gebhart/patrepeval huggingface dataset:
A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300 (2011)

A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography. The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and 5-hydroxymethylcytosine. Cleavage of 5mC-modified plasmids indicated that the sites S5mCNGS (S = C or G) are preferentially digested. The endonuclease activity requires the presence of adenosine triphosphate (ATP) or dATP whereas the non-hydrolyzable γ-S-ATP does not support activity. SauUSI activity was inhibited by ethylenediaminetetraacetic acid. It is most active in Mg(++) buffers. No companion methylase gene was found near the SauUSI restriction gene. The absence of a cognate methylase and cleavage of modified DNA indicate that SauUSI belongs to type IV restriction endonucleases, a group that includes EcoK McrBC and Mrr. SauUSI belongs to a family of highly similar homologs found in other sequenced S. aureus, S. epidermidis and S. carnosus genomes. More distant SauUSI orthologs can be found in over 150 sequenced bacterial/archaea genomes. Finally, we demonstrated the biological function of the type IV REase in restricting 5mC-modified plasmid DNA by transformation into clinical S. aureus strain SA564, and in restricting phage λ infection when the endonuclease is expressed in E. coli.
Transport spin polarization of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ni</mml:mi></mml:mrow><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Fe</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mi>−</mml:mi><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mo>:</mml:mo></mml:math>Electronic kinematics and band structure (2000)

We present measurements of the transport spin polarization of ${\mathrm{Ni}}_{x}{\mathrm{Fe}}_{1\ensuremath{-}x}$ $(0<~x<~1)$ using the recently developed point-contact Andreev reflection technique, and compare them with our first-principles calculations of the spin polarization for this system. Surprisingly, the measured spin polarization is almost composition independent. The results clearly demonstrate that the sign of the transport spin polarization does not coincide with that of the difference of the densities of states at the Fermi level. Calculations indicate that the independence of the spin polarization of the composition is due to compensation of density of states and Fermi velocity in the s and d bands.
Pseudo-aligned multilingual corpora (2007)

In machine translation, document alignment refers to finding correspondences between documents which are exact translations of each other. We define pseudo-alignment as the task of finding topical--as opposed to exact--correspondences between documents in different languages. We apply semisupervised methods to pseudo-align multilingual corpora. Specifically, we construct a topic-based graph for each language. Then, given exact correspondences between a subset of documents, we project the unaligned documents into a shared lower-dimensional space. We demonstrate that close documents in this lower-dimensional space tend to share the same topic. This has applications in machine translation and cross-lingual information analysis. Experimental results show that pseudo-alignment of multilingual corpora is feasible and that the document alignments produced are qualitatively sound. Our technique requires no linguistic knowledge of the corpus. On average when 10% of the corpus consists of exact correspondences, an on-topic correspondence occurs within the top 5 foreign neighbors in the lower-dimensional space while the exact correspondence occurs within the top 10 foreign neighbors in this this space. We also show how to substantially improve these results with a novel method for incorporating language-independent information.
Throughput comparison of IEEE 802.11ac and IEEE 802.11n in an indoor environment with interference (2015)

IEEE 802.11ac is an emerging standard that operates in 5GHz frequency band and provides high data rate as compared to IEEE 802.11n. In this paper we carry out experiments in a real indoor environment and quantify the gain in average throughput provided by IEEE 802.11ac compared to IEEE 802.11n in the presence of interference caused by other IEEE 802.11n sources. The experiments are performed for both Line of Sight (LoS) and Non-Line of Sight (NLoS) conditions. We note that IEEE 802.11n (2.4GHz) provides the worst average throughput due to the highly congested 2.4GHz frequency band in our experimental environment. We find that IEEE 802.11n (5GHz) with 40MHz channel width provides a gain of 36% in average throughput compared to 20MHz channel width at a distance of 20m from the wireless router in LoS conditions. Our experimental results reveal that IEEE 802.11ac achieves 42% better average throughput when compared to the IEEE 802.11n (5GHz) at a distance of 5m in LoS conditions. Similarly, IEEE 802.11ac provides 55% improvement over IEEE 802.11n (5GHz) at a distance of 15m in NLoS conditions. We conclude that IEEE 802.11ac can effectively handle interference caused by other IEEE 802.11n (5GHz) sources and provides higher throughput than IEEE 802.11n for both LoS and NLoS conditions.
Experimental study on vibration characteristics of metro tunnels with different track structures (2021)

To explore the vibration transmission characteristics and vibration reduction effects of metro tunnels with different track structures, the regular slab track section, the double-layer nonlinear vibration-damping fastener section and the isolated damping pad section in the Nanchang Metro Line 3 were selected respectively for the field hammer excitation test. Based on the field test results, the vibration transmission characteristics and the vibration reduction effects of metro tunnels with different track structures were analyzed. The results indicated that the vibration reduction effect of the isolated damping pads was best, followed by the double-layer nonlinear vibration-damping fasteners, while that of the regular slab tracks was worst; the double-layer nonlinear vibration-damping fastener section had obvious vibration reduction effect in the frequency range of 80 to 170 Hz, the isolated damping pad section had significant vibration reduction performance above 30 Hz; the vibration of the double-layer nonlinear vibration-damping fastener section and the isolated damping pad section was 5.6 dB and 10 dB less than the regular slab track section, respectively.
Investigation of readily processable thermoplastic‐toughened thermosets. III. Toughening BMIs and epoxy with a comb‐shaped imide oligomer (1998)

This is the third in a five-part series describing the preparation of tough, high-performance thermosets from low viscosity, autoclave-processable prepolymers. The first 2 articles described toughening of bismaleimides (BMI) and epoxy with linear imide thermoplastics of ∼ 1000 g/mol. Highly processable prepolymers were obtained, which resulted in increases in fracture toughness for BMI of ∼ 75–100%, while the fracture toughness of epoxy was increased by up to 220%. This article describes the preparation of a low-molecular-weight comb-shaped imide oligomer (∼ 4100 g/mol) and the effect of the oligomer architecture and end-group on BMI and epoxy prepolymer viscosity and fracture toughness. When an unreactive comb-shaped oligomer was incorporated in a BMI prepolymer (10% thermoplastic loading in the thermoset), the fracture toughness increased by 67% over that of an untoughed control, while a reactive oligomer increased the fracture toughness by 150% over an untoughened control. At 55°C, the viscosity of the solution of the reactive comb-shaped imide in B was only 6.2 Pa · S. When the oligomer was dissolved in epoxy resin, the viscosity was less than 0.2 Pa · S at 90°C, and the fracture toughness increased by 110 and 133% (at ∼ 13% loading in the thermoset), relative to an untoughened control, depending on the reactivity of the end group. The Tg and high-temperature modulus of BMI and epoxy remained approximately the same relative to the untoughened controls. © 1998 John Wiley & Sons, Inc. J. Appl. Polym. Sci. 70: 943–951, 1998
Map Location of the <i>Rpp1</i> Locus That Confers Resistance to Soybean Rust in Soybean (2007)

ABSTRACT Soybean rust (SBR), caused by Phakopsora pachyrhizi , was first discovered in North America in 2004 and has the potential to become a major soybean [ Glycine max (L.) Merr.] disease in the USA. Currently, four SBR resistance genes have been identified but not mapped on the soybean genetic linkage map. One of these resistance genes is the Rpp1 gene, which is present in the soybean accession PI 200492 The availability of molecular markers associated with Rpp1 will permit marker‐assisted selection and expedite the incorporation of this gene into U.S. cultivars. We compared simple sequence repeat (SSR) markers between ‘Williams 82’ and the BC 5 Williams 82 isoline L85‐2378, which contains the Rpp1 resistance allele from the soybean accession PI 200492 , for candidate regions that might contain Rpp1 One candidate region was found with the SSR marker BARC_Sct_187 on linkage group G. A population of BC 6 F 2:3 lines segregating for the Rpp1 resistance locus was genotyped in this region on linkage group G followed by inoculation with the P. pachyrhizi isolate India 73‐1 in the USDA‐ARS Biosafety Level 3 Plant Pathogen Containment Facility at Ft. Detrick, MD. The Rpp1 gene was mapped between SSR markers BARC_Sct_187 and BARC_Sat_064 on linkage group G.
The Stanmore Metal on Metal Total Hip Prosthesis Using a Three Pin Type Cup A Follow-up of 100 Arthroplasties Over Nine Years (1973)

Between April 1963 and June 1971, 108 total hip arthroplasties using the Stanmore 3 pin type cup were done on 101 patients (48 men and 53 women). The operation was done on 99 arthritic or deformed hips in 92 patients (7 bilateral). In the remaining 9 patients the operation was part of resection for primary bone tumor of the upper end of the femur (Table 1). These will be discussed separately. The particulars of the arthritic cases arc summarized in Table 2. Most of the patients operated upon have been elderly arthritics, but where joint replacements have been used in combination with extensive excision of the upper femur for tumor, age has not been a limiting factor. The ages ranged from 21 to 81 with a peak between 60–69 (Fig. 1). The cases shown in the 20–39 age group comprise 6 tumor replacements and one patient with ankylosing spondylitis.
Synthesis, characterization and nitric oxide release profile of nitrosylcobalamin (1998)

Nitrosylcobalamin, a vitamin B12-based, non-toxic carrier of nitric oxide (NO), has been synthesized, isolated and characterized in vitro. A UV/Vis analysis was performed confirming the reduction of the cobalt atom of hydroxocobalamin (vitamin B12a) with the binding of NO, causing a shift in the absorption spectra of CO3+ (lambdamax=530) to CO2+ (lambdamax=500) with the formation of nitrosylcobalamin. The extinction coefficient (epsilonmax) of nitrosylcobalamin, as calculated, was 4.8 (mM(-1), cm(-1)). An IR analysis determined the v(NO) vibrational frequency at 1652 cm(-1), supporting the binding of NO and suggesting a bent bonding geometry. NO release was maximized utilizing acidic conditions (pH 4.9, 32 degrees C) with a cumulative release of about 4610 nmol of NO in 675 h (calculated half-life of 210 h), representing 39% NO loading based on 11,890 nmol NO, theoretically possible (one NO per molecule of hydroxocobalamin). The cumulative NO release followed first-order kinetics and was pH dependent. NO release was minimal at pH 6.0 and 7.4 (37 degrees C), and undetected at pH 10 (37 degrees C). The possibility for nitrosylcobalamin to deliver NO (the active chemotherapeutic agent) to neoplastic cells is suggested because tumor cells, specifically leukemia cells, possess surface cell receptors for vitamin B12 which is readily utilized in the cellular proliferation process. Nitrosylcobalamin may offer a 'drug targeting' approach as a potential, biologically compatible and selective chemotherapeutic agent.
Quantized CNN: A Unified Approach to Accelerate and Compress Convolutional Networks (2017)

We are witnessing an explosive development and widespread application of deep neural networks (DNNs) in various fields. However, DNN models, especially a convolutional neural network (CNN), usually involve massive parameters and are computationally expensive, making them extremely dependent on high-performance hardware. This prohibits their further extensions, e.g., applications on mobile devices. In this paper, we present a quantized CNN, a unified approach to accelerate and compress convolutional networks. Guided by minimizing the approximation error of individual layer's response, both fully connected and convolutional layers are carefully quantized. The inference computation can be effectively carried out on the quantized network, with much lower memory and storage consumption. Quantitative evaluation on two publicly available benchmarks demonstrates the promising performance of our approach: with comparable classification accuracy, it achieves 4 to $6 \times $ acceleration and 15 to $20\times $ compression. With our method, accurate image classification can even be directly carried out on mobile devices within 1 s.
Measurement of the cleavage energy of graphite (2015)

The basal plane cleavage energy (CE) of graphite is a key material parameter for understanding many of the unusual properties of graphite, graphene and carbon nanotubes. Nonetheless, a wide range of values for the CE has been reported and no consensus has yet emerged. Here we report the first direct, accurate experimental measurement of the CE of graphite using a novel method based on the self-retraction phenomenon in graphite. The measured value, 0.37±0.01 J m(-2) for the incommensurate state of bicrystal graphite, is nearly invariant with respect to temperature (22 °C≤T≤198 °C) and bicrystal twist angle, and insensitive to impurities from the atmosphere. The CE for the ideal ABAB graphite stacking, 0.39±0.02 J m(-2), is calculated based on a combination of the measured CE and a theoretical calculation. These experimental measurements are also ideal for use in evaluating the efficacy of competing theoretical approaches.
A model of the pressure dependence of the enantioselectivity of <i>Candida rugosa</i>lipase towards (±)‐menthol (2001)

Transesterification of (+/-)-menthol using propionic acid anhydride and Candida rugosa lipase was performed in chloroform and water at different pressures (1, 10, 50, and 100 bar) to study the pressure dependence of enantioselectivity E. As a result, E significantly decreased with increasing pressure from E = 55 (1 bar) to E = 47 (10 bar), E = 37 (50 bar), and E = 9 (100 bar). To rationalize the experimental findings, molecular dynamics simulations of Candida rugosa lipase were carried out. Analyzing the lipase geometry at 1, 10, 50, and 100 bar revealed a cavity in the Candida rugosa lipase. The cavity leads from a position on the surface distinct from the substrate binding site to the core towards the active site, and is limited by F415 and the catalytic H449. In the crystal structure of the Candida rugosa lipase, this cavity is filled with six water molecules. The number of water molecules in this cavity gradually increased with increasing pressure: six molecules in the simulation at 1 bar, 10 molecules at 10 bar, 12 molecules at 50 bar, and 13 molecules at 100 bar. Likewise, the volume of the cavity progressively increased from about 1864 A(3) in the simulation at 1 bar to 2529 A(3) at 10 bar, 2526 A(3) at 50 bar, and 2617 A(3) at 100 bar. At 100 bar, one water molecule slipped between F415 and H449, displacing the catalytic histidine side chain and thus opening the cavity to form a continuous water channel. The rotation of the side chain leads to a decreased distance between the H449-N epsilon and the (+)-menthyl-oxygen (nonpreferred enantiomer) in the acyl enzyme intermediate, a factor determining the enantioselectivity of the lipase. Although the geometry of the preferred enantiomer is similar in all simulations, the geometry of the nonpreferred enantiomer gets gradually more reactive. This observation correlates with the gradually decreasing enantioselectivity E.
The changing faces of HP1: From heterochromatin formation and gene silencing to euchromatic gene expression (2011)

Heterochromatin protein 1 (HP1) is a positive regulator of active transcription in euchromatin. HP1 was first identified in Drosophila melanogaster as a major component of heterochromatin. Most eukaryotes have at least three isoforms of HP1, which are conserved in overall structure but localize differentially to heterochromatin and euchromatin. Although initial studies revealed a key role for HP1 in heterochromatin formation and gene silencing, recent progress has shed light on additional roles for HP1 in processes such as euchromatic gene expression. Recent studies have highlighted the importance of HP1-mediated gene regulation in euchromatin. Here, we focus on recent advances in understanding the role of HP1 in active transcription in euchromatin and how modification and localization of HP1 can regulate distinct functions for this protein in different contexts.
Effects of Processing Conditions on the Work Function and Energy-Level Alignment of NiO Thin Films (2010)

We have investigated NiO thin films prepared by in situ and ex situ ozone oxidation, as well as air-exposed and vacuum-annealed NiO films. The core-level and valence-level photoemission spectra, as well as the work function and energy-level alignment with a common hole-injection material, have been measured using X-ray photoemission spectroscopy and ultraviolet photoemission spectroscopy. We found that in situ oxidation results in the formation of a purely NiO film, while ex situ oxidation and air exposure result in a hydroxide-terminated NiO film. Work functions as high as 6.7 eV can be achieved for in situ-oxidized NiO; however, the work function decreases rapidly with time due to adsorption of residual gases in vacuum. The work functions of ex situ and air-exposed NiO were significantly lower, between 5.2 and 5.6 eV, due to hydroxylation of the oxide surface. We have examined the rate at which the work function decreases with air exposure and found there to be a very rapid initial decrease in work function, followed by a much slower continual decline. Despite the decrease in work function, energy-level alignment of α-NPD is not affected until the work function drops below a threshold value. We have also examined the effect of vacuum annealing of NiO and found that it becomes highly defective with oxygen vacancies, causing the Fermi level position of the oxide to move away from the valence band maximum and decreasing the work function.
Changes of human skin in subepidermal wound healing process (2008)

This non-invasive method using in vivo LCSM revealed chronological changes in the dermis and epidermis during wound healing. In addition, although a scar was not formed in any of study subjects, this microscopy revealed aspects similar to the fibrous tissue overgrowth or to melanocyte migration, both of which may relate to wound healing. These results indicate the usefulness of this non-invasive method in studies of wound healing and of scar formation.
A State-Space Model for Decoding Auditory Attentional Modulation from MEG in a Competing-Speaker Environment (2014)

Humans are able to segregate auditory objects in a complex acoustic scene, through an interplay of bottom-up feature extraction and top-down selective at-tention in the brain. The detailed mechanism underlying this process is largely unknown and the ability to mimic this procedure is an important problem in ar-tificial intelligence and computational neuroscience. We consider the problem of decoding the attentional state of a listener in a competing-speaker environment from magnetoencephalographic (MEG) recordings from the human brain. We de-velop a behaviorally inspired state-space model to account for the modulation of the MEG with respect to attentional state of the listener. We construct a decoder based on the maximum a posteriori (MAP) estimate of the state parameters via the Expectation-Maximization (EM) algorithm. The resulting decoder is able to track the attentional modulation of the listener with multi-second resolution using only the envelopes of the two speech streams as covariates. We present simula-tion studies as well as application to real MEG data from two human subjects. Our results reveal that the proposed decoder provides substantial gains in terms of temporal resolution, complexity, and decoding accuracy. 1
A system of analyzing and synthesizing facial images (1991)

A system is presented which analyzes and synthesizes the facial images. This system is focused on analysis and synthesis of facial features. Any particular image is assumed to be a weighted sum of facial image bases. The weights represent the facial features of the particular image. A method which analyzes and synthesizes the facial images on the basis of a three-dimensional facial shape model is presented. The method is extended so that the features of parts as well as the whole of the face can be analyzed and synthesized. Moreover, a procedure is developed for orthogonalizing the image bases for optimal description.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Distributed analog phase shifters with low insertion loss (1999)

This paper describes the design and fabrication of distributed analog phase-shifter circuits. The phase shifters consist of coplanar-waveguide (CPW) lines that are periodically loaded with varactor diodes. The circuits are fabricated on GaAs using standard monolithic processing techniques. The phase velocity on these varactor diode-loaded CPW lines is a function of applied reverse bias, thus resulting in analog phase-shifting circuits. Optimally designed circuits exhibit 0/spl deg/-360/spl deg/ phase shift at 20 GHz with a maximum insertion loss (IL) of 4.2 dB. To the best of our knowledge, this is the lowest reported IL for a solid-state analog phase shifter operating at 20 GHz.
High efficiency electrotransformation of Lactococcus lactis spp. lactis cells pretreated with lithium acetate and dithiothreitol (2007)

This investigation sought to improve still further transformation efficiencies and to provide a reliable high efficiency transformation system for L. lactis spp. lactis. The applied methodology, tested in two well-known strains, allows the production of large numbers of transformants and the construction of large recombinant libraries.
A 5-V only 16-kbit stacked-capacitor MOS RAM (1980)

A novel one-transistor-type MOS RAM is discussed. This memory cell gives a remarkable area reduction and/or increase in storage capacitance by stacking the main portion of the storage capacitor on the address transistor, bit lines, or field oxides. It is called a stacked-capacitor (STC) RAM. This STC memory has a three-level poly-Si structure. The stacked capacitor has poly-Si-Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> -poly-Si (or Al) structure. A 16-kbit STC RAM has been fabricated with 3-µm technology and operated successfully. Memory performance is strikingly improved by using STC cells.