gebhart/patrepeval huggingface dataset:
Free Radical Trapping as a Therapeutic Approach to Neuroprotection in Stroke: Experimental and Clinical Studies with NXY-059 and Free Radical Scavengers (2005)

There is substantial experimental evidence that free radicals are produced in the brain during ischemia, during reperfusion and during intracranial hemorrhage. Removal of pathologically produced free radicals is therefore a viable approach to neuroprotection. Four compounds with free radical scavenging activity (tirilazad, ebselen, edaravone) or free radical trapping properties (NXY-059) have been examined in experimental models of stroke and evaluated clinically as neuroprotective agents. Both experimental and clinical results are reviewed in this article. Ebselen was a modestly effective neuroprotectant in a rat transient middle cerebral artery occlusion (MCAO) model when given before the start of ischemia, but not when the insult was severe. Data from the permanent MCAO model and an embolic stroke model suggested a bell shaped dose-response curve. The weak preclinical profile may explain the lack of success in clinical trials. Preclinical data on tirilazad in animal models of acute ischemic stroke are neither comprehensive nor consistent. There was little evidence of efficacy in permanent MCAO or when the drug was given several hours post-occlusion. This may explain the negative clinical trials as these did not target patients likely to reperfuse and treatment started several hours after stroke onset. While preclinical data on subarachnoid hemorrhage demonstrated an attenuation of vasospasm the clinical data were inconsistent. There is very limited published preclinical data on edaravone but it has been approved in Japan as a neuroprotectant for the treatment of stroke. Evidence is based on a single placebo controlled trial in a relatively small number of patients. The status of possible development of edaravone outside of Japan is not known. NXY-059 has been found to be a very effective agent in transient and permanent MCAO and thromboembolic models of acute ischemic stroke. Its preclinical development has been governed by adherence with the recommendations of the Stroke Therapy Academic Industry Roundtable (STAIR) group and is now being investigated in Phase III clinical trials using a therapeutic time window and plasma concentrations that are effective in rat and primate models of stroke.
Anomalous Effects in Deuterated Systems. (1996)

Abstract : Excess power was measured in 28 out of 94 electrochemical experiments conducted using palladium or palladium alloy cathodes in heavy water. Reproducibility continues to be the major problem in this controversial research area. Based on our experiments, this lack of reproducibility stems from unknown variables in the palladium metal. The best reproducibility for excess power was obtained using palladium boron materials supplied by the Naval Research Laboratory. Our basic isoperibolic calorimeters were capable of measuring excess power with a sensitivity of +/- 1% of the input power or +/- 20 mW, whichever was larger. Calorimeters that are capable of detecting excess power levels of 1 watt per cubic centimeter of palladium are essential for research in this field. Results from our laboratory indicate that helium-4 is the missing nuclear product accompanying the excess heat. Thirty out of 33 experiments showed a correlation between either excess power and helium production or no excess power and no excess helium. The collection of the electrolysis gases in both glass and metal flasks place the helium-4 production rate at 10(exp 11) to 10(exp 12) atoms per second per watt of excess power. This is the correct magnitude for typical deuteron fusion reactions that yield helium-4 as a product. Anomalous radiation was detected in some experiments by the use of X-ray films, Geiger-Mueller counters, and by the use of sodium iodide detectors. There was never any significant production of tritium in any of our experiments.
Transgenic mice with muscle-specific insulin resistance develop increased adiposity, impaired glucose tolerance, and dyslipidemia. (1996)

Impaired skeletal muscle insulin receptor function is a feature of common forms of insulin resistance, including obesity and noninsulin-dependent diabetes mellitus. However, the extent to which this defect accounts for impaired muscle glucose disposal or altered in vivo glucose homeostasis remains to be established. We recently showed that transgenic mice that overexpress dominant-negative insulin receptors specifically in striated muscle have a severe defect in muscle insulin receptor-mediated signaling and modest hyperinsulinemia. Here we performed hindlimb perfusion studies to determine the impact of this defect on muscle glucose uptake and metabolism. Maximal rates of insulin-stimulated muscle 3-O-methylglucose transport were reduced by 32-40% in transgenic mice with proportional defects involving total hindlimb [14C]glucose uptake, lactate production, and muscle glycogen synthesis. To address the hypothesis that muscle insulin resistance could promote an increase in the accretion of body fat, carcass analysis was performed using two independent lines of transgenic mice. Although body weights were normal, transgenic mice had a 22-38% increase in body fat, with a reciprocal decrease (10-15%) in body protein. Mean gonadal fat pad weight was also increased in transgenic mice. Skeletal muscle histology and fiber type distribution were not affected. To determine whether muscle-specific insulin resistance was sufficient to cause impaired glucose tolerance, oral glucose tolerance tests were performed with 6-month-old transgenic and control mice. Fasting glucose levels were increased by 25%, and peak values were 22-40% higher in transgenic mice. Transgenic mice also had a 37% decrease in plasma lactate levels and modest increases in levels of plasma triglycerides and FFA (29% and 15%, respectively). We conclude that 1) severe defects in muscle insulin receptor function result in impaired insulin-stimulated glucose uptake and metabolism in this tissue; 2) muscle-specific insulin resistance can contribute to the development of obesity; and 3) a "pure" defect in insulin-mediated muscle glucose disposal is sufficient to result in impaired glucose tolerance and other features of the insulin resistance syndrome, including hyperinsulinemia and dyslipidemia.
Adaptation of a wheel loader automatic bucket filling neural network using reinforcement learning (2020)

Bucket-filling is a repetitive task in earth-moving operations with wheel-loaders, which needs to be automated to enable efficient remote control and autonomous operation. Ideally, an automated bucket-filling solution should work for different machine-pile environments, with a minimum of manual retraining. It has been shown that for a given machine-pile environment, a time-delay neural network can efficiently fill the bucket after imitation-based learning from 100 examples by one expert operator. Can such a bucket-filling network be automatically adapted to different machine-pile environments without further imitation learning by optimization of a utility or reward function? This paper investigates the use of a deterministic actor-critic reinforcement learning algorithm for automatic adaptation of a neural network in a new pile environment. The algorithm is used to automatically adapt a bucket-filling network for medium coarse gravel to a cobble-gravel pile environment. The experiments presented are performed with a Volvo L180H wheel-loader in a real-world setting. We found that the bucket-weights in the novel pile environment can improve by five to ten percent within one hour of reinforcement learning with less than 40 bucket-filling trials. This result was obtained after investigating two different reward functions motivated by domain knowledge.
[Dimethylsulfide emission in Qingdao near-shore waters and atmospheric dimethylsulfide concentration variation]. (2004)

To investigate the emission of dimethylsulfide in near-shore waters seriously disturbed by human activities in China, using the solid absorption-desorption and cryogenic preconcentration method, sampling and analysis of seawater and atmospheric DMS in Qingdao near-shore waters were carried out during 2001-2002. The results showed that the spatial distribution and seasonal variation of seawater DMS concentrations and sea-air fluxes were evident. In summer, the average of seawater DMS concentrations was highest, amounting to 1169.47 ng x L(-1) and lowest in spring, only 226.99 ng x L(-1). The obvious concentration gradient in estuarine, landscape and Olympic Game areas were observed in summer, but in spring and autumn is not so evident. Sea-air flux of DMS was mainly determined by seawater concentration, therefore the sea-air flux coincided with seawater concentration. Average atmospheric DMS concentration was higher in the summer (256.44 ng x m(-3)) and lower in the autumn (195.64 ng x m(-3)). The diurnal variation of atmospheric DMS was discussed in paper.
Connecting the innate and adaptive immune responses in mouse choroidal neovascularization via the anaphylatoxin C5a and γδT-cells (2016)

Neovascular age-related macular degeneration (AMD) is characterized by choroidal neovascularization (CNV). An overactive complement system is associated with AMD pathogenesis, and serum pro-inflammatory cytokines, including IL-17, are elevated in AMD patients. IL-17 is produced by complement C5a-receptor-expressing T-cells. In murine CNV, infiltrating γδT- rather than Th17-cells produce the IL-17 measurable in lesioned eyes. Here we asked whether C5a generated locally in response to CNV recruits IL-17-producing T-cells to the eye. CNV lesions were generated using laser photocoagulation and quantified by imaging; T-lymphocytes were characterized by QRT-PCR. CNV resulted in an increase in splenic IL-17-producing γδT- and Th17-cells; yet in the CNV eye, only elevated levels of γδT-cells were observed. Systemic administration of anti-C5- or anti-C5a-blocking antibodies blunted the CNV-induced production of splenic Th17- and γδT-cells, reduced CNV size and eliminated ocular γδT-cell infiltration. In ARPE-19 cell monolayers, IL-17 triggered a pro-inflammatory state; and splenocyte proliferation was elevated in response to ocular proteins. Thus, we demonstrated that CNV lesions trigger a systemic immune response, augmenting local ocular inflammation via the infiltration of IL-17-producing γδT-cells, which are presumably recruited to the eye in a C5a-dependent manner. Understanding the complexity of complement-mediated pathological mechanisms will aid in the development of an AMD treatment.
Ultrasensitive Mass Sensing with a Nanotube Electromechanical Resonator (2008)

Shrinking mechanical resonators to submicrometer dimensions (approximately 100 nm) has tremendously improved capabilities in sensing applications. In this Letter, we go further in size reduction using a 1 nm diameter carbon nanotube as a mechanical resonator for mass sensing. The performances, which are tested by measuring the mass of evaporated chromium atoms, are exceptional. The mass responsivity is measured to be 11 Hz x yg(-1) and the mass resolution is 25 zg at room temperature (1 yg = 10(-24) g and 1 zg = 10(-21) g). By cooling the nanotube down to 5 K in a cryostat, the signal for the detection of mechanical vibrations is improved and corresponds to a resolution of 1.4 zg.
Enantioselective Construction of Highly Functionalized Indoloquinolizines—congeners to Polycyclic Indole Alkaloids (1997)

Abstract Indolo[2,3‐ a ]quinolizines have been prepared in enantiomerically pure form by a very short and efficient synthetic sequence consisting of a) formation of imines of tryptophan esters, b) their enantioselective reaction with substituted silyloxydienes mediated by a chiral or an achiral boron Lewis acid, and c) subsequent ring closure initiated by conversion of the generated vinylogous amides into vinylogous imidoyl chlorides. With this strategy various substituents can be incorporated directly into the 1‐position of the heterocyclic framework of complex indole alkaloids by the choice of an appropriate silyloxydiene, so that subsequent derivatization of the alkaloid precursor at this position is rendered unnecessary.
4D Traction Force Microscopy Reveals Asymmetric Cortical Forces in Migrating <i>Dictyostelium</i> Cells (2010)

We present a 4D (x; y; z; t) force map of Dictyostelium cells crawling on a soft gel substrate. Vertical forces are of the same order as the tangential ones. The cells pull the substratum upward along the cell, medium, or substratum contact line and push it downward under the cell except for the pseudopods. We demonstrate quantitatively that the variations in the asymmetry in cortical forces correlates with the variations of the direction and speed of cell displacement.
Beyond breast density: a review on the advancing role of parenchymal texture analysis in breast cancer risk assessment (2016)

The objective is to provide a comprehensive reference for researchers in the field of parenchymal pattern analysis in breast cancer risk assessment, while indicating key directions for future research.
Atomic-Level Models of the Bacterial Carboxysome Shell (2008)

The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.
Mapping and Identification of GABAergic Neurons in Transgenic Mice Projecting to Cardiac Vagal Neurons in the Nucleus Ambiguus Using Photo-Uncaging (2009)

The neural control of heart rate is determined primarily by the activity of preganglionic parasympathetic cardiac vagal neurons (CVNs) originating in the nucleus ambiguus (NA) in the brain stem. GABAergic inputs to CVNs play an essential role in determining the activity of these neurons including a robust inhibition during each inspiratory burst. The origin of GABAergic innervation has yet to be determined however. A transgenic mouse line expressing green florescent protein (GFP) in GABAergic cells was used in conjunction with caged glutamate to identify both clusters and individual GABAergic neurons that evoke inhibitory GABAergic synaptic responses in CVNs. Transverse slices were taken with CVNs patch-clamped in the whole cell configuration. Sections containing both the pre-Botzinger complex as well as the calamus scriptorius were divided into approximately 90 quadrants, each 200 x 200 microm and were sequentially photostimulated. Inhibitory post synaptic currents (IPSCs) were recorded in CVNs after a 5-ms photostimulation of 50 microM caged glutamate. The four areas that contained GABAergic cells projecting to CVNs were 200 microm medial, 400 microm medial, 200 microm ventral, and 1,200 microm dorsal and 1,000 microm medial to patched CVNs. Once foci of GABAergic cells projecting to CVNs were determined, photostimulation of individual GABAergic neurons was conducted. The results from this study suggest that GABAergic cells located in four specific areas project to CVNs, and that these cells can be individually identified and stimulated using photouncaging to recruit GABAergic neurotransmission to CVNs.
Glycogen synthase kinase-3 as drug target: From wallflower to center of attention (2003)

Some 20 years ago, glycogen synthase kinase-3 (GSK-3) was categorized as one of several protein kinases that could phosphorylate glycogen synthase and regulate the glucose metabolism pathway. Today, GSK-3 is being identified as a ubiquitous serine/threonine protein kinase that participates in a multitude of cellular processes, ranging from cell membrane-to-nucleus signaling, gene transcription, translation, cytoskeletal organization to cell cycle progression and survival. Two functional aspects make GSK-3 a peculiar kinase: its activity is constitutive and downregulated after cell activation by phosphorylation or interaction with inhibitory proteins, and the enzyme prefers substrates that are specifically prepared, that is prephosphorylated, by other kinases. Its pleiotropic but unique activities have made GSK-3 a much sought-after target for the treatment of prevalent human diseases such as type 2 diabetes and Alzheimer's disease. Recent drug discovery efforts have identified small-molecule, orally active inhibitors of GSK-3. This accomplishment may represent the first step toward the development of novel therapeutic agents.
Using a neural-fuzzy approach for improving the perpendicular magnetic recording head manufacturing process (2010)

Magnetic write width targeting is a critical process in achieving high process yield and good quality in manufacturing perpendicular magnetic recording heads for hard disk drives. The current approach is an experimentally based feedback process in which the quality is highly dependent on the testing accuracy and the sensitivity assumptions. This paper proposes a new approach based on neural-fuzzy based modelling for improving the quality of the magnetic write width targeting. The model consists of a neural network for: 1) suggesting changes in the lapping parameters, together with a fuzzy reasoning mechanism; 2) obtaining fine-tuned lapping parameter values based on the parameters derived from the neural network. Through improvement in the magnetic write width targeting process, the overall process yield, and product quality can be improved and the overall cost of the magnetic recording heads will be significantly reduced.
Exploiting Social Networks for Large-Scale Human Behavior Modeling (2011)

The Cooperative Communities (CoCo) learning framework leverages everyday social connections between people to personalize classification models. By exploiting social networks, CoCo spreads the burden of providing training data over an entire community.
Stress compensation and noise reduction algorithms for robust speech recognition (2003)

The problem of speech recognition in noisy, stressful environments is addressed. The main contribution is the achievement of robust recognition in diverse environmental conditions through the formulation of a series of speech-enhancement and stress-compensation preprocessing algorithms. These preprocessors produce speech or recognition features less sensitive to varying factors caused by stress and noise. Results from four recognition scenarios based on such preprocessing are reported. Neutral, stressful, noisy neutral, and noisy stressful speech styles are considered. Noise reduction is based on constrained iterative speech enhancement. Stress compensation algorithms are based on formant location, bandwidth, and intensity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
AUTOMATED BLUR DETECTION AND REMOVAL IN AIRBORNE IMAGING SYSTEMS USING IMU DATA (2012)

Abstract. Images acquired by airborne sensors exhibit blur due to turbulent motion experienced by the aircraft. Significant amount of blur renders the images unusable for subsequent visual/automated analysis, requiring a re-flight. This necessitates quantifying the amount of blur in an image. Most approaches to blur quantification use image based methods to estimate the MTF (Modular Transfer Function) that indicates the amount of blur. Their limitations are – (1) MTF calculation requires presence of straight edges in the image scene, which may not always be available, (2) Due to the absence of an ideal edge, the amount of blur estimated is relative, and (3) It is computationally expensive and therefore may not be practical for blur detection in real time applications. Our solution uses the sensor motion as measured by an Inertial Measurement Unit (IMU) mounted in the camera system to calculate the motion experienced by the aircraft and the sensor during the time the shutter was actually open. This motion information together with the blur detection algorithm presented in this paper can provide an accurate quantification of blur in pixel units. Once we identify the images that exceed a given blur threshold, we use a blur removal algorithm that uses the IMU data and a natural image prior to compute per-pixel, spatially-varying blur, and then de-convolves an image to produce de-blurred images. The presented blur detection and removal methods are currently being used offline to quantify and remove the blur from images acquired by the UltraCam systems within the Global Ortho Program (Walcher, 2012), which generates ortho imagery for all of the continental US as well as Western Europe, from over 2.5 million images. Furthermore, the blur detection method will be incorporated in the camera software of all our operational and forthcoming UltraCam imaging systems for real-time blur quantification.
Stroke Controllable Fast Style Transfer with Adaptive Receptive Fields (2018)

The Fast Style Transfer methods have been recently proposed to transfer a photograph to an artistic style in real-time. This task involves controlling the stroke size in the stylized results, which remains an open challenge. In this paper, we present a stroke controllable style transfer network that can achieve continuous and spatial stroke size control. By analyzing the factors that influence the stroke size, we propose to explicitly account for the receptive field and the style image scales. We propose a StrokePyramid module to endow the network with adaptive receptive fields, and two training strategies to achieve faster convergence and augment new stroke sizes upon a trained model respectively. By combining the proposed runtime control strategies, our network can achieve continuous changes in stroke sizes and produce distinct stroke sizes in different spatial regions within the same output image.
QASMBench: A Low-Level Quantum Benchmark Suite for NISQ Evaluation and Simulation (2022)

The rapid development of quantum computing (QC) in the NISQ era urgently demands a low-level benchmark suite and insightful evaluation metrics for characterizing the properties of prototype NISQ devices, the efficiency of QC programming compilers, schedulers and assemblers, and the capability of quantum system simulators in a classical computer. In this work, we fill this gap by proposing a low-level, easy-to-use benchmark suite called QASMBench based on the OpenQASM assembly representation. It consolidates commonly used quantum routines and kernels from a variety of domains including chemistry, simulation, linear algebra, searching, optimization, arithmetic, machine learning, fault tolerance, cryptography, and so on, trading-off between generality and usability. To analyze these kernels in terms of NISQ device execution, in addition to circuit width and depth, we propose four circuit metrics including gate density, retention lifespan, measurement density, and entanglement variance, to extract more insights about the execution efficiency, the susceptibility to NISQ error, and the potential gain from machine-specific optimizations. Applications in QASMBench can be launched and verified on several NISQ platforms, including IBM-Q, Rigetti, IonQ and Quantinuum. For evaluation, we measure the execution fidelity of a subset of QASMBench applications on 12 IBM-Q machines through density matrix state tomography, comprising 25K circuit evaluations. We also compare the fidelity of executions among the IBM-Q machines, the IonQ QPU and the Rigetti Aspen M-1 system. QASMBench is released at: http://github.com/pnnl/QASMBench .