gebhart/patrepeval huggingface dataset:
Germinal‐center kinase‐like kinase co‐crystal structure reveals a swapped activation loop and C‐terminal extension (2016)

Germinal-center kinase-like kinase (GLK, Map4k3), a GCK-I family kinase, plays multiple roles in regulating apoptosis, amino acid sensing, and immune signaling. We describe here the crystal structure of an activation loop mutant of GLK kinase domain bound to an inhibitor. The structure reveals a weakly associated, activation-loop swapped dimer with more than 20 amino acids of ordered density at the carboxy-terminus. This C-terminal PEST region binds intermolecularly to the hydrophobic groove of the N-terminal domain of a neighboring molecule. Although the GLK activation loop mutant crystallized demonstrates reduced kinase activity, its structure demonstrates all the hallmarks of an "active" kinase, including the salt bridge between the C-helix glutamate and the catalytic lysine. Our compound displacement data suggests that the effect of the Ser170Ala mutation in reducing kinase activity is likely due to its effect in reducing substrate peptide binding affinity rather than reducing ATP binding or ATP turnover. This report details the first structure of GLK; comparison of its activation loop sequence and P-loop structure to that of Map4k4 suggests ideas for designing inhibitors that can distinguish between these family members to achieve selective pharmacological inhibitors.
Deeply Inverted Electron-Hole Recombination in a Luminescent Antibody-Stilbene Complex (2008)

The blue-emissive antibody EP2-19G2 that has been elicited against trans-stilbene has unprecedented ability to produce bright luminescence and has been used as a biosensor in various applications. We show that the prolonged luminescence is not stilbene fluorescence. Instead, the emissive species is a charge-transfer excited complex of an anionic stilbene and a cationic, parallel pi-stacked tryptophan. Upon charge recombination, this complex generates exceptionally bright blue light. Complex formation is enabled by a deeply penetrating ligand-binding pocket, which in turn results from a noncanonical interface between the two variable domains of the antibody.
Low power wide spectrum optical transmitter using avalanche mode LEDs in SOI CMOS technology (2017)

This paper presents a low power monolithically integrated optical transmitter with avalanche mode light emitting diodes in a 140 nm silicon-on-insulator CMOS technology. Avalanche mode LEDs in silicon exhibit wide-spectrum electroluminescence (400 nm < λ < 850 nm), which has a significant overlap with the responsivity of silicon photodiodes. This enables monolithic CMOS integration of optocouplers, for e.g. smart power applications requiring high data rate communication with a large galvanic isolation. To ensure a certain minimum number of photons per data pulse (or per bit), light emitting diode drivers must be robust against process, operating conditions and temperature variations of the light emitting diode. Combined with the avalanche mode light emitting diode's steep current-voltage curve at relatively high breakdown voltages, this conventionally results in high power consumption and significant heating. The presented transmitter circuit is intrinsically robust against these issues, thereby enabling low power operation.
Epoxidation of Cardanol’s Terminal Double Bond (2020)

In this investigation, the terminal double bonds of the side chain epoxidized cardanol glycidyl ether (SCECGE) molecule were further epoxidized in the presence of Oxone<sup>®</sup> (potassium peroxomonosulfate) and fluorinated acetone. Regular methods for the double bond epoxidation are not effective on the terminal double bonds because of their reduced electronegativity with respect to internal double bonds. The terminal double bond functionality of the SCECGE was epoxidized to nearly 70%, increasing the epoxy functionality of SCECGE from 2.45 to 2.65 epoxies/molecule as measured using proton magnetic nuclear resonance (<sup>1</sup>H-NMR). This modified material-side chain epoxidized cardanol glycidyl ether with terminal epoxies (TE-SCECGE)-was thermally cured with cycloaliphatic curing agent 4-4'-methylenebis(cyclohexanamine) (PACM) at stoichiometry, and the cured polymer properties, such as glass transition temperature (<i>T</i><sub>g</sub>) and tensile modulus, were compared with SCECGE resin cured with PACM. The <i>T</i><sub>g</sub> of the material was increased from 52 to 69 °C as obtained via a dynamic mechanical analysis (DMA) while the tensile modulus of the material increased from 0.88 to 1.24 GPa as a result of terminal double bond epoxidation. In addition to highlighting the effects of dangling side groups in an epoxy network, this modest increase in <i>T</i><sub>g</sub> and modulus could be sufficient to significantly expand the potential uses of amine-cured cardanol-based epoxies for fiber reinforced composite applications.
Standardized Mean Regional Method for Calculating Global Positron Emission Tomographic Measurements (1985)

A new "mean regional" method for calculating global hemispheric values of blood flow, blood volume, and metabolism with positron emission tomography is presented. It is based on a standardized set of regions defined according to coordinates in a stereotactic atlas of the brain. Region locations in each individual scan were determined by a localization technique that is independent of the appearance of the physiological images. Measurements obtained with this mean regional method minimize contributions from nonbrain structures such as ventricles or venous sinuses and provide the necessary basis for comparisons among different subjects and laboratories.
Ab initio Calculations of GaN Initial Growth Processes on GaAs(111)A and GaAs(111)B Surfaces (2001)

To understand the initial growth mechanism of GaN buffer layer on GaAs, the As desorption process from GaAs(111)A and GaAs(111)B surfaces was investigated by a first principle calculation method. The substrate orientation dependence of GaN buffer layer can be explained from the activation energies for As desorption processes.
Expanding the toolbox of the coinage bond: adducts involving new gold(iii) derivatives and bioactive molecules (2022)

X-ray analyses of some adducts between AuX 3 (X = Cl, Br) and several pyridine derivatives show short π-hole CiBs; computational studies reveal the attractive nature of these short contacts, confirming their key role in driving their crystal packing.
Three-Dimensional Bioprinting of Muscle Constructs for Reconstruction (2016)

Kim, Ji Hyun PhD; Seol, Young-Joon PhD; Ko, In Kap PhD; Kang, Hyun-Wook; Jackson, John PhD; Lee, Sang Jin; Yoo, James MD, PhD; Atala, Anthony MD, FACS Author Information
Médiation de qualité dans les systèmes d'information géographique (2005)

La prise de decision dans les domaines de l'amenagement du territoire, de la gestion des risques, de la gestion des transports, etc. Repose sur des donnees geographiques. Ces donnees sont diverses et de qualites variables, car elles sont issues d'observations plus ou moins imparfaites du monde reel. Les Systemes d'Information Geographique (SIG) actuels ne sont pas encore capables d'integrer a la fois des sources de donnees et leurs qualites. Il devient imperatif de surmonter ce probleme et d'offrir un systeme d'information qui guide l'utilisateur dans le choix des donnees qui satisfont au mieux ses besoins en termes de qualite. L'objectif de la these est d'apporter une solution a ce probleme en proposant un systeme d'integration qui prenne en compte la qualite des donnees a integrer. Le probleme consistera a satisfaire plusieurs besoins : gerer des sources de donnees geographiques autonomes, et prendre en compte des operateurs spatiaux ainsi que des informations de qualite.
Multigrid Algorithms for Tensor Network States (2012)

The widely used density matrix renormalization group (DRMG) method often fails to converge in systems with multiple length scales, such as lattice discretizations of continuum models and dilute or weakly doped lattice models. The local optimization employed by DMRG to optimize the wave function is ineffective in updating large-scale features. Here we present a multigrid algorithm that solves these convergence problems by optimizing the wave function at different spatial resolutions. We demonstrate its effectiveness by simulating bosons in continuous space and study nonadiabaticity when ramping up the amplitude of an optical lattice. The algorithm can be generalized to tensor network methods and combined with the contractor renormalization group method to study dilute and weakly doped lattice models.
How to ensure a good depth perception on a light field display (2020)

Information captured by the eye allows the human brain to extract depth cues from the scene, to analyze them and to understand a complex 3D scene. In real life all these depth cues are naturally present at the same time and consistent. Rendering them on a display for several viewers is not straightforward. Today no technology can fully achieve this requirement. Per definition, light field content is a collection of light rays that are corresponding to different viewpoints of the same scene. A light field display should be able to render these different viewpoints to a single viewer or to multiple viewers. The quality of a light field display will be measured by its ability to correctly render these different views and the expected depth cues. — In the paper we will define the technical requirements for a light field display to provide effective depth cues such as the binocular disparity, the motion parallax and the accommodation at a pixel resolution expected by the eye. These requirements will be evaluated with respect to existing technologies (e.g. integral imaging displays) or expected future ones (e.g. microLED displays). Simulation of light field displays will be proposed for different display sizes (smartphone, desktop or TV), resolution per view and pixel pitch. These simulations illustrate the main impact of the pixel pitch to reach the light field display goal in terms of depth cue requirements. — The last part of the paper will focus on the data generation issues. How to generate the necessary amount of views at the display side and what are the adapted data formats for such a purpose? The paper will be associated with supplementary videos that will illustrate the view generation topic using a dedicated data format that is optimized for current GPU processors. Video capture of early stage light field displays will also be provided.
Introduction to Thermal Insulating Materials and Silica Aerogels (2011)

The term 'thermal insulating materials' describes a class of materials which can improve the thermal efficiency by reducing the thermal conduction, convention and radiation between the inside and outside of the system. As a thermal insulating material, numerous industrial applications are possible including the automobile, aerospace, aviation, and petro- chemical. Especially, the silica aerogel, with their superior thermal insulating behavior, has been widely used as thermal insulating materials. Because the mechanical properties of the silica aerogel cannot meet the industrial demand, use of the silica aerogel is limited. This article aims to review the thermal insulating materials and silica aerogel, and to introduce the silica aerogel/polymer composites.
RNA editing enzyme APOBEC3A promotes pro-inflammatory M1 macrophage polarization (2021)

Pro-inflammatory M1 macrophage polarization is associated with microbicidal and antitumor responses. We recently described APOBEC3A-mediated cytosine-to-uracil (C > U) RNA editing during M1 polarization. However, the functional significance of this editing is unknown. Here we find that APOBEC3A-mediated cellular RNA editing can also be induced by influenza or Maraba virus infections in normal human macrophages, and by interferons in tumor-associated macrophages. Gene knockdown and RNA_Seq analyses show that APOBEC3A mediates C>U RNA editing of 209 exonic/UTR sites in 203 genes during M1 polarization. The highest level of nonsynonymous RNA editing alters a highly-conserved amino acid in THOC5, which encodes a nuclear mRNA export protein implicated in M-CSF-driven macrophage differentiation. Knockdown of APOBEC3A reduces IL6, IL23A and IL12B gene expression, CD86 surface protein expression, and TNF-α, IL-1β and IL-6 cytokine secretion, and increases glycolysis. These results show a key role of APOBEC3A cytidine deaminase in transcriptomic and functional polarization of M1 macrophages.
Arborization of Dendrites by Developing Neocortical Neurons Is Dependent on Primary Cilia and Type 3 Adenylyl Cyclase (2013)

The formation of primary cilia is a highly choreographed process that can be disrupted in developing neurons by overexpressing neuromodulatory G-protein-coupled receptors GPCRs or by blocking intraflagellar transport. Here, we examined the effects of overexpressing the ciliary GPCRs, 5HT6 and SSTR3, on cilia structure and the differentiation of neocortical neurons. Neuronal overexpression of 5HT6 and SSTR3 was achieved by electroporating mouse embryo cortex in utero with vectors encoding these receptors. We found that overexpression of ciliary GPCRs in cortical neurons, especially 5HT6, induced the formation of long (>30 μm) and often forked cilia. These changes were associated with increased levels of intraflagellar transport proteins and accelerated ciliogenesis in neonatal neocortex, the induction of which required Kif3a, an anterograde motor critical for cilia protein trafficking and growth. GPCR overexpression also altered the complement of signaling molecules within the cilia. We found that SSTR3 and type III adenylyl cyclase (ACIII), proteins normally enriched in neuronal cilia, were rarely detected in 5HT6-elongated cilia. Intriguingly, the changes in cilia structure were accompanied by changes in neuronal morphology. Specifically, disruption of normal ciliogenesis in developing neocortical neurons, either by overexpressing cilia GPCRs or a dominant-negative form of Kif3a, significantly impaired dendrite outgrowth. Remarkably, coexpression of ACIII with 5HT6 restored ACIII to cilia, normalized cilia structure, and restored dendrite outgrowth, effects that were not observed in neurons coexpressing ACIII and dominant-negative form of Kif3a. Collectively, our data suggest the formation of neuronal dendrites in developing neocortex requires structurally normal cilia enriched with ACIII.
Solar thermoelectricity via advanced latent heat storage (2016)

We report on a new modular, dispatchable, and cost-effective solar electricity-generating technology. Solar ThermoElectricity via Advanced Latent heat Storage (STEALS) integrates several state-of-the-art technologies to provide electricity on demand. In the envisioned STEALS system, concentrated sunlight is converted to heat at a solar absorber. The heat is then delivered to either a thermoelectric (TE) module for direct electricity generation, or to charge a phase change material for thermal energy storage, enabling subsequent generation during off-sun hours, or both for simultaneous electricity production and energy storage. The key to making STEALS a dispatchable technology lies in the development of a “thermal valve,” which controls when heat is allowed to flow through the TE module, thus controlling when electricity is generated. The current project addresses each of the three major subcomponents, (i) the TE module, (ii) the thermal energy storage system, and (iii) the thermal valve. The project also includes system-level and techno- economic modeling of the envisioned integrated system and will culminate in the demonstration of a laboratory-scale STEALS prototype capable of generating 3kWe.
A Broadband CMOS Amplitude Detector for On-Chip RF Measurements (2008)

This paper presents a CMOS RF amplitude detector as a practical integrated test device and demonstrates its application for on-chip testing. The proposed circuit performs full-wave rectification and generates a dc voltage proportional to the amplitude of an RF signal over a wide frequency range. The design considerations and analysis of operation for the employed class-AB rectifier are described. Fabricated in a standard 0.35-mum CMOS process, the RF detector uses only 0.031 of area and presents an equivalent input capacitance of 13 fF. Measurements show that this RF test device has a detection dynamic range of 30 dB from 900 MHz to 2.4 GHz. Experimental results for the application of the RF amplitude detector in the built-in measurement of the gain and compression of a 1.6-GHz low-noise amplifier fabricated in the same chip are also presented.
Room-temperature lasing at 1.82μm of GaInSb∕AlGaSb quantum wells grown on GaAs substrates using an interfacial misfit array (2007)

The authors report the device characteristics of GaInSb∕AlGaSb quantum well (QW) lasers monolithically grown on GaAs substrates. The 7.8% lattice mismatch between GaAs substrates and GaSb buffer layers can be completely accommodated by using an interfacial misfit (IMF) array. Room-temperature lasing operation is obtained from a 1.25-mm-long device containing six-layer Ga0.9In0.1Sb∕Al0.35Ga0.65Sb QWs at 1.816μm with a threshold current density of 1.265kA∕cm2. The observed characteristic temperature and temperature coefficient are 110K and 9.7Å∕K, respectively. This IMF technique will enable a wide range of lasing wavelengths from near-infrared to midwavelength-infrared regimes on a GaAs platform.
Des nanovecteurs hybrides pour la restitution retard de médicaments antitumoraux et antiviraux (2010)

The efficient delivery of drugs in the body requires the use of non-toxic nanocarriers. Most of the existing materials show poor drug loading and/or rapid release of the proportion of the drug that is simply adsorbed (or anchored) at the external surface of the nanocarrier. The new porous hybrid solids, with the ability to tune their structures and porosities are well suited to serve as nanocarriers for delivery and imaging applications. Here we show that specific non-toxic porous iron(III) - based metal - organic frameworks with engineered cores and surfaces, as well as imaging properties, function as superior nanocarriers for efficient controlled delivery of antitumour and retroviral drugs against cancer and AIDS. They also potentially associate therapeutics and diagnostics, and open the way for theranostics, or -personalized patient treatments. double dagger.
Prospective Analysis of Staphylococcus aureus Bacteremia in Nonneutropenic Adults With Malignancy (2000)

SAB in cancer patients is associated with significant morbidity from frequent metastatic infections or conditions including IE, as well as considerable mortality. Unknown initial infection site and 72-hour surveillance cultures positive for organisms were predictive of a complicated course and poor final outcome.
Off‐Chip Drivers (OCD) and ESD (2005)

This chapter contains sections titled: Off-Chip Drivers (OCD) Off-Chip Drivers: Mixed-Voltage Interface Off-Chip Drivers Self-Bias Well OCD Networks Off-Chip Drivers: Programmable Impedance (PIMP) OCD Networks Off-Chip Drivers: Universal OCDs Off-Chip Drivers: Gate-Array OCD Design Off-Chip Drivers: Gate-Modulated Networks Off-Chip Driver ESD Design: Integration of Coupling and Ballasting Techniques Off-Chip Driver ESD Design: Substrate-Modulated Resistor-Ballasted MOSFET Summary and Closing Comments Problems References
Transparent Informatics: A Foundation for Precision Medicine (2013)

On June 20th, 2013, the Arvados project was recognized by the White House Office of Science and Technology Policy at its 'Open Science' Champions of Change event. The free and open-source Arvados project and the public domain Harvard Personal Genome Project data could become important building blocks for precision medicine. We invite all organizations to adapt the work presented in this poster for use in clinical practice or biomedical research. We will further elaborate on our vision for "transparent informatics" resources in a subsequent article.
Medullary interplay for central tolerance (2011)

To establish central tolerance in T cells, Aire, a nuclear protein expressed in medullary thymic epithelial cells, not only induces the ectopic expression of various self-antigens but also facilitates the indirect presentation of medullary thymic epithelial cell (mTEC)–derived self-antigens by
Dynamic Biomolecule Sensing Bead Array Held by Optical Tweezers (2011)

We have developed a platform using optical tweezers to create dynamic arrays of functionalized microbeads in microfluidic channels. The array is then exposed to analyte signaling molecules and washes, and interrogated using fluorescence microscopy.
Acoustic event detection in real life recordings (2010)

This paper presents a system for acoustic event detection in recordings from real life environments. The events are modeled using a network of hidden Markov models; their size and topology is chosen based on a study of isolated events recognition. We also studied the effect of ambient background noise on event classifi-cation performance. On real life recordings, we tested recognition of isolated sound events and event detection. For event detection, the system performs recognition and temporal positioning of a se-quence of events. An accuracy of 24 % was obtained in classifying isolated sound events into 61 classes. This corresponds to the ac-curacy of classifying between 61 events when mixed with ambient background noise at 0dB signal-to-noise ratio. In event detection, the system is capable of recognizing almost one third of the events, and the temporal positioning of the events is not correct for 84 % of the time. 1.
Entanglement generation in a quantum network at distance-independent rate (2022)

Abstract We develop a protocol for entanglement generation in the quantum internet that allows a repeater node to use n -qubit Greenberger-Horne-Zeilinger (GHZ) projective measurements that can fuse n successfully entangled links , i.e., two-qubit entangled Bell pairs shared across n network edges, incident at that node. Implementing n -fusion, for n ≥ 3, is in principle not much harder than 2-fusions (Bell-basis measurements) in solid-state qubit memories. If we allow even 3-fusions at the nodes, we find—by developing a connection to a modified version of the site-bond percolation problem—that despite lossy (hence probabilistic) link-level entanglement generation, and probabilistic success of the fusion measurements at nodes, one can generate entanglement between end parties Alice and Bob at a rate that stays constant as the distance between them increases. We prove that this powerful network property is not possible to attain with any quantum networking protocol built with Bell measurements and multiplexing alone. We also design a two-party quantum key distribution protocol that converts the entangled states shared between two nodes into a shared secret, at a key generation rate that is independent of the distance between the two parties.
Voltage-dependent capacitors in power electronic multi-domain simulations (2010)

We discuss multi-domain simulation of power electronic systems where non-linear capacitors have a significant impact on the system behaviour, e.g. employing the MOSFET output capacitor Coss for soft switching or employing nonlinear thermal models in coupled electrical-thermal simulations. It is shown which errors can result from approximating non-linear capacitors with simple linear ones as proposed e.g. for Coss in datasheets. Furthermore a highly efficient implementation of non-linear capacitors in numerical circuit simulators is proposed.
Cartilage degradation and oxidative damage in osteoarthritic and rheumatoid arthritic patients (2003)

peer reviewed