gebhart/patrepeval huggingface dataset:
Replication based storage systems with local repair (2013)

We consider the design of regenerating codes for distributed storage systems that enjoy the property of local, exact and uncoded repair, i.e., (a) upon failure, a node can be regenerated by simply downloading packets from the surviving nodes and (b) the number of surviving nodes contacted is strictly smaller than the number of nodes that need to be contacted for reconstructing the stored file. Our codes consist of an outer MDS code and an inner fractional repetition code that specifies the placement of the encoded symbols on the storage nodes. For our class of codes, we identify the tradeoff between the local repair property and the minimum distance. We present codes based on graphs of high girth, affine resolvable designs and projective planes that meet the minimum distance bound for specific choices of file sizes.
Open-contact failure detection of via holes by using voltage contrast (2001)

We used two techniques to determine the sensitivity of a scanning-electron-microscope-based wafer-inspection system in detecting open-contact failures. (1) The correlation between the contact resistance and the brightness of the voltage-contrast image as captured by the system was obtained experimentally. (2) A voltage-contrast simulation was developed and applied to derive a correlation between resistance and brightness from these results. A close agreement between the experimental results and the calculated values was obtained. We succeeded in clarifying the determinants of the sensitivity of open-contact-failure detection. The brightness, over part of its range, appears to be proportional to log(R*I<SUB>p</SUB>) where R is the resistance and I<SUB>p</SUB> is the irradiating electron-beam current. This relationship indicates that the sensitivity of open-contact failure detection is determined by I<SUB>p</SUB>. Control of I<SUB>p</SUB> can be used to improve the voltage contrast, and this, in turn, can improve the sensitivity of detection.
Computational Modeling in Lignocellulosic Biofuel Production (2010)

Ab initio molecular dynamics (CPMD) coupled with metadynamics (MTD) simulations were used to investigate the free-energy surfaces of acid-catalyzed hydrolysis reactions of xylobiose disaccharide in the gas phase and in aqueous solution. Water and water structures were found to play a critical role in the hydrolysis reaction barrier. Proton partial desolvation associated with its migration to the ether linkage site, the protonation of the ether bond, and the subsequent breaking of the C-O bond were found to be the rate-limiting steps. The significant contribution to the reaction barrier caused by partial proton desolvation and migration could partially explain the biphasic phenomenon in xylan hydrolysis and highlight the importance of mass transport during biomass pretreatment.
Anterolateral C1—C2 Transarticular Fixation for Atlantoaxial Arthrodesis (2010)

We propose a new anterolateral stabilization technique for atlantoaxial instability based on less traumatic dissection of the upper cervical region, different instrumentation, and guidance by reliable landmarks. For anterolateral transarticular C1-C2 screw fixation, the gray ramus communicans to the C2 nerve is a reliable landmark for locating the entry for a screw on the C2 pars.
Product multi-lag high-order ambiguity function for blind equalization of polynomial phase signals (2002)

Blind equalization of multi-component polynomial phase signals (mc-PPS) may arise due to multipath propagation in mobile communications. Using the multi-lag high-order ambiguity function, an algorithm is proposed to estimate the parameters of PPS and FIR channel coefficients. Performance analysis is carried out and Cramer-Rao bounds are compared with simulation results.
A BIOMECHANICAL ANALYSIS OF POLYETHYLENE LINER CEMENTATION INTO A FIXED METAL ACETABULAR SHELL (2003)

When cementing a liner into a well-fixed shell, a surgeon should ensure that both the shell and the liner are textured, as interdigitation of the cement with the shell and the liner is crucial to the mechanical strength of this construct.
Tunable control of antibody immobilization using electric field (2015)

The controlled immobilization of proteins on solid-state surfaces can play an important role in enhancing the sensitivity of both affinity-based biosensors and probe-free sensing platforms. Typical methods of controlling the orientation of probe proteins on a sensor surface involve surface chemistry-based techniques. Here, we present a method of tunably controlling the immobilization of proteins on a solid-state surface using electric field. We study the ability to orient molecules by immobilizing IgG molecules in microchannels while applying lateral fields. We use atomic force microscopy to both qualitatively and quantitatively study the orientation of antibodies on glass surfaces. We apply this ability for controlled orientation to enhance the performance of affinity-based assays. As a proof of concept, we use fluorescence detection to indirectly verify the modulation of the orientation of proteins bound to the surface. We studied the interaction of fluorescently tagged anti-IgG with surface immobilized IgG controlled by electric field. Our study demonstrates that the use of electric field can result in more than 100% enhancement in signal-to-noise ratio compared with normal physical adsorption.
Cloning of rat brain succinyl-CoA:3-oxoacid CoA-transferase cDNA. Regulation of the mRNA in different rat tissues and during brain development (1987)

3-Oxoacid CoA-transferase, which catalyses the first committed step in the oxidation of ketone bodies, is uniquely regulated in developing rat brain. Changes in 3-oxoacid CoA-transferase activity in rat brain during the postnatal period are due to changes in the relative rate of synthesis of the enzyme. To study the regulation of this enzyme, we identified, with a specific polyclonal rabbit anti-(rat 3-oxoacid CoA-transferase), two positive cDNA clones (approx. 800 bp) in a lambda gtll expression library, constructed from poly(A)+ RNA from brains of 12-day-old rats. One of these clones (lambda CoA3) was subcloned into M13mp18 and subjected to further characterization. Labelled single-stranded probes prepared by primer extension of the M13mp18 recombinant hybridized to a 3.6 kb mRNA. Rat brain mRNA enriched by polysome immunoadsorption for a single protein of size 60 kDa which corresponds to the precursor form of 3-oxoacid CoA-transferase was also found to be similarly enriched for the hybridizable 3.6 kb mRNA complementary to lambda CoA3. Affinity-selected antibody to the lambda CoA3 fusion protein inhibited 3-oxoacid CoA-transferase activity present in rat brain mitochondrial extracts. The 3.6 kb mRNA for 3-oxoacid CoA-transferase was present in relative abundance in rat kidney and heart, to a lesser extent in suckling brain and mammary gland and negligible in the liver. The specific mRNA was also found to be 3-fold more abundant in the brain from 12-day-old rats as compared with 18-day-old foetuses and adult rats, corresponding to the enzyme activity and relative rate of synthesis profile during development. These data suggest that 3-oxoacid CoA-transferase enzyme activity is regulated at a pretranslational level.
ChemInform Abstract: Synthesis of Fluorinated Derivatives of Benzo(k)fluoranthene and Indeno(1,2,3‐cd)pyrene and 8,9‐Dihydro‐8,9‐epoxybenzo(k)fluoranthene. (1988)

Abstract Bromination of the o‐xylenes (I) and subsequent treatment with triphenylphosphine (II) results in the formation of the phosphonium salts (III) which undergo Wittig reaction with acenaphthenequinone (IV), forming the fluorobenzofluoranthenes (V).
Early detection of radiation-induced lung damage with X-ray dark-field radiography in mice (2020)

• Significant deviations from healthy lung due to irradiation were measured after 16 weeks with x-ray dark-field radiography (p = 0.004). • Significant deviations occur on average 10 weeks earlier for x-ray dark-field radiography in comparison to x-ray transmission radiography. • Sensitivity and specificity doubled when using x-ray dark-field radiography instead of x-ray transmission radiography.
The Space Optical Clocks Project: Development of high-performance transportable and breadboard optical clocks and advanced subsystems (2012)

The use of ultra-precise optical clocks in space ("master clocks") will allow for a range of new applications in the fields of fundamental physics (tests of Einstein's theory of General Relativity, time and frequency metrology by means of the comparison of distant terrestrial clocks), geophysics (mapping of the gravitational potential of Earth), and astronomy (providing local oscillators for radio ranging and interferometry in space). Within the ELIPS-3 program of ESA, the "Space Optical Clocks" (SOC) project aims to install and to operate an optical lattice clock on the ISS towards the end of this decade, as a natural follow-on to the ACES mission, improving its performance by at least one order of magnitude. The payload is planned to include an optical lattice clock, as well as a frequency comb, a microwave link, and an optical link for comparisons of the ISS clock with ground clocks located in several countries and continents. Undertaking a necessary step towards optical clocks in space, the EU-FP7-SPACE-2010-1 project no. 263500 (SOC2) (2011-2015) aims at two "engineering confidence", accurate transportable lattice optical clock demonstrators having relative frequency instability below 1\times10^-15 at 1 s integration time and relative inaccuracy below 5\times10^-17. This goal performance is about 2 and 1 orders better in instability and inaccuracy, respectively, than today's best transportable clocks. The devices will be based on trapped neutral ytterbium and strontium atoms. One device will be a breadboard. The two systems will be validated in laboratory environments and their performance will be established by comparison with laboratory optical clocks and primary frequency standards. In this paper we present the project and the results achieved during the first year.
High-NA EUV lithography exposure tool progress (Conference Presentation) (2018)

While EUV systems equipped with a 0.33 Numerical Aperture (NA) lens are readying to start high volume manufacturing, ASML and Zeiss are in parallel ramping up their activities on an EUV exposure tool with an NA of 0.55. The purpose of this high-NA scanner, targeting an ultimate resolution of 8nm, is to extend Moore’s law throughout the next decade. A novel lens design, capable of providing the required Numerical Aperture, has been identified; this lens will be paired with new, faster stages and more accurate sensors enabling the tight focus and overlay control needed for future process nodes. In this paper an update will be given on the status of the developments at Carl Zeiss and ASML. Next to this, we will address several topics inherent in the new design and smaller target resolution: M3D effects, polarization, focus control and stitching.
Figures S1-S6 & Tables S1 & S2 from Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress (2023)

&lt;p&gt;Merged supplementary Figures &amp; Figure legends and Tables &amp; Table legends&lt;/p&gt;
Temperature-dependent electrical conduction in porous silicon: Non-Arrhenius behavior (2001)

A model for the temperature dependence of electrical conduction in a porous silicon (PS) layer is introduced based on the consideration that the onset of electrical conduction is dependent on the formation of a continuous network of conducting sites extending the entire thickness of a PS layer. At an arbitrary temperature, a PS layer consists of both unblocked and blocked sites (blocking energies are larger than thermal fluctuation energy). The fraction of unblocked sites increases with temperature. At low temperatures (T < T1) a PS layer is mainly dominated by a continuous network of blocked sites, while discrete unblocked sites do not form any continuous network extending the entire thickness of a PS layer. At medium temperatures (T1 < T < T2) both continuous networks of unblocked and blocked sites appear in a PS layer. And at higher temperatures (T > T2), a PS layer is mainly dominated by a continuous network of unblocked sites, while discrete blocked sites do not form any continuous network extending the entire thickness of a PS layer. Contrary to the prevalent views, the overall temperature dependence of the electrical conductivity of a PS is not always Arrhenius: it obeys a Vogel-Tammann-Fulcher (VTF) law at T > T2, becomes insulating at T < T1, and exhibits the Arrhenius behavior only for T2 > T > T1. Both T1 and T2 are found to increase with the decrease silicon nanocrytallites sizes. The VTF behavior was derived using the mean-field approximation for Ising model and found to agree with experimental evidences.
The virC and virD operons of the Agrobacterium Ti plasmid are regulated by the ros chromosomal gene: analysis of the cloned ros gene (1991)

The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid. The ros gene was cloned from a genomic bank by electroporation and complementation in Agrobacterium cells. Reporter fusion to the ros gene indicates that the level of transcription is controlled in part by autoregulation. A consensus inverted repeat sequence present in the ros promoter and in the virC and virD promoters of pTiC58, pTiA6, and pRiA4b suggests that a specific Ros binding site exists in these promoters. In the virC and virD promoter region, this binding site is within a cluster of vir box consensus sequences in which the VirG protein binds. This suggests possible binding competition between Ros and VirG at the virC and virD promoters. That the Ros protein binds DNA is suggested by the presence of a 'zinc finger' consensus sequence in the protein.
New Particle Transport Methods for Design and Optimization of Spherical-Shell Transmission Measurements (2002)

This paper discusses new particle transport methods developed for accurate investigation of iron non-elastic scattering cross sections using the spherical-shell transmission method, employing iron shells with different thicknesses, and neutron time-of-flight spectroscopy of the scattered neutrons. New calculational techniques based on the deterministic and Monte Carlo methods have been developed for design and optimization of the experiment, and for identification and reduction of experimental uncertainties. The new methods include a new tallying option for the MCNP code and new quadrature sets for the 3-D parallel Sn code PENTRAN. The new tallying option is used to determine the optimum source energy versus target thickness, and among the new quadrature sets, the Pn-Tn with ordinate-splitting technique has resulted in accurate flux distributions as compared to Monte Carlo prediction.
Determination of m, e/m, and M p/m by the study of the isotope structure in hydrogen (1975)

Using a commercially available hydrogen–deuterium light source and a 3.4-m Ebert plane grating spectrograph, the wavelengths of the first six pairs of the Balmer series are obtained. From the results, first, the series limit, Rydberg constant, and ionization potential of hydrogen are found from the graph. Then, by means of formulas involving wave numbers of hydrogen and deuterium and by knowing the Faraday constant, the values of m, e/m, and Mp/m are determined. All the values are found to be in good agreement with accepted values. From the results, this experiment is recommended for an upper division optics and spectroscopy or quantum physics laboratory.
Electric currents applied during refractory period enhance contractility and systolic calcium in the ferret heart (2003)

We investigated the mechanism of positive inotropism of electric currents applied during the absolute refractory period. Ten Langendorff-perfused ferret hearts were instrumented to measure isovolumic left ventricular pressure (LVP) and the aequorin luminescence. Biphasic square-wave electric currents (+/-20 mA, total duration 30 ms) were delivered between pairs of electrodes. Six hearts were perfused at different extracellular Ca(2+) concentrations ([Ca(2+)](o); 1, 2, 4, and 8 mM). These signals increased LVP from 50.0 +/- 9.4 to 70.1 +/- 14.7, from 67.5 +/- 11.0 to 79.0 +/- 15.6, from 79.3 +/- 21.0 to 87.1 +/- 22.8, and from 84.6 +/- 24.0 to 91.8 +/- 28.5 mmHg at the respective [Ca(2+)](o) (P < 0.05). Peak free intracellular [Ca(2+)] ([Ca(2+)](i)) increased from 0.52 +/- 0.13 to 1.37 +/- 0.23, from 0.76 +/- 0.23 to 1.73 +/- 0.14, from 1.10 +/- 0.24 to 2.05 +/- 0.33, and from 1.41 +/- 0.36 to 2.24 +/- 0.36 microM/ml, respectively (P < 0.001). With the use of 1 mg/l propranolol with 1 mM [Ca(2+)](o), LVP and [Ca(2+)](i) were increased significantly from 48.7 +/- 8.18 to 56.3 +/- 6.11 mmHg and from 0.61 +/- 0.11 to 1.17 +/- 0.20 microM, respectively (P < 0.05). In conclusion, positive inotropism of such electrical currents was due to increased peak [Ca(2+)](i) and Ca(2+) responsiveness of the myofilaments did not change significantly.
Multiple Functions of the IKK-Related Kinase IKKε in Interferon-Mediated Antiviral Immunity (2007)

IKKepsilon is an IKK (inhibitor of nuclear factor kappaBkinase)-related kinase implicated in virus induction of interferon-beta (IFNbeta). We report that, although mice lacking IKKepsilon produce normal amounts of IFNbeta, they are hypersusceptible to viral infection because of a defect in the IFN signaling pathway. Specifically, a subset of type I IFN-stimulated genes are not activated in the absence of IKKepsilon because the interferon-stimulated gene factor 3 complex (ISGF3) does not bind to promoter elements of the affected genes. We demonstrate that IKKepsilon is activated by IFNbeta and that IKKepsilon directly phosphorylates signal transducer and activator of transcription 1 (STAT1), a component of ISGF3. We conclude that IKKepsilon plays a critical role in the IFN-inducible antiviral transcriptional response.
Method of CO and/or CO.sub.2 hydrogenation using doped mixed-metal oxides (2023)

A method of hydrogenation utilizing a reactant gas mixture comprising a carbon oxide and a hydrogen agent, and a hydrogenation catalyst comprising a mixed-metal oxide containing metal sites supported and/or incorporated into the lattice. The mixed-metal oxide comprises a perovskite, a pyrochlore, a fluorite, a brownmillerite, or mixtures thereof doped at the A-site or the B-site. The metal site may comprise a deposited metal, where the deposited metal is a transition metal, an alkali metal, an alkaline earth metal, or mixtures thereof. Contact between the carbon oxide, hydrogen agent, and hydrogenation catalyst under appropriate conditions of temperature, pressure and gas flow rate generate a hydrogenation reaction and produce a hydrogenated product made up of carbon from the carbon oxide and some portion of the hydrogen agent. The carbon oxide may be CO, CO.sub.2, or mixtures thereof and the hydrogen agent may be H.sub.2. In a particular embodiment, the hydrogenated product comprises an alcohol, an olefin, an aldehyde, a ketone, an ester, an oxo-product, or mixtures thereof.
Controlled deformation of vesicles by flexible structured media (2016)

Liquid crystalline (LC) materials, such as actin or tubulin networks, are known to be capable of deforming the shape of cells. Here, elements of that behavior are reproduced in a synthetic system, namely, a giant vesicle suspended in a LC, which we view as a first step toward the preparation of active, anisotropic hybrid systems that mimic some of the functionality encountered in biological systems. To that end, we rely on a coupled particle-continuum representation of deformable networks in a nematic LC represented at the level of a Landau-de Gennes free energy functional. Our results indicate that, depending on its elastic properties, the LC is indeed able to deform the vesicle until it reaches an equilibrium, anisotropic shape. The magnitude of the deformation is determined by a balance of elastic and surface forces. For perpendicular anchoring at the vesicle, a Saturn ring defect forms along the equatorial plane, and the vesicle adopts a pancake-like, oblate shape. For degenerate planar anchoring at the vesicle, two boojum defects are formed at the poles of the vesicle, which adopts an elongated, spheroidal shape. During the deformation, the volume of the topological defects in the LC shrinks considerably as the curvature of the vesicle increases. These predictions are confirmed by our experimental observations of spindle-like shapes in experiments with giant unilamellar vesicles with planar anchoring. We find that the tension of the vesicle suppresses vesicle deformation, whereas anchoring strength and large elastic constants promote shape anisotropy.
Learning Multisensory Integration and Coordinate Transformation via Density Estimation (2013)

Sensory processing in the brain includes three key operations: multisensory integration-the task of combining cues into a single estimate of a common underlying stimulus; coordinate transformations-the change of reference frame for a stimulus (e.g., retinotopic to body-centered) effected through knowledge about an intervening variable (e.g., gaze position); and the incorporation of prior information. Statistically optimal sensory processing requires that each of these operations maintains the correct posterior distribution over the stimulus. Elements of this optimality have been demonstrated in many behavioral contexts in humans and other animals, suggesting that the neural computations are indeed optimal. That the relationships between sensory modalities are complex and plastic further suggests that these computations are learned-but how? We provide a principled answer, by treating the acquisition of these mappings as a case of density estimation, a well-studied problem in machine learning and statistics, in which the distribution of observed data is modeled in terms of a set of fixed parameters and a set of latent variables. In our case, the observed data are unisensory-population activities, the fixed parameters are synaptic connections, and the latent variables are multisensory-population activities. In particular, we train a restricted Boltzmann machine with the biologically plausible contrastive-divergence rule to learn a range of neural computations not previously demonstrated under a single approach: optimal integration; encoding of priors; hierarchical integration of cues; learning when not to integrate; and coordinate transformation. The model makes testable predictions about the nature of multisensory representations.