gebhart/patrepeval huggingface dataset:
Structural profile of ultra‐high molecular weight polyethylene in acetabular cups worn on hip simulators characterized by confocal Raman spectroscopy (2011)

We applied a Raman confocal spectroscopic technique to quantitatively assess the structural features of two kinds of acetabular cups made of ultra-high molecular weight polyethylene. We wanted to know whether polyethylene cups belonging to different generations, and thus manufactured by different procedures, possess different molecular structures and how those differences affected their wear resistance. Emphasis was placed on oxidation profiles developed along the cross-sectional depth of the cups in the main wear zone developed during testing in a hip simulator. The micrometric lateral resolution of the laser beam, focused at surface or sub-surface sectional planes, enabled the visualization of highly resolved microstructural property profiles, including crystalline and amorphous phase fractions. Oxidation profiles retrieved from polyethylene cups belonging to different generations greatly differed after wear testing. The highly cross-linked polyethylene showed a lower degree of crystallinity and oxidation at an appreciably slower rate as compared to that belonging to an earlier generation.
Next-Generation Sequencing of Prostate Tumors Provides Independent Evidence of Xenotropic Murine Leukemia Virus-Related Gammaretrovirus Contamination (2011)

In 2006, xenotropic murine leukemia virus (MLV)-related gammaretrovirus (XMRV) was isolated from prostate cancer tissue ([9][1]). However, subsequent studies have yielded conflicting and controversial results, with widespread detection of XMRV suggested to be the result of contamination with mouse
A sight on the current nanoparticle-based gene delivery vectors (2014)

Nowadays, gene delivery for therapeutic objects is considered one of the most promising strategies to cure both the genetic and acquired diseases of human. The design of efficient gene delivery vectors possessing the high transfection efficiencies and low cytotoxicity is considered the major challenge for delivering a target gene to specific tissues or cells. On this base, the investigations on non-viral gene vectors with the ability to overcome physiological barriers are increasing. Among the non-viral vectors, nanoparticles showed remarkable properties regarding gene delivery such as the ability to target the specific tissue or cells, protect target gene against nuclease degradation, improve DNA stability, and increase the transformation efficiency or safety. This review attempts to represent a current nanoparticle based on its lipid, polymer, hybrid, and inorganic properties. Among them, hybrids, as efficient vectors, are utilized in gene delivery in terms of materials (synthetic or natural), design, and in vitro/in vivo transformation efficiency.
Real-World Image Super-Resolution by Exclusionary Dual-Learning (2022)

Real-world image super-resolution is a practical image restoration problem that aims to obtain high-quality images from in-the-wild input, has recently received considerable attention with regard to its tremendous application potentials. Although deep learning-based methods have achieved promising restoration quality on real-world image super-resolution datasets, they ignore the relationship between L1- and perceptual- minimization and roughly adopt auxiliary large-scale datasets for pre-training. In this paper, we discuss the image types within a corrupted image and the property of perceptual- and Euclidean- based evaluation protocols. Then we propose a method, Real-World image Super-Resolution by Exclusionary Dual-Learning (RWSR-EDL) to address the feature diversity in perceptual- and L1- based cooperative learning. Moreover, a noise-guidance data collection strategy is developed to address the training time consumption in multiple datasets optimization. When an auxiliary dataset is incorporated, RWSR-EDL achieves promising results and repulses any training time increment by adopting the noise-guidance data collection strategy. Extensive experiments show that RWSR-EDL achieves competitive performance over state-of-the-art methods on four in-the-wild image super-resolution datasets.
Optimization of an Angle-Aided Mirror Diversity Receiver for Indoor MIMO-VLC Systems (2016)

In this paper, we investigate the channel correlation problem which affects the performance of indoor multiple-input multiple-output (MIMO) visible light communication (VLC) systems. More specifically, in order to reduce the high correlation of channel matrix in MIMO-VLC intensity channel, we propose a non-imaging receiver called angle-aided mirror diversity receiver (AMDR) which utilizes not only a mirror placement but also a variation of orientation angle for the photodetector (PD) plane. Deploying a mirror helps reducing the correlation by blocking the reception of the light in one specific direction and by receiving additional light reflected in the mirror in another direction, while orienting the angle of PD plane into specific direction enables the directional reception of light. Applying a zero-forcing decorrelator at the receiver, we analyze the bit error rate (BER) performance for a 2×2 multiplexing MIMO-VLC system using a 2-dimensional geometric model. In particular, we formulate a min-max BER problem and find the optimal height of mirror and elevation angle of PD plane. Some selected numerical results validate our proposed optimal solution to our min-max BER problem and show that the BER performance of our proposed AMDR outperforms that of the previous non-imaging receivers.
The High Reactivity of Peroxiredoxin 2 with H2O2 Is Not Reflected in Its Reaction with Other Oxidants and Thiol Reagents (2007)

Peroxiredoxin 2 is a member of the mammalian peroxiredoxin family of thiol proteins that is important in antioxidant defense and redox signaling. We have examined its reactivity with various biological oxidants, in order to assess its ability to act as a direct physiological target for these species. Human erythrocyte peroxiredoxin 2 was oxidized stoichiometrically to its disulfide-bonded homodimer by hydrogen peroxide, as monitored electrophoretically under nonreducing conditions. The protein was highly susceptible to oxidation by adventitious peroxide, which could be prevented by treating buffers with low concentrations of catalase. However, this did not protect peroxiredoxin 2 against oxidation by added H(2)O(2). Experiments measuring inhibition of dimerization indicated that at pH 7.4 catalase and peroxiredoxin 2 react with hydrogen peroxide at comparable rates. A rate constant of 1.3 x 10(7) M(-1) s(-1) for the peroxiredoxin reaction was obtained from competition kinetic studies with horseradish peroxidase. This is 100-fold faster than is generally assumed. It is sufficiently high for peroxiredoxin to be a favored cellular target for hydrogen peroxide, even in competition with catalase or glutathione peroxidase. Reactions of t-butyl and cumene hydroperoxides with peroxiredoxin were also fast, but amino acid chloramines reacted much more slowly. This contrasts with other thiol compounds that react many times faster with chloramines than with hydrogen peroxide. The alkylating agent iodoacetamide also reacted extremely slowly with peroxiredoxin 2. These results demonstrate that peroxiredoxin 2 has a tertiary structure that facilitates reaction of the active site thiol with hydrogen peroxide while restricting its reactivity with other thiol reagents.
Shear-Induced Changes in Smooth HDPE Geomembrane Surface Topography (2000)

The shear strength of particulate material-“smooth” high density polyethylene (HDPE) geomembrane interfaces results predominantly from plowing and/or sliding of the particles at the interface. The relative contribution of particle sliding and plowing for a given “smooth” geomembrane surface is principally a function of the relative material hardness, the particle size and angularity, the normal stress, and the soil density. When plowing occurs, the geomembrane surface wears, resulting in altered surface roughness and changed interface strength. This paper summarizes the results of a study that quantified changes in surface roughness as a function of shearing displacement, normal stress, and soil particle shape. Increased particle angularity significantly increased both the geomembrane surface wear and the interface strength. Change in surface topography occurred relatively early in the shearing process with continued displacement inducing additional wear, but not substantially altering the surface roughness further. This study provides quantitative insight into the wear mechanisms of smooth geomembranes during interface shearing.
Galacto-oligosaccharides and bowel function (2007)

Background: Menopause induces various metabolic disorders due to the rapid decrease of the ovarian hormone estrogen. It is involved in increased risk of obesity, diabetes, dyslipidemia, and osteoporosis. The pigmented giant embryo cultivar is a promising food product for menopause-induced metabolic disorders. Objective: The effects of non-germinated and germinated Keunnunjami, a new blackish purple pigmented rice with a giant embryo, on glucose and bone metabolisms in ovariectomized rats were investigated. Design: The animals were fed with normal control diet (NC group) or control diet supplemented with either non-germinated Keunnunjami (KN group) or germinated Keunnunjami (GKN group) powder for 8 weeks. Results: The blood glucose and plasma insulin levels, adipokine concentrations, hepatic glucose-regulating enzyme activities, and bone resorption biomarker levels significantly decreased in KN and GKN groups compared to those of the control animals. Discussion: These findings illustrate that GKN group showed greater hypoglycemic activity and lower bone resorption than KN group, suggesting that germination could further improve the physiological property of Keunnunjami. Conclusion: Germinated Keunnunjami may have therapeutic potential against hyperglycemia and bone turnover imbalance caused by menopause.
EFFECT OF BUBBLES ON CELL VIABILITY IN A CIRCULAR-LUMEN ENDOTHELIALIZED MICROVASCULAR MODEL (2006)

A novel gas embolotherapy technique is being researched as a potential therapy for cancer. It involves the selective, acoustic vaporization of transvascular liquid perfluorocarbon droplets in or near a tumor, resulting in bubbles which can then stick within the tumor vasculature to occlude blood flow and “starve” the tumor. In achieving the desired outcome of ischemia of the tumor, it is hypothesized that the motion of bubbles within the vasculature would result in collateral endothelial cell injury and apoptosis, the extent of which being dependent on the bubble size and flow rate. A microvessel model has been designed for acoustic vaporization experiments as well as bubble flow experiments to investigate the above-mentioned hypothesis. The specific aim in the current work is to utilize the microvessel model in preliminary studies of the effects of bubble motion on endothelial cell injury and apoptosis. In a novel method of fabricating a microfluidic endothelialized model of a microvessel, a thin wire (diameter 50 to 200 micrometers, matching the desired microchannel dimension) threaded through a rectangular PVC mold was tightened into a straight line on a positioning device. The wire was sheathed in thin syringe needles inserted at both ends of the mold which was filled with a liquid elastomer, poly(dimethylsiloxane) (PDMS). After the PDMS was cured completely, the wire and syringe needles were extracted longitudinally from the cured PDMS, leaving a microchannel (due to the wire) and its inlet/outlet (due to the syringe needles). The microchannel was endothelialized at a density higher than 1x10E5 cells/cm 2 and maintained in an incubator with infusion of culture medium via a syringe pump. Air and PFC bubbles of different sizes were introduced into the microvessel model and moved at different flow rates. The viability of the cells within the microchannel was assessed with standard fluorescent microscopy and morphology studies. Our microvessel model has a circular lumen, optical clarity, gas permeability and is non-toxic to cells. The method of fabrication is also relatively simple and economical. The microchannel was successfully endothelialized, with >90% of the cells appearing viable in the assays, and the different parameters involved in optimal endothelialization of the microchannel were investigated. The effects of cell seeding parameters on cell viability, as well as preliminary findings regarding the effects of bubble size and speed, will be discussed. Ongoing work is aimed at quantifying the effects of bubble propagation and possible mechanisms of bioeffects.
Catalytic Asymmetric Conjugate Addition of Thiols to α,β‐Unsaturated Thioamides: Expeditious Access to Enantioenriched 1,5‐Benzothiazepines (2012)

Softly does it: The title reaction proceeded under proton transfer conditions with a catalyst prepared from commercially available reagents to afford the desired product in high enantioselectivity. The reaction was compatible with a free amino group, thus allowing for expeditious access to enantiomerically enriched 1,5-benzothiazepines, which are important chemical entities in medicinal chemistry.
Gas Generation and Accumulation in the West Siberian Basin (1999)

We appreciate the discussion by Murris (2001) and take the opportunity to clarify some of his objections and discuss some of the still open questions in more detail. Murris's main objections to the conclusions of Littke et al. (1999) concern, first, the influence of overpressure in the Lower Cretaceous and Upper Jurassic on hydrocarbon distribution and, second, the model of gas release by exsolution (degassing) from deep ground water as the main mechanism for accumulating the huge gas fields of northern West Siberia.

The first objective of Murris's discussion is how the overpressure in Jurassic strata might have influenced the distribution of hydrocarbons in the overlying Cretaceous sediments. Two crucial points regarding this question are the reason and timing of overpressuring and its influence on hydrocarbon movement.

We agree with Murris that the effect of compaction disequilibrium is not sufficient to explain the extent of overpressure in the Urengoy area and that hydrocarbon generation in the Bazhenov Formation has contributed to the buildup of overpressure. Two-dimensional basin modeling along a seismic line through the Urengoy field, however, showed that hydrocarbon generation in Jurassic source rocks (Bazhenov and the Tyumen formations) did only generate sufficient overpressure to explain the recent situation if the models were laterally completely sealed. This sealing appears to be highly unlikely. Furthermore, hydrocarbon generation ceased during the Miocene, when the tectonic movement started to lift the source rocks into shallower depths, where lower temperatures were reached. Thus, any overpressure caused by petroleum generation must have been preserved over a period of about 5-20 m.y. In addition, the overpressure is not restricted to the Jurassic Bazhenov Formation but extends into the Cretaceous, including the Achimov sands.

Uplift might have contributed to the overpressure, however. Maximum pore pressure from the stage of deepest burial might have …
Design and Implementation of an Autonomous Electric Vehicle for Self-Driving Control under GNSS-Denied Environments (2021)

In this study, the hardware and software design and implementation of an autonomous electric vehicle are addressed. We aimed to develop an autonomous electric vehicle for path tracking. Control and navigation algorithms are developed and implemented. The vehicle is able to perform path-tracking maneuvers under environments in which the positioning signals from the Global Navigation Satellite System (GNSS) are not accessible. The proposed control approach uses a modified constrained input-output nonlinear model predictive controller (NMPC) for path-tracking control. The proposed localization algorithm used in this study guarantees almost accurate position estimation under GNSS-denied environments. We discuss the procedure for designing the vehicle hardware, electronic drivers, communication architecture, localization algorithm, and controller architecture. The system’s full state is estimated by fusing visual inertial odometry (VIO) measurements with wheel odometry data using an extended Kalman filter (EKF). Simulation and real-time experiments are performed. The obtained results demonstrate that our designed autonomous vehicle is capable of performing path-tracking maneuvers without using Global Navigation Satellite System positioning data. The designed vehicle can perform challenging path-tracking maneuvers with a speed of up to 1 m per second.
Calpain inhibitor AK295 protects neurons from focal brain ischemia. Effects of postocclusion intra-arterial administration. (1994)

These data provide the first evidence that a peripherally administered calpain inhibitor can protect against ischemic brain damage. They offer further support for an important role of calpain proteolysis in the brain degeneration associated with cerebral ischemic events and suggest that selective calpain inhibitors provide a rational, novel, and viable means of treating such neurodegenerative problems.
Renal reabsorption in 3D vascularized proximal tubule models (2019)

Three-dimensional renal tissues that emulate the cellular composition, geometry, and function of native kidney tissue would enable fundamental studies of filtration and reabsorption. Here, we have created 3D vascularized proximal tubule models composed of adjacent conduits that are lined with confluent epithelium and endothelium, embedded in a permeable ECM, and independently addressed using a closed-loop perfusion system to investigate renal reabsorption. Our 3D kidney tissue allows for coculture of proximal tubule epithelium and vascular endothelium that exhibits active reabsorption via tubular-vascular exchange of solutes akin to native kidney tissue. Using this model, both albumin uptake and glucose reabsorption are quantified as a function of time. Epithelium-endothelium cross-talk is further studied by exposing proximal tubule cells to hyperglycemic conditions and monitoring endothelial cell dysfunction. This diseased state can be rescued by administering a glucose transport inhibitor. Our 3D kidney tissue provides a platform for in vitro studies of kidney function, disease modeling, and pharmacology.
Total Synthesis of Calyculin C (1998)

The study of phosphatases continues to flourish given their prominence in signal transduction pathways and the regulation of cell function. Our research efforts in this area focus on the potent inhibition of serine/threonine phosphatases, PP1 and PP2A, by a structurally diverse class of natural products. We herein report the completed total synthesis of the serine/threonine phosphatase inhibitor calyculin C (1) as part of an ongoing effort to elucidate key structural requirements for phosphatase inhibition by the aforementioned diverse class of natural products. Synthetic issues addressed include (1) the remote protecting group effect on Brown crotylboration diastereoselectivity during the introduction of the C10−C11 stereocenters and (2) the formation of the C25−C26 double bond using a fully deprotected C26−C37 phosphonium salt (3). In addition, the concurrent synthesis of 34R-calyculin C (29) clarified our previous C34-stereochemical assignment of C26−C37 phosphonium salts (3 and 27) (Ogawa, A. K.; DeMattei, J. A.; Scarlato, G. R.; Tellew, J. E.; Chong, L. S.; Armstrong, R. W. J. Org. Chem. 1996, 61, 6153).
CuBr Catalyzed C–N cross coupling reaction of purines and diaryliodonium salts to 9-arylpurines (2011)

CuBr was found to be an efficient catalyst for the C-N cross coupling reaction of purine and diaryliodonium salts. 9-Arylpurines were synthesized in excellent yields with short reaction times (2.5 h). The method represents an alternative to the synthesis of 9-arylpurines via Cu(II) catalyzed C-N coupling reaction with arylboronic acids as arylating agents.
SU‐FF‐T‐163: Development of An Inverse Optimization Package for Non‐Uniform Dose Distribution Based On Spatially Inhomogeneous Radiosensitivity (2006)

Purpose: To develop an inverse optimization algorithm that is capable of generating non‐uniform dose distribution with sub‐regional dose escalation based on spatially inhomogeneous radiosensitivity in the target, while keeping the critical structure doses as low as possible. Method and Materials: A matlab package with GUI was developed. The software system reads in structure contours, reference 3D‐dose distribution (e.g., conventional uniform dose), dose to each voxel from all beamlets, as well as the voxel radiosensitivity from biological images. This system is able to optimize beamlet weights based on sequential quadratic programming (SQP) method to achieve maximum equivalent uniform dose (EUD) for target and minimum EUD for critical structures. The beamlets were generated using a commercial planning system (XiO, CMS). The EUD was calculated based on 3D‐dose distribution and spatial radiosensitivity distribution which is extracted from biological images. Constraints that limit the doses to critical structures not to exceed the corresponding maximum for the reference plan are applied. Sample spatial radiosensitivity distributions based on physiological MRI of brain tumor were used to test the developed system. DVHs and EUDs for the uniform and non‐uniform dose distributions are compared. Results: Using the newly develop system, we have generated non‐uniform 3D‐dose distributions for selected patient cases. Sub‐regional dose escalation can be as high as 30% of the uniform dose as planned conventionally. The target EUDs are found to be higher than those for the uniform dose planned ignoring the spatial inhomogeneous radiosensitivity. The EUDs for organs at risk are found to be equal or lower than those for the uniform dose plans. Conclusion: We have developed a package that is capable of generating non‐uniform dose distributions optimized for spatially inhomogeneous radiosensitivity. Sub‐regional dose escalation may lead to increased treatment effectiveness as indicated by higher EUDs. The current development will impact biological image guided radiotherapy.
Functionalization and Isoreticulation in a Series of Metal–Organic Frameworks Derived from Pyridinecarboxylates (2016)

The partially fluorinated metal-organic frameworks (F-MOFs) have been constructed from 3-fluoro-4-pyridinecarboxylic acid and trans-3-fluoro-4-pyridineacrylic acid linkers using Mn(2+), Co(2+), and Cd(2+) metals via the solvothermal method, which show isostructural isomerism with their nonfluorinated counterparts synthesized using 4-pyridinecarboxylic acid and trans-4-pyridineacrylic acid, respectively. The simultaneous effect of partial fluorination and isoreticulation on structure and H2 adsorption has been studied systematically in isostructural nonfluorinated and partially fluorinated MOFs, which shows that the increment in the hydrogen uptake properties in F-MOFs is not a universal phenomenon but is rather system-specific and changes from one system to another.
Lattice QCD with 0, 2 and 4 quark flavors (1997)

We have done simulations of lattice QCD with different numbers of light dynamical quarks. Since we cannot reach the continuum limit with our current computers, we have done comparisons with 0 (quenched), 2 and 4 light quark flavors with the physical volume and lattice spacing constant, when these are determined from the mass of the rho. We find a 7% (2 standard deviation) difference in the nucleon to rho mass ratio for 2 and 4 quarks. More importantly, the effects of chiral symmetry breaking are dramatically decreased for the case of 4 light quarks.
Optical Coherence Tomography Longitudinal Evaluation of Retinal Nerve Fiber Layer Thickness in Glaucoma (2005)

A greater likelihood of glaucomatous progression was identified by OCT vs automated perimetry. This might reflect OCT hypersensitivity or true damage identified by OCT before detection by conventional methods.