gebhart/patrepeval huggingface dataset:
Peptide Aptamers That Bind to a Geminivirus Replication Protein Interfere with Viral Replication in Plant Cells (2006)

The AL1 protein of tomato golden mosaic virus (TGMV), a member of the geminivirus family, is essential for viral replication in plants. Its N terminus contains three conserved motifs that mediate origin recognition and DNA cleavage during the initiation of rolling-circle replication. We used the N-terminal domain of TGMV AL1 as bait in a yeast two-hybrid screen of a random peptide aptamer library constrained in the active site of the thioredoxin A (TrxA) gene. The screen selected 88 TrxA peptides that also bind to the full-length TGMV AL1 protein. Plant expression cassettes corresponding to the TrxA peptides and a TGMV A replicon encoding AL1 were cotransfected into tobacco protoplasts, and viral DNA replication was monitored by semiquantitative PCR. In these assays, 31 TrxA peptides negatively impacted TGMV DNA accumulation, reducing viral DNA levels to 13 to 64% of those of the wild type. All of the interfering aptamers also bound to the AL1 protein of cabbage leaf curl virus. A comparison of the 20-mer peptides revealed that their sequences are not random. The alignments detected seven potential binding motifs, five of which are more highly represented among the interfering peptides. One motif was present in 18 peptides, suggesting that these peptides interact with a hot spot in the AL1 N terminus. The peptide aptamers characterized in these studies represent new tools for studying AL1 function and can serve as the basis for the development of crops with broad-based resistance to single-stranded DNA viruses.
9-(3,4-dihydroxybutyl)guanine, a new inhibitor of herpesvirus multiplication (1983)

A new compound, 9-(3,4-dihydroxybutyl)guanine, has been synthesized and its antiherpes activity determined. 9-(3,4-Dihydroxybutyl)guanine was selectively phosphorylated by herpes simplex virus thymidine kinase and had a high affinity for this enzyme, with an inhibition constant of 1.5 microM. In cell culture, replication of different strains of herpes simplex virus types 1 and 2 was inhibited to the extent of 50% by 4 to 18 microM (RS)-9-(3,4-dihydroxybutyl)guanine. The (R)-enantiomer of this compound was more inhibitory than the (S)-enantiomer. Herpesvirus DNA synthesis was selectively inhibited by (RS)-9-(3,4-dihydroxybutyl)guanine in infected cells, and a low cellular toxicity was observed. (RS)-9-(3,4-Dihydroxybutyl)guanine had a therapeutic effect when applied topically to guinea pigs with cutaneous herpes simplex type 1 infections and to rabbits with herpes keratitis. Oral treatment of a generalized herpes simplex type 2 infection in mice had a therapeutic effect.
Reliable Face Alignment Using Two-Stage Aam (2008)

AAM (active appearance model) has been successfully applied to face and facial feature localization. However, its performance is sensitive to initial parameter values. In this paper, we propose a two-stage AAM for robust face alignment, which first fits an inner face-AAM model to the inner facial feature points of the face and then localizes the whole face and facial features by optimizing the whole face-AAM model parameters. Experiments show that the proposed face alignment method using two-stage AAM is more reliable to the background and the head pose than the standard AAM-based face alignment method.
Nonoxidative Direct Conversion of Methane on Silica-Based Iron Catalysts: Effect of Catalytic Surface (2019)

For a stable methane to olefins, aromatics, and hydrogen (MTOAH) reaction, 0.27–0.43 wt % Fe-containing silica catalysts were synthesized through various preparation methods and tested. The presence of Fe species in SiO2 mixtures increased the true and apparent densities of the catalysts during the melt-fusing process at 1700 °C. Several characterizations (i.e., H2-TPR, TEM, and XAS) revealed that partially reduced iron oxide (Fe3O4) predominantly existed in cristobalite (CRS) in the melt-fused catalysts. The Fe©CRS catalyst prepared from fayalite and quartz by the melt-fusing method showed a higher resistance to structural sintering and coke deposition than other Fe catalysts during MTOAH at 1020 °C. It also showed a 40% higher apparent activation energy for coke formation than for methane consumption in the temperature range of 1000 to 1040 °C. Increased CRS surfaces increased the coke selectivity, indicating that even the pure CRS surface acts as a chain reaction terminator to form coke. At the same space velocity (9400 h–1), the Fe©CRS catalyst was more selective in producing C2 (ethane, ethylene, and acetylene), C3–C5 olefins, and aromatics than pure CRS and other Fe catalysts. At a steady state, the Fe©CRS surface was most suitable for methane conversion, being 2.3 times more efficient than without a catalytic surface. The Fe©CRS catalyst exhibited a stable activity and low coke selectivity, even for 50 h, in the MTOAH reaction. EXAFS profiles showed that highly dispersed Fe carbide with Fe–Si coordination was formed in the Fe©CRS catalyst, and electronic structure calculations indicated that these confined Fe sites were more favorable for methyl radical formation and a high coke resistance than Fe3C clusters. By optimizing reaction parameters, the Fe©CRS catalyst exhibited 6.9–5.8% methane conversion and 86.2% C2 selectivity for 100 h with cofeeding of 50% H2 at 1080 °C.
Sub-15nm nanoimprint molds and pattern transfer (2009)

This work addresses the challenges in fabricating sub-10nm sized features, dense (sub-15nm half-pitch) arbitrary-pattern nanoimprint molds, as well as pattern transfer of the molds using nanoimprint. The molds were fabricated using an optimized electron-beam lithography process with hydrogen silsesquioxane (HSQ) resist. Two different mold-processing routes were investigated: (1) HSQ patterns on top of a silicon substrate were directly used for nanoimprint and (2) the HSQ patterns on the mold were transferred into the underlying silicon substrate to increase the aspect ratio of the patterns prior to imprint. After the nanoimprint, lift-off was carried out to demonstrate that the pattern could be transferred into functional materials. The difference between the two mold-processing routes is discussed. The results show excellent resolution transfer throughout the process flow to create sub-15nm half-pitch patterns in functional materials.
Arginine availability, arginase, and the immune response (2003)

The availability of arginine during critical illness may be regulated by arginase activity. Thus, arginase expression appears to be essential in the regulation of the cellular immune response and the inflammatory process during critical illness.
Studies for Synthesis of Phenol and Cyclohexanone (1961)

シクロヘキシルベンゼンの液相酸化によつてシクロヘキシルベンゼンハイドロパーオキサイドを生成する反応において, 誘導期, 定常連鎖反応速度, および反応系内の生成物最高濃度などの諸点からみて, 反応の最適条件を求めた。その結果反応温度は攪拌を強力に行なうならば, 110℃で充分であり, これに添加剤として本反応で得られるパーナキサイドを少量加えることにより好結果を与える。つぎに酸素分圧を上げることも本反応を有利に導く一手段である。本酸化反応の見掛けの活性化エネルギーは, 約20kcalである。その他添加剤としては, ステアリン酸ソーダ1%, ホルマリン2%を加えることも効果がある。酸化反応における, 吸収酸素量とパーオキサイド生成速度の関係, および反応系の酸性度の増加速度よりみて酸化の定常状態の途中から, 2次的な反応が起り, 酸, アルデヒドなどの生成副反応が主反応を次第に圧迫していることが判明した。なお吸収酸素に対するパーナキサイドの収率は90.8%であつた。上記で得た反応液を分解して, フェノールとシクロヘキサノンを得る分解反応において, 3弗化硼素または過塩素酸2～3%を添加し, 20℃, 22時間で完全に分解は終結し, フェノール約80%, シクロヘキサノン約78%収率で得られる。
High-responsivity graphene-on-silicon slot waveguide photodetectors (2016)

We demonstrated strong optical absorption in a graphene integrated silicon slot waveguide. Due to the increase in light intensity and decrease of optical mode confinement in the silicon slot, the graphene experienced an increased interaction to the in-plane light. A waveguide absorption of 0.935 dB μm(-1) was measured at 1.55 μm wavelengths. Based on the graphene-on-silicon slot waveguide, a compact and high-responsivity photodetector was demonstrated. Benefited from the lack of efficient electron cooling in the suspended graphene and the intensity enhancement effect in the nano slot, a maximum responsivity of 0.273 A W(-1) was achieved in the telecommunication band.
High Dimensional Nonlinear Learning using Local Coordinate Coding (2009)

This paper introduces a new method for semi-supervised learning on high dimensional nonlinear manifolds, which includes a phase of unsupervised basis learning and a phase of supervised function learning. The learned bases provide a set of anchor points to form a local coordinate system, such that each data point $x$ on the manifold can be locally approximated by a linear combination of its nearby anchor points, with the linear weights offering a local-coordinate coding of $x$. We show that a high dimensional nonlinear function can be approximated by a global linear function with respect to this coding scheme, and the approximation quality is ensured by the locality of such coding. The method turns a difficult nonlinear learning problem into a simple global linear learning problem, which overcomes some drawbacks of traditional local learning methods. The work also gives a theoretical justification to the empirical success of some biologically-inspired models using sparse coding of sensory data, since a local coding scheme must be sufficiently sparse. However, sparsity does not always satisfy locality conditions, and can thus possibly lead to suboptimal results. The properties and performances of the method are empirically verified on synthetic data, handwritten digit classification, and object recognition tasks.
Suppression of microbunching instability in the linac coherent light source (2004)

A microbunching instability driven by longitudinal space charge, coherent synchrotron radiation, and linac wakefields is studied for the linac coherent light source (LCLS) accelerator system. Since the uncorrelated (local) energy spread of electron beams generated from a photocathode rf gun is very small, the microbunching gain may be large enough to significantly amplify rf-gun generated modulations or even shot-noise fluctuations of the electron beam. The uncorrelated energy spread can be increased by an order of magnitude to provide strong Landau damping against the instability without degrading the free-electron laser performance. We study different damping options in the LCLS and discuss an effective laser heater to minimize the impact of the instability on the quality of the electron beam.
Physiologic disposition of lergotrile (1978)

Lergotrile, an ergot alkaloid, has been shown to be effective in treating disorders associated with elevated serum prolactin levels (e.g., galactorrhea-amenorrhea). Lergotrile has also been found to be a potent dopaminergic agonist and thus to be effective in Parkinson's disease. This study describes the physiologic disposition of lergotrile after administration to human volunteers. N-14CH3-lergotrile was rapidly absorbed from the gastrointestinal tract. Lergotrile was detected at low concentrations in plasma when subjects received large doses over extended periods of time. The major portion of radioactivity in plasma was attributed to the presence of circulating metabolites of lergotrile. Lergotrile metabolities were eliminated in the feces (ca. 60%), urine (ca. 20%), and breath (ca. 7% as 14CO2). A metabolite in feces was identified as 13-OH-lergotrile (up to 30% of the dose). A metabolite in urine was formed by conversion of the C8-acetonitrile group of lergotrile to a carboxyl group (about 10% of the dose). The presence of 14CO2 in the expired air after administering N-14C-methyl-lergotrile indicated that the drug was N-demethylated to form norlergotrile.
<title>Halftone Pictorial Encoding</title> (1977)

This report briefly reviews a new technique for pictorial encoding. Exploiting the characteristics of the human visual system, a halftone screening procedure is utilized to develop a binary-pixel representation of the image. This binary data is then encoded, enabling much less than 1 bit/pixel storage/communications cost. The proposed strategy is simple to implement, primarily digital, and capable of high speeds. Furthermore, the output image is most compatible with binary display and marking engine technologies.
Unique Substrate Recognition by Botulinum Neurotoxins Serotypes A and E (2006)

Botulinum neurotoxins (BoNTs) are zinc proteases that cleave SNARE proteins to elicit flaccid paralysis by inhibiting the fusion of neurotransmitter-carrying vesicles to the plasma membrane of peripheral neurons. There are seven serotypes of BoNT, termed A-G. BoNT serotype A and serotype E cleave SNAP25 at residues 197-198 and 180-181, respectively. Unlike other zinc proteases, the BoNTs recognize extended regions of SNAP25 for cleavage. The basis for this extended substrate recognition and specificity is unclear. Saturation mutagenesis and deletion mapping identified residues 156-202 of SNAP25 as the optimal cleavage domain for BoNT/A, whereas the optimal cleavage domain for BoNT/E was shorter, comprising residues 167-186 of SNAP25. Two sub-sites were resolved within each optimal cleavage domain, which included a recognition or active site (AS) domain that contained the site of cleavage and a binding (B) domain, which contributed to substrate affinity. Within the AS domains, the P1', P3, and P5 sites of SNAP25 contributed to scissile bond cleavage by LC/A, whereas the P1' and P2 sites of SNAP25 contributed to scissile bond cleavage by LC/E. These studies provide insight into the development of strategies for small molecule inhibitors of the BoNTs.
A novel integrated system for stormwater management (2001)

A novel integrated system for stormwater management is described. The system is made up of three key elements; a stormwater treatment stage, a stormwater storage stage, and a flow control/attenuation stage. The use of the system within a 'preventative' rather than 'curative' framework provides flexibility and significant cost savings in the implementation of effective stormwater management, especially in the urban environment. The system components are described in detail highlighting their benefits compared with conventional alternatives.
Self-testing and self-tuning of power system stabilizers using Prony analysis (1999)

This paper presents a new method for self-testing and self-tuning of power system stabilizers (PSSs) using Prony analysis. Prony analysis detects oscillation frequency, damping, phase and amplitude in measured waveforms. By applying this technique to signals of generator speed, output power, and generator internal induced voltage, weak damping oscillations are detected and the PSS parameters can be modified to damp the oscillations. When a disturbance occurs and a weak damping is detected, effectiveness of the installed PSS is verified by checking the phase angle between generator speed and internal induced voltage. Based on the test results, self-tuning is performed by changing phase compensation and gain parameters considering the phase lag of the excitation system. Simulation results show that the proposed method is effective both in a one-machine system and in a multimachine system. The method is especially useful for detecting and damping wide-area, low-frequency oscillation modes.
Imaging with intermolecular multiple-quantum coherences in solution NMR (1995)

NRC publication: Yes
Ultrafast diagnostics (1987)

Second order correlation techniques can be used to obtain a complete characterization of femtosecond pulses, in amplitude and phase. The importance of monitoring and controlling the frequency content of ultrashort pulses is discussed. Application of correlation techniques — in particular to three dimensional diagnostics — are reviewed. It is shown that depth scanning alone is sufficient to generate three dimensional images by up-conversion range gating.
<i>Arabidopsis CROOKED</i>encodes for the smallest subunit of the ARP2/3 complex and controls cell shape by region specific fine F-actin formation (2003)

The generation of a specific cell shape requires differential growth, whereby specific regions of the cell expand more relative to others. The Arabidopsis crooked mutant exhibits aberrant cell shapes that develop because of mis-directed expansion, especially during a rapid growth phase. GFP-aided visualization of the F-actin cytoskeleton and the behavior of subcellular organelles in different cell-types in crooked and wild-type Arabidopsis revealed that localized expansion is promoted in cellular regions with fine F-actin arrays but is restricted in areas that maintain dense F-actin. This suggested that a spatiotemporal distinction between fine versus dense F-actin in a growing cell could determine the final shape of the cell. CROOKED was molecularly identified as the plant homolog of ARPC5, the smallest sub-unit of the ARP2/3 complex that in other organisms is renowned for its role in creating dendritic arrays of fine F-actin. Rescue of crooked phenotype by the human ortholog provides the first molecular evidence for the presence and functional conservation of the complex in higher plants. Our cell-biological and molecular characterization of CROOKED suggests a general actin-based mechanism for regulating differential growth and generating cell shape diversity.
Accumulation of<i>S</i>-Adenosyl<scp>-l-</scp>Methionine Enhances Production of Actinorhodin but Inhibits Sporulation in<i>Streptomyces lividans</i>TK23 (2003)

S-Adenosyl-L-methionine synthetase (SAM-s) catalyzes the biosynthesis of SAM from ATP and L-methionine. Despite extensive research with many organisms, its role in Streptomyces sp. remains unclear. In the present study, the putative SAM-s gene was isolated from a spectinomycin producer, Streptomyces spectabilis. The purified protein from the transformed Escherichia coli with the isolated gene synthesized SAM from L-methionine and ATP in vitro, strongly indicating that the isolated gene indeed encoded the SAM-s protein. The overexpression of the SAM-s gene in Streptomyces lividans TK23 inhibited sporulation and aerial mycelium formation but enhanced the production of actinorhodin in both agar plates and liquid media. Surprisingly, the overexpressed SAM was proven by Northern analysis to increase the production of actinorhodin through the induction of actII-ORF4, a transcription activator of actinorhodin biosynthetic gene clusters. In addition, we found that a certain level of intracellular SAM is critical for the induction of antibiotic biosynthetic genes, since the control strain harboring only the plasmid DNA did not show any induction of actII-ORF4 until it reached a certain level of SAM in the cell. From these results, we concluded that the SAM plays important roles as an intracellular factor in both cellular differentiation and antibiotic production in Streptomyces sp.
A CFD/SEA Approach for Prediction of Vehicle Interior Noise due to Wind Noise (2009)

<div class="htmlview paragraph">For most car manufacturers, aerodynamic noise is becoming the dominant high frequency noise source (&gt; 500 Hz) at highway speeds. Design optimization and early detection of issues related to aeroacoustics remain mainly an experimental art implying high cost prototypes, expensive wind tunnel sessions, and potentially late design changes. To reduce the associated costs as well as development times, there is strong motivation for the development of a reliable numerical prediction capability. The goal of this paper is to present a computational approach developed to predict the greenhouse windnoise contribution to the interior noise heard by the vehicle passengers. This method is based on coupling an unsteady Computational Fluid Dynamics (CFD) solver for the windnoise excitation to a Statistical Energy Analysis (SEA) solver for the structural acoustic behavior. The basic strategy is to convert the time-domain pressure signals generated by CFD everywhere on the panels into structural power inputs, which in turn are used as input to an SEA model leading to the noise inside the cabin. This approach quantifies the windnoise contribution coming from different panels (e.g. side windows, windshield) at various locations inside the vehicle (driver and passenger headspace). In this paper the key technical and numerical aspects of the approach are presented, and interior noise predictions corresponding to real automotive cases are compared to experimental measurements. As examples of the usage, a vehicle exterior shape design study and an acoustic package optimization study are presented.</div>
LA EVALUACIÓN INSTITUCIONAL DE LA UNIVERSIDAD (1998)

Una evaluación institucional, cuando es correctamente realizada debe alcanzar los objetivos directos como: mejorar, rendir cuentas e informar. Sin embargo, otras consecuencias indirectas son posibles como: crear una cultura interna de calidad. Los fenómenos de calidad implican a muchos individuos que necesariamente pasan a ser conscientes de la necesidad de evaluar la calidad. Este resultado es valioso por si solo y se han obtenido resultados importantes como en el caso español: crear una cultura de responsabilidad ante la sociedad en general y ante los usuarios de la institución, en particular. Un efecto muy importante en instituciones españolas, con unas raices todavía recientes en la administración del estado; crear sistemas de información estadística para la gestión interna de las instituciones y para la información a la sociedad de cómo son los productos que la universidad está generando; crear sistemas de indicadores de rendimiento que sirvan que sirvan para recoger una información sintética, razonable y útil, del funcionamiento de las instituciones; crear un estímulo a la competencia positiva de las instituciones por la calidad que deberá transformarse en competencia por los alumnos y por los contratos con las empresas que dispondrán de criterios en que basar sus decisiones; la evaluación puede tener otras consecuencias. La primera deseable, la segunda no; disponer de unos criterios válidos para asignar recursos públicos a las instituciones según su calidad y eficacia y segundo establecer clasificaciones de instituciones. Pero existe el peligro de que se establezcan clasificaciones simplificadas. Existen muchas otras consecuencias y podemos pensar que los efectos serán benéficos. Si se acompañan de otros criterios búsqueda de la calidad como mejoras en los sistemas de financiación y sobre todo una decidida apertura de la universidad a las demandas de la sociedad.
In-Injection Port Thermal Desorption for Explosives Trace Evidence Analysis (1999)

A gas chromatographic method utilizing thermal desorption of a dry surface wipe for the analysis of explosives trace chemical evidence has been developed and validated using electron capture and negative ion chemical ionization mass spectrometric detection. Thermal desorption was performed within a split/splitless injection port with minimal instrument modification. Surface-abraded Teflon tubing provided the solid support for sample collection and desorption. Performance was characterized by desorption efficiency, reproducibility, linearity of the calibration, and method detection and quantitation limits. Method validation was performed with a series of dinitrotoluenes, trinitrotoluene, two nitroester explosives, and one nitramine explosive. The method was applied to the sampling of a single piece of debris from an explosion containing trinitrotoluene.
Remote monitoring of sitting behavior of people with spinal cord injury. (2007)

The clinical assessment of risk factors leading to pressure sores is normally undertaken in a hospital clinic. However, knowledge of the sitting behavior of the patient outside the clinic may more realistically and comprehensively identify these factors. Many patients, for example, are thought to sit habitually with more pressure on one buttock than the other, and this may significantly increase the risk. This sitting asymmetry may be due to the layout of a work area, the home, or a simple habit. Furthermore, busy wheelchair users may be too preoccupied to remember to reposition themselves regularly but may do so frequently at less hectic times. The applicants have developed a miniature remote pressure logger, which keeps a record of the sitting behavior of the wheelchair user. This study examines the feasibility of using the device for long-term monitoring of sitting pressure distributions during daylong wheelchair activities.