level). Furthermore, cell line-specific enhancer activity was detected in a fragment containing these DNase I-hypersensitive sites. The CD59 enhancer was mapped to between -1155 and -888 upstream of the 5'-end of exon 2. To investigate the enhancer activity in vivo, a new CD59 minigene was constructed by the addition of the enhancer fragment into CD59 minigene-1. High expressor CD59 transgenic mice were generated using the new minigene.
Design and operation of a silicon ring resonator for force sensing applications above 1 MHz (2009)

We present an integrated force probe based on a silicon bulk-mode MEMS resonator. This device uses a silicon ring with symmetrical tips vibrating in the elliptic vibration mode. The tips enable us to make mechanical interactions with surfaces or external objects. Both excitation and detection of the resonator are integrated thanks to electrostatic actuation and capacitive detection. Apart from optical and electrical characterizations of the fabricated device, we report for the first time on the interaction between the resonator tip and a hydrodynamic force applied thanks to a water droplet. This demonstrates a first step toward high frequency atomic force probes for liquid medium applications.
Haplotype block structures show significant variation among populations (2004)

Recent studies suggest that haplotypes tend to have block-like structures throughout the human genome. Several methods were proposed for haplotype block partitioning and for tagging single-nucleotide polymorphism (SNP) identification. In population genetics studies, several research groups compared block structures across human populations. However, the measures used to quantify population similarity are either less than satisfactory or nonexistent. In this article, we propose several similarity measures to facilitate the comparisons of haplotype structures, namely block boundaries and tagging SNPs, across populations. With these measures, we can more objectively compare haplotype block structures and tagging SNP sets between different populations. In addition, these measures allow us to compare the results of different methods for block partition and tagging SNP identification. When we applied these measures to a real data set on chromosome 10 in 16 worldwide populations, we found that in this genome region: 1) haplotype block boundaries vary among populations, with European and some African populations showing similar boundaries but other populations showing other patterns; 2) tagging SNP sets are generally similar for populations with similar haplotype block structures but differ if the block structures differ; and 3) all but one of the block finding methods we tested yield consistent results, although variations exist regarding consistency. Our tentative results show that at least in the genome region studied, it is unlikely that a common haplotype pattern exists for all human populations: many populations, even in the same geographical region, may have different haplotype patterns.
Precise time synchronization of two Milstar communications satellites without ground intervention (1997)

Satellite navigation and communication systems often require precise synchronization among spacecraft clocks. In the traditional method for achieving synchronization, a ground station makes time-offset measurements to the various spacecraft clocks, and then updates the time and frequency of each satellite as needed. Though straightforward in its implementation, disadvantages to the traditional approach include the large workload placed on the ground station, the need for multiple ground stations to view satellites in different geosynchronous positions, and unaccounted-for delays in atmospheric propagation. In early 1996 Milstar became the first satellite system to employ crosslinks for precise satellite time synchronization. At that time, the crystal oscillator clock onboard FLT-1, the first Milstar satellite, had its time and frequency tied (i.e., slaved) to the rubidium (Rb) atomic clock carried onboard FLT-2, the second Milstar satellite. The FLT-2 Rb atomic clock was controlled by the ground, while the slaving of FLT-1 to FLT-2 was accomplished without ground intervention: all timing information required by the slaving algorithm was obtained through the FLT-1 to FLT-2 satellite crosslink. In this paper we will first show the timekeeping capabilities of the two satellite clocks when operating independently, which indicate that both clocks are performing well. Then, we will present ground station measurements of FLT-1 and FLT-2 timekeeping that demonstrate satellite synchronization to better than 150 nsec without ground intervention. As satellites are added to the Milstar constellation, crosslink slaving will minimize ground station timekeeping activities, thereby lowering system operating costs. © 1997 John Wiley & Sons, Ltd.
Synthesis of some 4-anilino-3-quinolinecarboxylic acids and esters (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of some 4-anilino-3-quinolinecarboxylic acids and estersJ. William Hanifin, Rosemary Capuzzi, and Elliott CohenCite this: J. Med. Chem. 1969, 12, 6, 1096–1097Publication Date (Print):November 1, 1969Publication History Published online1 May 2002Published inissue 1 November 1969https://pubs.acs.org/doi/10.1021/jm00306a030https://doi.org/10.1021/jm00306a030research-articleACS PublicationsRequest reuse permissionsArticle Views35Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effect of Novel A<sub>2A</sub>Adenosine Receptor Agonist ATL 313 on<i>Clostridium difficile</i>Toxin A-Induced Murine Ileal Enteritis (2006)

Clostridium difficile is a spore-forming, anaerobic, gram-positive bacillus that releases two main virulence factors: toxins A and B. Toxin A plays an important pathogenic role in antibiotic-induced diarrhea and pseudomembranous colitis, a condition characterized by intense mucosal inflammation and secretion. Agonist activity at A2A adenosine receptors attenuates inflammation and damage in many tissues. This study evaluated the effects of a new selective A2A adenosine receptor agonist (ATL 313) on toxin A-induced injury in murine ileal loops. ATL 313 (0.5 to 5 nM) and/or the A2A adenosine receptor antagonist (ZM241385; 5 nM) or phosphate-buffered saline (PBS) were injected into ileal loops immediately prior to challenge with toxin A (1 to 10 microg/loop) or PBS. Intestinal fluid volume/length and weight/length ratios were calculated 3 h later. Ileal tissues were collected for the measurement of myeloperoxidase, adenosine deaminase activity, tumor necrosis factor alpha (TNF-alpha) production, histopathology, and detection of cell death by the TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) method. Toxin A significantly increased volume/length and weight/length ratios in a dose-dependent fashion. ATL 313 treatment significantly (P < 0.05) reduced toxin A-induced secretion and edema, prevented mucosal disruption, and neutrophil infiltration as measured by myeloperoxidase activity. ATL 313 also reduced the toxin A-induced TNF-alpha production and adenosine deaminase activity and prevented toxin A-induced cell death. These protective effects of ATL 313 were reversed by ZM241385. In conclusion, the A2A adenosine receptor agonist, ATL 313, reduces tissue injury and inflammation in mice with toxin A-induced enteritis. The finding of increased ileal adenosine deaminase activity following the administration of toxin A is new and might contribute to the pathogenesis of the toxin A-induced enteritis by deaminating endogenous adenosine.
Contact Hole Imaging In Stepper Lithography (1987)

Contact hole array imaging is compared to line-space grating imaging to determine the resolution of contact hole features printed by stepper lenses. Both calculated and experimental results are reported. Image intensity profiles, IIPs, have been calculated for selected cross-sections of square contact holes and equal line-space gratings. The calculations are done according to the method of Hopkins for circular aperture optical systems, partial coherence levels, fractional pupil fill (S), of 0.5 and 0.7, and various levels of optical defocus. The calculated results show that for S = 0.7, at resolution levels (i.e., half-pitch of equal line-space grating or the width of the square contact) greater than 0.9 λ/NA, the IIP of the lateral cross-sections of contact hole arrays to be equal to or better than that of the correspondingly dimensioned gratings. At resolution levels less than 0.9 λ/NA, the contact hole IIP degrades rapidly with respect to the grating IIP. A comparison of the lateral and diagonal cross-sections of contact holes with no defocus aberration shows that the shape of the contact changes from a 'square' to a 'circle' in the 1.25 to 1.00 λ/NA range. In the 1.0 λ.NA resolution region the lateral contact hole IIP has a greater intensity than that of the space of the grating. The effects of optical defocus on contact hole imaging are examined for g, h, and i-line stepper lens at the same λ/NA resolution levels. Contact hole IIPs degrade more rapidly with optical defocus than the correspondingly dimensioned grating IIPs. Experimental comparisons between contact hole and grating resist images are presented for several stepper lens systems. The comparison between calculated and experimental results shows significantly less than 'perfect' imaging for some stepper lenses. Contact hole imaging characteristics are much more sensitive to residual aberrations in the optical system and can be used as a relative measure of the magnitude of these aberrations.
The natural polyamine spermine functions directly as a free radical scavenger (1998)

The polyamines are small organic cations that are absolutely required for eukaryotic cell growth. Although their growth requirements are well established, the molecular functions of the polyamines are ill-defined. Oxidative damage to DNA by reactive oxygen species is a continual problem that cells must guard against to survive. The polyamine spermine, which is normally found in millimolar concentrations in the nucleus, is shown here to function directly as a free radical scavenger, and adducts formed as a result of this function are identified. These data suggest that spermine is a major natural intracellular compound capable of protecting DNA from free radical attack.
Size-tunable supramolecular nanoparticles mediated by ternary cucurbit[8]uril host–guest interactions (2013)

The formation of size-tunable, supramolecular nanoparticles (SNPs), employing cucurbit[8]uril-assisted naphthol-viologen charge-transfer complexes, is strongly time and temperature dependent. Yet, the ternary complex formation is fast at all temperatures employed. This indicates that SNP formation requires dynamic disassembly and reassembly of the constituting ternary complex units.
Catalytic Mechanism of Cytochrome P450 for 5′-Hydroxylation of Nicotine: Fundamental Reaction Pathways and Stereoselectivity (2011)

A series of computational methods were used to study how cytochrome P450 2A6 (CYP2A6) interacts with (S)-(-)-nicotine, demonstrating that the dominant molecular species of (S)-(-)-nicotine in CYP2A6 active site exists in the free base state (with two conformations, SR(t) and SR(c)), despite the fact that the protonated state is dominant for the free ligand in solution. The computational results reveal that the dominant pathway of nicotine metabolism in CYP2A6 is through nicotine free base oxidation. Further, first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations were carried out to uncover the detailed reaction pathways for the CYP2A6-catalyzed nicotine 5'-hydroxylation reaction. In the determined CYP2A6-(S)-(-)-nicotine binding structures, the oxygen of Compound I (Cpd I) can abstract a hydrogen from either the trans-5'- or the cis-5'-position of (S)-(-)-nicotine. CYP2A6-catalyzed (S)-(-)-nicotine 5'-hydroxylation consists of two reaction steps, that is, the hydrogen transfer from the 5'-position of (S)-(-)-nicotine to the oxygen of Cpd I (the H-transfer step), followed by the recombination of the (S)-(-)-nicotine moiety with the iron-bound hydroxyl group to generate the 5'-hydroxynicotine product (the O-rebound step). The H-transfer step is rate-determining. The 5'-hydroxylation proceeds mainly with the stereoselective loss of the trans-5'-hydrogen, that is, the 5'-hydrogen trans to the pyridine ring. The calculated overall stereoselectivity of ∼97% favoring the trans-5'-hydroxylation is close to the observed stereoselectivity of 89-94%. This is the first time it has been demonstrated that a CYP substrate exists dominantly in one protonation state (cationic species) in solution, but uses its less-favorable protonation state (neutral free base) to perform the enzymatic reaction.
A Block Copolymer for Functionalisation of Polymersome Surfaces (2008)

Abstract A block copolymer was designed to functionalise the surface of polystyrene‐based polymersomes via coaggregation. An α , ω ‐diacetylene‐functionalised poly(ethylene glycol) (PEG) was coupled to an azide‐terminated polystyrene via a Cu(I)‐catalysed cycloaddition to produce a PS‐ b ‐PEG polymer with an acetylene at its hydrophilic extremity. Incorporation of this ‘anchor’ compound in the bilayer of a polymersome places its bio‐orthogonal group at the surface of this aggregate. Its accessibility was demonstrated using an azido‐functionalised Candida antarctica Lipase B (CalB), which retained its activity while immobilised on the polymersome. magnified image
A uniformly stable conformal FDTD‐method in Cartesian grids (2003)

Abstract A conformal finite‐difference time‐domain algorithm for the solution of electrodynamic problems in general perfectly conducting 3D geometries is presented. Unlike previous conformal approaches it has the second‐order convergence without the need to reduce the maximal stable time step of conventional staircase approach. A novel proof for the local error rate for general geometries is given, and the method is verified and compared to other approaches by means of several numerical 2D examples. Copyright © 2003 John Wiley & Sons, Ltd.