gebhart/patrepeval huggingface dataset:
Sub-500 fs high power quasimonolithic FCPA laser using an all-solid step-index flexible PM VLMA Yb-doped fiber amplifier (2022)

We report on the design of a quasi-monolithic fiber chirped pulse amplification (FCPA) system operating at 1040 nm. Chirped-pulse amplification has been achieved using an all-solid step-index PM VLMA Yb-doped fiber, designed and drawn at Photonics Bretagne. The amplifier is integrated to the system through an internally developed mode field adapter (MFA), and bended with a 14 cm diameter, giving a truly single-mode behavior. 540 fs pulses are obtained without any fiber length optimization. An average power of 50 W has been achieved at the fundamental repetition rate of the laser, but also energies up to 41 µJ per pulse at lower repetition rate, pump power limited. The pulses are stretched using a thermally–controlled tunable chirped fibered Bragg grating (CFBG), allowing fine dispersion tuning, and compressed using a chirped volume Bragg grating (CVBG).
A Shannon-Theoretic Perspective on Fading Multihop Networks (2006)

We consider a frequency-flat fading multihop network with a single active source-destination pair terminals communicating over multiple hops through a set of intermediate relay terminals. We use Shannon-theoretic tools to analyze the tradeoff between energy efficiency and spectral efficiency (known as the power-bandwidth tradeoff) for a simple communication protocol based on time-division decode-and-forward relaying in meaningful asymptotic regimes of signal-to-noise ratio (SNR) under a system-wide power constraint on source and relay transmissions. The impact of multi-hopping and channel fading on the key performance measures of the high and low SNR regimes is investigated to shed new light on the possible enhancements in power/bandwidth efficiency and link reliability. In contrast to the common belief that in fading environments communicating over multiple hops suffers significantly in performance due to the worst link limitation, our results indicate that hopping could significantly improve the outage behavior over slow-fading networks and stabilize links against the random channel fluctuations. In particular, we prove that there exists an optimal number of hops that minimizes the end-to-end outage probability and characterize the dependence of this optimal number on the fading statistics and target energy and spectral efficiencies.
Kallistatin attenuates endothelial apoptosis through inhibition of oxidative stress and activation of Akt-eNOS signaling (2010)

Kallistatin is a regulator of vascular homeostasis capable of controlling a wide spectrum of biological actions in the cardiovascular and renal systems. We previously reported that kallistatin inhibited intracellular reactive oxygen species formation in cultured cardiac and renal cells. The present study was aimed to investigate the role and mechanisms of kallistatin in protection against oxidative stress-induced vascular injury and endothelial cell apoptosis. We found that kallistatin gene delivery significantly attenuated aortic superoxide formation and glomerular capillary loss in hypertensive DOCA-salt rats. In cultured endothelial cells, kallistatin suppressed TNF-α-induced cellular apoptosis, and the effect was blocked by the pharmacological inhibition of phosphatidylinositol 3-kinase and nitric oxide synthase (NOS) and by the knockdown of endothelial NOS (eNOS) expression. The transduction of endothelial cells with adenovirus expressing dominant-negative Akt abolished the protective effect of kallistatin on endothelial apoptosis and caspase activity. In addition, kallistatin inhibited TNF-α-induced reactive oxygen species formation and NADPH oxidase activity, and these effects were attenuated by phosphatidylinositol 3-kinase and NOS inhibition. Kallistatin also prevented the induction of Bim protein and mRNA expression by oxidative stress. Moreover, the downregulation of forkhead box O 1 (FOXO1) and Bim expression suppressed TNF-α-mediated endothelial cell death. Furthermore, the antiapoptotic actions of kallistatin were accompanied by Akt-mediated FOXO1 and eNOS phosphorylation, as well as increased NOS activity. These findings indicate a novel role of kallistatin in the protection against vascular injury and oxidative stress-induced endothelial apoptosis via the activation of Akt-dependent eNOS signaling.
Sound scattering from a thin rod in a viscous medium (1986)

Sound waves incident on a thin elastic rod whose radius is smaller than the wavelength of the incident sound induce flexural and uniform compressional oscillations in the rod. These elastic oscillations, in turn, radiate sound waves into the fluid medium and affect the scattered waves. This paper deals with an analytic study on sound scattering by, and acoustoelastic vibrations of, a thin elastic unbound rod in a viscous fluid. The shear viscosity of the fluid is considered in the solutions to boundary value problems concerning the sound scattering and the elastic response of the rod. Results show that the scattered compressional waves consist of the rigid-rod scattering of compressional waves, monopolar waves due to the uniform pulsating of the rod, and dipolar waves due to the flexural vibration of the rod. The scattered viscous waves consist of the rigid-rod scattering of viscous waves and dipolar waves due to the flexural vibration of the rod. Acoustic resonances occur when the effective inertia force of the rod balances the stiffness force of the rod. The fluid viscosity and the scattering of sound give rise to damping effects for the rod vibrations and signficantly affect the acoustic resonances.
Pure graphene oxide doped conducting polymer nanocomposite for bio-interfacing (2013)

Advanced materials that are highly biocompatible and easily modifiable with biomolecules are of great importance for bio-interfacing and the development of biodevices. Here, a biocompatible conducting polymer based nanocomposite was electrochemically synthesized through the electropolymerization of poly(3, 4-ethylene dioxythiophene) (PEDOT) in the presence of graphene oxide (GO) as the only dopant. GO contains many negatively charged carboxyl functional groups and is highly dispersible in aqueous solutions, enabling its facile incorporation and even distribution throughout the conducting polymer. PEDOT/GO films exhibited minimal cytotoxicity after 24 h and supported neuron growth with significantly longer neurites than a control PEDOT/PSS film, indicating that the PEDOT/GO film provides a positive growth signal to developing neurons. While some of the negatively charged functional carboxyl groups of GO "dope" the PEDOT, others are exposed freely on the surface of the nanocomposite allowing easy functionalization of the PEDOT/GO composite with biomolecules. Functional laminin peptide, RNIAEIIKDI (p20), was covalently bound to the surface of the PEDOT/GO film and maintained its bioactivity, as evidenced by an increased neurite outgrowth from neurons cultured on the functionalized composite surface. The ease of biomolecule functionalization of the PEDOT/GO nanocomposite, along with its low electrochemical impedance, minimal toxicity and permissiveness to neuron growth, underlines its potential as a material for widespread biosensing, neural interfacing and tissue engineering applications.
Electrochemical preparation of a rugate filter in silicon and its deviation from the ideal structure (2007)

Porous silicon single layers are formed by anodization of silicon in a hydrofluoric acid solution at different current densities. An accurate estimation of the etch rates and refractive indices is performed. The refractive index-depth profile of a porous silicon rugate filter (PSRF) prepared by sinusoidally modulating the current density during etch is investigated. The produced PSRF is found to have a periodic pseudo-sinusoidal variation of refractive index with depth. The sinusoidal current density waveform that was employed generates a nonideal refractive index-depth profile with an asymmetric period. It is found that this deformed refractive index profile affects the quality of the characteristic resonant peak of the rugate filter. A simple modification of the current density waveform can be implemented, which allows one to achieve a true sinusoidal refractive index-depth profile characteristic of a rugate filter. The modified current density waveform allows the generation of a PSRF with a low index contrast and a sharp resonant band. The ability of these structures to act as chemical vapor sensors is tested and compared with the existing literature. The filters exhibit a red-shift in the photonic feature upon exposure to saturated ethanol vapor. The modified signal does not impose a significant change on the filter sensitivity to ethanol vapor.
Diode-Pumped Solid State Laser Driver for Inertial Fusion Energy Power Plants (2004)

The two main types of laser drivers that have been employed to investigate inertial confinement fusion (ICF) are flashlamp-pumped Ndrglass lasers and KrF excimer systems. While Ndrglass has proved highly effective at elucidating key plasma physics issues involved in the ICF process,1 their basic system architecture lacks the efficiency and repetition rate required to serve as an economical driver for inertial fusion energy (IFE) power plants. In addition, significant developments are needed to show that electron beam-pumped KrF systems can attain the target irradiation parameters, as well as the system efficiency, reliability, and cost goals. The result of our recent conceptual studies have revealed that a diode-pumped solid state laser (DPSSL) might be a viable driver for an IFE power plant. In this work, we report on the results from our 4000 line computer code that encompasses the crucial physics and systems details needed to evaluate the resultant cost of electricity (COE). In this effort, we have not specifically addressed issues associated with the balance-of-plant, reactor vessel, and fusion gain curves, but instead employed community-accepted paradigms that account for the critical features of these aspects of the problem. In this way, we focused our attention of the design of the DPSSL, although it was considered in the context of the entire power plant economics and energy flow.
Dual Emissive Multinuclear Iridium(III) Complexes in Solutions: Linear Photophysical Properties, Two-Photon Absorption Spectra, and Photostability C (2018)

Linear steady-state and time-resolved spectroscopic properties, degenerate two-photon absorption (2PA) spectra, and photochemical stability of Irᴵᴵᴵ complexes TCQ[Irᴵᴵᴵ(ppz)₂]ₙ, (TCQ = tricycloquinazoline; ppz = 1-phenylpyrazole; n = 1 (1), n = 2 (2), and n = 3 (3)) are presented for liquid solutions. The analysis of the linear photophysical properties revealed the nature of the observed dual-component fluorescence–phosphorescence emission of 1–3 at room temperature. The values of 2PA cross sections were determined by open aperture Z-scans using a 1 kHz femtosecond laser system. The specific dependence of the 2PA efficiency on the number of ppz ligand units in 1–3 was determined. The quantum yields, Φₚₕ, for photochemical decomposition of TCQ[Irᴵᴵᴵ(ppz)₂]ₙ complexes were obtained for the first time using the absorption method [Corredor, C. C.; J. Photoch. Photobio. A2006, 184, 105−112] with continuous wave laser irradiation, and the highest stability of Φₚₕ ≈ 4 × 10–⁶ was shown for 2 in toluene.
Mesenchymal Stem Cell Stimulation of Tissue Growth Depends on Differentiation State (2010)

The osteochondral microenvironment involves a complex milieu of cues that facilitate proper tissue development, homeostasis, and repair. This environment is disrupted in disease states such as osteoarthritis. Mesenchymal stem cells (MSCs) are under clinical investigation for the treatment of osteoarthritis given their capacity to differentiate into chondrocytes as well as to secrete a wide array of biologically active factors that support cell proliferation and tissue formation. In fact, the therapeutic action of these cells in many clinical applications is now thought to be at least partially dependent on their secretory capacity. Previous work demonstrated that MSCs were capable of stimulating chondrocyte growth and tissue production, whereas tissue-derived osteoblasts were not stimulatory. This study investigated the stimulatory capacity of MSCs during osteogenesis and the impact of MSC phenotype on cartilage stimulation. Cell interactions were examined in 3 coculture systems to confirm that trends were not dependent on material: traditional cell culture insert coculture, bilayered poly(ethylene glycol) gels, and a scaffold comprised of a layer of poly(ethylene glycol) polymerized onto a poly(lactic-co-glycolic) acid-based scaffold. Results demonstrated that MSCs predifferentiated toward an osteogenic phenotype for 3 days exhibited enhanced stimulation of chondrocyte extracellular matrix production, whereas longer periods of predifferentiation decreased the magnitude of observed stimulation. Further, tissue formation by the MSCs themselves showed greater dependence on the coculture system than the presence of other cells or length of predifferentiation.
Characterizing subepithelial remodeling in eosinophilic esophagitis with PS-μOCT (2022)

Eosiophilic esophagitis (EoE) is an inflammatory disease of the esophagus, with long-term EoE causing fibrotic and hypertrophic restructuring of the sub-epithelial wall. We have developed a polarization-sensitive micro-optical coherence tomography (PS-µOCT) imaging device for its characterization. This device was used to quantify collagen at 15 sites on each of 5 swine esophagi, with results compared to histology. A linear mixed model with random intercept showed significant agreement between OCT and histology (slope = 0.41, 95% CI [0.22, 0.60], t(67) = 4.30, p = 5.8 x 10-5). This validates our technology and will allow longitudinal assessment of patient response to drug and diet, without endoscopic biopsy.
Graphical Models for Machine Learning and Digital Communication (1998)

A variety of problems in machine learning and digital communication deal with complex but structured natural or artificial systems. In this book, Brendan Frey uses graphical models as an overarching framework to describe and solve problems of pattern classification, unsupervised learning, data compression, and channel coding. Using probabilistic structures such as Bayesian belief networks and Markov random fields, he is able to describe the relationships between random variables in these systems and to apply graph-based inference techniques to develop new algorithms. Among the algorithms described are the wake-sleep algorithm for unsupervised learning, the iterative turbodecoding algorithm (currently the best error-correcting decoding algorithm), the bits-back coding method, the Markov chain Monte Carlo technique, and variational inference. Bradford Books imprint
Stratification of rate of lymph node metastasis according to risk factors and oncologic outcomes in patients who underwent radical resection for rectal neuroendocrine tumors (2023)

We found that the rate of lymph node metastasis increased significantly when the number of known risk factors is 2 or more.
New advances with REBL for maskless high-throughput EBDW lithography (2011)

REBL (Reflective Electron Beam Lithography) is a program for the development of a novel approach for highthroughput maskless lithography. The program at KLA-Tencor is funded under the DARPA Maskless Nanowriter Program. A DPG (digital pattern generator) chip containing over 1 million reflective pixels that can be individually turned on or off is used to project an electron beam pattern onto the wafer. The DARPA program is targeting 5 to 7 wafers per hour at the 45 nm node, and this paper will describe improvements to both increase the throughput as well as extend the system to the 2x nm node and beyond. This paper focuses on three specific areas of REBL technology. First, a new column design has been developed based on a Wien filter to separate the illumination and projection beams. The new column design is much smaller, and has better performance both in resolution and throughput than the first column which used a magnetic prism for separation. This new column design is the first step leading to a multiple column system. Second, the rotary stage latest results of a fully integrated DPG CMOS chip with lenslets will be reviewed. An array of over 1 million micro lenses which is fabricated on top of the CMOS DPG chip has been developed. The microlens array eliminates crosstalk between adjacent pixels, maximizes contrast between on and off states, and provides matching of the NA between the DPG reflector and the projection optics.
MMSE interference suppression for joint acquisition and demodulation in CDMA systems (2002)

Minimum mean squared error (MMSE) demodulation for direct-sequence CDMA systems eliminates the near-far problem, and can be implemented adaptively (i.e., without explicit knowledge of the parameters of the multiple-access interference), given a training sequence for the desired transmission. However, prior to timing acquisition, the receiver does not know the phase of the training sequence, i.e., it does not know, for a given observation interval, which bit of the training sequence contributes the most signal energy. Conceivably, this timing information could be obtained using conventional acquisition techniques by correlating over long enough intervals and applying enough power control to resolve the near-far problem. In this paper, however, we present an adaptive approach to the problem of near-far resistant joint acquisition and demodulation. Our method is to use a training sequence with a short period P, and run P adaptive algorithms either serially or in parallel, one for each assumed phase of the training sequence. The adaptive algorithm that yields the least mean squared error (MSE) corresponds to the correct phase, and yields in addition an MMSE correlator that can be used for continued training or for decision-directed adaptation. Thus, acquisition results in a near-far resistant demodulator that implicitly accounts for the timings and amplitudes of all the transmissions without explicitly estimating even the timing of the desired signal. We note that a method for joint acquisition and demodulation that does not require a training sequence has also been devised.
High temperature photonic crystal fiber tip sensor (2010)

We demonstrate a temperature sensor consisting of a 2-dimensional, Silicon (Si), Photonic Crystal (PC) attached to the facet of a standard single-mode optical fiber. The 2-D PC sensors are fabricated on standard Si wafers, using a single mask and a combination of isotropic and anisotropic etching, and micro-assembled onto the facets of the optical fibers by Si welding. The temperature of the Si-PC sensor is monitored by measuring its reflectance spectrum in the 1250 nm to 1650 nm wavelength range. The measured reflectivity peak shifts from 100°C to 700°C is 0.1036 nm/°C. The observed spectral shift and temperature sensitivity are significantly higher than other high temperature fiber Bragg grating sensors, and comparable to long-period fiber gratings sensors. The high sensitivity along with the compactness and robustness gives these sensors the strong potential for use in harsh environments.
Ex vivo MR microscopy of a human brain with multiple sclerosis: Visualizing individual cells in tissue using intrinsic iron (2020)

Changes in iron accumulation within cells gave rise to imaging contrast seen between cortical lesions and normal cortex, as well as the patchy signal in NAWM. Densely packed myelin and collagen deposition also contributed to MRM signal changes. Even though we studied only one block each from normal appearing and cortical lesions, such studies can help better understand the origins of histopathological and microstructural correlates of MRI signal changes in multiple sclerosis and contextualize the interpretation of lower-resolution in vivo MRI scans.
IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback (2019)

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This paper analyzes the feasibility of applying Darwins algorithms to the problem of protein sequence alignment. In addition to a behavioral analysis of Darwin when aligning proteins, we propose an algorithmic improvement to Darwins alignment algorithm, GACT, in the form of a multi-pass variant that increases its accuracy on protein sequence alignment. Concretely, our proposed multi-pass variant of GACT achieves on average 14\\% better alignment scores.
Antiviral Effects of Lamivudine, Emtricitabine, Adefovir Dipivoxil, and Tenofovir Disoproxil Fumarate Administered Orally Alone and in Combination to Woodchucks with Chronic Woodchuck Hepatitis Virus Infection (2008)

Adefovir dipivoxil (ADV) and tenofovir disoproxil fumarate (TDF) are nucleotide analogs that inhibit the replication of wild-type hepatitis B virus (HBV) and lamivudine (3TC)-resistant virus in HBV-infected patients, including those who are coinfected with human immunodeficiency virus. The combination of ADV or TDF with other nucleoside analogs is a proposed strategy for managing antiviral drug resistance during the treatment of chronic HBV infection. The antiviral effect of oral ADV or TDF, alone or in combination with 3TC or emtricitabine (FTC), against chronic woodchuck hepatitis virus (WHV) infection was evaluated in a placebo-controlled study in the woodchuck, an established and predictive model for antiviral therapy. Once-daily treatment for 48 weeks with ADV plus 3TC or TDF plus FTC significantly reduced serum WHV viremia levels from the pretreatment level by 6.2 log(10) and 6.1 log(10) genome equivalents/ml serum, respectively, followed by TDF plus 3TC (5.6 log(10) genome equivalents/ml), ADV alone (4.8 log(10) genome equivalents/ml), ADV plus FTC (one survivor) (4.4 log(10) genome equivalents/ml), TDF alone (2.9 log(10) genome equivalents/ml), 3TC alone (2.7 log(10) genome equivalents/ml), and FTC alone (2.0 log(10) genome equivalents/ml). Individual woodchucks across all treatment groups also demonstrated pronounced declines in serum WHV surface antigen, characteristically accompanied by declines in hepatic WHV replication and the hepatic expression of WHV antigens. Most woodchucks had prompt recrudescence of WHV replication after drug withdrawal, but individual woodchucks across treatment groups had sustained effects. No signs of toxicity were observed for any of the drugs or drug combinations administered. In conclusion, the oral administration of 3TC, FTC, ADV, and TDF alone and in combination was safe and effective in the woodchuck model of HBV infection.
L’académie et la réforme de l’enseignement secondaire (2009)

info:eu-repo/semantics/published