gebhart/patrepeval huggingface dataset:
Ig‐like transcript 4 as a cellular receptor for soluble complement fragment C4d (2015)

Complement regulation leads to the generation of complement split products (CSPs) such as complement component (C)4d, a marker for disease activity in autoimmune syndromes or antibody-mediated allograft rejection. However, the physiologic role of C4d has been unknown. By screening murine thymoma BW5147 cells expressing a cDNA library generated from human monocyte-derived dendritic cells with recombinant human C4d, we identified Ig-like transcript (ILT)4 and ILT5v2 as cellular receptors for C4d. Both receptors, expressed on monocytes, macrophages, and dendritic cells, also interacted with the CSPs C3d, C4b, C3b, and iC3b. However, C4d did not bind to classic complement receptors (CRs). Interaction between cell surface-resident ILT4 and soluble monomeric C4d resulted in endocytosis of C4d. Surprisingly, binding of soluble ILT4 to C4d covalently immobilized to a cellular surface following classic complement activation could not be detected. Remarkably, C4d immobilized to a solid phaseviaits intrinsic thioester conferred a dose-dependent inhibition of TNF-α and IL-6 secretion in monocytes activatedviaFc-cross-linking of up to 50% as compared to baseline. Similarly, C4d conferred an attenuation of intracellular Ca(2+)flux in monocytes activatedviaFc-cross-linking. In conclusion, ILT4 represents a scavenger-type endocytotic CR for soluble monomeric C4d, whereas attenuation of monocyte activation by physiologically oriented C4d on a surface appears to be dependent on a yet to be identified C4d receptor.-Hofer, J., Forster, F., Isenman, D. E., Wahrmann, M., Leitner, J., Hölzl, M. A., Kovarik, J. K., Stockinger, H., Böhmig, G. A., Steinberger, P., Zlabinger, G. J. Ig-like transcript 4 as a cellular receptor for soluble complement fragment C4d.
Cloud Advisor - A Framework towards Assessing the Trustworthiness and Transparency of Cloud Providers (2014)

We propose a Cloud Advisor framework that couples two salient features: trustworthiness and transparency measurement. It provides a mechanism to measure trustworthiness based on the history of the cloud provider taking into account evidence support and to measure transparency based on the Cloud Controls Matrix (CCM) framework. The selection process is based on a set of assurance requirements that if are met by the cloud provider or if it has been considered in a tool it could bring assurance and confidence to cloud customers.
Bioengineered corporal tissue for structural and functional restoration of the penis (2009)

Various reconstructive procedures have been attempted to restore a cosmetically acceptable phallus that would allow normal reproductive, sexual, and urinary function in patients requiring penile reconstruction. However, these procedures are limited by a shortage of native penile tissue. We previously demonstrated that a short segment of the penile corporal body can be replaced using naturally derived collagen matrices with autologous cells. In the current study, we examined the feasibility of engineering the entire pendular penile corporal bodies in a rabbit model. Neocorpora were engineered from cavernosal collagen matrices seeded with autologous cells using a multistep static/dynamic procedure, and these were implanted to replace the excised corpora. The bioengineered corpora demonstrated structural and functional parameters similar to native tissue and male rabbits receiving the bilateral implants were able to successfully impregnate females. This study demonstrates that neocorpora can be engineered for total pendular penile corporal body replacement. This technology has considerable potential for patients requiring penile reconstruction.
Characterization of the Key Aroma Compounds in an American Bourbon Whisky by Quantitative Measurements, Aroma Recombination, and Omission Studies (2008)

Thirty-one of the 45 odor-active compounds previously identified by us in an American Bourbon whisky were quantified by stable isotope dilution assays. Also for this purpose, new synthetic pathways were developed for the synthesis of the deuterium-labeled whisky lactone as well as for gamma-nona- and gamma-decalactone. To obtain the odor activity values (OAVs), the concentrations measured were divided by the odor thresholds of the odorants determined in water/ethanol (6:4 by vol.). Twenty-six aroma compounds showed OAVs >1, among which ethanol, ethyl (S)-2-methylbutanoate, 3-methylbutanal, 4-hydroxy-3-methoxybenzaldehyde, (E)-beta-damascenone, ethyl hexanoate, ethyl butanoate, ethyl octanoate, 2-methylpropanal, (3S,4S)- cis-whiskylactone, (E, E)-2,4-decadienal, 4-allyl-2-methoxyphenol, ethyl-3-methylbutanoate, and ethyl 2-methylpropanoate showed the highest values. The overall aroma of the Bourbon whisky could be mimicked by an aroma recombinate consisting of the 26 key odorants in their actual concentrations in whisky using water/ethanol (6:4 by vol.) as the matrix. Omission experiments corroborated the importance of, in particular, 4-hydroxy-3-methoxybenzaldehyde, (3S,4S)-cis-whiskylactone, ethanol, and the entire group of esters for the overall aroma of the Bourbon whisky.
Forward–adjoint fluorescence model: Monte Carlo integration and experimental validation (1997)

The adjoint form of the photon transport equation is applied to a generalized fluorescence detection problem, and its accuracy is empirically tested. This approach can be interpreted as mathematically reversing the temporal flow of fluorescent photons; that is, they are tracked from the detector back to potential sites of origin in the scattering medium. The result is a distribution of potential fluorescing sites that, when properly normalized, gives a probability field of the relative importance of the photon starting position and direction to the resulting signal. This adjoint solution can be combined with the temporally forward-derived distribution of absorbed excitation photons to evaluate the fluorescence excitation detection scheme. This bypasses the normal, temporal derivation wherein the fluorescence transport solution is dependent on the result of the excitation transport solution.
Functional reconstitution in lipid vesicles of influenza virus M2 protein expressed by baculovirus: evidence for proton transfer activity (1994)

The influenza virus M2 protein was expressed from a recombinant baculovirus in Spodoptera frugiperda Sf9 cells, purified and reconstituted into artificial membrane vesicles. The specific inhibitor amantadine overcame the toxic activity of the protein and boosted the rate of M2 synthesis by a factor of 10, allowing yields of about 1 mg of purified M2 protein per g of Sf9 cells. M2 protein expressed in this system was phosphorylated and palmitoylated and displayed properties similar to the authentic virus protein. Purified wild-type M2 protein and an amantadine-resistant mutant M2 (M2 delta) with a deletion in the trans-membrane domain (amino acids 28 to 31) were incorporated into lipid vesicles, which were loaded with the fluorescent pH indicator pyranine. On imposition of an ionic gradient, M2 caused a decrease in intravesicular pH, which was susceptible to inhibition by 0.1 to 1 microM-rimantadine or N-ethyl-rimantadine. M2 delta behaved similarly but exhibited the expected drug resistance. These experiments indicate that isolated M2 functions as an ion channel and demonstrates in vitro M2-mediated proton translocation.
Intramolecular Asymmetric Amidations of Sulfonamides and Sulfamates Catalyzed by Chiral Dirhodium(II) Complexes (2004)

Abstract Enantioselective intramolecular amidation of aliphatic sulfonamides was achieved for the first time by means of chiral carboxylatodirhodium(II) catalysts in conjunction with PhI(OAc) 2 and MgO in high yields and with enantioselectivities of up to 66% ( Scheme 3, Table 1 ). The best results were obtained with [Rh 2 {( S )‐nttl) 4 ] and [Rh 2 {( R )‐ntv) 4 ] as catalysts (( S )‐nttl=( αS )‐ α ‐( tert ‐butyl)‐1,3‐dioxo‐2 H ‐benz[ de ]isoquinoline‐2‐acetato, ( R )‐nto=( αR )‐ α ‐isopropyl‐1,3‐dioxo‐2 H ‐benz[ de ] isoquinoline‐2‐acetato). In addition, these carboxylatodirhodium(II) catalysts were also efficient in intramolecular amidations of aliphatic sulfamates esters, although the enantioselectivity of these latter reactions was significantly lower ( Scheme 4, Table 3 ).
Expression of Blood Group Lewis b Determinant from Lewis a: Association of this Novel .alpha.(1,2)-L-Fucosylating Activity with the Lewis Type .alpha.(1,3/4)-L-Fucosyltransferase (1995)

Blood group H type 1 [Fuc alpha (1,2)Gal beta (1,3)GlcNAc beta-->] is known as the precursor structure of the blood group determinant, Lewis b [Fuc alpha (1,2)Gal beta (1,3)(Fuc alpha (1,4))GlcNAc beta-->]. Recently, a new biosynthetic route for Lewis b from Lewis a [Gal beta (1,3)(Fuc alpha (1,4))GlcNAc-->] was identified in human gastric carcinoma cells, colon carcinoma Colo 205, and ovarian tumor. The present study demonstrates the association of this new type of alpha (1,2)-L-fucosyltransferase (FT) activity with the Lewis-type alpha (1,3/4)-L-FT as follows: (i) the alpha (1,4)- and novel alpha (1,2)-FT activities of Colo 205 were much less inhibited than the alpha (1,3)-FT activity by N-ethylmaleimide [Ki(microM) = 714.0, 119.0, and 6.5 respectively]. (ii) The alpha (1,4)- and novel alpha (1,2)-FT activities emerged from a Sephacryl S-200 column in identical positions. (iii) A specific inhibitor (copolymer from 3-sulfo-Galbeta(1,3)GlcNAcbeta-O-allyl and acrylamide) of alpha(1,4)-FT activity inhibited both alpha(1,4)- and alpha(1,2)-FT activities in Sephacryl S-200 column effluent to almost the same extent (approximately 80%); (iv) separation of the Lewis-type alpha(1,3/4)-FT from the plasma-type alpha(1,3)-FT by specific elution of the affinity column (bovine IgG glycopep-Sepharose) with lactose and further purification on a Sephacryl S-100 HR column showed that (a) the alpha(1,3)-FT activity was the inherent capacity of the Lewis-type FT (Colo 205 fraction L) since approximately 90% of both the alpha(1,4)- and alpha(1,3)-FT activities is inhibited by the copolymer, (b) the unique ability of catalyzing the alpha(1,2)-L-fucosylation of Gal in Lewis a structure and also the alpha(1,3)-L-fucosylation of Glc in lactose-based structure belonged to the Lewis type enzyme (Colo 205 fraction L), (c) a measurement of the [14C]fucosyl products arising from the two acceptors Galbeta(1,3)(4,6-di-O-Me)GlcNAcbeta-O-Bn and 3-sulfo-Galbeta(1,3)GlcNAcbeta-O-A1 (specific for alpha(1,2) and alpha(1,4), respectively) taken in the same incubation mixture showed mutual inhibition by the acceptors ([Km for the alpha(1,4)-specific acceptor, 3-sulfo-Galbeta(1,3)GlcNAcbeta-O-A], increased from 32 to 50 microM in the presence of 7.5 mM Galbeta(1,3)(4,6-di-O-Me)GlcNAcbeta-O-Bn, whereas Ki for the mutual inhibition of alpha(1,2)-FT activity by the former was 102 microM], and (d) the Lewis-type FT, in contrast to the plasma type FT, was highly effective in fucosylating complex glycopeptides. (iv) A cloned FT (FT III:Lewis type) and the Colo 205 Lewis-type FT (fraction L) showed similar activities toward various acceptors; the enzymatic product resulting from the action of cloned FT on Galbeta(1,3)(Fucalpha(1,4))GlcNAc-beta-O-Bn was identified by FAB mass spectrometry as the difucosyl compound. (v) An examination of six human cell lines indicated that the novel alpha(1,2)-FT activity associates with the alpha(1,4)-FT activity.
Structural Analysis of Glycosaminoglycans in Animals Bearing Mutations in sugarless, sulfateless, andtout-velu (2000)

Mutations that disrupt developmental patterning in Drosophila have provided considerable information about growth factor signaling mechanisms. Three genes recently demonstrated to affect signaling by members of the Wnt, transforming growth factor-beta, Hedgehog, and fibroblast growth factor families in Drosophila encode proteins with homology to vertebrate enzymes involved in glycosaminoglycan synthesis. We report here the biochemical characterization of glycosaminoglycans in Drosophila bearing mutations in sugarless, sulfateless, and tout-velu. We find that mutations in sugarless, which encodes a protein with homology to UDP-glucose dehydrogenase, compromise the synthesis of both chondroitin and heparan sulfate, as would be predicted from a defect in UDP-glucuronate production. Defects in sulfateless, a gene encoding a protein with similarity to vertebrate N-deacetylase/N-sulfotransferases, do not affect chondroitin sulfate levels or composition but dramatically alter the composition of heparin lyase-released disaccharides. N-, 6-O-, and 2-O-sulfated disaccharides are absent and replaced entirely with an unsulfated disaccharide. A mutation in tout-velu, a gene related to the vertebrate Exostoses 1 heparan sulfate co-polymerase, likewise does not affect chondroitin sulfate synthesis but reduces all forms of heparan sulfate to below the limit of detection. These findings show that sugarless, sulfateless, and tout-velu affect glycosaminoglycan biosynthesis and demonstrate the utility of Drosophila as a model organism for studying the function and biosynthesis of glycosaminoglycans in vivo.
Removing noise using block DCT in Magnetic Resonance Images (2011)

Magnetic Resonance Imaging (MRI) is a medical imaging technique that has proven to be particularly valuable for examination of the soft tissues in the body. In this paper, a new denoising technique is proposed to remove the Rician noise from Magnetic Resonance Images using block DCT transform. It is well known that the noise in magnetic resonance imaging has a Rician distribution. Unlike additive Gaussian noise, Rician noise is signal dependent, and separating signal from noise is a difficult task. The proposed method adopt a weighted averaging schedule which uses direct component of small block DCTs to evaluate the weights. The proposed approaches were compared with other transform method such as wavelete thresholding methods, and produced much better results.
A multi-loop voltage feedback filterless class-D switching audio amplifier using unipolar pulse-width-modulation (2004)

Voltage feedback is frequently used in class-D switching audio power amplifiers. This paper discusses the design and implementation of a low-cost filterless class-D, unipolar pulse-width modulation switching audio amplifier having a multi-loop voltage feedback scheme. Classical frequency-compensation techniques are used to design and stabilize the three voltage feedback loops implemented in this application. This design method proves to be a cost-effective solution for designing high-fidelity (hi-fi) audio amplifiers. The cost is reduced because no output filter is used, the required switching frequency is half of the one needed if bipolar PWM was used, and no current sensor is needed for feedback purposes. The output impedance is extremely low due to the reduction of the successive voltage loops, making the amplifier less load dependent. Simulation results show that a total harmonic distortion (THD) of 0.005% can be achieved using this topology, as well as a flat frequency response, free of phase distortion in the audio band. Experimental results show the feasibility of this control scheme, since a THD of 0.05% was achieved with a laboratory prototyped amplifier. A comparison of the performance of this audio amplifier with that of some commercial class-D audio amplifiers, reveals that our design can seriously compete with some of the ICs leading the market at a lower cost.
Nicotinamide Riboside, an Unusual, Non‐Typical, Substrate of Purified Purine‐Nucleoside Phosphorylases (1997)

Nicotinamide 1-beta-D-riboside (Nir), the cationic, reducible moiety of the coenzyme NAD+, has been confirmed as an unusual substrate for purified purine-nucleoside phosphorylase (PNP) from a mammalian source (calf spleen). It is also a substrate of the enzyme from Escherichia coli. The Km values at pH 7, 1.48 mM and 0.62 mM, respectively, were 1-2 orders of magnitude higher than for the natural substrate inosine, but the Vmax values were comparable, 96% and 35% that for Ino. The pseudo first-order rate constants, Vmax/Km, were 1.1% and 2.5% for the calf spleen and E. coli enzymes. The aglycon, nicotinamide, was neither a substrate nor an inhibitor of PNP. Nir was a weak inhibitor of inosine phosphorolysis catalyzed by both enzymes, with Ki values close to the Km for its phosphorolysis, consistent with simple competitive inhibition; this was further confirmed by Dixon plots. Phosphorolysis of the fluorescent positively charged substrate 7-methylguanosine was also inhibited in a competitive manner by both Ino and Nir. Phosphorolysis of Nir by both enzymes was inhibited competitively by several specific inhibitors of calf spleen and E. coli PNP, with Ki values similar to those for inhibition of other natural substrates. The pH dependence of the kinetic constants for the phosphorolysis of Nir and of a variety of other substrates, was extensively investigated, particularly in the alkaline pH range, where Nir exhibited abnormally high substrate activity relative to the reduced reaction rates of both enzymes towards other anionic or neutral substrates. The overall results are discussed in relation to present concepts regarding binding and phosphorolysis of substrates by PNP based on crystallographic data of enzyme-inhibitor complexes, and current studies on enzymatic and nonenzymatic mechanisms of the cleavage of the Nir glycosidic bond.
Building Functionalized Peptidomimetics:  Use of Electroauxiliaries for Introducing <i>N</i>-Acyliminium Ions into Peptides (2006)

A series of silyl-substituted amino acids have been synthesized, inserted into peptides, and then employed as precursors for oxidatively generating reactive N-acyliminium ions. Both electrochemical and chemical oxidation procedures have been employed. N-Acyliminium ion generation in a solid-phase substrate as well as application to a small library of functionalized dipeptides has been demonstrated. Limitations in terms of how electron-rich the silyl groups can be as well as the compatibility of multiple silyl groups within a longer peptide are defined.
Architecture for Secure and Private Vehicular Communications (2007)

The deployment of vehicular communication (VC) systems is strongly dependent on their security and privacy features. In this paper, we propose a security architecture for VC. The primary objectives of the architecture include the management of identities and cryptographic keys, the security of communications, and the integration of privacy enhancing technologies. Our design approach aims at a system that relies on well-understood components which can be upgraded to provide enhanced security and privacy protection in the future. This effort is undertaken by SeVeCom (http://www.sevecom.org), a transversal project providing security and privacy enhancing mechanisms compatible with the VC technologies currently under development by all EU funded projects.
105-kW peak-power double-clad fiber laser (2003)

A diode-pumped Yb-doped double-clad fiber laser operating in a Q-switched regime is described. By exploiting pulsed pump light and stimulated Brillouin scattering of the gain fiber, a peak power of 105 kW has been demonstrated, which is an order of magnitude greater than that of conventional Q-switched fiber devices. Pulse energy of 0.5 mJ and pulse duration of 5 ns have been achieved.
Coordinate system matching for neuromagnetic and morphological reconstruction overlay (1995)

The overlay of functional and morphological images is an essential tool for advanced and improved functional diagnosis showing the correlation between spatial structures or lesions and functional areas. We present an improved coordinate system matching technique. The well known method of three orthogonal coils combined in one coilset for an angular-independent measure is validated for the use of first- or higher order gradiometers instead of magnetometers. The coilset localization procedure was modified with lock-in detection and current feedback for better long range sensitivity. Real measurements with the 31-channel Philips-MEG system have been carried out. A very good localization accuracy below the measuring area with deviations below 2 mm was found. For coordinate system matching, a 3-D cursor with surface images from segmented MR-data was implemented and an optimized, weighted least squares fit transformation algorithm between functional and morphological systems was developed. The resulting transformations consist of weighted shifts and best-fit rotations and lead to deviations of marker positions in the mm range, depending mainly on the spatial accuracy of the marker fixation.
The blind Newton sensitivity attack (2006)

Until now, the sensitivity attack was considered as a serious threat to the robustness and security of spread spectrum-based schemes, since it provides a practical method of removing watermarks with minimum attacking distortion. Nevertheless, it had not been used to tamper other watermarking algorithms, as those which use side-information. Furthermore the sensitivity attack has never been used to obtain falsely watermarked contents, also known as forgeries. In this paper a new version of the sensitivity attack based on a general formulation is proposed; this method does not require any knowledge about the detection function nor any other system parameter, but just the binary output of the detector, thus being suitable for attacking most known watermarking methods, both for tampering watermarked signals and obtaining forgeries. The soundness of this new approach is tested by empirical results.
The EphA4 receptor regulates dendritic spine remodeling by affecting β1-integrin signaling pathways (2007)

Remodeling of dendritic spines is believed to modulate the function of excitatory synapses. We previously reported that the EphA4 receptor tyrosine kinase regulates spine morphology in hippocampal pyramidal neurons, but the signaling pathways involved were not characterized (Murai, K.K., L.N. Nguyen, F. Irie, Y. Yamaguchi, and E.B. Pasquale. 2003. Nat. Neurosci. 6:153-160). In this study, we show that EphA4 activation by ephrin-A3 in hippocampal slices inhibits integrin downstream signaling pathways. EphA4 activation decreases tyrosine phosphorylation of the scaffolding protein Crk-associated substrate (Cas) and the tyrosine kinases focal adhesion kinase (FAK) and proline-rich tyrosine kinase 2 (Pyk2) and also reduces the association of Cas with the Src family kinase Fyn and the adaptor Crk. Consistent with this, EphA4 inhibits beta1-integrin activity in neuronal cells. Supporting a functional role for beta1 integrin and Cas inactivation downstream of EphA4, the inhibition of integrin or Cas function induces spine morphological changes similar to those associated with EphA4 activation. Furthermore, preventing beta1-integrin inactivation blocks the effects of EphA4 on spines. Our results support a model in which EphA4 interferes with integrin signaling pathways that stabilize dendritic spines, thus modulating synaptic interactions with the extracellular environment.
Hierarchical maximum entropy density estimation (2007)

We study the problem of simultaneously estimating several densities where the datasets are organized into overlapping groups, such as a hierarchy. For this problem, we propose a maximum entropy formulation, which systematically incorporates the groups and allows us to share the strength of prediction across similar datasets. We derive general performance guarantees, and show how some previous approaches, such as hierarchical shrinkage and hierarchical priors, can be derived as special cases. We demonstrate the proposed technique on synthetic data and in a real-world application to modeling the geographic distributions of species hierarchically grouped in a taxonomy. Specifically, we model the geographic distributions of species in the Australian wet tropics and Northeast New South Wales. In these regions, small numbers of samples per species significantly hinder effective prediction. Substantial benefits are obtained by combining information across taxonomic groups.