gebhart/patrepeval huggingface dataset:
Recognition and Blocking of HIV-1 gp41 Pre-transmembrane Sequence by Monoclonal 4E10 Antibody in a Raft-like Membrane Environment (2006)

The conserved (664)DKWASLWNWFNITNWLWYIK(683) (preTM) sequence preceding the transmembrane anchor of human immunodeficiency virus (HIV-1) gp41 glycoprotein subunit is accessible to the broadly neutralizing 4E10 antibody and, therefore, constitutes a potential target for vaccine design. Recently reported structural data are compatible with preTM insertion into the viral external membrane monolayer in the gp41 pre-fusion state (Zhu, P., Liu, J., Bess, J., Chertova, E., Lifson, J. D., Grisé, H., Ofek, G. A., Taylor, K. A., and Roux, K. H. (2006) Nature 441, 847-852). Here we demonstrate that the broadly neutralizing 4E10 antibody is able to specifically block the membrane-restructuring activity of a peptide mimic inserted into membranes. Recognition and restructuring blocking occurred in the presence of cholesterol, whereas transmembrane versions as those promoted in 1-palmitoyl-2-oleoylphosphatidylcholine:sphingomyelin mixtures could not be effectively arrested. Spectrofluorimetric assays using rhodamine-labeled peptides revealed that recognition correlated better with pore-formation blocking than with membrane-fusion inhibition. The capacity of the antibody to recognize preTM peptides in a raft-like environment was further corroborated employing planar-supported lipid layers and fluorescence microscopy. These data support that membrane-bound epitope recognition by 4E10 results in clustering reorganization of preTM at the membrane interface. We propose that this process might interfere with the formation of fusion-competent complexes at the low spike densities existing in the HIV-1 membrane. This work comprises the first experimental report on a lipid-modulated antibody capacity to bind a membrane-bound epitope sequence and arrest its restructuring activity.
3D head pose estimation with optical flow and depth constraints (2004)

A method is presented to estimate 3D head poses effectively by hybrid sensing of depth and gray information. Depth information is used to generate clean head segmentation even in a cluttered scene. Based on the segmentation result, sparse optical flow at head region is extracted and used for 3D head motion estimation in video rate. This method is shown to be effective through experiments on video sequences. Our method provides an alternative way for 3D head pose estimation from an image sequence in the current computer vision literature. Moreover, the depth information is incorporated into the estimation step as regularization for noisy motion estimation problem.
Molecular Cloning of Full-Length HIV-1 Genomes Directly from Plasma Viral RNA (1996)

Human immunodeficiency virus type 1 (HIV-1) in plasma reflects the replicating virus population at any point in time in vivo. Studies of the relationship of the complete HIV-1 genome to pathogenesis therefore need to focus on plasma virions. Since dual infections and recombination can occur in vivo, cloning an intact plasma virus genome as a single full-length molecule is desirable. For these reasons, we developed an efficient method to clone full-length HIV-1 genomes directly from plasma viral RNA. This method used reverse transcription and long polymerase chain reaction (PCR) amplification. Virion-associated RNA was isolated from plasma samples and then reverse-transcribed to make cDNA for PCR amplification. Two different strategies were employed to amplify the full-length genome: one amplified a 9-kb fragment, and the other amplified two overlapping 5-kb fragments. Although both strategies were successful, the second was preferable for amplifying HIV-1 genomes from samples with low viral titers. By directly ligating the PCR-derived fragments into a phagemid vector, we constructed clones that comprised full-length HIV-1 RNA genomes. Using this technique, we have constructed hundreds of clones containing full-length HIV-1 genomes derived from the plasma of HIV-1-infected individuals, some of whom had low HIV-1 titers. Different HIV-1 molecular species were cloned from a single clinical sample, as demonstrated by restriction site polymorphism. This method provides a tool for studying complete HIV-1 genomes in relation to pathogenic processes.
Controlling the Pore Size and Morphology of Mesoporous Silica (2010)

Mesoporous silica with a hexagonally ordered pore structure (SBA-15) has been synthesized. Through variations in the synthesis conditions several morphologies, such as fibers, sheets and separate rods, have been realized. Furthermore, additions of heptane and NH4F make it possible to synthesize SBA-15 with pores as large as 18 nm in the sheet morphology. Mechanisms for the formation of different morphologies have been suggested. In the case of fibers and sheets, the amount of heptane present during the synthesis determines the final morphology. For low concentrations, the heptane enters the micelles and increases the pore size while the particles (crystallites) attaches to each other end to end. When the heptane concentration increases, the heptane droplets increase in size, and above a critical droplet size the crystallites attach with one short end towards the droplet, forming the sheet morphology. The crystallites can also be separated. This is the case of the rod morphology. The separation is performed by shortening the stirring time and increasing the HCl concentration. The increased amount of HCl increases the hydration rate of the silica precursor, which can be used to control the thickness and length of the rods. Furthermore, the reaction time has been decreased from 20 h for all morphologies to less than 4 hours. The materials have been characterized with nitrogen sorption, electron microscopy and x-ray diffraction. Also, thermogravimetric analysis and fourier transformed infrared spectroscopy have been used for studying the removal of surfactants.
AMP-Activated Protein Kinase and Type 2 Diabetes (2006)

AMP-activated protein kinase (AMPK) is an enzyme that works as a fuel gauge, being activated in situations of high-energy phosphate depletion. Upon activation, AMPK functions to restore cellular ATP by modifying diverse metabolic pathways. AMPK is activated robustly by skeletal muscle contraction and myocardial ischemia, and may be involved in the stimulation of glucose transport and fatty acid oxidation produced by these stimuli. In liver, activation of AMPK results in enhanced fatty acid oxidation and in decreased production of glucose, cholesterol, and triglycerides. Recent studies have shown that AMPK is the cellular mediator for many of the metabolic effects of drugs such as metformin and thiazolidinediones, as well as the insulin sensitizing adipocytokines leptin and adiponectin. These data, along with evidence from studies showing that chemical activation of AMPK in vivo with 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR) improves blood glucose concentrations and lipid profiles, make this enzyme an attractive pharmacological target for the treatment of type 2 diabetes and other metabolic disorders.
Interaction of Metals with Suspended Graphene Observed by Transmission Electron Microscopy (2012)

In this Perspective, we present an overview of how different metals interface with suspended graphene, providing a closer look into the metal-graphene interaction by employing high-resolution transmission electron microscopy, especially using high-angle dark field imaging. All studied metals favor sites on the omnipresent hydrocarbon surface contamination rather than on the clean graphene surface and present nonuniform distributions, which never result in continuous films but instead in clusters or nanocrystals, indicating a weak interaction between the metal and graphene. This behavior can be altered to some degree by surface pretreatment (hydrogenation) and high-temperature vacuum annealing. Graphene etching is observed in a scanning transmission electron microscope (STEM) under high vacuum and 60 kV electron beam acceleration voltage conditions for all metals, except for Au. This unusual metal-mediated etching sheds new light on the metal-graphene interaction; it might explain the observed higher frequency of cluster nucleation for certain transition metals and might have implications regarding controlled nanomanipulation, that is, for self-assembly and sculpturing of future graphene-based devices.
Molecular Predictors of Outcome With Gefitinib in a Phase III Placebo-Controlled Study in Advanced Non–Small-Cell Lung Cancer (2006)

EGFR gene copy number was a predictor of clinical benefit from gefitinib in ISEL. Additional studies are warranted to assess these biomarkers fully for the identification of patients most likely to benefit from gefitinib treatment.
Diversity of plasmids and plasmid-encoded phenotypic traits in Xanthomonas campestris pv. Vesicatoria (1990)

Tesis para obtener el grado de Doctor of Philosophy, de la University of Florida (Estados Unidos), en 1990
The computer simulation of RNA folding involving pseudoknot formation (1991)

The algorithm and the program for the prediction of RNA secondary structure with pseudoknot formation have been proposed. The algorithm simulates stepwise folding by generating random structures using Monte Carlo method, followed by the selection of helices to final structure on the basis of both their probabilities of occurrence in a random structure and free energy parameters. The program versions have been tested on ribosomal RNA structures and on RNAs with pseudoknots evidenced by experimental data. It is shown that the simulation of folding during RNA synthesis improves the results. The introduction of pseudoknot formation permits to predict the pseudoknotted structures and to improve the prediction of long-range interactions. The computer program is rather fast and allows to predict the structures for long RNAs without using large memory volumes in usual personal computer.
Phase and Antigenic Variation in Bacteria (2004)

Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. This form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. This review provides an overview of the many bacterial proteins and structures that are under the control of phase or antigenic variation. The context is mainly within the role of the proteins and variation for pathogenesis, which reflects the main body of literature. The occurrence of phase variation in expression of genes not readily recognizable as virulence factors is highlighted as well, to illustrate that our current knowledge is incomplete. From recent genome sequence analysis, it has become clear that phase variation may be more widespread than is currently recognized, and a brief discussion is included to show how genome sequence analysis can provide novel information, as well as its limitations. The current state of knowledge of the molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the way in which these mechanisms form part of the general regulatory network of the cell is addressed. Arguments both for and against a role of phase and antigenic variation in immune evasion are presented and put into new perspective by distinguishing between a role in bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies.
Hydrogen from methane in a single-step process (1999)

Addition of a calcium-based CO2 acceptor to commercial steam methane reforming catalyst permits the production of 95+% H2 in a single-step process. The combined reforming, shift, and CO2 separation reactions have been studied using a laboratory-scale fixed-bed reactor as a function of temperature, steam-to-methane ratio, acceptor-to-catalyst ratio, feed gas flow rate, and methane content of the feed gas. The combined reactions were sufficiently rapid above 550°C that equilibrium was closely approached at all reaction conditions studied. The H2 content of the product gas was relatively independent of temperature with the primary impurity at lower temperatures being CH4. Higher temperatures resulted in increased CH4 conversion but decreased carbon oxide removal leaving CO and CO2 as the primary impurities. Potential advantages of the single-step process, in addition to reducing the number of processing steps, include improved energy efficiency, elimination of the need for shift catalysts, and reduction in the temperature of the primary reactor by 150–200°C. Key unanswered problems involving the single-step process include continuous separation of catalyst and acceptor and the durability of the acceptor for multiple cycle operation.
Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface (2016)

Flavivirus nonstructural protein 5 (NS5) consists of methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, which catalyze 5'-RNA capping/methylation and RNA synthesis, respectively, during viral genome replication. Although the crystal structure of flavivirus NS5 is known, no data about the quaternary organization of the functional enzyme are available. We report the crystal structure of dengue virus full-length NS5, where eight molecules of NS5 are arranged as four independent dimers in the crystallographic asymmetric unit. The relative orientation of each monomer within the dimer, as well as the orientations of the MTase and RdRp domains within each monomer, is conserved, suggesting that these structural arrangements represent the biologically relevant conformation and assembly of this multi-functional enzyme. Essential interactions between MTase and RdRp domains are maintained in the NS5 dimer via inter-molecular interactions, providing evidence that flavivirus NS5 can adopt multiple conformations while preserving necessary interactions between the MTase and RdRp domains. Furthermore, many NS5 residues that reduce viral replication are located at either the inter-domain interface within a monomer or at the inter-molecular interface within the dimer. Hence the X-ray structure of NS5 presented here suggests that MTase and RdRp activities could be coordinated as a dimer during viral genome replication.
Directly measuring the spatio-temporal electric field of focusing ultrashort pulses (2007)

We present the first technique for directly measuring (without assumptions) the spatio-temporal intensity and phase of a train of ultrashort pulses at and near a focus. Our method uses an experimentally simple and high-spectral resolution variant of spectral interferometry (SEA TADPOLE). To illustrate our technique, we measured the spatio-temporal electric field in and around the foci of several different types of lenses. To confirm our results, we also simulated these measurements by numerically propagating a pulse through each of the lenses used. From one set of measurements, we made a movie showing a focusing pulse with severe chromatic aberration.
Ex vivo expansion of megakaryocyte progenitor cells from normal bone marrow and peripheral blood and from patients with haematological malignancies (2002)

A number of haematological and non-haematological malignancies can be successfully treated using high-dose chemotherapy +/- irradiation followed by haematopoietic progenitor cell transplantation. Post transplant, thrombocytopenia and neutropenia always occur and patients require platelet transfusions. It may be possible to reduce the period of thrombocytopenia by re-infusion of ex vivo expanded megakaryocyte progenitors (MP), derived from the progenitor cell graft. We have investigated the expansion of MP from CD34+ enriched cells from normal bone marrow (NBM) and peripheral blood (PB) and remission BM or PB samples from patients with haematological malignancies. CD34+ cells were cultured in serum-free medium supplemented with thrombopoietin (TPO), interleukin 1 (IL-1), IL-6 and stem cell factor (SCF) for 7 d, then cell proliferation was assessed by flow cytometry using lineage-specific markers. It was possible to significantly expand the number of MP cells from all sources. There were no major differences in yields of MP from normal BM or PB, or BM from multiple myeloma and non-Hodgkin's lymphoma patients. However, expansion of MP in acute myeloid leukaemia samples was lower than all other samples and the number of megakaryocyte colony-forming units was reduced. Several cytokine combinations were evaluated to optimize MP expansion from NBM. Equivalent yields of MP were obtained using TPO and one of IL-1, IL-3, granulocyte-macrophage colony-stimulating factor or SCF, suggesting that large cytokine combinations are not necessary for this procedure. It should be possible to scale up the culture conditions described to produce effective MP doses for clinical transplantation.
Structural Study of the N,N′-Dimethylpropyleneurea Solvated Lanthanoid(III) Ions in Solution and Solid State with an Analysis of the Ionic Radii of Lanthanoid(III) Ions (2010)

The structures of the N,N'-dimethylpropyleneurea (dmpu) solvated lanthanoid(III) ions have been studied in dmpu solution (La-Nd, Sm-Lu) and in solid iodide salts (La-Nd, Sm, Gd-Lu) by extended X-ray absorption fine structure (EXAFS), and single crystal X-ray diffraction (La, Pr, Nd, Gd, Tb, Er, Yb, and Lu); the EXAFS studies were performed on both K and L(III) absorption edges. Because of the space-demanding properties of dmpu upon coordination, dmpu solvated metal ions often show coordination numbers lower than those found in corresponding hydrates and solvates of oxygen donor solvents without steric requirements beyond the size of the donor atom. All lanthanoid(III) ions are seven-coordinate in solution, except lutetium(III) which is six-coordinated in regular octahedral fashion, whereas in the solid iodide salts the dmpu solvated lanthanoid(III) ions are all six-coordinate in regular octahedral fashion. A comparison of Ln-O bond lengths in a large number of lanthanoid(III) complexes with neutral oxygen donor ligands and different configurations shows that the metal ion-oxygen distance is specific for each coordination number with a narrow bond distance distribution. This also shows that the radius of the coordinated oxygen atom in these compounds can be assumed to be 1.34 A as proposed for coordinated water, while for ethers such as tetrahydrofuran (thf) it is somewhat larger. Using this atomic radius of oxygen in coordinated water molecules, we have calculated the ionic radii of the lanthanoid(III) ions in four- to nine-coordination and evaluated using the bond lengths reported for homo- and heteroleptic complexes in oxygen donor solvates in solution and solid state. This yields new and revised ionic radii which in some instances are significantly different from the ionic radii normally referenced in the literature, including interpolated values for the elusive promethium(III) ion.
Apparent convergence (at 2-monoacylglycerol level) of phosphatidic acid and 2-monoacylglycerol pathways of synthesis of chylomicron triacylglycerols. (1991)

Dietary fats are converted into chylomicron triacylglycerols via the 2-monoacylglycerol and phosphatidic acid pathways of acylglycerol formation. In view of the known positional and fatty acid specificity of the acyltransferases, the triacylglycerol structures resulting from the two pathways would be expected to differ, but this has not been demonstrated. We have performed stereospecific analyses on the chylomicron triacylglycerols from rats fed menhaden oil and the corresponding fatty acid alkyl esters, which would be expected to be assimilated via the monoacylglycerol and the phosphatidic acid pathways, respectively. The results show a remarkable similarity between the two triacylglycerol types in the fatty acid composition of the sn-1 and sn-3 positions, along with marked differences in the composition of the sn-2 positions. The triacylglycerols from rats fed oil retained about 85% of the original fatty acids in the sn-2 position, including a high proportion of the long chain polyunsaturates (e.g., 5-7% 20:5 and 4-5% 22:6). The triacylglycerols from rats fed the alkyl ester contained large amounts of endogenous fatty acids in the sn-2 position (e.g., 18% 16:1, 14% 18:1, 14% 18:2, and 2.5% 20:4), which approximated the composition of the sn-2 position of the presumed phosphatidic acid intermediates. The sn-1 position contained a much higher proportion of polyunsatured fatty acids (e.g., 12-13% 20:5, 5-6% 22:6) than the sn-2 position (e.g. 2-3% 20:5, 0-0.6% 22:6) of triacylglycerols from rats fed the ester. We conclude that the chylomicron triacylglycerols arising via the 2-monoacylglycerol and the phosphatidic acid pathways differ mainly in the composition of the fatty acids in the sn-2 position. The similarity in the acids of the sn-1 and sn-3 positions of the chylomicron triacylglycerols from rats fed oil or ester is consistent with a hydrolysis of the acylglycerol products of the phosphatidic acid pathway to 2-monoacylglycerols prior to reconversion to triacylglycerols via the monoacylglycerol pathway and secretion as chylomicrons.
Kinetic effects near the magnetopause (1994)

Boundary conditions for magnetopause processes such as reconnection can be understood by studying the properties of magnetosheath plasma as it flows toward this transition. This manuscript reviews the role of electromagnetic ion cyclotron instabilities in constraining ion temperature anisotropies in the magnetosheath. Linear Vlasov theory and hybrid computer simulations have demonstrated that the inverse correlation between the proton anisotropy and the parallel proton {beta} observed from AMPTE/CCE in the subsolar sheath is due to wave-particle scattering by ion cyclotron anisotropy instabilities. Recent research on this topic is reviewed and the application of this inverse correlation to a successful bounded anisotropy model of proton temperatures in the sheath is described.
[Studies on porcine reproductive and respiratory syndrome virus morphogenesis in Marc-145 cell and the ultrastructural changes of the infected cells]. (2007)

Electron microscopy was employed for ultrastructural observation of Marc-145 cells infected with porcine reproductive and respiratory syndrome virus (PRRSV) SC1 strain and studied the virus morphogenesis in infected cells. The results demonstrated that PRRSV was spherical and enveloped. The virion is 45-65 nm in diameter and its nucleocapsid was approximately 25-30 nm. PRRSV entered Marc-145 cells by endocytosis, and replicated in the cytoplasm. The mature viruses were released from infected cells by budding or exocytosis. The main ultrastructural changes of the infected cells were as follows: increased number of cytoplasmic vacuoles, dilated endoplasmic reticulum, mitochondria underwent hyperplasia with its ridges swollen, sloughed, and eventually vacuolated. Typical apoptosis was also observed in the infected Marc-145 cells, which included microvilli sloughing off the cell, appearance of apoptotic bodies and cell fragmentation.