gebhart/patrepeval huggingface dataset:
Portable and scalable FPGA-based acceleration of a direct linear system solver (2012)

FPGAs have the potential to serve as a platform for accelerating many computations including scientific applications. However, the large development cost and short life span for FPGA designs have limited their adoption by the scientific computing community. FPGA-based scientific computing and many kinds of embedded computing could become more practical if there were hardware libraries that were portable to any FPGA-based system with performance that scaled with the size of the FPGA. To illustrate this idea we have implemented one common super-computing library function: the LU factorization method for solving systems of linear equations. This paper describes a method for making the design both portable and scalable that should be illustrative if such libraries are to be built in the future. The design is a software-based generator that leverages both the flexibility of a software programming language and the parameters inherent in an hardware description language. The generator accepts parameters that describe the FPGA capacity and external memory capabilities. We compare the performance of our engine executing on the largest FPGA available at the time of this work (an Altera Stratix III 3S340) to a single processor core fabricated in the same 65nm IC process running a highly optimized software implementation from the processor vendor. For single precision matrices on the order of 10,000 × 10,000 elements, the FPGA implementation is 2.2 times faster and the energy dissipated per useful GFLOP operation is a factor of 5 times less. For double precision, the FPGA implementation is 1.7 times faster and 3.5 times more energy efficient.
Growth, Optical Properties, and Scintillation Light Yield of CaF2:Ce Crystals with Different Ce Concentration (2010)

Present work describes the first detailed γ-ray light yield of Ce 3+ perturbed emission in CaF 2 host. (1-, 3-, 5-, 10-, and 20-mol %-) Ce 3+ -doped single crystalline CaF 2 scintillator crystals were grown by the micro-pulling-down method. Their transmittances were measured to be approximately 80% at UV to visible wavelengths. All the crystals exhibited emission peaks at approximately 330 nm, which were identified as the Ce 3+ perturbed emission, when they were irradiated by 1 GBq 137 Cs. The photoluminescence decay kinetics was measured to be about 40 ns for all the crystals. Scintillation light yield in unit of photons/MeV (ph/MeV) was measured, and the 5% sample showed the highest light yield of around 900 ph/MeV with 2 µs shaping time.
BINDING OF ACTIVATED PROTEIN C TO A SPECIFIC RECEPTOR ON HUMAN MONONUCLEAR PHAGOCYTES INHIBITS INTRACELLULAR CALCIUM SIGNALING AND MONOCYTE-DEPENDENT PROLIFERATIVE RESPONSES1,2 (1995)

Upon activation, mononuclear phagocytes (Mphi) play key roles in the development of septic shock and multiple host immune responses, but details of the regulation of Mphi activation are little understood. We recently showed that the physiologic anticoagulant molecule, activated protein C (APC), blocks responses of human blood Mphi, alveolar Mphi, or THP-1 cells induced by LPS, IFN-gamma, or PMA, including TNF-alpha production and down-regulation of several LPS binding-related proteins. We now report a possible mechanism of action through inhibition of the rapid intracellular calcium signaling that occurs at the onset of Mphi activation, and characterization of a specific Mphi receptor for APC. Flow cytometry studies using Fluo-3 showed that Mph activation by Fc-receptor cross-linking or rIFN-gamma caused a rapid increase in free intracellular calcium, a primary event in multiple signal transduction pathways, which was blocked by pretreatment with APC. Consistent with this, addition of APC inhibited PHA-induced T cell proliferation in a dose- and time-dependent manner. Peak suppression (> 70%) required addition of APC within the first hour of 72 hr cocultures of Mphi and lymphocytes, and proliferative responses were not restored by addition of IL-2 or TNF-alpha. Biochemical studies showed that 125I-labeled APC bound specifically to M phi in a time-dependent and saturable manner. Scatchard analysis indicated there were 180,690 binding sites for APC per cell, which were of high affinity (Kd value of 12.9 mM). Binding of 125I-APC was doubled by activation of Mphi with LPS, and bound APC was not displaced by the zymogen, protein C (PC), or by enzymatically inactive (diisopropyl fluorophosphate- or PPACK-treated) APC, indicating an absolute requirement for the active site of APC in its binding to Mphi. APC binding was blocked by a polyclonal Ab to human PC/APC, but not by protein S, factor Va or Xa, or a polyclonal antithrombomodulin antibody. When 125I-APC was crosslinked to its receptor, immunoprecipitated and analyzed by SDS-PAGE under reducing conditions, a covalent complex (110-115 kD) of 125I-APC (62 kD) and its receptor was seen. In addition, a Mphi membrane protein of 50-55 kD, as determined by SDS-PAGE, was affinity-purified using an APC-Affigel column, and confirmed by ligand binding. Taken together, our findings document the presence of a M phi surface receptor for APC, which appears distinct from a recently described endothelial receptor for PC and APC, and which may be involved in the inhibitory effects of APC on activation of human Mphi, including Mphi-dependent T cell proliferation.
A General Method for the Synthesis of Nanostructured Large‐Surface‐Area Materials through the Self‐Assembly of Functionalized Nanoparticles (2004)

A general synthetic method for the preparation of nanostructured materials with large surface area was developed by using nanoparticle building blocks. The preparation route involves the self-assembly of functionalized nanoparticles in a liquid-crystal phase. These nanoparticles are functionalized by using difunctional amino acid species to provide suitable interactions with the template. Optimum interactions for self-assembly of the nanoparticles in the liquid-crystal phase were achieved with one -NH2 group anchored to the nanoparticle surface per 25 A(2). To maximize the surface area of these materials, the wall thicknesses are adjusted so that they are composed of a monolayer of nanoparticles. To form such materials, numerous parameters have to be controlled such as the relative volume fraction of the nanoparticles and the template and size matching between the hydrophilic component of the copolymer and nanoparticles. The surface functionalization renders our synthetic route independent of the nanoparticles and allows us to prepare a variety of nanostructured composite materials that consist of a juxtaposition of different discrete oxide nanoparticles. Examples of such materials include CeO2, ZrO2, and CeO2-Al(OH)3 composites.
ChemInform Abstract: Aluminum‐Catalyzed Asymmetric Alkylations of Pyridyl‐Substituted Alkynyl Ketones with Dialkylzinc Reagents. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Design of the American Wake Experiment (AWAKEN) field campaign (2022)

Abstract The American WAKE experimeNt (AWAKEN) is a multi-institutional collaborative field campaign, starting in March 2022, that will gather an unprecedented data set including both atmospheric observations and wind plant operational data. This comprehensive data set will be used to characterize the wind plant performance and turbine loading in different operational and atmospheric conditions and validate the use of different wind plant control strategies and simulation frameworks. An extensive field campaign like AWAKEN requires proper coordination and long-term planning to be successful. In this paper, we review the major activities planned during AWAKEN to provide information for current and future project partners. Specifically, we provide information about the project sites, their planned instruments, and how these will relate to the scientific objectives of the overall AWAKEN project.
Detection or Modulation at 35 Gbit/s with a Standard CMOS-processed Optical Waveguide (2012)

Light modulation and detection within a single SOI waveguide is demonstrated at 1550 nm. Multi-functional devices allow simplified transceiver systems. Savings in the number of fabrication steps increase the yield and reduce costs.
International Union of Immunological Societies: 2017 Primary Immunodeficiency Diseases Committee Report on Inborn Errors of Immunity (2017)

Beginning in 1970, a committee was constituted under the auspices of the World Health Organization (WHO) to catalog primary immunodeficiencies. Twenty years later, the International Union of Immunological Societies (IUIS) took the remit of this committee. The current report details the categorization and listing of 354 (as of February 2017) inborn errors of immunity. The growth and increasing complexity of the field have been impressive, encompassing an increasing variety of conditions, and the classification described here will serve as a critical reference for immunologists and researchers worldwide.
Efficient Nonlinear Autoregressive Neural Network Architecture for Real-Time Biomedical Applications (2022)

Medical devices, such as continuous glucose monitors (CGMs) and drug-delivery pumps, are often combined in closed-loop systems for treating chronic diseases. Generally, these systems consist of sensors and actuators whose operation is modulated based on sensed stimuli. Closed-loop systems may be susceptible to a number of different security and reliability issues which may result in incorrect operation which may endanger patients. Nonlinear autoregressive neural networks (NARNNs) may be used in such systems for error detection and correction due to their predictive capabilities; however, an efficient implementation is needed for use in wearables and biomedical implants. In this paper, we present an area-and energy-efficient, pipelined NARNN hardware architecture suitable for such constrained devices. The architecture was tested on FPGA to confirm functionality, then synthesized targeting the SAED 32nm EDK. This NARNN implementation requires an estimated area of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$0.02 mm^{2},0.54\mu s$</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$0.76 nJ$</tex> per inference.
Erratum: “Clifford quantum cellular automata: Trivial group in 2D and Witt group in 3D” [J. Math. Phys. 62, 092202 (2021)] (2022)

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ZnO/ZnO2/Pt Janus Micromotors Propulsion Mode Changes with Size and Interface Structure: Enhanced Nitroaromatic Explosives Degradation under Visible Light (2018)

Self-motile mesoporous ZnO/Pt-based Janus micromotors accelerated by bubble propulsion that provide efficient removal of explosives and dye pollutants via photodegradation under visible light are presented. Decomposition of H<sub>2</sub>O<sub>2</sub> (the fuel) is triggered by a platinum catalytic layer asymmetrically deposited on the nanosheets of the hierarchical and mesoporous ZnO microparticles. The size-dependent motion behavior of the mesoporous micromotors is studied; the micromotors with average size ∼1.5 μm exhibit enhanced self-diffusiophoretic motion, whereas the fast bubble propulsion is detected for micromotors larger than 5 μm. The bubble-propelled mesoporous ZnO/Pt Janus micromotors show remarkable speeds of over 350 μm s<sup>-1</sup> at H<sub>2</sub>O<sub>2</sub> concentrations lower than 5 wt %, which is unusual for Janus micromotors based on dense materials such as ZnO. This high speed is related to efficient bubble nucleation, pinning, and growth due to the highly active and rough surface area of these micromotors, whereas the ZnO/Pt particles with a smooth surface and low surface area are motionless. We discovered new atomic interfaces of ZnO<sub>2</sub> introduced into the ZnO/Pt micromotor system, as revealed by X-ray diffraction (XRD), which contribute to enhance their photocatalytic activity under visible light. Such coupling of the rapid movement with the high catalytic performance of ZnO/Pt Janus micromotors provides efficient removal of nitroaromatic explosives and dye pollutants from contaminated water under visible light without the need for UV irradiation. This paves the way for real-world environmental remediation efforts using microrobots.
Quasicontinuum Models for Interface Multiscale Model (2004)

A strategy of coupling length scales from atomistic to continuum is investigated on the basis of quasicontinuum model for interface fracture problems. In the model, an atomistic region of the interest is discretized by finite elements and the positions of atoms are prescribed by means of nodal displacements of the elements with shape function for the reduction of the degrees of freedom. Total energy of the system consists of interatomic potentials, and minimized through variational method employed in conventional finite element formulation. In this study, we deal with the fracture behavior of Cu-Fe interface crack in two dimensional problems, and investigate the adequate discretization manner around the crack tip in use of quasicontinuum method.
Glutamatergic Signaling by Mesolimbic Dopamine Neurons in the Nucleus Accumbens (2010)

Recent evidence suggests the intriguing possibility that midbrain dopaminergic (DAergic) neurons may use fast glutamatergic transmission to communicate with their postsynaptic targets. Because of technical limitations, direct demonstration of the existence of this signaling mechanism has been limited to experiments using cell culture preparations that often alter neuronal function including neurotransmitter phenotype. Consequently, it remains uncertain whether glutamatergic signaling between DAergic neurons and their postsynaptic targets exists under physiological conditions. Here, using an optogenetic approach, we provide the first conclusive demonstration that mesolimbic DAergic neurons in mice release glutamate and elicit excitatory postsynaptic responses in projection neurons of the nucleus accumbens. In addition, we describe the properties of the postsynaptic glutamatergic responses of these neurons during experimentally evoked burst firing of DAergic axons that reproduce the reward-related phasic population activity of the mesolimbic projection. These observations indicate that, in addition to DAergic mechanisms, mesolimbic reward signaling may involve glutamatergic transmission.
Locally Enhanced Relative Humidity for Scanning Probe Nanolithography (2005)

The formation of a water meniscus between a sharp tip and a solid surface is one of the prevailing requirements for scanning probe microscope (SPM)-based lithographies, such as dip-pen nanolithography (DPN) and conductive tip induced oxidation. The water meniscus functions as a medium for the oxidation of or mass transfer to the solid surface. Here we report a simple, efficient, and effective approach to enhance the local relative humidity and thus increase the size of the water meniscus by bringing a water-containing capillary tube to the proximity of the tip-surface contact area. The enhancement in local relative humidity is confirmed via an increase in the measured tip-surface adhesion forces and the widths of DPN generated parallel lines. Compared to the global control of relative humidity for the whole lithography system, the short distance between the "water reservoir" and the tip-surface contact area enables rapid increase in the local vapor pressure of water, less perturbation, and minimal erosion to the state-of-the-art electronics. As a result, most scanning probe lithography experiments at high relative humidity can now be performed in a reasonable time frame.
Medical intervention in parent‐reported infant gastro‐oesophageal reflux: A population‐based study (2014)

In the first year of life, approximately 14% of the population seek medical advice for GOR symptoms. The use of anti-reflux medication in the general community remains high, despite the absence of evidence that it is appropriate or effective for uncomplicated GOR.
Resource management simulator for radiology departments. (2007)

We propose a new system to manage modalities in radiology departments. Our system introduces a novel method to accurately estimate some indexes in order to provide an analysis of resource plans within three broad categories: financial affairs, patient satisfaction, and productivity. The main idea is to simulate the operational status of modalities. Results from a preliminary hospital evaluation show that use of the system results in more efficient resource management.
Characterization of a flocculation-like phenotype in Cryptococcus neoformans and its effects on pathogenesis (2006)

We investigated the phenomenon of cell-cell aggregation (flocculation) in a serotype D strain of Cryptococcus neoformans (ATCC 24067, isolate RC-2). Cell aggregation into clumps of 5-40 cells (clump+ cells) occurred during the early log phase and disappeared in the beginning of the stationary phase (clump- cells). The cell aggregation phenomenon was medium dependent. Clump+ cells could be dispersed by either vortexing or proteinase K digestion. Most importantly, the transient change in cellular phenotype changed several important host-pathogen interactions. Adherence of clump+ cells to murine macrophage-like cells J774.16 was significantly (P < 0.001) enhanced compared with adherence of clump- cells. Furthermore, complement-mediated phagocytosis efficacy of dispersed clump+ cells was significantly higher (P < 0.001) compared with clump- cells. Similar findings were documented with an in vivo phagocytosis assay. Infection of mice with a low inoculum (10(4)) of clump+ cells resulted in lower fungal burden when compared with mice infected with clump- cells. Accordingly, mice infected with clump+ cells survived significantly longer than mice infected with clump- cells. These results indicate that the cellular phenotype undergoes significant changes that result in a transient flocculation-like phenotype. We hypothesize that this cell-cell aggregation is the result of changes in protein content in the polysaccharide capsule. We conclude from our data that the change in cellular phenotype has a dramatic effect on cell adherence, and on complement-mediated phagocytosis, both of which can affect the pathogenesis of the disease in the host. Our results underscore the complexity of studies that investigate host pathogen interactions and may explain differences and inconsistencies observed in in vitro and in vivo assays.
Conformation of apolipoprotein B-100 in the low density lipoproteins of tangier disease. Identification of localized conformational response to triglyceride content. (1990)

The low density lipoproteins (LDL) from patients with Tangier disease are enriched in triglycerides, 27% of LDL mass versus 7% for normal LDL. To study whether this unique LDL core lipid composition affects the surface disposition of apolipoprotein (apo) B-100, we analyzed the LDL by protease digestion and in competitive radioimmunoassays. Limited proteolytic digestion of Tangier LDL by Staphylococcus aureus V8 protease generated a prominent fragment of 120 kDa (cleavage site at residue 1076), which was not visible in similarly digested normal LDL. In competitive radioimmunoassay, Tangier LDL bound weakly to the apoB-specific monoclonal antibody MB20, compared with control LDL. We localized the MB20 epitope between residues 1031 and 1084 of apoB-100, probably very near residue 1076. DNA sequencing of exon 21 of apoB genomic clones (coding for residues 1014-1084) from a Tangier patient revealed no difference from the normal DNA sequence, thus eliminating a protein polymorphism as a basis for the altered protease sensitivity and antibody binding. When the triglyceride contents of Tangier LDL were reduced to 10% of mass by incubation with normal high density lipoproteins, production of the 120-kDa fragment by proteolysis decreased and MB20 binding increased in affinity, implying a change toward normal conformation of apoB-100. Thus, using two independent techniques, proteolytic digestion and binding of monoclonal antibodies, we have demonstrated an alternative conformation of apoB-100 in the vicinity of residue 1076, which reflects the content of triglycerides in the LDL particle.
Novel High‐Temperature Antiferroelectric‐Based Dielectric NaNbO 3 – NaTaO 3 Solid Solutions Processed in Low Oxygen Partial Pressures (2012)

The (1− x ) NaNbO 3 –( x ) NaTaO 3 solid solution was investigated for x ≤ 0.4 in terms of new high‐temperature and high‐permittivity dielectric system that is suitable for base metal inner electrode capacitor applications. The addition of Ta significantly enhanced the resistivity of the dielectric, resulting in superior resistivity than the dielectrics‐formulated BaTiO 3 systems that dominate the multilayer ceramic capacitor dielectric devices. The voltage dependence of the permittivity was also superior to BaTiO 3 ‐based materials, providing higher capacitance at higher temperatures. A transmission electron microscopy study illustrated that the grains had so‐called core‐shell structure. According to the electron diffraction analysis, the core region had an inhomogeneous structure between antiferroelectric and ferroelectric phases, and shell region had an incommensurate ferroelectric‐like structure. The core and shell region had Nb ‐ and Ta ‐rich composition, respectively, and their interface was compositionally sharp, implying that shell region was formed via a liquid phase during the sintering process with an incongruent Ta dissolution reprecipitation. We anticipate that these or similar materials based on the alkali‐niobate perovskites can be further enhanced to provide capacitor solutions from 150°C to 250°C, which is an important range for a number of new AC–DC invertor and engine control units.
C–O and C–X Bond-Forming Reactions with Pd(II)/MWCNT (2015)

Key words nanoparticles - carbon nanotubes - C–H bond activation - palladium
Nanoparticle removal from EUV photomasks using laser induced plasma shockwaves (2006)

In recent years, it has been demonstrated that nanoparticles can be detached and removed from substrates using laser-induced plasma (LIP) shockwaves. While it was experimentally established the effectiveness of the LIP technique for removing nanoparticles in the sub-100nm range, the removal mechanisms were not well-understood. In this article, we introduce a set of particle removal mechanisms based on moment resistance of the particle-substrate bond and discuss their effectiveness and applicability in laser-induced plasma shock nanoparticle removal. The mechanical interactions between nanoparticles and shockwaves are studied by utilizing molecular dynamic simulation approach. The forces and moments acting on nanoparticles are calculated and are related to the detachment mechanisms. It is demonstrated that sub-100nm particles can be detached from various substrates. Experiments and simulations are performed to study the effect of LIP on optical and EUVL/LTEM substrates in terms of substrate damage. Initial experiments and simulations reveal the window of safe operation of LIP and the mechanisms responsible for material alterations if any at close distances of operation of LIP above the substrate.