gebhart/patrepeval huggingface dataset:
Mutations in the Human AAA+ Chaperone p97 and Related Diseases (2016)

A number of neurodegenerative diseases have been linked to mutations in the human protein p97, an abundant cytosolic AAA<sup>+</sup> (ATPase associated with various cellular activities) ATPase, that functions in a large number of cellular pathways. With the assistance of a variety of cofactors and adaptor proteins, p97 couples the energy of ATP hydrolysis to conformational changes that are necessary for its function. Disease-linked mutations, which are found at the interface between two main domains of p97, have been shown to alter the function of the protein, although the pathogenic mutations do not appear to alter the structure of individual subunit of p97 or the formation of the hexameric biological unit. While exactly how pathogenic mutations alter the cellular function of p97 remains unknown, functional, biochemical and structural differences between wild-type and pathogenic mutants of p97 are being identified. Here, we summarize recent progress in the study of p97 pathogenic mutants.
Effect of Temperature on Glycerol Retention in the Halotolerant Algae <i>Dunaliella</i> and <i>Asteromonas</i> (1980)

Algae of the genera Dunaliella and Asteromonas can maintain extremely high concentration gradients (>10(4)) of glycerol between the intracellular space and the medium. This unique ability is highly temperature-dependent. Treating the algae for several minutes at temperatures exceeding 60 C causes complete release of all the internally held glycerol; 50% release occurs around 50 C, but essentially none is released below 40 C. A similar behavior was observed in several species of Dunaliella, and one of Asteromonas and is independent of the salt concentration of the medium. The underlying mechanism may involve a temperature-dependent conformational transition of a component of the cellular membrane which is essential for glycerol impermeability.
Chromatin remodeling of the interleukin-2 gene: Distinct alterations in the proximal versus distal enhancer regions (1998)

Known transcription factor-DNA interactions in the minimal enhancer of the murine interleukin-2 gene (IL-2) do not easily explain the T cell specificity of IL-2 regulation. To seek additional determinants of cell type specificity, in vivo methodologies were employed to examine chromatin structure 5' and 3' of the 300 bp IL-2 proximal promoter/enhancer region. Restriction enzyme accessibility revealed that until stimulation the IL-2 proximal promoter/enhancer exists in a closed conformation in resting T and non-T cells alike. Within this promoter region, DMS and DNase I genomic footprinting also showed no tissue-specific differences prior to stimulation. However, DNase I footprinting of the distal -600 to -300 bp region revealed multiple tissue-specific and stimulation-independent DNase I hypersensitive sites. Gel shift assays detected T cell-specific complexes binding within this region, which include TCF/LEF or HMG family and probable Oct family components. Upon stimulation, new DNase I hypersensitive sites appeared in both the proximal and distal enhancer regions, implying that there may be a functional interaction between these two domains. These studies indicate that a region outside the established IL-2 minimal enhancer may serve as a stable nucleation site for tissue-specific factors and as a potential initiation site for activation-dependent chromatin remodeling.
Progress and problems in vaccination against necrotic enteritis in broiler chickens (2014)

Necrotic enteritis in broilers is caused by Clostridium perfringens type A strains that produce the NetB toxin. It is one of the diseases that gained worldwide importance the last decade. Prevention strategies include avoiding predisposing factors, such as coccidiosis, and in-feed supplementation of a variety of feed additives. For protection against a toxin-producing bacterium, vaccination with modified toxin or other secreted immunogenic proteins seems a logical preventive tool. Formalin inactivated crude supernatant has been used for vaccination initially. Recently, several studies have been carried out to identify the most important immunogenic and protective proteins that can be used for vaccination. These include the NetB toxin, but also multiple other proteins. There is evidence that immunization with single proteins is not protective against severe challenge and that combinations of different antigens are needed. Most published studies used multiple dosage vaccination regimens that are not relevant for practical use in the broiler industry. Single vaccination regimens at day-old seem to be non-protective. This review describes the history of vaccination strategies against necrotic enteritis in broilers and gives an update on future vaccination strategies that are applicable in the field. These may include breeder hen vaccination, in ovo vaccination and live attenuated vectors to be used in feed or in drinking water.
Water Oxidation Catalysis Beginning with Co<sub>4</sub>(H<sub>2</sub>O)<sub>2</sub>(PW<sub>9</sub>O<sub>34</sub>)<sub>2</sub><sup>10–</sup> When Driven by the Chemical Oxidant Ruthenium(III)tris(2,2′-bipyridine): Stoichiometry, Kinetic, and Mechanistic Studies en Route to Identifying the True Catalyst (2013)

Stoichiometry and kinetics are reported for catalytic water oxidation to O2 beginning with the cobalt polyoxometalate Co4(H2O)2(PW9O34)210– (Co4POM) and the chemical oxidant ruthenium(III)tris(2,2′-bipyridine) (Ru(III)(bpy)33+). This specific water oxidation system was first reported in a 2010 Science paper (Yin et al. Science 2010, 328, 342). Under standard conditions employed herein of 1.0 μM Co4POM, 500 μM Ru(III)(bpy)33+, 100 μM Ru(II)(bpy)32+, pH 7.2, and 0.03 M sodium phosphate buffer, the highest O2 yields of 22% observed herein are seen when Ru(II)(bpy)32+ is added prior to the Ru(III)(bpy)33+ oxidant; hence, those conditions are employed in the present study. Measurement of the initial O2 evolution and Ru(III)(bpy)33+ reduction rates while varying the initial pH, [Ru(III)(bpy)33+], [Ru(II)(bpy)32+], and [Co4POM] indicate that the reaction follows the empirical rate law: −d[Ru(III)(bpy)33+]/dt = (k1 + k2)[Co4POM]soluble[Ru(III)(bpy)33+]/[H+], where the rate constants k1 ∼ 0.0014 s–1 and k2 ∼ 0.0044 s–1 correspond to the water oxidation and ligand oxidation reactions, and for O2 evolution, d[O2]/dt = (k1/4)[Co4POM]soluble[Ru(III)(bpy)33+]/[H+]. Overall, at least seven important insights result from the present studies: (i) Parallel WOC and Ru(III)(bpy)33+ self-oxidation reactions well documented in the prior literature limit the desired WOC and selectivity to O2 in the present system to ≤28%. (ii) The formation of a precipitate from ∼2 Ru(II)(bpy)32+/3 Co4(H2O)2(PW9O34)210– with a Ksp = (8 ± 7) × 10–25 (M5) greatly complicates the reaction and interpretation of the observed kinetics, but (iii) the best O2 yields are still when Ru(II)(bpy)32+ is preadded. (iv) CoOx is 2–11 times more active than Co4POM under the reaction conditions, but (v) Co4POM is still the dominant WOC under the Co4POM/Ru(III)(bpy)33+ and other reaction conditions employed. The present studies also (vi) confirm that the specific conditions matter greatly in determining the true WOC and (vii) allow one to begin to construct a plausible WOC mechanism for the Co4POM/Ru(III)(bpy)33+ system.
Ultrasonic Press–Fitting: A New Assembly Technique (2014)

The superposition of ultrasonic frequency vibrations to conventional machining techniques is known and practiced since the 1950s under the name of ultrasonic machining. Using ultrasound, many good properties appear including reduced thrust force, improved surface finish, reduced residual stress in machined material, etc…In this paper we present a new assembly technique based on the same principles: ultrasonic press–fitting. Feasibility and energy reduction are demonstrated through experiments under industrial production conditions.
Synthesis of TiO<sub>2</sub> nanorings and nanorods on TCO substrate by potentiostatic anodization of titanium powder (2011)

Abstract Various TiO 2 nanostructures, such as nanorings, nanorods were synthesized via potentiostatic anodization of titanium powder under different conditions. The morphology of the obtained TiO 2 nanostructures can be easily tuned by varying applied voltage. The crystal structure, compositional information and morphological structures were characterized by X‐ray diffraction (XRD), X‐ray photoelectron spectra (XPS) and field emission scanning electronic microscopy (FESEM). XRD and XPS analysis confirmed the anodization products were TiO 2 . A possible formation mechanism was suggested on the basis of the shape evolution of TiO 2 nanostructures observed by FESEM. The results revealed that the applied voltage played an important role in the formation of various nanostructures. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A solution for an ideal planar multi-gates process for ultimate CMOS? (2010)

We demonstrate for the first time high-performant planar multi-gates devices with Si-conduction channel of 4nm, allowing drive current up to 1350μA/μm @I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> =0.4nA/μm (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dd</sub> =1.1V, CET=1.9nm). But as future multi-gates transistors need to have reduced capacitances and a simple robust process, we also demonstrate in this paper an ideal planar self-aligned solution, based on the direct exposure of a HSQ layer through a 5nm Si-channel. This opens the way to an easy planar multi-gate process for ultimate CMOS (11nm node & below), fully co-integrable with conventional devices.
Collaborative filtering with fine-grained trust metric (2009)

Similarity-based collaborative filtering systems are vulnerable to the data sparsity, cold-start, and robustness problems. Computational trust models are promising alternative solutions to alleviate these problems by replacing similarity metric with trust metric. However, they often have some shortages that rely on users' explicit trust statements. A fine-grained model computing trust from user ratings is more reasonable and gets more nonintrusive for average users. We propose a novel trust-based recommendation model for this purpose. Experiments on a large real dataset show that the proposed model has better performance in terms of MAE, coverage, and F-metric than the conventional collaborative filtering model.
DVB-H: Digital Broadcast Services to Handheld Devices (2006)

This paper gives a brief review of the new Digital Video Broadcasting-Handheld(DVB-H) standard. This is based on the earlier standard DVB-T, which is used for terrestrial digital TV broadcasting. The new extension brings features that make it possible to receive digital video broadcast type services in handheld, mobile terminals. The paper discusses the key technology elements-4K mode and in-depth interleavers, time slicing and additional forward error correction-in some detail. It also gives extensive range of performance results based on laboratory measurements and real field tests. Finally it presents viewpoints relevant for DVB-H network design and system use in general.
A vector-based approach for power supply noise analysis in test compaction (2006)

Excessive power supply noise can lead to overkill during delay test. A static test vector compaction solution is described to prevent such overkill. Low-cost power supply noise models are developed and used in compaction. An error analysis of these models is given. This paper improves on prior work in terms of models and algorithm to increase accuracy and performance. Experimental results are given on ISCAS89 circuits
Enzymatic Regional Methylation Assay: A Novel Method to Quantify Regional CpG Methylation Density (2001)

We have developed a novel quantitative method for rapidly assessing the CpG methylation density of a DNA region in mammalian cells. After bisulfite modification of genomic DNA, the region of interest is PCR amplified with primers containing two dam sites (GATC). The purified PCR products are then incubated with 14C-labeled S-adenosyl-L-methionine (SAM) and dam methyltransferase as an internal control to standardize DNA quantity. This is followed by an incubation with 3H-labeled SAM and SssI methyltransferase for methylation quantification. By use of standard mixtures of cell line DNA with a defined methylation status in every assay, the ratio (3H/14C signal) of each sample can be converted into percentage values to assess the methylation density of the amplified sequence. This methylation-sensitive technique, termed ERMA (Enzymatic Regional Methylation Assay) provides several advantages over existing methods used for methylation analysis as it determines an exact measurement of the methylation density of the region studied. We demonstrate a use of this technique in determining the methylation density of the promoter region of the tumor suppressor gene p15INK4B and changes that occur after treatment with demethylating agents.
Spectrometer employing a micro-Fresnel lens (1995)

The dispersion characteristics of a diffractive micro-Fresnel lens (MFL) which is mass-produced for a laser diode collimator are examined for novel applications. The MFL's resolving power (Rayleigh criterion for resolution) at the design wavelength is calculated to be comparable to that of conventional dispersing prisms of the same size. A simple spectrometer with an MFL (4.5 mm diameter, 14.83 mm focal length at 0.78 μm design wavelength) and a movable pinhole (PH), is fabricated. The optimum PH diameter for both resolving power and light efficiency is 5 m, and the resolution and efficiency at the design wavelength are estimated to be 3.7 nm and 85%, respectively. The measurable spectral range determined from both the diffraction efficiency and the free spectral range of the MFL almost covers the entire visible region. The absorption spectrum of KMnO<sub>4</sub> solution is roughly obtained using the spectrometer. The space between the MFL and the PH, and the PH's movable length, which are required for spectroscopy, are as short as 20 and 7 mm, respectively. The simple and straight-line-structured spectroscopic system utilizing a more cost-efficient MFL may lead to the realization of less expensive and compact spectrometers.
Plasmonic Modulators for Near-Infrared Photonics on a Silicon-on-Insulator Platform (2013)

A CMOS compatible interference-based Mach-Zehnder modulator with each arm comprising a metal-insulator-silicon-insulator-metal structure and a simpler, single-arm variant is considered for electro-optic and electroabsorption modulation, respectively, using finite-element electromagnetic simulations. In the calculation of electron density profiles in bias-induced accumulation layers, the size-quantization effects at oxide-silicon interfaces are considered. These are then used to find the complex refractive index profiles across the structure, in its biased and unbiased states, and eventually the modulator insertion loss and extinction ratio, as they depend on various structural parameters. Furthermore, an alternative modulator, comprising a metalized stub filled with SiGe/Ge multiple quantum wells or quantum dots in a silicon matrix, coupled to a dielectric waveguide structure is also investigated using 3-D finite-element simulations. The principle behind its modulation is the change of electromagnetic field profile after the stub, relative to the incoming mode, which happens when the absorption of the stub material varies. This affects the field coupling into a single-mode output waveguide, resulting in a controllable transmission.
Single ring resonator QPSK modulator (2015)

We propose a new implementation of a QPSK modulator using a simple single ring resonator. That requires only < π/10 phase shift. Signal generated have a better dispersion tolerance than from a single phase modulator.
Dual-Gate E/E- and E/D-Mode AlGaAs/InGaAs pHEMTs for Microwave Circuit Applications (2007)

In this paper, we developed dual-gate enhancement/enhancement-mode (E/E-mode) and enhancement/depletion-mode (E/D-mode) AlGaAs/InGaAs pHEMTs for high-voltage and high-power device applications. These dual-gate devices had a higher breakdown voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">br</sub> ) and maximum oscillation frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ). This could be obtained because there were two depletion regions, and the total electrical field was shared between the two regions, leading to lower output conductance (g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> ) and lower gate-to-drain capacitance (C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">gd</sub> ). The dual-gate device can be operated at a higher drain-to-source voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ds</sub> ), resulting in better linear gain and output power performance, as compared to a conventional single-gate E-mode GaAs pHEMT device. The maximum oscillation frequency obtained using the dual-gate E/E-mode device increased from 78 to 123 GHz. When operated at 2.4 GHz, the maximum RF output power of the single-gate E-mode and dual-gate E/D-mode devices increased from 636 to 810 mW/mm, respectively. We also produced a 2.4-GHz high-gain and high-power density two-stage power amplifier using dual-gate E/E and E/D-mode transistors. A linear gain of 40 dB and a maximum output power of 24 dBm were obtained.
CHANGE MANAGEMENT IN CONSTRUCTION PROJECTS (2008)

Decisions are made everyday in construction processes based on incomplete information, assumptions and the personal experience of the construction professionals. Project changes and/or adjustments are inevitable as they are a fact-of-life at all stages of a project’s life cycle. Managing changes effectively is crucial to the success of a construction project. Change management in construction requires an integrated solution to discipline and coordinate the process, for example, documentation, drawing, process, flow, information, cost, schedule and personnel. The construction industrial needs an effective construction change management process. This paper summarizes various aspects of the existing construction change management processes and provides a comprehensive literature review as well as some comments on possible future directions.
Bacterial Two-Hybrid Analysis of Interactions between Region 4 of the ς <sup>70</sup> Subunit of RNA Polymerase and the Transcriptional Regulators Rsd from <i>Escherichia coli</i> and AlgQ from <i>Pseudomonas aeruginosa</i> (2001)

A number of transcriptional regulators mediate their effects through direct contact with the sigma(70) subunit of Escherichia coli RNA polymerase (RNAP). In particular, several regulators have been shown to contact a C-terminal portion of sigma(70) that harbors conserved region 4. This region of sigma contains a putative helix-turn-helix DNA-binding motif that contacts the -35 element of sigma(70)-dependent promoters directly. Here we report the use of a recently developed bacterial two-hybrid system to study the interaction between the putative anti-sigma factor Rsd and the sigma(70) subunit of E. coli RNAP. Using this system, we found that Rsd can interact with an 86-amino-acid C-terminal fragment of sigma(70) and also that amino acid substitution R596H, within region 4 of sigma(70), weakens this interaction. We demonstrated the specificity of this effect by showing that substitution R596H does not weaken the interaction between sigma and two other regulators shown previously to contact region 4 of sigma(70). We also demonstrated that AlgQ, a homolog of Rsd that positively regulates virulence gene expression in Pseudomonas aeruginosa, can contact the C-terminal region of the sigma(70) subunit of RNAP from this organism. We found that amino acid substitution R600H in sigma(70) from P. aeruginosa, corresponding to the R596H substitution in E. coli sigma(70), specifically weakens the interaction between AlgQ and sigma(70). Taken together, our findings suggest that Rsd and AlgQ contact similar surfaces of RNAP present in region 4 of sigma(70) and probably regulate gene expression through this contact.
Methane Oxidation over a V<sub>2</sub>O<sub>5</sub> Catalyst in the Liquid Phase (2006)

The selective oxidation of methane by V2O5 catalysts in oleum has been studied. The effects of the reaction temperature, the concentration of V2O5, and the residence time on the conversion of methane and the yield of methanol were investigated. We have found that methane was transformed to methyl bisulfate first, and the methyl bisulfate was then hydrolyzed to methanol. The process of the selective oxidation of methane was involved in electrophilic alternative mechanisms by V2O5 catalysts, and the sulfur trioxide in oleum was necessary for the reaction systems. The methane oxidation reaction was determined to be a first-order reaction, based on the pressure−time relationship. The maximum methanol yield of 45.5% and the methane conversion of 54.5% were obtained at a V2O5 concentration of 0.0175 mol, a reaction temperature of 453 K, a methane pressure of 4.0 MPa, a reaction time of 2 h, and the sulfur trioxide content in oleum is ∼50%.
Empirical Predictions of Wheat Head Blight in the Northern Argentinean Pampas Region (2001)

In Argentina, head blight (caused by Fusarium graminearum Schwabe), is a highly risky disease of wheat ( Triticum aestivum L. emm. Thell), although its occurrence is sporadic, depending on prevalent environmental variables. This unpredictability has stimulated the development of predictive models of head blight occurrence that, if successful, would help growers in the selection of control strategies. As a result of our earlier work, empirical equations for predicting head blight incidence were developed at Pergamino INTA Experiment Center (Lat., 33° 56′S), associating temperature and moisture variables with mean disease observations from many wheat cultivars. In the current study our objective was to validate two of these meteorological based equations developed for Pergamino to predict wheat head blight incidence and severity at Zavalla (Lat., 33° 1′S) and Oliveros (Lat., 32° 33′S) in moderately susceptible to susceptible cultivars for the years 1993 to 1995. Even though the t ‐test determined nonsignificant differences between mean observed disease values versus predicted values, a graphic method and a deviation examination showed an underestimation at high disease levels. Simple analyses of sensitivity were able to detect the improvement in incidence and severity goodness of fit estimations that resulted from increasing the maximum temperature threshold and the heat accumulation defining the length of the wheat critical period for infection. This study showed that meteorological based empirical equations developed for Pergamino can be useful for predicting disease intensity at more northern locations in the Pampas region, making only a few changes in temperature thresholds.
On Hyperbolic F- Structure Manifold (2010)

In this paper, we have defined Hyperbolic F-structure manifold and Hyperbolic metric F-structure manifold with some theoremsrelated to projection and rank. The integrability conditions for the manifold have been obtained and some related results are derived. We have defined Pseudo Projective curvature tensor W, Pseudo conformal curvature tensor C, Pseudo conharmonic curvature tensor L, Pseudo concircular curvature tensor V, Pseudo H-Projective curvature tensor P, Pseudo H-conharmonic curvature tensor S and Pseudo Bochner curvature tensor B in Hyperbolic F-structure manifold. Recurrence and Recurrence symmetry of different kinds have been defined and theorems of recurrent and recurrent symmetry of this manifold have been proved.