gebhart/patrepeval huggingface dataset:
Functional Homologies between Avian and Human Alphaherpesvirus VP22 Proteins in Cell-to-Cell Spreading as Revealed by a New <i>cis</i> -Complementation Assay (2008)

VP22, encoded by the UL49 gene of Marek's disease virus (MDV), is indispensable for virus cell-to-cell spreading. We show herein that MDV UL49 can be functionally replaced with avian and human viral orthologs. Replacement of MDV VP22 with that of avian gallid herpesvirus 3 or herpesvirus of turkey, whose residue identity with MDV is close to 60%, resulted in 73 and 131% changes in viral spreading, respectively. In contrast, VP22 replacement with human herpes simplex virus type 1 resulted in 14% plaque formation. Therefore, heterologous avian and human VP22 proteins share sufficient structural homology to support MDV cell-to-cell spreading, albeit with different efficiencies.
A parametric approach for handling local variation effects in timing analysis (2009)

In this paper we propose a new methodology, called parametric on chip variation (POCV) analysis, to determine local process variation effects on the timing of designs. The proposed methodology requires relative delay and parasitic variations of cells and interconnects, respectively. Once this information is provided, delays and arrival times are propagated to calculate slacks as a function of these relative variations. A key characteristic of the POCV analysis is that it does not require a statistical library characterization or statistical RC extraction. The POCV method has been implemented in a timing analysis software, and tested on multiple production designs on 65nm and 45nm technology nodes, including multi-million instance designs. Our observation was that compared to the existing methods, POCV removes unrealistical pessimism on the setup paths and captures risks on the hold paths, with no changes to the existing timing sign-off environment.
Subsurface oxide plays a critical role in CO <sub>2</sub> activation by Cu(111) surfaces to form chemisorbed CO <sub>2</sub> , the first step in reduction of CO <sub>2</sub> (2017)

A national priority is to convert CO<sub>2</sub> into high-value chemical products such as liquid fuels. Because current electrocatalysts are not adequate, we aim to discover new catalysts by obtaining a detailed understanding of the initial steps of CO<sub>2</sub> electroreduction on copper surfaces, the best current catalysts. Using ambient pressure X-ray photoelectron spectroscopy interpreted with quantum mechanical prediction of the structures and free energies, we show that the presence of a thin suboxide structure below the copper surface is essential to bind the CO<sub>2</sub> in the physisorbed configuration at 298 K, and we show that this suboxide is essential for converting to the chemisorbed CO<sub>2</sub> in the presence of water as the first step toward CO<sub>2</sub> reduction products such as formate and CO. This optimum suboxide leads to both neutral and charged Cu surface sites, providing fresh insights into how to design improved carbon dioxide reduction catalysts.
Electrical characteristics of scaled CMOSFET's with source/drain regions fabricated by 7° and 0° tilt-angle implantations (1995)

The differences of electrical characteristics in trench-isolated n-well CMOSFET's with LDD- and EPS-regions fabricated by 7/spl deg/ and 0/spl deg/ tilt-angle phosphorous implantations are measured and qualitatively explained. The CMOSFET's have channel lengths ranging from 5 to 0.4 /spl mu/m and a channel width of 10 /spl mu/m. The differences in impurity profiles due to the channeling ions by 0/spl deg/-implantation cause the clear changes in the punchthrough-current characteristics and the substrate bias-voltage dependences of threshold voltages for both n- and p-MOSFET's. Meanwhile n- and p-MOSFET's fabricated by 7/spl deg/ and 0/spl deg/ implantations show nearly the same characteristics of threshold voltages and subthreshold swings which are almost determined by the impurity profiles in each channel region because the impurity profiles are scarcely affected by the channeling ions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Nativism or Response to Globalization? Business Reaction to Immigration Reform (2006)

Industries such as agriculture, service, health care, construction, and meat packing and processing have relied heavily on immigrant labor and have voiced opposition to the restrictive immigration reform passed recently by the House of Representatives which would provide no amnesty, no path to legalization, and which would reduce the number of worker visas. Other industries and coalitions favor tighter border security and punitive action toward undocumented immigrants and those who hire them. I propose that the position these businesses take toward immigration reform is more a response to globalization than one of nativism. Faculty Mentor: Johanna Brenner
Oxidative stress in symptom‐free HCV carriers: relation with ALT flare‐up (2001)

This study suggests that symptom-free HCV carriers with impaired redox state have a higher risk of aminotransferase flare-up; therefore the impaired oxidative balance may have a prognostic significance on disease activity.
Micromachined packaging for chemical microsensors (1988)

The critical issues involved in chemical microsensor packaging and encapsulation are reviewed and a hybrid solution is presented. In the design approach, the microsensor is divided into two principal physical parts, an electrode and electronics-containing substrate, and a micromachined membrane package. The fabrication and the resultant performance of each part are independently optimizable. The final microsensor is constructed by first binding the two parts together at the wafer level, followed by die separation, and then lead attachment. The micromachined membrane-holders are then filled with liquid membranes to yield functioning sensors. A calcium-ion sensor fabricated by this method is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High-Speed Electronic Circuits for 100 Gb/s Transport Networks (2010)

An overview of state-of-the-art high-speed electronic circuits for major 100G modulation schemes is given. The results show the trade-off between electrical performance and energy efficiency and lead to design considerations for future transceiver electronics.
The mechanism of texture formation during film growth: The roles of preferential sputtering and shadowing (1996)

Nonequilibrium molecular dynamics simulations have been employed to develop a mechanistic model for the development of an out-of-plane (fiber) texture in polycrystalline thin films. The depositing atoms preferentially sputter film atoms from grains with high surface energies. As the film grows, an atomic shadowing mechanism leads to the lateral growth of the grains with a height advantage—eventually leading to the occlusion of randomly oriented grains.
Location and Clonal Analysis of Stem Cells and Their Differentiated Progeny in the Human Ocular Surface (1999)

We have analyzed the proliferative and differentiation potential of human ocular keratinocytes. Holoclones, meroclones, and paraclones, previously identified in skin, constitute also the proliferative compartment of the ocular epithelium. Ocular holoclones have the expected properties of stem cells, while transient amplifying cells have variable proliferative potential. Corneal stem cells are segregated in the limbus, while conjunctival stem cells are uniformly distributed in bulbar and forniceal conjunctiva. Conjunctival keratinocytes and goblet cells derive from a common bipotent progenitor. Goblet cells were found in cultures of transient amplifying cells, suggesting that commitment for goblet cell differentiation can occur late in the life of a single conjunctival clone. We found that conjunctival keratinocytes with high proliferative capacity give rise to goblet cells at least twice in their life and, more importantly, at rather precise times of their life history, namely at 45-50 cell doublings and at approximately 15 cell doublings before senescence. Thus, the decision of conjunctival keratinocytes to differentiate into goblet cells appears to be dependent upon an intrinsic "cell doubling clock. " These data open new perspectives in the surgical treatment of severe defects of the anterior ocular surface with autologous cultured conjunctival epithelium.
Discovering a proof for the fixed point theorem: a case study (1988)

The relationship of ionizing radiation to the age-related ophthalmological findings of the 1978-1980 ophthalmological examination of A-bomb survivors of Hiroshima and Nagasaki has been reanalyzed using DS86 eye organ dose estimates. The main purpose of this reevaluation was to determine whether age and radiation exposure, as measured using the recently revised dosimetry information (DS86), have an additive, synergistic, or antagonistic effect. The data in this study are limited to axial opacities and posterior subcapsular changes, for which a definite radiation-induced effect has been observed in Hiroshima and Nagasaki A-bomb survivors. The best model fitting for axial opacities gives a significant positive effect for both linear dose and linear age-related regression coefficients and a significant negative effect for an interaction between radiation dose and age. Such a negative interaction implies an antagonistic effect in that the relative risks in relation to radiation exposure doses become smaller with an increase in age. On the other hand, the best-fitting relationship for posterior subcapsular changes suggested a linear-quadratic dose and linear age-related effect. The estimate of the quadratic dose coefficient shows a highly negative correlation with age, but the negative quadratic dose term is extremely small and is of little biological significance.
Selective Homogeneous Hydrogenation of Biogenic Carboxylic Acids with [Ru(TriPhos)H]<sup>+</sup>: A Mechanistic Study (2011)

Selective hydrogenation of biogenic carboxylic acids is an important transformation for biorefinery concepts based on platform chemicals. We herein report a mechanistic study on the homogeneously ruthenium/phosphine catalyzed transformations of levulinic acid (LA) and itaconic acid (IA) to the corresponding lactones, diols, and cyclic ethers. A density functional theory (DFT) study was performed and corroborated with experimental data from catalytic processes and NMR investigations. For [Ru(TriPhos)H](+) as the catalytically active unit, a common mechanistic pathway for the reduction of the C═O functionality in aldehydes, ketones, lactones, and even free carboxylic acids could be identified. Hydride transfer from the Ru-H group to the carbonyl or carboxyl carbon is followed by protonation of the resulting Ru-O unit via σ-bond metathesis from a coordinated dihydrogen molecule. The energetic spans for the reduction of the different functional groups increase in the order aldehyde < ketone < lactone ≈ carboxylic acid. This reactivity pattern as well as the absolute values are in full agreement with experimentally observed activities and selectivities, forming a rational basis for further catalyst development.
Echo target determination using acoustic round trip delay for voice over IP conferences (2003)

This paper proposes a method for determining acoustic echo cancellation targets by combining acoustic round trip delay data and psyche-acoustic echo target data. An accurate determination of echo targets is required to minimize detrimental switched-loss attenuation effects. The nonlinear processor (NLP) can use the proposed echo cancellation targets to lower the amount of switched-loss attenuation added by the echo suppression system. Lower levels of switched-loss attenuation increase the system gain and reduce unwanted half-duplex effects. Most voice over Internet protocol (VoIP) conferencing products can use the proposed echo suppression system because it is ITU-T H.323 compliant.
A 4–41 GHz Singly Balanced Distributed Mixer Using GaAs pHEMT Technology (2007)

A broadband singly balanced distributed mixer is developed using a 0.15-mum GaAs pHEMT foundry process. It is the first time that the charge-injection approach is applied to a distributed mixer. With the advantage of charge-injection, the mixer achieves a high conversion gain with low dc consumption. The fabricated distributed mixer with an integrated broadband transformer has a compact chip size of 2mmtimes1mm. Measurement results show that the mixer achieves a conversion gain of better than 3.5dB over a broadband frequency from 4-41GHz, with a relatively low dc power consumption of 100mW
Two Wound-Inducible Soybean Cysteine Proteinase Inhibitors Have Greater Insect Digestive Proteinase Inhibitory Activities than a Constitutive Homolog (1996)

Diverse functions for three soybean (Glycine max L. Merr.) cysteine proteinase inhibitors (CysPIs) are inferred from unique characteristics of differential regulation of gene expression and inhibitory activities against specific Cys proteinases. Based on northern blot analyses, we found that the expression in leaves of one soybean CysPI gene (L1) was constitutive and the other two (N2 and R1) were induced by wounding or methyl jasmonate treatment. Induction of N2 and R1 transcript levels in leaves occurred coincidentally with increased papain inhibitory activity. Analyses of kinetic data from bacterial recombinant CysPI proteins indicated that soybean CysPIs are noncompetitive inhibitors of papain. The inhibition constants against papain of the CysPIs encoded by the wound and methyl jasmonate-inducible genes (57 and 21 nM for N2 and R1, respectively) were 500 to 1000 times lower than the inhibition constant of L1 (19,000 nM). N2 and R1 had substantially greater inhibitory activities than L1 against gut cysteine proteinases of the third-instar larvae of western corn rootworm and Colorado potato beetle. Cysteine proteinases were the predominant digestive proteolytic enzymes in the guts of these insects at this developmental stage. N2 and R1 were more inhibitory than the epoxide trans-epoxysuccinyl-L-leucylamide-(4-guanidino)butane (E-64) against western corn rootworm gut proteinases (50% inhibition concentration = 50, 200, and 7000 nM for N2, R1, and E-64, respectively). However, N2 and R1 were less effective than E-64 against the gut proteinases of Colorado potato beetle. These results indicate that the wound-inducible soybean CysPIs, N2 and R1, function in host plant defense against insect predation, and that substantial variation in CysPI activity against insect digestive proteinases exists among plant CysPI proteins.
Partial purification of novel differentiation-inducing substances(s) from hot water extract of Japanese pine cone. (1986)

The effects of hot-water extract of pine cone (PCE) of Pinus parviflora Sieb. et Zucc. on the growth and differentiation of ML-1 cells, derived from a patient with human myeloblastic leukemia, were investigated. Growth of ML-1 cells was slightly inhibited at 3% (v/v) PCE, and a cytotoxic effect appeared at greater than 10%. Growth inhibition was accompanied by conversion to morphologically macrophage-like cells with alpha-naphthyl acetate esterase activity. In contrast, PCE dose-dependently increased the Fc receptor and nitroblue tetrazolium (NBT)-reducing activity up to 3%; above 3% its effect declined. Most of the cytotoxic activity was extracted from PCE with ethanol, and separated from the insoluble pellet, which contained the differentiation-inducing activity. The differentiation-inducing activity was eluted near the void volume on Sephadex G-200 gel filtration, with a 260-fold increase in the specific activity.
Efficient Ensemble-Based Closed-Loop Production Optimization (2009)

Summary With the advances in smart well technology, substantially higher oil recovery can be achieved by intelligently managing the operations in a closed-loop optimization framework. The closed-loop optimization consists of two parts: geological model updating and production optimization. Both of these parts require gradient information to minimize or maximize an objective function: squared data mismatch or the net present value (or other quantities depending on financial goals), respectively. Alternatively, an ensemble-based method can acquire the gradient information through the correlations provided by the ensemble. Computation of the optimal controls in this way is nearly independent of the number of control variables, reservoir simulator, and simulation solver. In this paper, we propose an ensemble-based closed-loop optimization method that combines a novel ensemble-based optimization scheme (EnOpt) with the ensemble Kalman filter (EnKF). EnKF has recently been found suitable for sequential data assimilation in large-scale nonlinear dynamics. It adjusts reservoir model variables to honor observations and propagates uncertainty in time. EnOpt optimizes the expectation of the net present value based on the updated reservoir models. The proposed method is fairly robust, completely adjoint-free and can be readily used with any reservoir simulator. The ensemble-based closed-loop optimization method is illustrated with a waterflood example subject to uncertain reservoir description. Results are compared with other possible reservoir operation scenarios, such as wells with no controls, reactive control, and optimization with known geology. The comparison shows that the ensemble-based closed-loop optimization is able to history match the main geological features and increase the net present value to a level comparable with the hypothetical case of optimizing based on known geology.
Investigation of readily processable thermoplastic-toughened thermosets: IV. BMIs toughened with hyperbranched polyester (1999)

This is the fourth article in a series describing efforts to produce tough, high-performance thermosets from very low viscosity prepolymers which are autoclave processable. Hydroxy-terminated hyperbranched polyester (HBP) with a systematically increased molar mass was used to toughen bismaleimide (BMI). HBP was dissolved in the allyl phenol component, B, of a two-part BMI, to yield homogeneous solutions. The BMI monomer, A, was dissolved in the solution of HBP in B to give homogeneous prepolymers. The fracture toughness (KIc) of neat resin plaques was measured by compact tension, while the Tg and storage moduli (E′, at 55 and 200°C) were determined by DMA. At 9% loading, the KIc of the BMI increased steadily with HBP molecular weight up to 138% over the control with G5 HBP (Mn ∼ 14,000 g/mol); however, significant decreases in both the Tg and E′ resulted, indicating incomplete phase separation of the thermoplastic. A linear hydroxy-terminated polyester (Mn ∼ 5400 g/mol) with a repeat unit structure which was similar to the HBP's was prepared and used as a control. The linear polyester (LPE) toughened the BMI nearly as effectively as did the HBP and caused a smaller decrease in the Tg and E′. The viscosity of solutions of HBP and LPE in B were essentially the same at lower loadings in B, but at higher loadings, the HBP viscosity increased faster than did that of the LPE. The viscosity increase was end group-dependent. Preliminary morphological results are presented to show the effect of the thermoplastic architecture, loading, and end group on the cured thermoset. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 1809–1817, 1999
Classification of radar signatures by autoregressive model fitting and cluster analysis (1989)

Ninety radar signatures were digitally recorded during the probing of ten different land and marine objects with a pulsed coherent Doppler radar. Their spectra were evaluated on the basis of the Marple algorithm for autoregressive model fitting. An attempt at classification is made. The method consists in representing the radar signatures as points in four-dimensional space and identifying the obtained clusters of four-dimensional points with the observed objects. The cluster analysis is carried out assuming that the classification parameters have different clustering lengths.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The slot line in uniplanar MMIC's: propagation characteristics and loss analysis (2002)

Slotline structures as used in uniplanar MMICs (monolithic microwave integrated circuits) are analyzed, including a full-wave description of conductor loss. It is found that such lines support a fundamental wave mode that differs basically from the conventional slotline type. Results on propagation characteristics are presented, taking into account the influence of metallization thickness. The differences between the propagation behavior of the MMIC slotline and that of conventional slotlines are clarified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
DNA topoisomerase II mutant of Saccharomyces cerevisiae: topoisomerase II is required for segregation of daughter molecules at the termination of DNA replication. (1984)

A temperature-sensitive DNA topoisomerase II mutant of the yeast Saccharomyces cerevisiae has been identified. Genetic analysis shows that a single recessive nuclear mutation is responsible for both temperature-sensitive growth and enzymatic activity. Thus, topoisomerase II is essential for viability and the mutation is most probably in the structural gene. Experiments with synchronized mutant cells show that at the nonpermissive temperature cells can undergo one, and only one, round of DNA replication. These cells are arrested at medial nuclear division. Analysis of 2-microns plasmid DNA from these cells shows it to be in the form of multiply intertwined catenated dimers. The results suggest that DNA topoisomerase II is necessary for the segregation of chromosomes at the termination of DNA replication.
Suppressive Effect of Captopril on Platelet Aggregation in Essential Hypertension (1984)

Effects of captopril on platelet aggregation were studied in 12 essential hypertensive subjects. At the same time, the effects of captopril and angiotensin II on platelet aggregation in vitro were examined in 20 volunteers. A 50-mg oral dose of captopril was administered daily to hypertensive subjects for 2 weeks; the dose was then increased to 100 mg daily for the next 2 weeks. Values of platelet aggregation induced by ADP, epinephrine, collagen, and arachidonic acid before captopril treatment were 71.9 +/- 4.5, 77.3 +/- 4.2, 72.4 +/- 4.1, and 70.8 +/- 4.3% (mean +/- SE), respectively. Two weeks after daily administration of 50 mg captopril, these values were 56.7 +/- 4.5, 50.8 +/- 7.6, 64.0 +/- 4.6, and 60.9 +/- 3.9%, respectively, with significant reduction of platelet aggregation (p less than 0.001, p less than 0.01, p less than 0.01, and p less than 0.005, respectively). Daily administration of 100 mg captopril also had a significant suppressive effect on platelet aggregation. Changes of platelet count and serum lipids were not significant. In vitro, captopril and angiotensin II added to platelet-rich plasma had no effect on platelet aggregation. These results show that the suppressive effect of captopril on platelet aggregation is a secondary action in vivo.
Heritability of wing-beat frequency in Anopheles quadrimaculatus. (2002)

The repeatability of male wing-beat frequency measurements of Anopheles quadrimaculatus was determined by using mosquitoes allowed free flight in a confined space. Heritability of the wing-beat frequency trait was estimated for a laboratory and a wild-strain population of An. quadrimaculatus by using free-flight measurement with a parent-offspring regression of offspring on dams. Repeatability was 0.75 for free flight. Wing-beat frequency rose for the 1st day after adult emergence and then became steady. Female heritability of wing-beat frequency was 21.6% for colony and 24.0% for wild-strain mosquitoes. Male heritability was 57.2% for colony and 53.7% for wild-strain mosquitoes. Male heritability was significantly different from 0 when probabilities were combined across both populations.