gebhart/patrepeval huggingface dataset:
Channel-Opening Mechanism of a Kainate-Activated Glutamate Receptor:  Kinetic Investigations Using a Laser-Pulse Photolysis Technique<sup>†</sup> (1998)

Kainate is an excitatory neurotransmitter that binds to the kainate and AMPA receptor subtypes of the glutamate receptor and triggers the formation of cation permeable transmembrane channels in these receptors. In the present report the channel-opening mechanism of the AMPA receptors by kainate has been determined in rat hippocampal neurons using two different kinetic methods, namely, the rapid-flow method (cell-flow) with a 10 ms time resolution and a laser-pulse photolysis technique with a approximately 65 microseconds time resolution. The whole-cell currents induced by kainate, using the cell-flow method, are nondesensitizing and inhibited significantly by CNQX and hence pertain to activation of the AMPA receptors and not the kainate receptors. The cell-flow measurements were used to evaluate the constants pertaining to the minimum mechanism that could account for the concentration of the receptor in the open-channel form over a 500-fold range of kainate concentration. These constants, namely, the intrinsic dissociation constant of kainate from the AMPA receptor and the channel-opening equilibrium constant, were determined to be 140 +/- 30 microM and 8 +/- 2, respectively. On the other hand, the kinetics of the steps leading to channel opening was evaluated using the laser-pulse photolysis techniques. In this technique whole-cell currents were obtained by releasing kainate in the submillisecond time scale near the cell by photolysis of N-(alpha-carboxy-2-nitrobenzyl) kainate. The concentration of the released kainate was calculated by comparing the whole-cell currents obtained from the laser-pulse photolysis experiments with the whole currents obtained with 100 microM kainate on the same cell using cell-flow measurements. The rate constants for channel opening and closing were then determined from the observed rate constants for the current rise obtained as a function of kainate concentration. These rates were 5000 +/- 2000 and 640 +/- 30 s-1, respectively. The rate and equilibrium constants obtained in the present report allow an evaluation of the fraction of the receptors in the open-channel form as a function of time and kainate concentration, hence providing insight into the role of kainate in neuronal signal transmission.
Influence of Hydraulic Retention Time on Extent of PCE Dechlorination and Preliminary Characterization of the Enrichment Culture (2001)

The extent of tetrachloroethene (PCE) dechlorination in two chemostats was evaluated as a function of hydraulic retention time (HRT). The inoculum of these chemostats was from an upflow anaerobic sludge blanket (UASB) reactor that rapidly converts PCE to vinyl chloride (VC) and ethene. When the HRT was 2.9 days, PCE was converted only to cis-dichloroethene (cDCE). When the HRT was 11 days, the end products were VC and ethene. Further studies showed that the dechlorinating microbial community in the UASB reactor contained two distinct populations, one of which converted PCE to cDCE and the other cDCE to VC and ethene. Methanogenic activity was very low in these cultures. The cDCE dechlorinating culture apparently has a lower growth rate than the PCE dechlorinating culture, and as a result, at a shorter HRT, the cDCE dechlorinating culture was washed out from the system leading to incomplete dechlorination of PCE. Both enrichment cultures used pyruvate or hydrogen as electron donors for dechlorination. Acetate was the carbon source (but not energy source) when hydrogen was used. Both cultures had undefined nutrient requirements and needed supplements of cell extract obtained from the mixed culture in the UASB reactor. However, the two cultures were different in their response to the addition of an inhibitor of methanogenesis (2-bromoethanesulfonate [BES]). BES inhibited the dechlorinating activity of the enriched cDCE dechlorinating culture, but had no influence on the PCE dechlorinating culture. Preliminary studies on BES inhibition are presented.
SPAD Image Sensor With Analog Counting Pixel for Time-Resolved Fluorescence Detection (2013)

This paper presents a 32 × 32 pixel image sensor for time-gated fluorescence lifetime detection based on single-photon avalanche diodes. The sensor, fabricated in a high-voltage 0.35- μm CMOS technology, uses an analog counting approach to minimize the area occupation of pixel electronics while maintaining a nanosecond timing resolution and shot-noise-limited operation. The all nMOS pixel is formed by 12 transistors and features 25- μm pitch and 20.8% fill factor. The chip includes a phase-locked loop circuit for gating window generation, working at a maximum repetition frequency of 40 MHz, while the sensor can be gated at frequency up to 80 MHz using an external delay generator. Optical characterization with a picosecond-pulsed laser showed a minimum gating window width of 1.1 ns. Example images acquired in both continuous and time-gated mode are presented, together with a lifetime image obtained with the sensor mounted on a fluorescence microscope.
A physically-based facial skin model to simulate facial expressions on digitally scanned 3D models (2007)

In this paper we present a physically-based 3D facial skin model based on biomechanical properties of human facial anatomy. The skin model is mainly formed of two DNURBS surfaces as a two layered membrane structure. The model represents the soft tissue layer which covers the skull and is attached to the skull via muscle insertion points. The model is fitted on digitally scanned 3D facial surfaces and controlled via DNURBS control points, which are spatially close to muscle insertion points. The face (skin model) is modified by displacing control points to mimic muscle contraction in order to simulate facial expressions. The system is solved and the simulations are displayed on a graphics workstation, where near real-time performance is achieved as opposed to many other existing physically- based methods.
Prevention and treatment of cancer with indole-3-carbinol. (2001)

Indole-3-carbinol (I-3-C) is a naturally occurring constituent of many plant foods. Oral administration of I-3-C has been shown to manipulate estrogen metabolism in humans in a possibly beneficial manner. I-3-C increases the 2/16-hydroxyestrone ratio, a ratio found to be predictive of breast cancer risk in some prospective studies. Animal and in vitro studies have identified a number of other possibly beneficial effects of I-3-C and its metabolites, including inhibition of estrogen binding and modulation of oncogene expression. A chemopreventive effect of I-3-C has been demonstrated in a number of animal models. Some chemical carcinogenesis models have found a tumor promoting effect of I-3-C, however. Epidemiological studies support the hypothesis that high intakes of I-3-C may have broad chemopreventive effect. Preliminary human trials have demonstrated that I-3-C is well tolerated and has a sustained estrogen modifying effect. I-3-C is a good candidate for clinical trial in women at increased risk of developing breast cancer.
Optimization of the cyclotide framework to improve cell penetration properties (2015)

Cell penetrating peptides have been regarded as promising vectors to deliver hydrophilic molecules inside cells. Although they are great tools for research and have high potential as drug delivery systems, their application as drugs is impaired by their low stability in serum. Cyclotides, cyclic disulfide-rich peptides from plants, are ultra-stable molecules that have inspired applications in drug design as they can be used as scaffolds to stabilize linear bioactive sequences. Recently, they have also been shown to possess cell-penetrating properties. The combination of their remarkable stability and cell-penetrating properties opens new avenues for the application of peptides to bind to and inhibit intracellular proteins. Nevertheless, for a broader application of these molecules as vectors is of utmost importance to improve their cellular internalization efficiency. In this study we successfully modified MCoTI-II, one of the most widely studied cyclotide scaffolds in drug design, and improved its internalization properties. The internalization of the newly designed MCoTI-II is as efficient as the gold standard cell-penetrating peptide (CPP) TAT and maintains all the required features as a template to graft desired bioactivities.
Syntheses of heterocyclic compounds. CDLI. Alternative photolytic total syntheses of O-methylandrocymbine and kreysigine (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of heterocyclic compounds. CDLI. Alternative photolytic total syntheses of O-methylandrocymbine and kreysigineT. Kametani, Y. Satoh, S. Shibuya, M. Koizumi, and K. FukumotoCite this: J. Org. Chem. 1971, 36, 24, 3733–3736Publication Date (Print):December 1, 1971Publication History Published online1 May 2002Published inissue 1 December 1971https://pubs.acs.org/doi/10.1021/jo00823a015https://doi.org/10.1021/jo00823a015research-articleACS PublicationsRequest reuse permissionsArticle Views64Altmetric-Citations7LEARN 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
Application of generalized partial volume estimation for mutual information based registration of high resolution SAR and optical imagery (2008)

Mutual information (MI) has proven its effectiveness for automated multimodal image registration for numerous remote sensing applications like image fusion. We analyze MI performance with respect to joint histogram bin size and the employed joint histogramming technique. The affect of generalized partial volume estimation (GPVE) utilizing B-spline kernels with different histogram bin sizes on MI performance has been thoroughly explored for registration of high resolution SAR (TerraSAR-X) and optical (IKONOS-2) satellite images. Our experiments highlight possibility of an inconsistent MI behavior with different joint histogram bin size which gets reduced with an increase in order of B-spline kernel employed in GPVE. In general, bin size reduction and/or increasing B-spline order have a smoothing affect on MI surfaces and even the lowest order B-spline with a suitable histogram bin size can achieve same pixel level accuracy as achieved by the higher order kernels more consistently.
Quantitative morphology and regional and laminar distributions of senile plaques in Alzheimer's disease (1985)

Senile (neuritic) plaques are one of the two major neuropathologic hallmarks of Alzheimer's disease. Despite their obvious importance (e.g., they are significantly correlated with severity of dementia), there is little present information about their etiology, the specific neuronal elements that form them, or a quantitative definition of where in cortex they occur. We have sought clues to these issues by quantifying regional and laminar distributions of neocortical plaques and setting these data against the present wealth of information on neocortical cytoarchitecture and neurotransmitter-specific circuitry. Senile plaques are significantly more numerous in associative regions of neocortex than in sensory areas and are significantly more numerous in cortical laminae dominated by their role in corticocortical, associative relations. Plaques are also largest in those laminae characterized by large pyramidal cells subserving input/output functions. The quantitative distribution of senile plaques in Alzheimer's disease does not necessarily correspond to innervation patterns for any known subcortical afferent system. This, coupled with the finding that several different neurotransmitters can be immunocytochemically co-localized with plaques, casts doubts on a primary role of cholinergic deterioration in plaque etiology, and opens the possibility that neocortical senile plaques may derive from pathologic events initiated in the neocortex.
Low-frequency amplifiers for PVDF film sensors (2008)

This paper proposes instrumental ion amplifiers for use with large area Polyvinylidine Diflouride (PVDF) sensors designed to detect rodent motion. The sensor behaves as a pressure-to-voltage converter in series with a parasitic capacitance. Motion signals critical for classifying rodent behavior range from 0.5 Hz to 20 Hz. Amplification on the order of 20 dB is required for the pass-band before digitization. Amplifier A is presently used in art experimental system. This amplifier has slow response time with noticeable drift. Amplifier B is designed to overcome these obstacles. It is more complex but reduces the drift and noise floor, while decreasing the response time. Performance is evaluated with metrics based on low-frequency drift and noise-floor power computed over a 19-hour period and with recovery time from saturation. The comparison shows amplifier B with a faster response and lower drift than amplifier A.
Equal Reverberance Matching of Music (2009)

This study explores the reverberance of music in simulated auditoria. It investigates the effects of gain on the reverberance of an anechoic music recording convolved with auditorium impulse responses. Based on objective loudness modelling, our hypothesis is that gain has a positive effect on reverberance (even though it has no effect on reverberation time). In a subjective experiment, participants adjusted decay rate of auditorium impulse responses convolved with an anechoic music sample in order to match the reverberance of each music stimulus to that of a reference music sample. Results support the hypothesis, and are similar to those of a previous study in which auditorium impulse responses (without convolution) were matched similarly for reverberance.
A real‐time respiratory motion monitoring system using <scp>KINECT</scp>: Proof of concept (2012)

It is feasible to use the KINECT for respiratory motion tracking. Traces are similar to those of a clinically used strain gauge system. The KINECT-based system provides a new and economical way to monitor respiratory motion.
Properties of P3-esters of nucleoside triphosphates as substrates for RNA polymerase from Escherichia coli (1981)

P3-[(2,4-Dinitrophenyl)amino]ethyl (DNPNHEt) and P3-methyl phosphate esters of nucleoside 5'-triphosphates have been synthesized. Their properties as substrates in the initiation and elongation steps of transcription have been examined by using RNA polymerase from Escherichia coli and poly[d(A-T)] or T7 DNA as templates. It is shown that transcription can be initiated by ATP-EtNHDNP and that 2,4-dinitrophenyl residues are incorporated at the 5' end of the RNA molecules. Steady-state kinetic experiments of abortive initation on promoters A1 and A3 of T7 DNA revealed that ATP-EtNHDNP, ADP-EtNHDNP, and ATP-OCH3 have lower Km values and markedly reduced Vmax values compared to those of ATP. The two classes of esters, NTR-EtNHDNP and NTP-OCH3, were found to differ regarding their utilization as substrates for elongation. Both ATP-OCH3 and UTP-OCH3 are substrates for transcription. However, only the pyrimidine derivatives of NTP-EtNHDNP are elongation substrates which release DNPNHEt-PP upon utilization. This dramatic difference between the purine and pyrimidine derivatives of NTP-EtNHDNP reflects a selective process in the transcriptional complex for purines and pyrimidines.
Effect of caries disclosing agents on bond strengths of total-etch and self-etching primer dentin bonding systems to resin composite. (2002)

This study examined the effect of caries disclosing dyes on composite to dentin shear bond strengths of a total etch, one-bottle and two self-etching, non-rinsing primer dental adhesives. Two caries disclosing dyes were evaluated, Seek and Snoop, with three dentin adhesives, Prime & Bond NT, Prompt L-Pop and Clearfil SE Bond. Extracted human molars stored in 0.2% sodium azide were sectioned longitudinally to expose dentin and embedded in acrylic, leaving the dentin exposed. Each dentin adhesive had three test groups (n=12); a control and one with each of the caries disclosing dyes. The control group had the dentin conditioned and the adhesive applied following the manufacturer's instructions. The caries disclosing dye groups had the dentin first treated for 10 seconds with the disclosing dye, rinsed, then the dentin adhesives were applied as in the controls. A column of Tetric Ceram was bonded after dentin adhesive placement to each specimen and light cured. Specimens were stored in room temperature water for 24 hours, thermocycled for 1,000 cycles between 5 degrees C and 55 degrees C and tested in shear until failure. Mean +/- SD shear bond values (SBV) were determined in MPa. A one-way ANOVA and Student Neuman Keuls multiple comparison test within each DBS were performed at a significance level ofp<0.05 to analyze the caries disclosing dyes input on SBV versus the controls. Surface analysis to determine the nature of the type of dentin/composite fracture/ separation was also performed. For the fracture analysis data, a Chi-Square test was performed at a significance level of p<0.05. The results of this study indicate that using the two tested caries disclosing dyes, with a total etch, one bottle and two self-etching, non-rinsing primer dental adhesives did not negatively affect the dentin-to-composite shear bond strengths of the three tested dentin bonding systems (p>0.05).
Chemoselective Hydrogenation of Nitro Compounds with Supported Gold Catalysts (2006)

The selective reduction of a nitro group when other reducible functions are present is a difficult process that often requires stoichiometric amounts of reducing agents or, if H2 is used, the addition of soluble metals. Gold nanoparticles supported on TiO2 or Fe2O3 catalyzed the chemoselective hydrogenation of functionalized nitroarenes with H2 under mild reaction conditions that avoided the accumulation of hydroxylamines and their potential exothermic decomposition. These chemoselective hydrogenation gold catalysts also provide a previously unknown route for the synthesis of the industrially relevant cyclohexanone oxime from 1-nitro-1-cyclohexene.
Correlation of E protein binding with cell susceptibility to dengue 4 virus infection (1992)

Supernatant culture fluids from dengue virus type 4 (DEN-4)-infected cultures of monkey kidney Vero cells and Aedes albopictus C6/36 cells contained the virion structural proteins; secreted NS1 was found only in supernatants from infected Vero cells. Using supernatant culture fluids from [35S]methionine-labelled, virus-infected Vero and C6/36 cells, binding of radiolabelled viral proteins was examined with various cell lines varying in susceptibility to DEN-4 infection. Binding of viral E protein was observed with the highly infectible Vero and LLC-MK2 cell lines, whereas a very small degree of binding was seen with four other cell lines (mouse fibroblast L929, bovine kidney MDBK, human hepatoma Hep G2 and primary human endothelial cells) which are less susceptible to DEN-4 infection. The results suggest that cell susceptibility to DEN-4 may be determined largely at the stage of virus binding, i.e. by the presence of a cell receptor capable of binding viral E protein.
Design, Synthesis, and Structural Analysis of Influenza Neuraminidase Inhibitors Containing Pyrrolidine Cores (2001)

The discovery of (+/-)-(2S,3R,4R)-2-(trifluoroacetamido)methyl-3-amino-1-(N'-ethyl-N'-isopropylcarbamyl)pyrrolidine-4-carboxylic acid (A-192558, 20e) as a potent inhibitor of influenza neuraminidase (NA) is described. Efficient syntheses of two core structures, cis-3-(allyloxycarbonyl)amino-1-(9'-fluorenylmethoxycarbonyl)pyrrolidine-4-carboxylic acid (7) and tert-butyl (+/-)-(2S,3R,4R)-2-aminomethyl-3-bis(tert-butyloxycarbonyl)amino-1-(N'-ethyl-N'-isopropylcarbamyl)pyrrolidine-4-carboxylate (18b), were developed. Starting with these core structures and using available structural information of the NA active site as the guide, analogues were synthesized in both the tri- and tetrasubstituted pyrrolidine series by means of high-throughput parallel synthesis in solid or solution phase for expeditious SAR. These studies accelerated the identification of (+/-)-(2S,3R,4R)-2-(trifluoroacetamido)methyl-3-amino-1-(N-ethyl-N-isopropylcarbamyl)pyrrolidine-4-carboxylate (20e, A-192558) as the most potent NA inhibitor in this series (IC50 = 0.2 microM against NA A and 8 microM against NA B). The X-ray crystallographic structure of A-192558 bound to NA revealed the predicted interaction of the carboxylic group with the positively charged pocket (Arg118, Arg292, Arg371) and interaction of the trifluoroacetamino residue with the hydrophobic pocket (Ile222, Trp178) of the enzyme active site. Surprisingly, the ethyl and isopropyl groups of the urea functionality induced a conformational change of Glu276, turning the Glu276/Glu277 hydrophilic pocket, which normally accommodates the triglycerol side chain of substrate sialic acid, into an induced hydrophobic pocket.
Surface Interactions of C<sub>2</sub> and C<sub>3</sub> Polyols with γ-Al<sub>2</sub>O<sub>3</sub> and the Role of Coadsorbed Water (2012)

The formation of surface species from two- and three-carbon polyols on γ-Al(2)O(3) in the presence and absence of coadsorbed water is investigated. Aqueous-phase adsorption isotherms indicate that competitive adsorption between water and polyol inhibits the uptake of the polyol molecules on γ-Al(2)O(3) and that the polyol with the most hydroxyl groups, glycerol, experienced the greatest uptake. Deuterium solid echo pulse NMR measurements support the fact that glycerol strongly interacts with γ-Al(2)O(3) in the presence of physisorbed water and that ethylene glycol interacts with γ-Al(2)O(3) only after the physisorbed water has been removed. In situ high-vacuum FT-IR analysis combined with DFT simulations demonstrate that glycerol readily forms a multidentate alkoxy species through its primary hydroxyl groups with coordinatively unsaturated Al atoms of γ-Al(2)O(3) in the presence of physisorbed water. This surface species exhibits a bridging alkoxy bond from one of its primary hydroxyl groups and a strong interaction with the remaining primary hydroxyl group. FT-IR analysis of 1,3-propanediol on γ-Al(2)O(3) also demonstrates the formation of a multidentate alkoxy species in the presence of coadsorbed water. In contrast, polyols with hydroxyl groups only on the one- and two-carbon atoms, ethylene glycol, and 1,2-propanediol do not form alkoxy bonds with the γ-Al(2)O(3) surface when coadsorbed water is present. These polyols will form alkoxy bonds to γ-Al(2)O(3) when coadsorbed water is removed, and these alkoxy species are removed when water is readsorbed on the sample. The formation of strongly bound, stable multidentate alkoxy species by ethylene glycol and 1,2-propanediol on γ-Al(2)O(3) is prevented by steric limitations of vicinal alcohol groups.
Maggot Debridement Therapy (2005)

This clinical in vivo study supports in vitro studies in which containment of maggots was found to reduce the effectiveness of maggot debridement therapy.