gebhart/patrepeval huggingface dataset:
Fast quantum state control of a single trapped neutral atom (2007)

We demonstrate the initialization, readout, and high-speed manipulation of a qubit stored in a single $^{87}\mathrm{Rb}$ atom trapped in a submicrometer-sized optical tweezer. Single-qubit rotations are performed on a time scale below $100\phantom{\rule{0.3em}{0ex}}\mathrm{ns}$ using two-photon Raman transitions. Using the spin-echo technique, we measure an irreversible dephasing time of $34\phantom{\rule{0.3em}{0ex}}\mathrm{ms}$. The readout of the single atom qubit is at the quantum projection noise limit when averaging up to 1000 individual events.
Reduction of Stale Flavor Development in Low-Heat Skim Milk Powder via Epicatechin Addition (2005)

The influence of epicatechin (EC) on off-flavor development in low-heat skim milk powder samples during processing and storage was investigated. Milk powder samples were prepared from a concentrated skim milk (control) plus a concentrated skim milk with EC (treatment). Volatile extracts of the powders were analyzed by aroma extract dilution analysis (AEDA) at 0 days and after 17 months of storage in conjunction with sensory analysis of the flavor attributes. The treatment milk powders with EC added prior to drying reported a reduction in the formation of three main compounds, 4-hydroxy-2,5-dimethyl-3-(2H)-furanone, o-aminoacetophenone, and furfural, by 8-, 4-, and 4-fold for the 0 day old samples, while for the 17 month aged samples o-aminoacetophenone was the major compound reduced in formation by 8-fold, respectively, based on the flavor dilution factors reported. The sensory evaluations indicated that the treatment milk powders for 0 day old and 17 month aged samples were statistically lower (alpha = 0.05) in stale flavor intensity in comparison to the respective control samples, while no differences were noted in bitterness intensity.
Obstacle Detection and Tracking for the Urban Challenge (2009)

This paper describes the obstacle detection and tracking algorithms developed for Boss, which is Carnegie Mellon University 's winning entry in the 2007 DARPA Urban Challenge. We describe the tracking subsystem and show how it functions in the context of the larger perception system. The tracking subsystem gives the robot the ability to understand complex scenarios of urban driving to safely operate in the proximity of other vehicles. The tracking system fuses sensor data from more than a dozen sensors with additional information about the environment to generate a coherent situational model. A novel multiple-model approach is used to track the objects based on the quality of the sensor data. Finally, the architecture of the tracking subsystem explicitly abstracts each of the levels of processing. The subsystem can easily be extended by adding new sensors and validation algorithms.
Hormones and Vasoprotection (1999)

There is a strong link between menopause and increased cardiovascular disease incidence in women, and observational studies suggest that postmenopausal hormone replacement therapy reduces cardiovascular disease risk by about half. Observational studies suffer from important limitations, however, and the only published prospective controlled trial of the effects of hormone replacement therapy on cardiovascular outcomes, the Heart Estrogen-Progestin Replacement Study (HERS), showed no net benefit of continuous estrogen plus synthetic progestin treatment in women with established coronary disease. Fundamental mechanistic studies of the cellular and molecular events by which hormones protect (or fail to protect) blood vessels from damage are needed to define the role of postmenopausal hormone replacement therapy in cardiovascular disease prevention. Most studies suggest that estrogen inhibits the neointimal response to acute injury in normal blood vessels, but this vasoprotective effect was not seen in vessels with preexisting atherosclerosis. Studies from our laboratory in the rat carotid injury model have shown that estrogen inhibits neointima formation via effects on all 3 layers of the vascular wall, including inhibition of medial smooth muscle cell migration and proliferation, stimulation of regrowth of endothelium, and inhibition of adventitial cell migration into neointima. Our laboratory is currently using transduced (lacZ) syngeneic fibroblasts as 'reporter' cells to delineate the factors that stimulate migration of adventitial cells into neointima after vascular injury and their modulation by estrogen and the other sex hormones. These fundamental studies will establish more rational strategies for therapeutic intervention in vascular diseases, including the basis for future gene therapy.
Osmotic and SANS Observations on Sodium Polyacrylate Hydrogels in Physiological Salt Solutions (2000)

The volume transition induced by the addition of calcium into lightly cross-linked fully neutralized sodium polyacrylate hydrogels, swollen in 40 mM NaCl solutions, is investigated by osmotic swelling pressure and small-angle neutron scattering (SANS) measurements. In this reversible transition, the polymer volume fraction φ changes by more than an order of magnitude. The longitudinal osmotic modulus Mos deduced from macroscopic measurements shows an abrupt increase at the transition. The intensity of the scattered radiation can be decomposed into a static and a dynamic component. The former exhibits Porod scattering behavior, while the latter obeys an Ornstein−Zernike relation. The observed intensity of the dynamic part has a maximum at the transition and exhibits a functional dependence on the calcium concentration, which is similar to that of the osmotic susceptibility φ2/Mos, determined from direct osmotic measurements.
Prediction error as a criterion for operator length (1971)

Abstract Prediction error filtering has been widely used for deconvolution. The mean squared error in prediction is a monotonically nonincreasing function of operator length, and the value of the error is readily available from the Wiener-Levinson algorithm. In general, the value of this error for the infinitely long operator is not known a priori. It is shown that the final value of the error can be obtained by considering the Kolmogorov spectrum factorization. Simple criteria can then be established for operator effectiveness and length.
DNA Adduct Formation in Precision-Cut Rat Liver and Lung Slices Exposed to Benzo[a]pyrene (2003)

Chemical-DNA adducts provide an integrated measure of exposure, absorption, bioactivation, detoxification, and DNA repair following exposure to a genotoxic agent. Benzo[a]pyrene (BaP), a prototypical polycyclic aromatic hydrocarbon (PAH), can be bioactivated by cytochrome P-450s (CYPs) and epoxide hydrolase to genotoxic metabolites which form covalent adducts with DNA. In this study, we utilized precision-cut rat liver and lung slices exposed to BaP to investigate tissue-specific differences in chemical absorption and formation of DNA adducts. To investigate the contribution of bioactivating CYPs (such as CYP1A1 and CYP1B1) on the formation of BaP-DNA adducts, animals were also pretreated in vivo with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin) prior to in vitro incubation of tissue slices with BaP. Furthermore, the tissue distribution of BaP and BaP-DNA adduct levels from in vivo studies were compared with those from the in vitro tissue slice experiments. The results indicate a time- and concentration-dependent increase in tissue-associated BaP following exposure of rat liver and lung tissue slices to BaP in vitro, with generally higher levels of BaP retained in lung tissue. Furthermore, rat liver and lung slices metabolized BaP to reactive intermediates that formed covalent adducts with DNA. Total BaP-DNA adducts increased with concentration and incubation time. Adduct levels (fmol adduct/microg DNA) in lung slices were greater than liver at all doses. Liver slices contained one major and two minor adducts, while lung slices contained two major and 3 minor adducts. The tissue-specific qualitative profile of these adducts in tissue slices was similar to that observed from in vivo studies, further validating the use of this model. Pretreatment of animals with TCDD prior to in vitro incubation with BaP potentiated the levels of DNA adduct formation. TCDD pretreatment altered the adduct distribution in lung but not in liver slices. Together, the results suggest that tissue-specific qualitative and quantitative differences in BaP-DNA adducts could contribute to the lung being a target tissue for BaP carcinogenesis. Furthermore, the results validate the use of precision-cut tissue slices incubated in dynamic organ culture as a useful model for the study of chemical-DNA adduct formation.
Oxidative stabilities of soybean oils that lack lipoxygenases (1996)

Abstract Lipoxygenase (LOX)‐null soybean lines that lack LOX 2, or LOX 2 and 3, and contain normal (8.0–8.6%) or low (2.0–2.8%) linolenate (18∶3) amounts were evaluated for their oil qualities and storage stabilities. Soybean oils of six genotypes were extracted by both laboratory‐scale and pilot‐plant systems and were refined, bleached, and deodorized in the laboratory. Citric acid was added to oils during the cool‐down stage of deodorization. Two replications, separated at the point of conditioning, were evaluated for each genotype. Under storage conditions of 55–60°C in the dark, soybean oils with low 18∶3 contents were significantly ( P <‐0.05) more stable as measured by peroxide values than were oils with normal 18∶3 contents, regardless of the LOX content of the beans. The volatile analysis showed few differences between oils with low and high 18∶3 contents or among oils from beans that lack different LOX enzymes. After 16 d of storage, the amount of 1‐octen‐3‐ol was significantly greater in oils with low 18∶3 content, and soybean oils from beans with normal LOX content had a significantly ( P <‐0.05) lower amount of 1‐octen‐3‐ol than did the oils that lacked LOX enzymes. Storage at 35°C under light showed no differences in volatile amounts or sensory evaluations after 14 d of storage. During storage, peroxide values tended to be lower in oils from beans with normal 18∶3 content and in oils from beans with normal LOX content. Generally, the abscence of LOX 2 or LOX 2 and 3, although having a small effect on lipid oxidation, was not as important to oil quality as was the 18∶3 content.
Cytoplasmic Tail of Moloney Murine Leukemia Virus Envelope Protein Influences the Conformation of the Extracellular Domain: Implications for Mechanism of Action of the R Peptide (2002)

The envelope (Env) protein of Moloney murine leukemia virus (MoMuLV) is a homotrimeric complex whose monomers consist of linked surface (SU) and transmembrane (TM) proteins cleaved from a precursor protein by a cellular protease. In addition, a significant fraction of virion-associated TM is further processed by the viral protease to remove the C-terminal 16 amino acids of the cytoplasmic domain, the R peptide. This cleavage greatly enhances the fusogenicity of the protein and is necessary for the formation of a fully functional Env protein complex. We have previously proposed that R peptide cleavage enhances fusogenicity by altering the conformation of the ectodomain of the protein (Y. Zhao et al., J. Virol. 72:5392-5398, 1998). Using a series of truncation and point mutants of MoMuLV Env, we now provide direct biochemical and immunological evidence that the cytoplasmic tail and the membrane-spanning region of Env can influence the overall structure of the ectodomain of the protein and alter the strength of the SU-TM interaction. The R-peptide-truncated form of the protein, in particular, exhibits a markedly different conformation than the full-length protein.
Mixing and Fluid Dynamics Effects in Particle Precipitation Processes (2016)

Precipitation defined as the rapid formation of moderately soluble crystalline or amorphous solid particles from a liquid solution under high supersaturation conditions is considered. It involves the simultaneous and fast occurrence of primary nucleation and growth of particles together with the secondary processes such as aggregation and breakage. It is shown how the effects of fluid flow and mixing affect the subprocesses forming the overall precipitation process. Examples are presented for reactive precipitation and antisolvent precipitation with supercritical fluids applied as the antisolvents.The elementary subprocesses forming the overall precipitation process (i.e. macro-, meso-, micromixing, chemical reaction, nucleation and growth of particles, aggregation and breakage) are characterized by the related time constants and the application of time constants in the modeling and scale-up of precipitation processes is presented. The effects of turbulence on particle formation are simulated using mechanistic models, CFD and population balances (including the method of moments and the quadrature method of moments). The results of modeling are compared with experimental data.Finally, it is shown in the context of practical applications to what extent the approaches discussed in this paper can be applied to “design” particles.
Dither-motor design with concurrent sensing and actuating piezoelectric materials (Ring laser gyroscope) (1994)

The authors present an analytical model to predict the model parameters of a dither-motor structure in a ring laser gyroscope in which the piezoelectric sensor and actuator are employed as driving mechanisms to avoid the problem of so-called lock-in effects. It is shown that the natural frequency of a dither motor is strongly influenced by: (1) the inertia and stiffness of piezoelectric elements and bonding layers, (2) the location of piezoelectric elements, and (3) the interaction between structural vibration and piezoelectric actuation. Conventionally. piezoelectric elements are used for sensor and actuator independently. A technique for utilizing each of the piezoelectric elements concurrently for dither rate sensing and dither motion actuation is also developed. Experimental results show that the system performance and reliability can be significantly increased by accurately predicting the fundamental structural frequency and by implementing the concurrent sensing/actuating technique.
Absolute Quantification of Multisite Phosphorylation by Selective Reaction Monitoring Mass Spectrometry (2006)

Multisite phosphorylation is an important mechanism for achieving intricate regulation of protein function. Here we extended the absolute quantification of abundance (AQUA) methodology and validated its applicability to quantitatively study multisite phosphorylation. As a test case, we chose the conserved inhibitory site of the cyclin-dependent kinases (CDKs), Cdk1, Cdk2, and Cdk3, which are important regulators of cell cycle transitions and apoptosis. Inhibitory phosphorylation at Thr(14) and Tyr(15) of the CDKs is modulated by complex regulatory mechanisms involving multiple kinases and phosphatases. Yet the resulting quantitative dynamics among the four possible phosphorylated and non-phosphorylated versions of CDKs (T14p-Y15p, T14p-Y15, T14-Y15p, and T14-Y15) has not been investigated to date. Hence we used the heavy isotope-labeled tryptic peptides spanning the inhibitory site as internal standards and quantified all four versions by LC-selected reaction monitoring. Quantification of the phosphorylation status of the inhibitory site in the cell extracts provided novel quantitative insights. 1) The transition to mitotic phase was dominated by the conversion of "T14p-Y15p" to the "T14-Y15" form, whereas the two monophosphorylated forms were considerably lower in abundance. 2) The amount of all four forms decreased during the progression of apoptosis but with differing kinetics. Analysis of immunoprecipitated Cdk1 and Cdk2 revealed that the inhibitory site phosphorylation state of both kinases at different stages of the cell cycle followed the same trend. Quantitative immunoblotting using antibodies to Cdk1 and Cdk2 and to the T14-Y15p form suggested that quantification by AQUA was reliable and accurate. These results highlight the utility of internal standard peptides to achieve accurate quantification of multisite phosphorylation status.
Automatic Extraction of Power Lines From Aerial Images (2007)

There has been little investigation for the automatic extraction of power lines from aerial images due to the low resolution of aerial images in the past decades. With increasing aerial photogrammetric technology and sensor technology, it is possible for photogrammetrists to monitor the status of power lines. This letter analyzes the property of imaged power lines and presents an algorithm to automatically extract the power line from aerial images acquired by an aerial digital camera onboard a helicopter. This algorithm first uses a Radon transform to extract line segments of the power line, then uses the grouping method to link each segment, and finally applies the Kalman filter technology to connect the segments into an entire line. We compared our algorithm with the line mask detector method and the ratio line detector, and evaluated their performances. The experimental results demonstrated that our algorithm can successfully extract the power lines from aerial images regardless of background complexity. This presented method has successfully been applied in China National 863 project for power line surveillance, 3-D reconstruction, and modeling.
Recombinant expression and antigenic properties of a 32-kilodalton extracellular alkaline protease, representing a possible virulence factor from Aspergillus fumigatus (1994)

A 32-kDa nonglycosylated alkaline protease (EC 3.4.1.14) with elastolytic activity, secreted by the opportunistic pathogen Aspergillus fumigatus ATCC 42202, is suggested to be a virulence factor of this fungus. The enzyme is a serine protease of the subtilisin family, and its cDNA nucleotide sequence has recently been reported. We have cloned the cDNA encoding the mature protease into a high-level Escherichia coli expression plasmid and produced the recombinant protease as a fusion protein with a six-adjacent-histidine affinity tag at the carboxy terminus. Subsequently, the recombinant protease was purified to homogeneity, with affinity chromatography yielding 30 to 40 mg of recombinant protease per liter of E. coli culture. Refolded recombinant protease, in comparison with native protease, demonstrated weak enzymatic activity but similar immunochemical characteristics as analyzed by antigen-specific enzyme-linked immunosorbent assay (ELISA), competition ELISA, and immunoblotting assays. To assess the allergenic potential of the protease, sera from patients with allergic bronchopulmonary aspergillosis and sera from healthy control individuals were analyzed by ELISA and immunoblotting techniques. Sera from patients with allergic bronchopulmonary aspergillosis did not have protease-specific immunoglobulin E (IgE) antibodies and, remarkably, did not show significantly elevated protease-specific IgG antibody levels compared with those in sera from healthy control individuals. This suggests that the alkaline protease from A. fumigatus does not elicit IgE antibodies and has weak immunogenicity, a property which may explain fungus persistence in allergic individuals.
Calibrated waveform measurement with high-impedance probes (2003)

We develop an on-wafer waveform calibration technique that combines a frequency-domain mismatch correction to account for the effects of the probe on the measurement with an oscilloscope calibration. The mismatch correction is general and can be applied to any type of microwave probe, including scanning and internal-node probes for noninvasive integrated-circuit tests. We show that, for the commercial high-impedance probe we used, this calibration approach allows accurate on-wafer waveform reconstruction for a variety of probe ground configurations.
Dual frequency dielectrophoresis with interdigitated sidewall electrodes for microfluidic flow‐through separation of beads and cells (2009)

This paper presents a novel design and separation strategy for lateral flow-through separation of cells/particles in microfluidics by dual frequency coupled dielectrophoresis (DEP) forces enabled by vertical interdigitated electrodes embedded in the channel sidewalls. Unlike field-flow-fractionation-DEP separations in microfluidics, which utilize planar electrodes on the microchannel floor to generate a DEP force to balance the gravitational force and separate objects at different height locations, lateral separation is enabled by sidewall interdigitated electrodes that are used to generate non-uniform electric fields and balanced DEP forces along the width of the microchannel. In the current design, two separate AC electric fields are applied to two sets of independent interdigitated electrode arrays fabricated in the sidewalls of the microchannel to generate differential DEP forces that act on the cells/particles flowing through. Individual particles (cells or beads) will experience DEP forces differently due to the difference in their dielectric properties. The balance of the differential DEP forces from the electrode arrays will position dissimilar particles at distinct equilibrium planes across the width of the channel. When coupled with fluid flow, this results in lateral separation along the width of the microchannel and the separated particles can thus be automatically directed into branched channel outlets leading to different reservoirs for downstream processing. In this paper, we present the design and analysis of lateral separation enabled by dual frequency coupled DEP, and cell/bead and cell/cell separations are demonstrated with this lateral separation strategy. With vertical interdigitated electrodes on the sidewall, the height of the microchannel can be increased without losing the electric field strength in contrast to other multiple frequency DEP devices with planar electrodes. As a result, populations of cells can be separated simultaneously instead of one by one to enable high-throughput sorting microfluidic devices.
Deep hashing for compact binary codes learning (2015)

In this paper, we propose a new deep hashing (DH) approach to learn compact binary codes for large scale visual search. Unlike most existing binary codes learning methods which seek a single linear projection to map each sample into a binary vector, we develop a deep neural network to seek multiple hierarchical non-linear transformations to learn these binary codes, so that the nonlinear relationship of samples can be well exploited. Our model is learned under three constraints at the top layer of the deep network: 1) the loss between the original real-valued feature descriptor and the learned binary vector is minimized, 2) the binary codes distribute evenly on each bit, and 3) different bits are as independent as possible. To further improve the discriminative power of the learned binary codes, we extend DH into supervised DH (SDH) by including one discriminative term into the objective function of DH which simultaneously maximizes the inter-class variations and minimizes the intra-class variations of the learned binary codes. Experimental results show the superiority of the proposed approach over the state-of-the-arts.
A 1.33 µm InAs/GaAs quantum dot laser with a 46 cm<sup>−1</sup>modal gain (2008)

We report on 1.33 µm quantum dot (QD) lasers grown on GaAs substrates that show a modal gain of 45 cm−1, low threshold current density of 150 A cm−2 and room-temperature continuous wave output power of 2.5 W. The active region is based on ten InAs/InGaAs/GaAs quantum dot layers formed by activated phase separation. High structural quality of the active region is achieved, owing to minimization of the total amount of strained material per QD layer. The optical confinement factor is increased by exploiting high Al composition (80%) in the cladding layers. A modal gain over 20 cm−1 in the 1315–1345 nm wavelength range is revealed by the Hakki–Paoli technique at a low current density of 500 A cm−2.