gebhart/patrepeval huggingface dataset:
Identification, Characterization, and Molecular Detection of <i>Alfalfa mosaic virus</i> in Potato (2006)

ABSTRACT Alfalfa mosaic virus (AMV) was detected in potato fields in several provinces in Canada and characterized by bioassay, enzyme-linked immunosorbent assay, and reverse-transcription polymerase chain reaction (RT-PCR). The identity of eight Canadian potato AMV isolates was confirmed by sequence analysis of their coat protein (CP) gene. Sequence and phylogenetic analysis indicated that these eight AMV potato isolates fell into one strain group, whereas a slight difference between Ca175 and the other Canadian AMV isolates was revealed. The Canadian AMV isolates, except Ca175, clustered together among other strains based on alignment of the CP gene sequence. To detect the virus, a pair of primers, AMV-F and AMV-R, specific to the AMV CP gene, was designed based on the nucleotide sequence alignment of known AMV strains. Evaluations showed that RT-PCR using this primer set was specific and sensitive for detecting AMV in potato leaf and tuber samples. AMV RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 tubers. Restriction analysis of PCR amplicons with SacI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by restriction fragment length polymorphism analysis may be a useful approach for screening potato samples on a large scale for the presence of AMV.
Enhancement of Anti-Cancer Activity of Cisdiaminedichloroplatinum by the Protein-Bound Polysaccharide of <i>Coriolus Versicolor</i> QUEL (PS-K) <i>in vitro</i> (1994)

The protein-bound polysaccharide of Coriolus versicolor QUEL (PS_K) expresses superoxide dismutase (SOD) mimicking activity. Examination was made of the effects of PS-K on cancer cell lines following administration of the anti-cancer drug cisdiaminedichloroplatinum (cisplatin). Cell proliferation of each cell line was inhibited markedly by cisplatin from 0.5 to 5 micrograms/0.5 ml per well. Fifty percent of the inhibitory concentration (IC50) was 0.33 micrograms/0.5 ml per well in NRK-49F and human ovarian cancer cells, and 1.5 micrograms/0.5 ml per well in H4-II-E. PS-K 50 micrograms/0.5 ml per well prevented cytotoxicity due to cisplatin toward NRK-49F, but enhanced the cytotoxicity on H4-II-E and human ovarian cancer cells. Increase in lipid peroxide and decrease in SOD activity were observed following an IC50 dose of cisplatin. With PS-K 50 micrograms/0.5 ml per well, all the above were augmented in H4-II-E and ovarian cancer cells, but diminished in NRK-49F cell line. PS-K may have effect on cancer patients through its combining with cisplatin.
A Novel SNR Estimation Algorithm for OFDM (2005)

In this paper, we extend the traditional SNR estimation algorithms defined in complex AGWN channel to time variant linear channel and present a new SNR estimation algorithm for OFDM system. We compare our algorithm with two moment-based algorithms. Simulation results show that the new algorithm performs better in large Doppler frequency environments and is insensitive to the statistical characteristics of the channel.
Inactivation of Prions and Amyloid Seeds with Hypochlorous Acid (2016)

Hypochlorous acid (HOCl) is produced naturally by neutrophils and other cells to kill conventional microbes in vivo. Synthetic preparations containing HOCl can also be effective as microbial disinfectants. Here we have tested whether HOCl can also inactivate prions and other self-propagating protein amyloid seeds. Prions are deadly pathogens that are notoriously difficult to inactivate, and standard microbial disinfection protocols are often inadequate. Recommended treatments for prion decontamination include strongly basic (pH ≥~12) sodium hypochlorite bleach, ≥1 N sodium hydroxide, and/or prolonged autoclaving. These treatments are damaging and/or unsuitable for many clinical, agricultural and environmental applications. We have tested the anti-prion activity of a weakly acidic aqueous formulation of HOCl (BrioHOCl) that poses no apparent hazard to either users or many surfaces. For example, BrioHOCl can be applied directly to skin and mucous membranes and has been aerosolized to treat entire rooms without apparent deleterious effects. Here, we demonstrate that immersion in BrioHOCl can inactivate not only a range of target microbes, including spores of Bacillus subtilis, but also prions in tissue suspensions and on stainless steel. Real-time quaking-induced conversion (RT-QuIC) assays showed that BrioHOCl treatments eliminated all detectable prion seeding activity of human Creutzfeldt-Jakob disease, bovine spongiform encephalopathy, cervine chronic wasting disease, sheep scrapie and hamster scrapie; these findings indicated reductions of ≥103- to 106-fold. Transgenic mouse bioassays showed that all detectable hamster-adapted scrapie infectivity in brain homogenates or on steel wires was eliminated, representing reductions of ≥~105.75-fold and >104-fold, respectively. Inactivation of RT-QuIC seeding activity correlated with free chlorine concentration and higher order aggregation or destruction of proteins generally, including prion protein. BrioHOCl treatments had similar effects on amyloids composed of human α-synuclein and a fragment of human tau. These results indicate that HOCl can block the self-propagating activity of prions and other amyloids.
Virus‐Templated Nickel Phosphide Nanofoams as Additive‐Free, Thin‐Film Li‐Ion Microbattery Anodes (2019)

Transition metal phosphides are a new class of materials generating interest as alternative negative electrodes in lithium-ion batteries. However, metal phosphide syntheses remain underdeveloped in terms of simultaneous control over phase composition and 3D nanostructure. Herein, M13 bacteriophage is employed as a biological scaffold to develop 3D nickel phosphide nanofoams with control over a range of phase compositions and structural elements. Virus-templated Ni<sub>5</sub> P<sub>4</sub> nanofoams are then integrated as thin-film negative electrodes in lithium-ion microbatteries, demonstrating a discharge capacity of 677 mAh g<sup>-1</sup> (677 mAh cm<sup>-3</sup> ) and an 80% capacity retention over more than 100 cycles. This strong electrochemical performance is attributed to the virus-templated, nanostructured morphology, which remains electronically conductive throughout cycling, thereby sidestepping the need for conductive additives. When accounting for the mass of additional binder materials, virus-templated Ni<sub>5</sub> P<sub>4</sub> nanofoams demonstrate the highest practical capacity reported thus far for Ni<sub>5</sub> P<sub>4</sub> electrodes. Looking forward, this synthesis method is generalizable and can enable precise control over the 3D nanostructure and phase composition in other metal phosphides, such as cobalt and copper.
Infectious in vivo and in vitro transcripts from a full-length cDNA clone of PVY-N605, a Swiss necrotic isolate of potato virus Y. (1997)

A full-length cDNA clone of the potato virus Y (PVY) genome was obtained after cloning difficulties in Escherichia coli were overcome. These difficulties were mainly due to the expression of the CI gene from upstream prokaryotic promoter-like elements within the PVY genome. To overcome this problem, PVY cDNA was maintained in two subclones which were ligated before infection. A plasmid in which these two fragments were contained could be propagated in some E. coli strains but was unstable and yielded only low levels of plasmid DNA. Replacement of the 35S promoter by the SP6 promoter slightly increased the stability of the plasmid and its RNA transcripts were infectious when capped with m7G(5')ppp(5')G. Using two inoculation methods (mechanical or biolistic) the cDNA and its RNA transcript proved infectious on three Nicotiana species and on Solanum tuberosum.
Technical and economic characteristic analysis on 35 and 10kV Electronic Transformer (2010)

This paper describes the advantages and disadvantages of several configuration schemes for 35 and 10kV transformer in the Intelligent Substation, through technical and economic analysis, it shows that the advantages of Combined Electronic Transformers.
Application of fuzzy logic in automated cow status monitoring (2000)

Sensors for measuring yield, temperature and electrical conductivity of milk, and activity can be used for automated cow status monitoring. Fuzzy logic was used for the classification of mastitis alerts with the objective to reduce the number of false positive alerts, while keeping the level of detected cases of mastitis at the same level. Input for the fuzzy logic model were alerts from the detection model and additional information. The output was a classification, true or false, of each alert. Only alerts that were classified true should be presented to the herd manager. The additional information was used to check whether deviating sensor measurements were caused by mastitis or by other influences. The fuzzy logic model was tested on a data set from cows milked in an automatic milking system. All clinical cases without measurement errors were classified correctly. The number of false positive alerts from a subset of 25 cows was reduced from 1266 to 64, by applying the fuzzy logic model.
Active site conformational changes upon reaction intermediate biotinyl‐5'‐AMP binding in biotin protein ligase from <i>Mycobacterium tuberculosis</i> (2014)

Protein biotinylation, a rare form of post-translational modification, is found in enzymes required for lipid biosynthesis. In mycobacteria, this process is essential for the formation of their complex and distinct cell wall and has become a focal point of drug discovery approaches. The enzyme responsible for this process, biotin protein ligase, substantially varies in different species in terms of overall structural organization, regulation of function and substrate specificity. To advance the understanding of the molecular mechanism of biotinylation in Mycobacterium tuberculosis we have biochemically and structurally characterized the corresponding enzyme. We report the high-resolution crystal structures of the apo-form and reaction intermediate biotinyl-5'-AMP-bound form of M. tuberculosis biotin protein ligase. Binding of the reaction intermediate leads to clear disorder-to-order transitions. We show that a conserved lysine, Lys138, in the active site is essential for biotinylation.
Polyimide-Surface-Modified Silica Tubes:  Preparation and Cryogenic Properties (2007)

The silica tubes were synthesized by template self-assembly from d,l-tartaric acid and hydrolysis of tetraethoxysilane (TEOS), and their surfaces were modified by a 3-aminopropyltriethoxysilane coupling agent. Thereafter, a series of polyimide (PI)-surface modified silica tube (ST) hybrid films was prepared from PMDA-ODA in N,N-dimethylacetamide as a solvent using an in situ polymerization process combined with ultrasonic dispersion and multistep curing. The resulting silica tubes and the hybrid films were characterized using XRD, SEM, TEM, FTIR, and UV−vis. The cryogenic mechanical properties at 77 K and dynamic mechanical properties of the hybrid films were studied. The results indicated that the strength, modulus, and failure strain of the hybrid films were all increased compared with those of the pure PI film when the silica tube content was at 1−3 wt %. The cryogenic tensile strength and modulus were generally higher than those at room temperature, whereas the cryogenic failure strain was lower than that at room temperature. The elastic modulus of the hybrid films exhibited a monotonically increasing trend. The cryogenic failure strain of hybrid films with 1−3 wt % silica tube contents was greater than with 15 wt %, indicating a good ductility at 77 K. The glass-transition temperature of the hybrid films increased with the increase in silica tube content.
Module Partitioning and Interlaced Data Placement Schemes to Reduce Conflicts in Interleaved Memories (1994)

In interleaved memories, interference between concurrently active vector streams results in memory bank conflicts and reduced bandwidth. In this paper, we present two schemes for reducing inter-vector interference. First, we propose a memory module partitioning technique in which disjoint access sets are created for each of the concurrent vectors. Various properties of the involved address mapping are presented. Then we present an interlaced data placement scheme, where the simultaneously accessed vectors are interlaced and stored to the memory. Performance of the two schemes are evaluated by trace driven simulation. It is observed that the schemes have significant merit in reducing the interference in interleaved memories and increasing the effective memory bandwidth. The schemes are applicable to memory systems for superscalar processors, vector supercomputers and parallel processors.
Association of 24-Hour Cortisol Production Rates, Cortisol-Binding Globulin, and Plasma-Free Cortisol Levels with Body Composition, Leptin Levels, and Aging in Adult Men and Women (2004)

The present study was designed to examine the hypothesis that hypothalamic-pituitary-adrenal axis activity as measured by 24-h cortisol production rate (CPR) and plasma levels of free cortisol is linked to increased body fat in adults, and that increased cortisol levels with aging results from increased CPR. Fifty-four healthy men and women volunteers with a wide range of body mass indexes and ages underwent measurement of CPR by isotope dilution measured by gas chromatography-mass spectroscopy, cortisol-binding globulin, and free cortisol in pooled 24-h plasma, body composition, and leptin. Cortisol clearance rates were determined from the 10-h disappearance curves of hydrocortisone after steady-state infusion in a separate group of lean and obese subjects with adrenal insufficiency. Although CPR significantly increased with increasing body mass index and percentage body fat, free cortisol levels remained independent of body composition and leptin levels due to increased cortisol clearance rates. CPR and free cortisol levels were, however, significantly higher in men than women. In addition, 24-h plasma free cortisol levels were increased with age in association with increased CPR, independent of body size. This increase in hypothalamic-pituitary-adrenal axis activity may play a role in the alterations in body composition and central fat distribution in men vs. women and with aging.
Smart body contact for SOI MOSFETs (2003)

Summary form only given. SOI MOSFETs exhibit various floating-body effects due to the lack of a contact to the channel region. These effects can show up as a kink in the saturation region of I/sub DS/-V/sub DS/ characteristics (higher drive current) and an improvement of the subthreshold slope, or can be as severe as latch-up of the SOI MOSFET at large drain biases. The easiest was to eliminate floating-body effects is to provide a contact to the channel region to deep it at or below the source potential. One problem with providing a body contact is that the increased transistor drive current due to the floating-body effects is lost even in the saturation region, where it may be desirable for high-speed circuit operation. Here, a scheme for providing a smart body contact is presented. This contact acts as a low-resistance channel contact at low gate voltages to keep the transistor off and avoid latch-up. At high-gate voltages, the resistance of this body contact becomes very high and allows the MOSFET channel to float, which increases the drain current due to both MOS body effect and bipolar action.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structure Determination of the Two-Domain (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mn>1</mml:mn><mml:mo>×</mml:mo><mml:mn>4</mml:mn></mml:math>) Anatase<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi>TiO</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>(</mml:mo><mml:mn>001</mml:mn><mml:mo>)</mml:mo></mml:math>Surface (2000)

The reconstructed anatase ${\mathrm{TiO}}_{2}(001)$ surface has been investigated by low-energy electron diffraction (LEED), x-ray photoelectron spectroscopy (XPS), and angle-resolved mass spectroscopy of recoiled ions (AR-MSRI). Prior investigations have observed or considered only a $(1\ifmmode\times\else\texttimes\fi{}1)$ unreconstructed termination for this surface with no detailed structural analysis. Our LEED results indicate a previously unobserved two-domain $(1\ifmmode\times\else\texttimes\fi{}4)$ reconstruction after sputtering and annealing the $(1\ifmmode\times\else\texttimes\fi{}1)$ surface. The XPS data for this reconstruction indicate the presence of only ${\mathrm{Ti}}^{4+}$. Simulations of the AR-MSRI experimental data indicate a best fit for a microfaceted surface, revealing both (103) and $(\overline{1}03)$ surface planes.
Realization of All-optical Ultrafast Logic Gates using Triple Core Asymmetric Nonlinear Directional Coupler (2001)

Article Realization of All-optical Ultrafast Logic Gates using Triple Core Asymmetric Nonlinear Directional Coupler was published on April 1, 2001 in the journal Journal of Optical Communications (volume 22, issue 2).
Environment-Adaptive Concurrent Companding and Bias Control for Efficient Power-Amplifier Operation (2010)

The design of power-efficient orthogonal frequency division multiplexing (OFDM) transmitters suffers from a major bottleneck due to the high peak-to-average ratio (PAR) of OFDM signals as the efficiency of a linear RF power amplifier (PA) reduces drastically due to backoff requirements. In this paper, we propose a system-level approach for dynamic power reduction in OFDM transmitters with varying channels. The proposed methodology uses adaptive baseband companding/expanding of the OFDM signal along with concurrent PA rebiasing to save power. Using channel quality information for dynamic PAR adaptation, the proposed approach achieves a PAR reduction of as high as 7.25 dB, under favorable channels. This translates to a power savings of 5.5× compared with static PAs and 3.6× compared with adaptive PAs with only output-power adaptation.
CLOUDFARM: An Elastic Cloud Platform with Flexible and Adaptive Resource Management (2014)

Elasticity is a key feature of current cloud computing platforms. Dependent on their demand tenants can dynamically scale up and down their applications. To increase their revenue, cloud providers are used to over-provision their clusters, but they still have to reserve capacity to avoid that services get unresponsive and cause SLO violation during bursts. In this paper, we propose CLOUDFARM, a PaaS architecture with an adaptive SLO-based resource management mechanism. It introduces new flexible SLAs backed with a respective development model and management interface for end-user services. According to their SLAs and the price tenants pay, services can be selectively downgraded to overcome short-term peaks, e.g. While preparing for scale-out. Providers can deploy services optimistically and thus maximize their data center utilization and revenue.
Object Detectors Emerge in Deep Scene CNNs (2015)

With the success of new computational architectures for visual processing, such as convolutional neural networks (CNN) and access to image databases with millions of labeled examples (e.g., ImageNet, Places), the state of the art in computer vision is advancing rapidly. One important factor for continued progress is to understand the representations that are learned by the inner layers of these deep architectures. Here we show that object detectors emerge from training CNNs to perform scene classification. As scenes are composed of objects, the CNN for scene classification automatically discovers meaningful objects detectors, representative of the learned scene categories. With object detectors emerging as a result of learning to recognize scenes, our work demonstrates that the same network can perform both scene recognition and object localization in a single forward-pass, without ever having been explicitly taught the notion of objects.
Introduction to this special section: Reverse time migration (2010)

Reverse time migration (RTM) received its name because its inventors were literally running the time axis of their modeling programs backward and computationally sending waves back into a model of the Earth to make images. By extrapolating waves in time, rather than along the vertical direction, waves could go all directions rather than just within some angle of the vertical. Initial RTM images were astounding for the steep dips they rendered that other methods missed. Equally importantly, because the wave propagation in an RTM algorithm is “complete”, the velocity model didn't have to be smoothed; complex models were no problem as they were with Kirchhoff methods, the main competing steep-dip imaging method. These advantages are easily understood in the context of poststack migration and the exploding reflector model. Prestack RTM is slightly more complicated, requiring simulations of both source and receiver wavefields, but the advantages of extrapolating the time axis remain. Even though this “time reversal of the physics” is conceptually appealing, practical application of RTM languished over the years since its inception in the early 1980s. We think this was partly due to cost, partly due to issues such as internal scattering leading to image artifacts and the difficulties and cost of producing high-quality image gathers, and, finally, partly due to the insufficiency of the data we acquired. We think it's fair to say that RTM is only truly justified on 3D data; so, RTM had to wait for the 3D revolution.