gebhart/patrepeval huggingface dataset:
Functional characterisation of tetanus and botulinum neurotoxins binding domains (1999)

Tetanus and botulinum neurotoxins constitute a family of bacterial protein toxins responsible for two deadly syndromes in humans (tetanus and botulism, respectively). They bind with high affinity to neurons wherein they cause a complete inhibition of evoked neurotransmitter release. Here we report on the cloning, expression and use of the recombinant fragments of the heavy chains of tetanus neurotoxin and botulinum neurotoxin serotypes A, B and E as tools to study the neurospecific binding of the holotoxins. We found that the recombinant 50 kDa carboxy-terminal domains of tetanus and botulinum neurotoxins alone are responsible for the specific binding and internalisation into spinal cord cells in culture. Moreover, we provide evidence that the recombinant fragments block the internalization of the parental holotoxins in a dose-dependent manner, as determined by following the neurotoxin-dependent cleavage of their targets VAMP/synaptobrevin and SNAP-25. In addition, the recombinant binding fragments cause a significant delay in the paralysis induced by the corresponding holotoxin on the mouse phrenic nerve-hemidiaphragm preparation. Taken together, these results show that the carboxy-terminal domain of tetanus and botulinum neurotoxins is necessary and sufficient for the binding and internalisation of these proteins in neurons and open the possibility to use them as tools for the functional characterisation of the intracellular transport of clostridial neurotoxins.
Contrast Sensitivity and Reading Through Multifocal Intraocular Lenses (1992)

Multifocal intraocular lenses are intended to increase depth of focus for patients with cataracts, but optical considerations predict reduced retinal-image contrast. We evaluated visual performance through multifocal intraocular lenses by measuring contrast sensitivity functions and reading speed for age-matched groups with multifocal and monofocal intraocular lenses and two normal control groups. Contrast sensitivity functions of the patients with multifocal lenses did not differ significantly for optical distances differing by 2.5 diopters, indicating substantial depth of focus. Normal and monofocal contrast sensitivity functions were nearly identical, and both were about a factor of two higher than multifocal contrast sensitivity functions. Patients with multifocal lenses showed deficits in reading speed only for low-contrast text (less than 30%) and small letters (0.2 degree and 1.0 degree).
Generation of Monoclonal Rheumatoid Factors after Immunization with Collagen II‐Anti‐Collagen II Immune Complexes (1986)

Two monoclonal IgG rheumatoid factors were obtained after hybridization of spleen cells from DBA/1 mice immunized with immune complexes containing native collagen type II and a monoclonal anti-collagen II antibody. One of these rheumatoid factors reacted not only with purified murine Fc fragments, but also with Fab fragments of the anti-collagen II antibody used for immunization, whereas no reactivity was seen with Fab fragments from normal mouse IgG. The findings demonstrate the ability of immune complexes encompassing native collagen type II to induce production of IgG rheumatoid factors, and suggest that an idiotypic relationship may exist between certain rheumatoid factors and anti-collagen II antibodies.
Panther: Fast Top-k Similarity Search in Large Networks (2015)

Estimating similarity between vertices is a fundamental issue in network analysis across various domains, such as social networks and biological networks. Methods based on common neighbors and structural contexts have received much attention. However, both categories of methods are difficult to scale up to handle large networks (with billions of nodes). In this paper, we propose a sampling method that provably and accurately estimates the similarity between vertices. The algorithm is based on a novel idea of random path, and an extended method is also presented, to enhance the structural similarity when two vertices are completely disconnected. We provide theoretical proofs for the error-bound and confidence of the proposed algorithm. We perform extensive empirical study and show that our algorithm can obtain top-k similar vertices for any vertex in a network approximately 300x faster than state-of-the-art methods. We also use identity resolution and structural hole spanner finding, two important applications in social networks, to evaluate the accuracy of the estimated similarities. Our experimental results demonstrate that the proposed algorithm achieves clearly better performance than several alternative methods.
Bit allocation for dependent quantization with applications to multiresolution and MPEG video coders (1994)

We address the problem of efficient bit allocation in a dependent coding environment. While optimal bit allocation for independently coded signal blocks has been studied in the literature, we extend these techniques to the more general temporally and spatially dependent coding scenarios. Of particular interest are the topical MPEG video coder and multiresolution coders. Our approach uses an operational rate-distortion (R-D) framework for arbitrary quantizer sets. We show how a certain monotonicity property of the dependent R-D curves can be exploited in formulating fast ways to obtain optimal and near-optimal solutions. We illustrate the application of this property in specifying intelligent pruning conditions to eliminate suboptimal operating points for the MPEG allocation problem, for which we also point out fast nearly-optimal heuristics. Additionally, we formulate an efficient allocation strategy for multiresolution coders, using the spatial pyramid coder as an example. We then extend this analysis to a spatio-temporal 3-D pyramidal coding scheme. We tackle the compatibility problem of optimizing full-resolution quality while simultaneously catering to subresolution bit rate or quality constraints. We show how to obtain fast solutions that provide nearly optimal (typically within 0.3 dB) full resolution quality while providing much better performance for the subresolution layer (typically 2-3 dB better than the full-resolution optimal solution).
Normalization of microRNA expression levels in quantitative RT-PCR assays: Identification of suitable reference RNA targets in normal and cancerous human solid tissues (2008)

Proper normalization is a critical but often an underappreciated aspect of quantitative gene expression analysis. This study describes the identification and characterization of appropriate reference RNA targets for the normalization of microRNA (miRNA) quantitative RT-PCR data. miRNA microarray data from dozens of normal and disease human tissues revealed ubiquitous and stably expressed normalization candidates for evaluation by qRT-PCR. miR-191 and miR-103, among others, were found to be highly consistent in their expression across 13 normal tissues and five pair of distinct tumor/normal adjacent tissues. These miRNAs were statistically superior to the most commonly used reference RNAs used in miRNA qRT-PCR experiments, such as 5S rRNA, U6 snRNA, or total RNA. The most stable normalizers were also highly conserved across flash-frozen and formalin-fixed paraffin-embedded lung cancer tumor/NAT sample sets, resulting in the confirmation of one well-documented oncomir (let-7a), as well as the identification of novel oncomirs. These findings constitute the first report describing the rigorous normalization of miRNA qRT-PCR data and have important implications for proper experimental design and accurate data interpretation.
A simple approach to modeling cross-talk in integrated circuits (1994)

A simple engineering approach for rapid simulation of cross-talk in mixed-mode IC's using SPICE is presented. A side-by-side comparison of several cross-talk reduction schemes has shown that while an SOI-based process provides high isolation from cross-talk at low operating frequencies, its benefit is lost at high frequencies. Simple guard ring substrate contacts appear to be the technique best suited for preventing cross-talk at high operating frequencies. Lumped parameter equivalent circuits have also been developed to represent different isolation schemes in SPICE. The isolation characteristics of test structures employing the above techniques are computed using SPICE and the results compared with two-dimensional device simulation. The results are also compared with experimental measurements on actual silicon to validate the models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of the envelope proteins of pseudorabies virus (1984)

Previously we have reported that among the proteins of purified pseudorabies virions there are four major glycoproteins (T. Ben-Porat and A. S. Kaplan, Virology 41:265-273, 1970). Several minor glycoproteins can also be identified by two-dimensional gel electrophoresis. Removal of the viral envelope with Triton X-100 selectively removes from the virions all of the glycoproteins as well as several non-glycosylated proteins. Sedimentation analysis or chromatography of these proteins reveals that several are complexed with one another, some being covalently linked via disulfide bridges. Analysis of the proteins by immunoprecipitation with monoclonal antibodies reactive with the membrane proteins showed also that three of the four major virus glycoproteins (125K, 74K, and 58K; gIIa, gIIb, and gIIc, respectively) are linked covalently by disulfide bridges. Furthermore, all three share extensive sequence homology as indicated by the identity of their antigenic determinants and by partial peptide mapping; they probably originate from a single protein precursor. The fourth major glycoprotein (98K; gIII) is not complexed to any other protein. Three minor glycoproteins (130K [gI], 98K [gIV], and 62K [gV]), which form a noncovalently linked complex with a 115K nonglycosylated protein, have also been identified. Of the monoclonal antibodies used in this study, only those reactive with the major 98K glycoprotein (gIII) inhibit virus adsorption and neutralize virus infectivity in the absence of complement. However, all react with surface components of the virion, indicating that the proteins with which they react are exposed on the surface of the virions. A nomenclature for the pseudorabies virus glycoproteins is proposed.
Crosslinking-induced morphology change of latex nanoparticles: A study of RAFT-mediated polymerization in aqueous dispersed media using amphiphilic double-brush copolymers as reactive surfactants (2014)

Amphiphilic double-brush copolymers (DBCs) with each graft site quantitatively carrying both a hydrophilic poly(ethylene oxide) (PEO) graft and a hydrophobic polystyrene (PSt) graft are synthesized by sequential reversible addition-fragmentation chain transfer (RAFT) polymerization and ring-opening metathesis polymerization (ROMP). These DBCs are used as both surfactants and polyfunctional RAFT agents in the radical polymerization of St in aqueous dispersed media. Miniemulsions with narrowly dispersed St-based nanodroplets are readily obtained after ultrasonication of the reaction mixtures. Without the presence of crosslinker, chain-extension polymerization of St from the DBCs yields well-defined polymeric latexes with narrow size distributions. However, with the presence of divinylbenzene (DVB) as the crosslinker, vesicular polymeric nanoparticles are formed as the major product. Such crosslinking-induced change in morphology of the resulting latex nanomaterials may be ascribed to the increase of interfacial curvature in the heterophase systems during crosslinking polymerization. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 3250–3259
A Review of Integrative Imputation for Multi-Omics Datasets (2020)

Multi-omics studies, which explore the interactions between multiple types of biological factors, have significant advantages over single-omics analysis for their ability to provide a more holistic view of biological processes, uncover the causal and functional mechanisms for complex diseases, and facilitate new discoveries in precision medicine. However, omics datasets often contain missing values, and in multi-omics study designs it is common for individuals to be represented for some omics layers but not all. Since most statistical analyses cannot be applied directly to the incomplete datasets, imputation is typically performed to infer the missing values. Integrative imputation techniques which make use of the correlations and shared information among multi-omics datasets are expected to outperform approaches that rely on single-omics information alone, resulting in more accurate results for the subsequent downstream analyses. In this review, we provide an overview of the currently available imputation methods for handling missing values in bioinformatics data with an emphasis on multi-omics imputation. In addition, we also provide a perspective on how deep learning methods might be developed for the integrative imputation of multi-omics datasets.
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores (2006)

The method improves performance over existing state-of-the-art methods of MHC class II peptide binding predictions by using a custom, knowledge-based representation of peptides. Similarity scores, in contrast to a fixed-length, pocket-specific representation of amino acids, provide a flexible and powerful way of modelling MHC binding, and can easily be applied to other dynamic sequence problems.
Integrated diagnostic analysis of inertial confinement fusion capsule performance (2013)

A conceptual model is developed for typical inertial confinement fusion implosion conditions that integrates available diagnostic information to determine the stagnation properties of the interior fill and surrounding shell. Assuming pressure equilibrium at peak compression and invoking radiative and equation-of-state relations, the pressure, density, and electron temperature are obtained by optimized fitting of the experimental output to smooth, global functional forms. Typical observational data that may be used includes x-ray self-emission, directional neutron time-of-flight signals, neutron yield, high-resolution x-ray spectra, and radiographic images. This approach has been validated by comparison with radiation-hydrodynamic simulations, producing semi-quantitative agreement. Model results implicate poor kinetic energy coupling to the hot core as the primary cause of the observed low thermonuclear burn yields.
The interdependence of glycolytic and pentose cycle intermediates in ad libitum fed rats. (1986)

Equilibrium constants for reactions catalyzed by ribulose-5-phosphate 3-epimerase, [sigma xylulose-5-P]/[sigma ribulose-5-P] = 1.82, ribose-5-phosphate isomerase, [sigma Rib-5-P]/[sigma ribulose-5-P] = 1.20, transaldolase, [sigma erythrose-4-P] [sigma Fru-6-P]/[sigma sedoheptulose-7-P] [sigma glyceraldehyde 3-P] = 0.37, and transketolase, [sigma Fru-6-P] [sigma glyceraldehyde 3-P]/[sigma erythrose-4-P] [sigma xylulose-5-P] = 29.7 and [sigma Rib-5-P] [sigma xylulose-5-P]/[sigma sedoheptulose-7-P] [sigma glyceraldehyde 3-P] = 0.48, were redetermined under physiological conditions. The equilibrium constant for the combined glucose-6-P dehydrogenase and 6-phosphoglucono-gamma-lactonase reaction, [6-phosphogluconate3-] [NADPH] [H+]2/[Glc-6-P2-] [NADP+], was found to be at least 1 X 10(-9). Using these redetermined equilibrium constants, calculated values of pentose cycle intermediates, based on near equilibrium assumptions and the tissue content of Fru-6-P and glyceraldehyde 3-P, were found to be in good agreement with measured values for male Wistar rats injected with saline, 20 mumol/g pyruvate, 20 mumol/g gluconate, and 20 mumol/g ribose. Measured and calculated values for pentose cycle intermediates in saline injected animals were ribulose-5-P; 3.8 +/- 0.4 and 2.4 +/- 0.1 nmol/g; xylulose-5-P, 5.9 +/- 0.6 nmol/g and 4.3 +/- 0.2 nmol/g; sedoheptulose-7-P, 41.5 +/- 2.4 and 37.6 +/- 2.9 nmol/g; and combined sedopheptulose-7-P and Rib-5-P, 43.0 +/- 2.8 nmol/g and 40.5 +/- 3.0 nmol/g; liver content of erythrose-4-P was less than the detection limits of the assay, 2 nmol/g. Calculated erythrose-4-P was 0.23 +/- 0.01 nmol/g. Liver content of 6-phosphogluconate was 8.5 +/- 0.7 nmol/g. The free cytosolic [NADP+]/[NADPH] ratio calculated from the 6-phosphogluconate dehydrogenase redox couple, 0.0030 +/- 0.0002, was also in good agreement with that calculated from the malic enzyme redox couple, 0.0051 +/- 0.0007, and the isocitrate dehydrogenase redox couple, 0.0066 +/- 0.0008. These data indicate the interdependence of the liver content of glycolytic intermediates and pentose cycle intermediates in ad libitum fed rats.
Recent advances in insulated gate bipolar transistor technology (1990)

Device design of the insulated gate bipolar transistor (IGBT) has been optimized to reduce the distributed transmission-line effect. In addition, cell geometry is chosen to yield high latchup current capability and low forward-voltage drop simultaneously. The vertical structure is optimized to enhance both the turn-off speed and the safe operating area of the IGBTs. The turn-off time of the n-IGBT has been shortened to be as low as 40 ns. The p-channel IGBT latchup current has been improved four to six times over the previously reported results through innovative design and processes. An open-base bipolar transistor model has been implemented to investigate transient IGBT characteristics.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Altered Constitutive Expression of Fatty Acid-metabolizing Enzymes in Mice Lacking the Peroxisome Proliferator-activated Receptor α (PPARα) (1998)

Peroxisome proliferator-activated receptor alpha (PPARalpha) is a member of the steroid/nuclear receptor superfamily and mediates the biological and toxicological effects of peroxisome proliferators. To determine the physiological role of PPARalpha in fatty acid metabolism, levels of peroxisomal and mitochondrial fatty acid metabolizing enzymes were determined in the PPARalpha null mouse. Constitutive liver beta-oxidation of the long chain fatty acid, palmitic acid, was lower in the PPARalpha null mice as compared with wild type mice, indicating defective mitochondrial fatty acid catabolism. In contrast, constitutive oxidation of the very long chain fatty acid, lignoceric acid, was not different between wild type and PPARalpha null mice, suggesting that constitutive expression of enzymes involved in peroxisomal beta-oxidation is independent of PPARalpha. Indeed, the PPARalpha null mice had normal levels of the peroxisomal acyl-CoA oxidase, bifunctional protein (hydratase + 3-hydroxyacyl-CoA dehydrogenase), and thiolase but lower constitutive expression of the D-type bifunctional protein (hydratase + 3-hydroxyacyl-CoA dehydrogenase). Several mitochondrial fatty acid metabolizing enzymes including very long chain acyl-CoA dehydrogenase, long chain acyl-CoA dehydrogenase, short chain-specific 3-ketoacyl-CoA thiolase, and long chain acyl-CoA synthetase are also expressed at lower levels in the untreated PPARalpha null mice, whereas other fatty acid metabolizing enzymes were not different between the untreated null mice and wild type mice. A lower constitutive expression of mRNAs encoding these enzymes was also found, suggesting that the effect was due to altered gene expression. In wild type mice, both peroxisomal and mitochondrial enzymes were induced by the peroxisome proliferator Wy-14,643; induction was not observed in the PPARalpha null animals. These data indicate that PPARalpha modulates constitutive expression of genes encoding several mitochondrial fatty acid-catabolizing enzymes in addition to mediating inducible mitochondrial and peroxisomal fatty acid beta-oxidation, thus establishing a role for the receptor in fatty acid homeostasis.
Enzymic Modification of Insoluble Amylose in Organic Solvents (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic Modification of Insoluble Amylose in Organic SolventsFerdinando F. Bruno, Joseph A. Akkara, Madhu Ayyagari, David L. Kaplan, Richard Gross, Graham Swift, and Jonathan S. DordickCite this: Macromolecules 1995, 28, 26, 8881–8883Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ma00130a028https://doi.org/10.1021/ma00130a028research-articleACS PublicationsRequest reuse permissionsArticle Views226Altmetric-Citations48LEARN 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
Accuracy of Various Types of Neugebauer Model (1993)

In characterizing a color hardcopy device, it is necessary to establish the relationship between the input signals that drive the device and the colorimetric response of the device to these signals. Most printing devices are not adequately characterized by a simple linear transformation; hence one is left with the choice of either measuring the printer's colorimetric response at numerous points throughout the input signal space, or deriving a model to predict the printer's response. In this paper, we examine a model based approach to device characterization. In particular, we focus on a model developed by Hans Neugebauer for binary color printers employing a rotated halftone dot screen. In their simplest form, the so called &#x201C;Neugebauer equations&#x201D; are used to predict the broadband reflectance of a halftone pattern printed on paper. In this paper, we investigate the accuracy of the basic Neugebauer equations and several of its modifications. These equations involve some basic constraints which we will assume to be fulfilled throughout the discussion.An important application of the Neugebauer model is the calibration of binary color printers. Calibration, which requires a mapping from colorimetric signal space to the printer signal space, is the inverse problem of device characterization. Hence, calibration requires that the Neugebauer model be inverted. Since the Neugebauer equations are nonlinear, the inversion is not trivial, and requires numerical or statistical approaches (see [3] for examples). In this paper, we do not deal with the inverse calibration problem; rather, we focus only on the forward characterization problem. We evaluate and compare the use of various Neugebauer models to predict the colorimetric response of a Xerox 5775 color printer. This printer uses xerographic technology with four colorants, and has a resolution of 406 &#xD7; 1624 dpi.