gebhart/patrepeval huggingface dataset:
Protein Knockdown Using Methyl Bestatin−Ligand Hybrid Molecules: Design and Synthesis of Inducers of Ubiquitination-Mediated Degradation of Cellular Retinoic Acid-Binding Proteins (2010)

Induction of selective degradation of target proteins by small molecules (protein knockdown) would be useful for biological research and treatment of various diseases. To achieve protein knockdown, we utilized the ubiquitin ligase activity of cellular inhibitor of apoptosis protein 1 (cIAP1), which is activated by methyl bestatin (MeBS, 2). We speculated that formation of an artificial (nonphysiological) complex of cIAP1 and a target protein would be induced by a hybrid molecule consisting of MeBS (2) linked to a ligand of the target protein, and this would lead to cIAP1-mediated ubiquitination and subsequent proteasomal degradation of the target protein. To verify this hypothesis, we focused on cellular retinoic acid-binding proteins (CRABP-I and -II) and designed hybrid molecules (compounds 4) consisting of MeBS (2) coupled via spacers of various lengths to all-trans retinoic acid (ATRA, 3), a ligand of CRABPs. Compounds 4 induced selective loss of CRABP-I and -II proteins in cells. We confirmed that 4b induced formation of a complex of cIAP1 and CRABP-II in vitro and induced proteasomal degradation of CRABP-II in cells. When neuroblastoma IMR-32 cells were treated with 4b, the level of CRABP-II was reduced and cell migration was inhibited, suggesting potential value of CRABP-II-targeting therapy for controlling tumor metastasis. Our results indicate that 4b possesses sufficient activity, permeability, and stability in cells to be employed in cellular assays. Hybrid molecules such as 4 should be useful not only as chemical tools for studying the biological/physiological functions of CRABPs but also as candidate therapeutic agents targeting CRABPs.
How Neurons Know That It's C-c-c-c-cold Outside (2002)

NEUROSCIENCEA spate of papers published this month offers two answers to the question of how nerve cells transmit cold sensations. Sometimes specialized sensors for menthol, the active ingredient in mint, do the job; other times neurons choreograph the movement of ions in response to cold in the absence of a specific receptor. Researchers suspect that the two mechanisms operate in concert, either in separate populations of cells or together in the same neurons.
Early hematopoietic recovery after single unit unrelated cord blood transplantation in adults supported by co-infusion of mobilized stem cells from a third party donor. (2006)

Our strategy offers prompt engraftment with a low rate of complications in a feasible alternative protocol that overcomes the current limitations of a single CB-transplant in adults.
Regulatory T Cells and Human Myeloid Dendritic Cells Promote Tolerance via Programmed Death Ligand-1 (2010)

Immunotherapy using regulatory T cells (Treg) has been proposed, yet cellular and molecular mechanisms of human Tregs remain incompletely characterized. Here, we demonstrate that human Tregs promote the generation of myeloid dendritic cells (DC) with reduced capacity to stimulate effector T cell responses. In a model of xenogeneic graft-versus-host disease (GVHD), allogeneic human DC conditioned with Tregs suppressed human T cell activation and completely abrogated posttransplant lethality. Tregs induced programmed death ligand-1 (PD-L1) expression on Treg-conditioned DC; subsequently, Treg-conditioned DC induced PD-L1 expression in vivo on effector T cells. PD-L1 blockade reversed Treg-conditioned DC function in vitro and in vivo, thereby demonstrating that human Tregs can promote immune suppression via DC modulation through PD-L1 up-regulation. This identification of a human Treg downstream cellular effector (DC) and molecular mechanism (PD-L1) will facilitate the rational design of clinical trials to modulate alloreactivity.
Ultrahigh field induced strain and polarization response in electron irradiated poly(vinylidene fluoride-trifluoroethylene) copolymer (1998)

The influence of electron dosage on the field induced strain, dielectric constant, and polarization response has been investigated in electron irradiated poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE)) 50/50 copolymer. It was found that under suitable electron dosage an ultrahigh electrostrictive strain can be achieved. Interestingly, material after irradiation exhibits many features resembling those of relaxor ferroelectrics, suggesting that the electron irradiation breaks up the coherent polarization domain in normal ferroelectric P(VDF-TrFE) copolymer into nano-polar regions that transform the material into a relaxor ferroelectric. In addition, many of the material properties including the field induced polarization, the electrostrictive strain, and elastic modulus exhibit irregular change (non-monotonical) with electron dosage, indicating a complex relation among the crosslinking density, crystallinity, crystallite size, and molecular conformation in determining the material responses.
Dynamic nature of the quaternary structure of the vesicular stomatitis virus envelope glycoprotein (1990)

The envelope glycoprotein (G protein) of vesicular stomatitis virus probably exists in the viral envelope as a trimer of identical subunits. Depending on the conditions of solubilization, G protein may dissociate into monomers. G protein solubilized with the detergent octyl glucoside was shown to exist as oligomeric forms by sedimentation velocity analysis and chemical cross-linking. G protein was modified with either fluorescein isothiocyanate or rhodamine isothiocyanate. Resonance energy transfer between fluorescein and rhodamine labels was observed upon mixing the two labeled G proteins in octyl glucoside. This result provided further evidence that G protein in octyl glucoside is oligomeric and indicated that the subunits are capable of exchange to form mixed oligomers. Resonance energy transfer was independent of G protein concentration in the range examined (10-80 nM) and was not observed when labeled G proteins were mixed with fluorescein or rhodamine that was not conjugated to protein. Resonance energy transfer decreased upon incorporation of G protein into Triton X-100, consistent with sedimentation velocity data that G protein in Triton X-100 is primarily monomeric. Kinetic analysis showed that the subunit exchange reaction had a half-time of about 3 min at 27 degrees C that was independent of G protein concentration. These data indicate that the exchange occurs through dissociation of G protein trimers into monomers and dimers followed by reassociation into timers. Thus, in octyl glucoside, G protein must exist as an equilibrium between monomers and oligomers. This implies that monomers are capable of self-assembly into trimers.
Biosynthesis and degradation of peptides derived from Xenopus laevis prohormones (1987)

Peptides present in the skin secretion of the South African frog, Xenopus laevis, have been analysed by fast atom bombardment mass spectrometry and h.p.l.c. in the mass range 500-3200 Da. We have investigated the effects of successive glandular secretions induced by noradrenaline injections on these peptide levels and have found that the replenishment of the whole range of peptides is complete within 2-6 days. Intact secretory vesicles free of cellular contaminants contain a relatively large number of peptides with molecular masses in the range 2400-2700 Da. We have termed these peptides primary products or spacer peptides, since they originate from spacer regions of the precursors to xenopsin and caerulein. However, if the secretory vesicles are disrupted during the collection procedure and the solution containing the secretion is kept at room temperature for up to 2 h, relatively little of the larger peptides remain. By comparing the relative levels of the various peptides present in these secretions we have found that the larger peptides are proteolytically cleaved into smaller fragments by a novel cleavage at the N-terminal side of a lysine residue (at Xaa-Lys bonds where Xaa is Leu, Gly, Ala or Lys). Preliminary evidence has been obtained suggesting that the larger intact peptides possess lytic activity whereas the smaller proteolytic fragments appear relatively inactive. This may represent a mechanism by which the secretions are rendered harmless to the frog itself, since prolonged exposure would be expected to result in toxic effects. The dorsal glands of X. laevis thus appear similar to endocrine glands, since they are involved in peptide biosynthesis, secretion and subsequent proteolytic degradation.
Solvent-dependent oxidations of 5- and 6-azaindoles to trioxopyrrolopyridines and functionalised azaindoles (2008)

A regioselective synthesis of 4,7-dimethoxy 5- and 6-azaindoles 2 has been achieved, based on the appropriate choice of ortho-directing or ortho-repulsing groups in the formylation of a pyridine ring. Studies on the regioselectivity of the formylation step and on the preparation of azidoacrylate intermediates 4 are described in this paper. The reactivity of the 5- and 6-azaindole structures towards BBr3-mediated selective monodemethylation and oxidative demethylation reactions were also investigated. The regioselectivity of the deprotection was confirmed using a chemical approach. Oxidation reactions were then carried out on either dimethoxy- or hydroxymethoxyazaindoles, in different solvents, using [bis(trifluoroacetoxy)iodo]benzene. In acetonitrile–water, trioxopyrrolopyridines 12 were obtained, whereas the formation of functionalised azaindoles 17 was observed in acetonitrile–methanol. The tautomeric structure of the trioxopyrrolopyridines was proved by X-ray diffraction analysis.
Di-, Tri-, and Tetravalent Dendritic Galabiosides That Inhibit Hemagglutination by Streptococcus suis at Nanomolar Concentration (1997)

Galabiose (Galα1-4Gal) derivatives were coupled to carrier molecules having mono-, di-, tri-, and tetrameric functionalities, thus creating mono- to tetravalent dendritic galabiosides (1−9). The di- to tetravalent galabiosides were several hundred times more efficient than the monomeric galabiosides in inhibiting hemagglutination by the Gram-positive bacterium Streptococcus suis, resulting in complete inhibition at low nanomolar concentrations. This is unprecedented in the field of inhibition of bacterial adhesion by soluble compounds.
Data-Dependent Modulation of Solid-Phase Extraction Capillary Electrophoresis for the Analysis of Complex Peptide and Phosphopeptide Mixtures by Tandem Mass Spectrometry:  Application to Endothelial Nitric Oxide Synthase (1999)

Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) of peptides in conjunction with automated sequence database searching of the resulting collision-induced dissociation (CID) spectra has become a powerful method for the identification of purified proteins or the components of protein mixtures. The success of the method is critically dependent on the manner by which the peptides are introduced into the mass spectrometer. In this report, we describe a capillary electrophoresis-based system for the automated, sensitive analysis of complex peptide mixtures. The system consists of an ESI-MS/MS instrument, a solid-phase extraction (SPE)-capillary zone electrophoresis (CZE) device for peptide concentration and separation, and an algorithm written in Instrument Control Language (ICL) which modulates the electrophoretic conditions in a data-dependent manner to optimize available time for the generation of high-quality CID spectra of peptides in complex samples. We demonstrate that the data-dependent modulation of the electric field significantly expands the analytical window for each peptide analyzed and that the sensitivity of the SPE-CZE technique is not noticeably altered by the procedure. By applying the technique to the analysis of in vivo phosphorylation sites of endothelial nitric oxide synthase (eNOS), we demonstrate the power of this system for the MS/MS analysis of minor peptide species in complex samples such as phosphopeptides generated by the proteolytic digestion of a large protein, eNOS, phosphorylated at low stoichiometry.
Layers of opportunity: nanostructured polymer assemblies for the delivery of macromolecular therapeutics (2006)

Layer-by-layer approaches to the fabrication of nanostructured polymer assemblies have contributed to the design of thin films and composites of interest in a variety of areas. Here, we highlight recent contributions from our laboratory toward the design of multilayered assemblies that erode controllably and predictably in physiological environments and permit spatial and temporal control over the administration of macromolecular therapeutics, such as DNA. Our approach makes use of assemblies fabricated from hydrolytically degradable polyamines. We place this work in the context of recent progress from other laboratories and discuss new opportunities and connections that illustrate the potential of these layered assemblies as platforms for the controlled release of one or several therapeutic agents.
A multiversion model for multimedia data warehouse (2005)

The traditional multidimensional models have a static structure where members of dimensions are computed in a unique way. However, multimedia data is often characterized by descriptors that can be obtained by various computation modes. We define these computation modes as "functional versions" of the descriptors. We propose a Functional Multiversion Multidimensional Model by integrating the concept of "version of dimension". This concept defines dimensions with members computed according to various functional versions. This new approach integrates a choice of computation modes of these members into the model, in order to allow the user to choose the best representation of data. We implement a multimedia data warehouse in the medical field by integrating the multimedia data of a therapeutic study into a multidimensional model. We formally define a conceptual model and we present a prototype for this study
In situ molecular imaging of a hydrated biofilm in a microfluidic reactor by ToF-SIMS (2014)

A novel microfluidic reactor for biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) was constructed to enable two-dimensional chemical imaging of hydrated biofilms. We demonstrate the detection of characteristic fatty acid fragments from microfluidic reactor-grown biofilms and illustrate advantages of hydrated-state ToF-SIMS imaging.
A New Approach to Low-Cost High-Efficiency Automotive Gas Turbines (1997)

&lt;div class="htmlview paragraph"&gt;The automotive gas turbine has not been adopted for many reasons, among which are that the materials required have been expensive, and the fuel consumption has been unremarkable. A new approach is to use a marked reduction in blade speeds (and therefore in blade and disk stresses) through multistaging, allowing the use of injection-molded compressor components and low-cost ceramic materials (e.g. technology developed for automotive turbochargers) for all hot parts. The pressure ratio will also be lowered and the heat-exchanger effectiveness increased. The resulting engine is larger than existing experimental turbines but still smaller and lighter than an equivalent spark-ignition or compression-ignition engine, with a marked improvement in projected fuel efficiency.&lt;/div&gt;
User Plane Architecture of 3rd Generation Mobile Telecommunication Network (1999)

This paper presents modifications that are proposed to the 3rd generation packet data network in 3GPP (3rd Generation Partnership Project). The scope of the paper is the user plane of the packet data network. The UMTS (Universal Mobile Telecommunications System) network architecture is based on the GPRS (General Packet Radio Service). In this paper, the proposed UMTS packet data network is presented and compared to the GPRS. In the comparison, modifications are highlighted and tasks of different protocols and their differences are evaluated. The comparison of protocols concentrates on the user plane or parts that affect to the user plane data transfer. A comparison of the advantages and drawbacks is made. Finally, the paper concludes the network modifications and changes on functional split.
Fecal calprotectin as an index of intestinal inflammation (2001)

The assessment of inflammatory activity in intestinal disease in man can be done using a variety of different techniques, from measurement of conventional noninvasive acute-phase inflammatory markers in plasma (C-reactive protein and the erythrocyte sedimentation rate) to the direct assessment of disease activity by intestinal biopsy. However, most of these techniques have significant limitations when it comes to assessing functional components of the disease that relate to activity and prognosis. Here we briefly review the value of a novel emerging intestinal function test, fecal calprotectin. Single stool assay of neutrophil-specific proteins (calprotectin, lactoferrin) give the same quantitative data on intestinal inflammation as the 4-day fecal excretion of indium-111-labeled white cells. Elevated levels of fecal calprotectin have been demonstrated in patients with NSAID-induced enteropathy and have been used in the diagnosis of colorectal cancer. Fecal calprotectin is increased in over 95% of patients with inflammatory bowel disease (IBD) and correlates with clinical disease activity. It reliably differentiates between patients with IBD and irritable bowel syndrome (IBS). More importantly, at a given fecal calprotectin concentration in patients with quiescent IBD, the test has a specificity and sensitivity in excess of 85% in predicting clinical relapse of disease. This suggests that relapse of IBD is closely related to the degree of intestinal inflammation and suggests that targeted treatment at an asymptomatic stage of the disease may be indicated. (c) 2001 Prous Science. All rights reserved.
Effect of environmental factors and precursors on oxalic acid production, mycelial biomass and virulence of a potential bioherbicide isolate of Sclerotium rolfsii SC64 produced in liquid culture (2011)

Abstract The fungus Sclerotium rolfsii is presently under development as a bioherbicide for broadleaf weed species using fungus-infested substrates as application material in this laboratory. The effect of environmental factors and three precursors (citric acid, ascorbic acid, and sodium succinate) on mycelial growth, oxalic acid production, and virulence by SC64 in liquid culture were investigated. The results showed that for mycelia growth the optimum liquid medium was Modified Richard's solution (MRS) among the five tested media, but potato dextrose broth (PDB) produced the maximum oxalic acid production and virulence on detached Solidago canadensis leaves. When PDB was used as the basic medium, the oxalic acid/mycelial dry weight (mg g–1) ratio reached the peak 4 days after inoculation. The optimum temperature for oxalic acid production was at 27°C, but increased mycelial dry weight and virulence were observed at 30°C. The optimum range of initial pH value for oxalic acid accumulation was 4.0–6.0, with the optimal pH 5.0; highest mycelial growth was with an initial pH 3.5–6.0 (optimum pH 5.0) and subsequently pH 3.5–5.5 (maximum at pH 3.5). Both mycelial dry weight and oxalic acid production showed a decreasing trend as a result of the precursor of oxalic acid being added to PDB. Among the three precursors, the greatest decrease in mycelial dry weight, and oxalic acid production was caused by sodium succinate. This clarification of optimal conditions for production of mycelial biomass while insuring high concentrations of oxalic acid and high virulence should be useful for further development of this fungus as biocontrol agent.
Delay and area optimization in standard-cell design (1990)

This paper presents a heuristic approach to the optimal selection of standard cells in VLSI circuit design. We are considering a cell library composed of several templates (3-5) for each type of cell. These templates differ in area, driving capabilities, intrinsic delay, and capacitive loading. When realizing a logically synthesized circuit, we select the best templates from the cell library to minimize the total area of the cells under delay constraints. We have found a very successful heuristic approach to attack this discrete optimization problem.
Functional Substitution by TAT-Utrophin in Dystrophin-Deficient Mice (2009)

These results are, to our knowledge, the first to establish the efficacy and feasibility of TAT-utrophin-based constructs as a novel direct protein-replacement therapy for the treatment of skeletal and cardiac muscle diseases caused by loss of dystrophin.
Introduction of anti-fouling coatings at the surface of supramolecular elastomeric materials via post-modification of reactive supramolecular additives (2017)

A covalent anti-fouling is introduced at the surface of supramolecular ureidopyrimidinone (UPy) based materials to prevent both protein and cell adhesion.
Coordinated Expression of MUC2 and CDX-2 in Mucinous Carcinomas of the Lung Can Be Explained by the Role of CDX-2 as Transcriptional Regulator of MUC2 (2004)

International audience
Structure of reactively magnetron sputtered Hf-N films (1984)

In spite of the technical interest in the Hf-N system the form of the phase diagram is not yet clear, and therefore it is difficult to predict the phase composition of thin films. In this letter Hf-N films have been prepared by reactive dc planar magnetron sputtering and the phase composition of the films investigated by x-ray diffraction. Between the α-Hf and HfN single phase regions a multiphase region was found consisting of α-Hf, ε-Hf3N2, and/or ζ-Hf4N3 and also HfN in the nitrogen rich part. For the mononitride a lattice parameter of 4.54 Å was found which is slightly higher than reported bulk vlaues. This deviation is caused by intrinsic stresses in the films. If the nitrogen content is increased above that of the mononitride, the (111) interplanar distance increases further while all other interplanar distances decrease. At still higher nitrogen contents new reflections start to appear indicating a new phase. In this region the films also change from being conducting and nontransparent to electrically insulating and transparent.
Comparative Sequence Analysis on Different Strains of Swine Influenza Virus Sub-type H1N1 for Neuraminidase and Hemagglutinin (2010)

The swine flu is an infectious disease of swine and human, causing a huge amount of death to both. The aim of this study was to analyse the mutation possibility of swine influenza virus sub-type A/Swine/Nebraska/(H1N1) from swine of Nebraska. The H1N1 amino acid sequences of neuraminidase (GenBank Acc. No: ABR28650) and hemagglutinin (GenBank Acc. No: ABR28647) were analyzed for mutations using BLASTP and ClustalW programs. Our in silico analysis predicted that hemagglutinin and neuraminidase of swine influenza virus are sensitive to mutations at positions 225, 283 and 240, 451 respectively. These mutations were significant for its pathogenic nature because they are involved in change in polarity or hydrophobicity. Domain and motif search shows that mutations were detected in NA (T240A, G451S) and HA (I283V) at a predicted site of N-myristoylation. Secondary structure analysis predicted that no structural conformation changes were observed in HA and NA at positions 225, 283 and 240, 451 respectively. The program PROTMUTATION was developed in Perl CGI programming using Needleman-Wunsch algorithm for global sequence alignment. This program was used to monitor the mutations and predicts the trend of mutations.