gebhart/patrepeval huggingface dataset:
Deep learning with feature embedding for compound-protein interaction prediction (2016)

Abstract Accurately identifying compound-protein interactions in silico can deepen our understanding of the mechanisms of drug action and significantly facilitate the drug discovery and development process. Traditional similarity-based computational models for compound-protein interaction prediction rarely exploit the latent features from current available large-scale unlabelled compound and protein data, and often limit their usage on relatively small-scale datasets. We propose a new scheme that combines feature embedding (a technique of representation learning) with deep learning for predicting compound-protein interactions. Our method automatically learns the low-dimensional implicit but expressive features for compounds and proteins from the massive amount of unlabelled data. Combining effective feature embedding with powerful deep learning techniques, our method provides a general computational pipeline for accurate compound-protein interaction prediction, even when the interaction knowledge of compounds and proteins is entirely unknown. Evaluations on current large-scale databases of the measured compound-protein affinities, such as ChEMBL and BindingDB, as well as known drug-target interactions from DrugBank have demonstrated the superior prediction performance of our method, and suggested that it can offer a useful tool for drug development and drug repositioning.
Spatiotemporal Dynamics of Human Cognition (1999)

It is still largely unknown how the complex cortical neural network of the human brain can process information so rapidly. Multichannel evoked potential recordings with millisecond time resolution and spatiotemporal analysis methods now allow us to address this question and to unravel the temporal dynamics of the large-scale neurocognitive networks.
Diminished Primary and Secondary Influenza Virus-Specific CD8<sup>+</sup>T-Cell Responses in CD4-Depleted Ig<sup>−/−</sup>Mice (2000)

Optimal expansion of influenza virus nucleoprotein (D(b)NP(366))-specific CD8(+) T cells following respiratory challenge of naive Ig(-/-) microMT mice was found to require CD4(+) T-cell help, and this effect was also observed in primed animals. Absence of the CD4(+) population was consistently correlated with diminished recruitment of virus-specific CD8(+) T cells to the infected lung, delayed virus clearance, and increased morbidity. The splenic CD8(+) set generated during the recall response in Ig(-/-) mice primed at least 6 months previously showed a normal profile of gamma interferon production subsequent to short-term, in vitro stimulation with viral peptide, irrespective of a concurrent CD4(+) T-cell response. Both the magnitude and the localization profiles of virus-specific CD8(+) T cells, though perhaps not their functional characteristics, are thus modified in mice lacking CD4(+) T cells.
Kaempferol as Selective Human MAO-A Inhibitor: Analytical Detection in Calabrian Red Wines, Biological and Molecular Modeling Studies (2016)

The purpose of this work was to determine the kaempferol content in three red wines of Calabria, a southern Italian region with a great number of certified food products. Considering that wine cultivar, climate, and soil influence the qualitative and quantitative composition in flavonoids of Vitis vinifera L. berries, the three analyzed samples were taken from the 2013 vintage. Moreover, the Gaglioppo samples, with assigned Controlled Origin Denomination (DOC), were also investigated in the production of years 2008, 2010, and 2011. In addition to the analysis of kaempferol, which is present in higher concentration than in other Italian wines, in vitro assays were performed to evaluate, for the first time, the inhibition of the human monoamine oxidases (hMAO-A and hMAO-B). Molecular recognition studies were also carried out to provide insight into the binding mode of kaempferol and selectivity of inhibition of the hMAO-A isoform.
Computerized Colposcopy: Results of a Pilot Study and Analysis of Its Clinical Relevance (1995)

The integration of computer imaging and colposcopy can improve the colposcopic diagnostic accuracy. An inexperienced colposcopist may benefit from computerized support to obtain the most appropriate histologic specimen, and eventually access to distant consultation via modem or through on-line services. An additional advantage is the ability to develop a space-saving permanent record of digitized images readily available to review a patient's cervical history or perform effective programs of quality control in colposcopy.
Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems (2014)

RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on time scales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of evaluating these networks in vivo. Here, we adapt an Escherichia coli-based cell-free transcription-translation (TX-TL) system for rapidly prototyping RNA networks. We used this system to measure the response time of an RNA transcription cascade to be approximately five minutes per step of the cascade. We also show that this response time can be adjusted with temperature and regulator threshold tuning. Finally, we use TX-TL to prototype a new RNA network, an RNA single input module, and show that this network temporally stages the expression of two genes in vivo.
Difusión de los resultados de una investigación (2006)

En este número trataremos los pasos a seguir para realizar una publicación del trabajo de investigación elaborado, en concreto desarrollaremos como confeccionar el abstract para presentar a una reunión científica y de que manera debemos elaborar un artículo original para su publicación en una revista científica. Centro de Trabajo: Técnico de la Unidad de Formación e Investigación del Area 11 de Atención Primaria del Servicio Madrileño de Salud Fecha del Trabajo: 25/04/2006
Analýza citlivosti referenčních úrokových sazeb PRIBOR na změny repo sazby České národní banky [An analysis of PRIBOR interest rates sensitivity to changes in Czech national bank repo rate] (2004)

Since 1980's many central banks have been changing their monetary strategy to explicit inflation targeting. This new monetary concept is based on management of short-term interest rates in the context of relation between inflation prediction and central bank inflation target. Therefore we try to analyze the crucial problems of efficiency of the inflation targeting strategy - the causality and sensitivity between interest rates on Prague interbank market (PRIBOR) and Czech National Bank repo rate. For this purpose we use the framework of expectation theory with the term premium and simple deterministic regression models. We found out that as repo rate was sticky it led to higher volatility of PRIBOR before repo rate change and when the maturity of PRIBOR was increasing the sensitivity of PRIBOR to repo rate changes was strongly decreasing. In our opinion it's the result of at least partial adjustment of PRIBOR before repo rate changes.
Modelling line edge roughness in periodic line-space structures by Fourier optics to improve scatterometry (2014)

In the present paper, we propose a 2D-Fourier transform method as a simple and efficient algorithm for stochastical and numerical studies to investigate the systematic impacts of line edge roughness on light diffraction pattern of periodic line-space structures. The key concept is the generation of ensembles of rough apertures composed of many slits, to calculate the irradiance of the illuminated rough apertures far away from the aperture plane, and a comparison of their light intensities to those of the undisturbed, ’non-rough’ aperture. We apply the Fraunhofer approximation and interpret the rough apertures as binary 2D-gratings to compute their diffraction patterns very efficiently as the 2D-Fourier transform of the light distribution of the source plane. The rough edges of the aperture slits are generated by means of power spectrum density (PSD) functions, which are often used in metrology of rough geometries. The mean efficiencies of the rough apertures reveal a systematic exponential decrease for higher diffraction orders if compared to the diffraction pattern of the unperturbed aperture. This confirms former results, obtained by rigorous calculations with computational expensive finite element methods (FEM) for a simplified roughness model. The implicated model extension for scatterometry by an exponential damping factor for the calculated efficiencies allows to determine the standard deviation σ r of line edge roughness along with the critical dimensions (CDs), i.e., line widths, heights and other profile properties in the sub-micrometer range. First comparisons with the corresponding roughness value determined by 3D atomic force microscopy (3D AFM) reveal encouraging results.
Stochastic clustered-dot dithering (1999)

A new technique for building stochastic clustered-dot screens is being proposed. A large dither matrix comprising thousands of stochastically laid out screen dots is constructed by first laying out the screen dot centers. Screen dot centers are obtained by placing discrete disks of a chosen radius at free cell locations when traversing the dither array cells according to either a discretely rotated Hilbert space-filling curve or a random space-filling curve. After Delauney triangulation of the screen dot centers, the maximal surface of each screen dot is computed and isointensity regions are created. This isointensity map is converted into an antialiased gray scale image, i.e., into an array of preliminary threshold values. These threshold values are renumbered to obtain the threshold values of the final dither threshold array. By changing the disk radius, the screen dot size can be adapted to the characteristics of particular printing devices. Larger screen dots may improve the tone reproduction of printers having important dot gain
Cleaning of carbon contaminated vacuum ultraviolet-optics: Influence on surface roughness and reflectivity (1992)

The loss of transmission of optical elements by irradiation is a big problem of all synchrotron radiation laboratories. A major reason for the reduced transmission is the contamination with graphitic carbon that is due to adsorbed and cracked hydrocarbons. In accordance with earlier experiments at other storage rings, a cleaning procedure was developed at BESSY which consists of an oxygen discharge suspended by an rf cavity. The atomic oxygen that is created in the plasma reacts with the carbon to CO and CO2 and dissolves from the surface. The investigations focused on the items: (a) influence of the cleaning procedure on the reflectivity, (b) its influence on the surface roughness of the optical element, and (c) transfer of the procedure to other elements (e.g., vacuum ultraviolet detectors, diodes, different substrates). For an in-situ check of the cleaning efficiency, the reflectivity of gold-and carbon-coated test samples was measured before and after cleaning using the BESSY HE-TGM 2 beamline. The microroughness was investigated employing different surface sensitive techniques like scanning electron microscopy, scanning tunneling microscopy, and interferometry.
pH-Sensitive siRNA Nanovector for Targeted Gene Silencing and Cytotoxic Effect in Cancer Cells (2010)

A small interfering RNA (siRNA) nanovector with dual targeting specificity and dual therapeutic effect is developed for targeted cancer imaging and therapy. The nanovector is composed of an iron oxide magnetic nanoparticle core coated with three different functional molecules: polyethyleneimine (PEI), siRNA, and chlorotoxin (CTX). The primary amine group of PEI is blocked with citraconic anhydride that is removable at acidic conditions, not only to increase its biocompatibility at physiological conditions but also to elicit a pH-sensitive cytotoxic effect in the acidic tumor microenvironment. The PEI is covalently immobilized on the nanovector via a disulfide linkage that is cleavable after cellular internalization of the nanovector. CTX as a tumor-specific targeting ligand and siRNA as a therapeutic payload are conjugated on the nanovector via a flexible and hydrophilic PEG linker for targeted gene silencing in cancer cells. With a size of ∼60 nm, the nanovector exhibits long-term stability and good magnetic property for magnetic resonance imaging. The multifunctional nanovector exhibits both significant cytotoxic and gene silencing effects at acidic pH conditions for C6 glioma cells, but not at physiological pH conditions. Our results suggest that this nanovector system could be safely used as a potential therapeutic agent for targeted treatment of glioma as well as other cancers.
Laser-diode side-pumped Nd:YAlO_3 laser at 108 and 134 μm (1989)

We report efficient pulsed operation of a b-axis Nd:YAIO(3) laser rod at 1.08 and 1.34 microm side-pumped by laser-diode arrays. Optical slope efficiencies of 27% and 20% were obtained at these wavelengths. Polarized absorption spectra were taken for Nd:YAlO(3) along the three principal axes in the region of the pump bands from 780 to 830 nm.
Retinoic Acid Receptor γ1 (RARγ <sub>1</sub> ) Levels Control RARβ <sub>2</sub> Expression in SK-N-BE2(c) Neuroblastoma Cells and Regulate a Differentiation-Apoptosis Switch (1998)

Vitamin A and its derivatives (retinoids) have profound effects on the proliferation and differentiation of many cell types and are involved in a diverse array of developmental and physiological regulatory processes, including those responsible for the development of the mature nervous system. Retinoid signals are mediated by retinoic acid (RA) receptors (RARs) and retinoid X receptors (RXRs), which show distinct spatio-temporal patterns of expression during development and in adult tissues. We have used SK-N-BE2(c) neuroblastoma cells to study the effects of reciprocal regulation of expression of various RARs. We show that in these cells RARgamma1 acts as a repressor of RARbeta2 transcription in the absence of an agonist. In the presence of RA, the expression of RARgamma1 is reduced and that of RARbeta2 is induced. Overexpression of RARgamma1 neutralizes the effects of RA on RARbeta induction. Expression of an RARgamma1-specific antisense construct leads to the constitutive expression of RARbeta2. Although both overexpression of RARgamma1 and its reduction of expression can result in inhibition of cell proliferation, they induce different morphological changes. Reduction of RARgamma1 (and induction of RARbeta) leads to increased apoptosis, whereas RARgamma1 overexpression leads to differentiation in the absence of apoptosis. Thus, RARgamma1 appears to control a differentiation-apoptosis switch in SK-N-BE2(c) neuroblastoma cells.
Purification and characterization of a human pituitary growth factor (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurification and characterization of a human pituitary growth factorJohn M. Rowe, Stephen F. Henry, and Henry G. FriesenCite this: Biochemistry 1986, 25, 21, 6421–6425Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://pubs.acs.org/doi/10.1021/bi00369a012https://doi.org/10.1021/bi00369a012research-articleACS PublicationsRequest reuse permissionsArticle Views21Altmetric-Citations5LEARN 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
Prestack Data Enhancement Using Local Traveltime Approximation (2010)

The quality of recorded seismic data depends on many factors such as complexity of the subsurface, strong noise level, the topography of the earth’s surface, near surface inhomogeneities etc. We propose to use a local common offset (CO) approximation for traveltime stacking surface description. It allows to approximate traveltimes of reflection events in the vicinity of arbitrary ray and thus arbitrary offset. We present the general workflow and the implementation of a signal enhancement scheme.
Investigations on the influence of phosphonates in dispersing iron oxide (rust) by polymeric additives for industrial water applications (2014)

The performance of polymeric and non-polymeric additives as iron oxide (rust) dispersants in aqueous system has been investigated.The polymers evaluated include: homopolymers of acrylic acid, aspartic acid; copolymers of acrylic acid:vinyl acetate; acrylic acid: hydroxylpropyl acrylate, maleic acid:sulfonated styrene; and terpolymer of acrylic acid:2acrylamido-2-methyl propane sulfonic acid:sulfonated styrene.Phosphonates (or nonpolymeric additives) tested include: hydroxyphosphono acetic acid, HPA; aminotris(methylenephosphonic acid), AMP; hydroxyethylidene 1,1-diphosphonic acid, HEDP; 2-phosphonobutane 1,2,4-tricarboxylic acid, PBTC; and polyamino polyether methylene phosphonic acid, PAPEMP.Based on the performance data, polymers effectiveness as iron oxide dispersants is: terpolymer > copolymer > homopolymer.Under similar experimental conditions, phosphonates exhibit poor performance as iron oxide dispersants.It has also been observed that presence of phosphonates exhibit antagonistic effect on the performance of polymers.
Scanning tunneling microscopy of Si(001) (1986)

The atomic structure of the Si(001) surface has been examined with use of scanning tunneling microscopy (STM). The STM images reveal a dimer-type reconstruction and are inconsistent with chain and vacancy models. Both buckled and nonbuckled dimers are observed, giving rise to regions of (2\ifmmode\times\else\texttimes\fi{}1), c(4\ifmmode\times\else\texttimes\fi{}2), and p(2\ifmmode\times\else\texttimes\fi{}2) symmetry. The surface has a high density of vacancy-type defects, which appear to induce or stabilize buckling of the dimers at room temperature. The STM images also reveal the atomic structure at steps and defects. At high annealing temperature the step density increases dramatically, eventually leading to faceting.
UV curable pressure‐sensitive adhesives for fabricating semiconductors. I. Development of easily peelable dicing tapes (2003)

Abstract In order to develop easily peelable dicing tapes from diced wafers, UV curing of various pressure‐sensitive adhesives (PSAs) was studied. After UV irradiation, the adhesive strength of a PSA composition including a diacrylourethane oligomer (UDA) decreased drastically compared with other compositions. Because of network formation via UV irradiation, this composition had a greater volume contraction that might yield microvoids at the interface between the adhesive and the wafer, resulting in the loose adhesion. Its storage modulus increased up to about 1000 times that before UV curing, which was due to the crosslinking of the UDA component. It was suggested that the increased crosslinking density and the high internal coagulant energy of the UDA backbone structure caused a remarkable decrease of the adhesive strength. Furthermore, it was ascertained that the UV‐irradiated UDA adhesives left few residual deposits on the wafer released from the tape. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 436–441, 2003
TT virus: Preferential distribution in CD19<sup>+</sup> peripheral blood mononuclear cells and lack of viral integration (2001)

In order to determine whether peripheral blood mononuclear cells (PBMC) contain proviral DNA or double-stranded replicative forms of TT virus (TTV) and to define which cell subset harbors TTV, we analyzed 126 PBMC DNA samples by PCR, using the NG059/NG061/NG063 and the T801/T935 primer sets. TTV sequences were detected in nearly 20% (25/126) of PBMC DNA samples. Analysis of PBMC subsets revealed that TTV was preferentially distributed in CD19(+) cells. TTV DNA was also detected in CD3(+)/CD19(+) double-depleted cells but was undetectable in CD3(+) cells. After degradation of single-stranded DNA using mung bean nuclease (MBN), TTV could not be detected in previously TTV-positive PBMC DNA samples nor in DNA from CD19(+) cells, CD3(+)-depleted, and CD3(+)/CD19(+) double-depleted cells, indicating the lack of TTV DNA integration and the absence of viral double-stranded replicative intermediates in PBMC or PBMC subset cells. Our data indicate that PBMC and PBMC subsets are not the major sites of TTV replication.
High-frequency acousto-electric single-photon source (2000)

We propose a single optical photon source for quantum cryptography based on the acoustoelectric effect. Surface acoustic waves (SAWs) propagating through a quasi-one-dimensional channel have been shown to produce packets of electrons that reside in the SAW minima and travel at the velocity of sound. In our scheme, the electron packets are injected into a p-type region, resulting in photon emission. Since the number of electrons in each packet can be controlled down to a single electron, a stream of single- (or N-) photon states, with a creation time strongly correlated with the driving acoustic field, should be generated.
Trace analysis of polyaromatic hydrocarbons in water using multiphoton ionization-membrane introduction mass spectrometry (1998)

We have combined the resonance-enhanced multiphoton ionization (REMPI) technique with membrane introduction mass spectrometry to significantly enhance its performance in the direct analysis of select polyaromatic hydrocarbons (PAHs) in water. We have used UV radiation from a pulsed KrF (λ = 248nm) excimer laser to selectively ionize PAHs sampled directly from their aqueous solutions by a silicone membrane probe. The ionization and mass analysis is carried out using a modified GCQ ion trap mass spectrometer. The REMPI method provides exceptional selectivity as demonstrated in the detection of parts-per-trillion levels of pyrene in the presence of abundant background neutrals from the matrix, pump-oil, membrane and other sources. The instrumentation and experimental results using naphthalene and pyrene are presented. The selectivity and sensitivity of standard electron impact ionization is also compared with 248 nm multiphoton ionization to illustrate the improvements in performance. © 1998 John Wiley & Sons, Ltd. This paper was produced under the auspices of the US Government and it is therefore not subject to copyright in the US.