gebhart/patrepeval huggingface dataset:
The T cell receptor gene usage by simian immunodeficiency virus gag-specific cytotoxic T lymphocytes in rhesus monkeys (1996)

MHC class I-restricted CTL play an important role in limiting the spread of HIV-1 in the infected individual. Elucidating the molecular interactions of CTL with the virus is, therefore, of central importance for characterizing the immune control of this infection. In exploring this CTL response, we have defined the TCR usage by SIVmac Gag-specific CTL in rhesus monkeys. Thirty-nine CTL clones were generated from PBL of three SIVmac-infected monkeys expressing the MHC class I Mamu-A*01 gene product, all of which were shown to recognize a single SIVmac Gag peptide in association with Mamu-A*01. Sixty-six percent of CTL clones derived from two monkeys early after infection expressed TCR genes of the V beta 13 family; 70% of these V beta 13+ CTL clones expressed a TCR heterodimer composed of V alpha 1 and V beta 13 gene products. In addition, there appeared to be a selection of a single conserved amino acid and restricted CDR3 lengths in junctional regions of TCR beta-chains expressed by the V beta 13+ CTL clones. These findings indicate significant structural constraints on the CTL-TCR interaction with the AIDS virus. Interestingly, 55% of the CTL clones derived from the third animal at a later time following infection employed genes of the V beta 6 family in their TCR. Despite the preferential use of TCR V family genes by the CTL clones, the SIVmac Gag-specific CTL response was clearly polyclonal; TCR expressed by these CTL clones displayed varied sequences in their CDR3 regions. Other V gene families, including V beta 23, V alpha 8, and V alpha 20, were used in TCR expressed by SIVmac Gag-specific CTL clones. These studies, therefore, indicate that the TCR repertoire of SIVmac Gag-specific CTL that share a peptide and MHC class I recognition specificity can be diverse. Such a broad CTL-TCR repertoire may be advantageous for the host in containing an AIDS virus infection.
Allosteric Inhibition of the SARS‐CoV‐2 Main Protease: Insights from Mass Spectrometry Based Assays** (2020)

Abstract The SARS‐CoV‐2 main protease (M pro ) cleaves along the two viral polypeptides to release non‐structural proteins required for viral replication. M Pro is an attractive target for antiviral therapies to combat the coronavirus‐2019 disease. Here, we used native mass spectrometry to characterize the functional unit of M pro . Analysis of the monomer/dimer equilibria reveals a dissociation constant of K d =0.14±0.03 μM, indicating M Pro has a strong preference to dimerize in solution. We characterized substrate turnover rates by following temporal changes in the enzyme‐substrate complexes, and screened small molecules, that bind distant from the active site, for their ability to modulate activity. These compounds, including one proposed to disrupt the dimer, slow the rate of substrate processing by ≈35 %. This information, together with analysis of the x ‐ray crystal structures, provides a starting point for the development of more potent molecules that allosterically regulate M Pro activity.
Development of high-density DNA array based signature-tagged mutagenesis and its application for the discovery of novel Y. pseudotuberculosis virulence-associated genes (2000)

Conference Abstract| October 01 2000 Development of high-density DNA array based signature-tagged mutagenesis and its application for the discovery of novel Y. pseudotuberculosis virulence-associated genes A. V. Karlyshev; A. V. Karlyshev 1Department of Infectious Diseases, London School of Hygiene and Tropical Medicine, University of London, Keppel St., London WC1E 7HT, UK Search for other works by this author on: This Site PubMed Google Scholar P. C. Oyston; P. C. Oyston 2Defence Evaluation and Research Agency, CBD Porton Down, Salisbury, Wiltshire SP4 OJQ, UK Search for other works by this author on: This Site PubMed Google Scholar K. Williams; K. Williams 1Department of Infectious Diseases, London School of Hygiene and Tropical Medicine, University of London, Keppel St., London WC1E 7HT, UK Search for other works by this author on: This Site PubMed Google Scholar R. W. Titball; R. W. Titball 2Defence Evaluation and Research Agency, CBD Porton Down, Salisbury, Wiltshire SP4 OJQ, UK Search for other works by this author on: This Site PubMed Google Scholar R. Davis; R. Davis 3Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 943305–5307 Search for other works by this author on: This Site PubMed Google Scholar E. A. Winzeler; E. A. Winzeler 4Novartis Institute for Functional Genomics, 3115 Merryfield Row, Suite 200, San Diego, CA 92121–1125 Search for other works by this author on: This Site PubMed Google Scholar B. W. Wren B. W. Wren 1Department of Infectious Diseases, London School of Hygiene and Tropical Medicine, University of London, Keppel St., London WC1E 7HT, UK Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 2000 Biochemical Society2000 Biochem Soc Trans (2000) 28 (5): A232. https://doi.org/10.1042/bst028a232 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation A. V. Karlyshev, P. C. Oyston, K. Williams, R. W. Titball, R. Davis, E. A. Winzeler, B. W. Wren; Development of high-density DNA array based signature-tagged mutagenesis and its application for the discovery of novel Y. pseudotuberculosis virulence-associated genes. Biochem Soc Trans 1 October 2000; 28 (5): A232. doi: https://doi.org/10.1042/bst028a232 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2000 Biochemical Society2000 Article PDF first page preview Close Modal You do not currently have access to this content.
Computational Methods for Calculating Accurate Enthalpies of Formation, Ionization Potentials, and Electron Affinities (1998)

In this chapter we describe two methods being used in computational thermochemistry. The first is Gaussian-2 theory, which is based on a sequence of well-defined ab initio molecular orbital calculations. It has proven to be a useful technique for the calculation of accurate bond energies, enthalpies of formation, ionization potentials, electron affinities, and proton affinities. The second is density functional theory which is developing as a cost-effective procedure for studying molecular properties and energies.
Emergent Dynamics of Thymocyte Development and Lineage Determination (2007)

Experiments have generated a plethora of data about the genes, molecules, and cells involved in thymocyte development. Here, we use a computer-driven simulation that uses data about thymocyte development to generate an integrated dynamic representation-a novel technology we have termed reactive animation (RA). RA reveals emergent properties in complex dynamic biological systems. We apply RA to thymocyte development by reproducing and extending the effects of known gene knockouts: CXCR4 and CCR9. RA simulation revealed a previously unidentified role of thymocyte competition for major histocompatability complex presentation. We now report that such competition is required for normal anatomical compartmentalization, can influence the rate of thymocyte velocities within chemokine gradients, and can account for the disproportion between single-positive CD4 and CD8 lineages developing from double-positive precursors.
QoE-driven resource optimization for user generated video content in next generation mobile networks (2011)

The increasing popularity of user-generated content and the high quality upstreaming capabilities of mobile phones indicate a prevalence of video traffic in the uplink of next generation mobile net works. Need arises for optimizing the network resource allocation while preserving the user satisfaction. In this paper, we propose a service-centric approach for uplink distribution of real-time user generated content based on the Quality of Experience (QoE) and popularity of the video content. In case of limited network resources, the proposed approach assigns more resources for popular contents while maintaining a minimum guaranteed QoE for the less popular ones. We compare our service-centric approach with a QoE-driven one that does not consider video popularity and evaluate both approaches for the uplink of an LTE system. The simulation results show that a significant gain in terms of average user satisfaction can be achieved.
Drosophila NAB (dNAB) is an orphan transcriptional co‐repressor required for correct CNS and eye development (2002)

The mammalian NAB proteins have been identified previously as potent co-repressors of the EGR family of zinc finger transcription factors. Drosophila NAB (dNAB), like its mammalian counterparts, binds EGR1 and represses EGR1-mediated transcriptional activation from a synthetic promoter. In contrast, dNAB does not bind the Drosophila EGR-related protein klumpfuss. dnab RNA is expressed exclusively in a subset of neuroblasts in the embryonic and larval central nervous system (CNS), as well as in several larval imaginal disc tissues. Here, we describe the creation of targeted deletion mutations in the dnab gene and the identification of additional, EMS-induced dnab mutations by genetic complementation analysis. Null alleles in dnab cause larval locomotion defects and early larval lethality (L1-L2). A putative hypomorphic allele in dnab instead causes early adult lethality due to severe locomotion defects. In the dnab -/- CNS, axon outgrowth/guidance and glial development appear normal; however, a subset of eve+ neurons forms in reduced numbers. In addition, mosaic analysis in the eye reveals that dnab -/- clones are either very small or absent. Similarly, dNAB overexpression in the eye causes eyes to be very small with few ommatidia. These dramatic eye-specific phenotypes will prove useful for enhancer/suppressor screens to identify dnab-interacting genes.
Physical processes associated with the deactivation of dopants in laser annealed silicon (2002)

Laser annealing is being investigated as an alternative method to activate dopants and repair the lattice damage from ion implantation. The unique properties of the laser annealing process allow for active dopant concentrations that exceed equilibrium solubility limits. However, these super-saturated dopant concentrations exist in a metastable state and deactivate upon subsequent thermal processing. Previously, this group compared the electrical characteristics of the deactivation behavior of common dopants (P, B, and Sb) across a range of concentrations and annealing conditions. Boron and antimony were shown to be stable species against deactivation while P and As deactivate quickly at temperatures as low as 500 °C. In this work, we present additional data to understand the underlying physical mechanisms involved in the deactivation process. It is proposed that As and P deactivate through the formation of small dopant—defect clusters while B and Sb deactivate through precipitation.
Functions of Nanoparticles and Surfactants in Enhanced Oil Recovery: Molecular Dynamics Studies (2017)

Abstract The roles of nanoparticles in enhanced oil recovery (EOR) are typically associated with stabilization of foams and emulsions (Fakoya et al. 2017) and with oil detachment due to creation of wedge effect in confined oil-water-rock contact region (Wasan et al. 2003). This publication focuses on these and other functions of nanoparticles in EOR applications, often performed in synergy with surfactant mixtures, e.g. abrasive removal of oil films from rock surfaces, wettability alteration, and improved transport of surfactant molecules through porous media. Conventional and non-equilibrium Molecular Dynamics (MD) techniques were applied to simulate behavior of nanoparticles and surfactant molecules on oil-water-rock interfaces in stationary and flow conditions and compute the energies of interactions between the components of the studied systems as well as interfacial tensions in them. Moving nanoparticles were found to be effective in detachment of oil film from rock surfaces. Increased temperature and addition of surface-active agent further enhance the oil-sweeping capability of colloidal nanosuspensions. Changes in interfacial tension as well as density profile computations showed that functionalized silica nanoparticles and related surfactant-nanoparticle compositions clearly exhibit surface active properties on oil-water interfaces that can be fine-tuned and utilized in EOR applications. The wettability-altering potential and surfactant-transporting capability of nanoparticles are also demonstrated. Oil-sweeping, wettability-altering, and surfactant-transporting capabilities of nanoparticles are demonstrated on the molecular level for the first time. Authors also believe that it is the first systematic numerical study of nanoparticle's and surfactant's contribution to the changes in interfacial tension on oil-water interface.
Electrochemical Synthesis and Nanofabrication of Materials for Magnetic and Ultrasound Sensors Application (2008)

We present the new approach to synthesize materials and nanostructures with application for magnetic field and ultrasound sensing. Our results indicate that electrodeposition at the nanoscale electrode geometry (nanocontacts) is an effective process that can deliver the ferromagnetic metal/oxide materials with desired composition and properties. These materials are the essential part of the nanocontact based device architecture which is investigated as the model system for magnetic filed sensor application. As an opposite process to electrodeposition, the dealloying i.e. a selective metal dissolution is used as fabrication process to create a high surface to volume ratio nanoporous metal structures. These structures are used as capacitive transducer for ultrasound sensor application. We present the preliminary results which demonstrate that thin layer - of nanoporous metal electrodes can be used as an inexpensive sensing device for ultrasound in electrolytes.
Development of Ligands for the Peripheral Benzodiazepine Receptor (2006)

The peripheral benzodiazepine receptor (PBR) initially characterised as a high affinity binding site for diazepam, is densely distributed in most peripheral organs whilst only moderately expressed in the healthy brain. The predominant cell type expressing the PBR at regions of central nervous system (CNS) pathology are activated microglial cells. Under neuroinflammatory conditions there is an over-expression of PBR binding sites indicating that measurements of PBR density can act as a useful index of brain disease activity. The PBR is now considered a significant therapeutic and diagnostic target which has provided the impetus for PBR ligand development. There are several classes of PBR ligands available including benzodiazepines (Ro5-4864), isoquinoline carboxamides (PK 11195), indoleacetamides (FGIN-1-27), phenoxyphenyl-acetamides (DAA1106) and pyrazolopyrimidines (DPA-713). Subsequent conformationally restrained isoquinoline and indoleacetamide analogues have been synthesised in an attempt to yield PBR ligands with superior affinity and brain kinetics. Even though the PBR has been linked to a number of biochemical processes, including cell proliferation, apoptosis, steroidogenesis, porphyrin transport and immunomodulation, its exact physiological role is yet to be deciphered. Selective PBR ligands with favourable in vivo binding properties and kinetics is required to gain a more complete understanding on the normal functioning of the PBR and the chemical pathways underlying several pathological conditions. Novel PBR ligands with unique binding properties and functional activity may also generate information on the localisation of the PBR and the possibility of PBR subtypes. This review highlights the main classes of PBR ligands to date. In addition the biological activity and therapeutic potential of certain PBR ligands is discussed.
The Flash-lag Effect in Amblyopia (2021)

We demonstrate a reduced FLE both in the AE as well as the FE of patients with amblyopia, suggesting a global visual processing deficit. We suggest it may be attributed to a more limited spatiotemporal extent of facilitatory anticipatory activity within the amblyopic primary visual cortex.
α-Synuclein Tertiary Contact Dynamics (2007)

Tertiary contact formation rates in alpha-synuclein, an intrinsically disordered polypeptide implicated in Parkinson's disease, have been determined from measurements of diffusion-limited electron-transfer kinetics between triplet-excited tryptophan:3-nitrotyrosine pairs separated by 10, 12, 55, and 90 residues. Calculations based on a Markovian lattice model developed to describe intrachain diffusion dynamics for a disordered polypeptide give contact quenching rates for various loop sizes ranging from 6 to 48 that are in reasonable agreement with experimentally determined values for small loops (10-20 residues). Contrary to expectations, measured contact rates in alpha-synuclein do not continue to decrease as the loop size increases (>/=35 residues), and substantial deviations from calculated rates are found for the pairs W4-Y94, Y39-W94, and W4-Y136. The contact rates for these large loops indicate much shorter average donor-acceptor separations than expected for a random polymer.
Noise factors in detection of minute marks by domain wall displacement (2000)

Causes of data errors by DWDD and dominant noise factors which determine the density are discussed. Dropout of data mainly occurs during readout by domain wall displacement at mark length less than 110 nm. The bit shift causes serious data error when window width is shorter than 70 nm. A novel method has been introduced to analyze the jitter by reading the signal many times for the same area and by averaging the waveform. The space-dependent jitter obtained by averaging is 8.8 nm and is greater than the time-dependent jitter of 6.7 nm caused by the shot noise, the laser noise, and the system noise as well as caused by the fluctuation of the domain wall displacement. Comparison with the ordinary structured MO media has revealed that a bit length of 77 nm will be available when the space-dependent jitter is reduced to 3.8 nm which is the value for ordinary structured media.
Temperature dependent and magnetic field dependent terahertz spectroscopy of In<sub>1-x</sub>Mn<sub>x</sub>As (2007)

We report temperature and magnetic field dependent terahertz time domain spectroscopy measurements on InMnAs. The temperature dependent transmission is shown to vary with Mn content and applied magnetic field strength.
Strategies of transport of microstructural variables for remeshing - application to texture induced mechanical anisotropy in metals (2006)

International audience
Establishment of subcellular fractionation techniques to monitor the intracellular fate of polymer therapeutics II. Identification of endosomal and lysosomal compartments in HepG2 cells combining single-step subcellular fractionation with fluorescent imaging (2007)

As they are often designed for lysosomotropic, endosomotropic and/or transcellular delivery, an understanding of intracellular trafficking pathways is essential to enable optimised design of novel polymer therapeutics. Here, we describe a single-step density gradient subcellular fractionation method combined with fluorescent detection analysis that provides a new tool for characterisation of endocytic traffic of polymer therapeutics. Hepatoma (HepG2) cells were used as a model and cell breakage was optimised using a cell cracker to ensure assay of the whole cell population. After removal of unbroken cells and nuclei, the cell lysate as a post-nuclear supernatant (PNS) was layered onto an iodixanol (OptiPrep) density gradient optimised to 5-20%. Early endosomes, late endosomes and lysosomes were identified from gradient fractions by immunoblotting for marker proteins early endosome antigen 1 (EEA 1) and lysosomal associated membrane protein 1 (LAMP 1) using horseradish peroxidase or fluorescently-labelled secondary antibodies. Lysosomes were also detected using N-acetyl-beta-glucosamindase (Hex A) activity. In addition, cells were incubated with Texas-red labelled transferrin (TxR-Tf) for 5 min to specifically label early endosomes and this was directly detected from SDS-PAGE gels. Internalised macromolecules and colloidal particles can potentially alter vesicle buoyant density. To see if typical macromolecules of interest would alter vesicle density or perturb vesicle traffic, HepG2 cells were incubated with dextran or a polyethyleneglycol (PEG)-polyester dendron G4 (1 mg/ml for 24 h). The PEG-polyester dendron G4 caused a slight redistribution of endocytic structures to lower density fractions but immunofluorescence microscopy showed no obvious dendron effects. In conclusion, the combined subcellular fractionation with fluorescent imaging approach described here can be used as a tool for both fundamental cell biology research and/or the quantitative localisation of polymer therapeutics in the endocytic pathway.
Quantization of massive vector fields in curved space–time (1999)

We develop a cannonical quantization for massive vector fields on a globally hyperbolic Lorentzian manifold.
Supplementary Table 1 from The Neuroblastoma-Associated F1174L ALK Mutation Causes Resistance to an ALK Kinase Inhibitor in ALK-Translocated Cancers (2023)

Supplementary Table 1 from The Neuroblastoma-Associated F1174L ALK Mutation Causes Resistance to an ALK Kinase Inhibitor in ALK-Translocated Cancers
Brownian Dynamics Simulation of Peeling a Strongly-Adsorbed Polymer Molecule from a Frictionless Substrate (2013)

We used brownian dynamics to study the peeling of a polymer molecule, represented by a freely jointed chain, from a frictionless surface in an implicit solvent with parameters representative of single-stranded DNA adsorbed on graphite. For slow peeling rates, simulations match the predictions of an equilibrium statistical thermodynamic model. We show that deviations from equilibrium peeling forces are dominated by a combination of Stokes (viscous) drag forces acting on the desorbed section of the chain and a finite rate of hopping over a desorption barrier. Characteristic velocities separating equilibrium and nonequilibrium regimes are many orders of magnitude higher than values accessible in force spectroscopy experiments. Finite probe stiffness resulted in disappearance of force spikes due to desorption of individual links predicted by the statistical thermodynamic model under displacement control. Probe fluctuations also masked sharp transitions in peeling force between blocks of distinct sequences, indicating limitation in the ability of single-molecule force spectroscopy to distinguish small differences in homologous molecular structures.