gebhart/patrepeval huggingface dataset:
Abstract LB-457: Multiplexing protein and DNA biomarkers on a single analytical platform (2012)

Abstract We have recently developed a non-invasive assay that combines protein and DNA biomarkers for triaging bladder cancer patients and demonstrated that this multi-analyte approach improves clinical performance. This assay combines detection in urine of Matrix Metalloproteinase-2 (MMP-2) protein, hypermethylation of two DNA markers (Twist1 and Nid2) and mutation detection of the FGFR3 gene. To eliminate the need to perform separate analytical procedures for protein and DNA, and to decrease assay complexity and cost while increasing assay throughput, we are now developing a method for simultaneous detection of protein and DNA biomarkers on a qPCR platform. To this end, we have identified and characterized six DNA aptamers that specifically bind Matrix Metalloprteinase-2 (MMP-2). DNA aptamers are single stranded DNA oligos that can bind specifically to their target molecules, including proteins. Once bound to the protein, these aptamers can then be used as templates for quantitative PCR-mediated protein detection. We have developed qPCR assays for each of the six MMP-2-specific aptamers, and demonstrate detection limits for each aptamer as low as 5x102 copies. Kinetic and equilibrium analysis was used to determine the KD constant for the aptamers. High affinity interactions were observed for all aptamers, with two aptamers having the highest affinity and calculated KD values of 15 and 10nM. Using one of these aptamers, we bound MMP-2 protein to the aptamer in solution and then immunoprecipitated the protein/aptamer complexes using biotin-labeled MMP-2-specific antibodies. Immunoprecipitated complexes were then quantitated using the aptamer-specific qPCR assay. In this study, we show that by qPCR, we can efficiently detect 10-12 mol/L of MMP-2 using the aptamer as the detection molecule. This level of MMP-2 protein detection is equivalent to commercially available ELISA assays. To further improve performance and to take advantage of the known specificity of aptamers, we intend to develop a system that uses one aptamer for detection and a second biotin-labeled aptamer for immunoprecipitation. We subsequently demonstrate the ability to multiplex the aptamer qPCR assay with our qPCR assay for FGFR3 and intend to add the other DNA markers into this multiplex system in the future. This is the first demonstration of simultaneous detection of protein and DNA biomarkers using a single analytical platform. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-457. doi:1538-7445.AM2012-LB-457
Autonome Entdeckung in den chemischen Wissenschaften, Teil I: Fortschritt (2019)

Abstract In dem zweiteiligen Aufsatz wird der Beitrag von Automation zu verschiedenen Aspekten der chemischen Entdeckung untersucht. In Teil 1 definieren wir die Arten von Entdeckung in den chemischen Wissenschaften – Entdeckung von Materie (Molekülen, Materialien, Gegenständen), Entdeckung von Prozessen und Entdeckung von Modellen – und beschreiben ihre Vereinheitlichung als Suchproblem. Anschließend formulieren wir eine Reihe von Fragen, die für die Bewertung des Autonomiegrads einer Entdeckung relevant sind. Den Abschluss bilden zahlreiche Fallstudien in den Bereichen Synthesechemie, Wirkstoffentdeckung, anorganische Chemie und Materialwissenschaften, bei denen Entdeckungen durch Rechenunterstützung und Automation beschleunigt oder erst ermöglicht werden. Die Studien machen deutlich, wie die rasanten Entwicklungen in der Hardware‐Automation und im maschinellen Lernen unaufhörlich die Art der experimentellen Forschung und der Modellierung verändern. Im zweiten Teil werden anhand der Fallstudien die noch ungelösten Aufgaben auf dem Gebiet benannt und diskutiert.
Numerical Investigation of Linear Low-Pressure Turbine Cascade with Periodic Unsteadiness Generating Device (2020)

Front-loaded high-lift low-pressure turbine blade airfoils, such as the L2F by the Air Force Research Laboratory at Wright-Patterson Air Force Base, promise overall efficiency gains and weight reductions. However, compared to more conventional designs, the endwall losses are increased. The increased losses were partially traced back to a stronger passage vortex. This has prompted wind tunnel experiments at the Air Force Research Laboratory aimed at understanding the unsteady wake effect on the coherence of the passage vortex. In the experiments, a periodic unsteadiness generating device was employed to introduce unsteady wakes. Implicit large-eddy simulations for a chord Reynolds number of 50,000 were carried out in support of the experiments to obtain additional insight into the unsteady wake effect on the passage vortex dynamics. Visualizations of the phase-averaged periodic wakes obtained from the experiments and simulations are in reasonable agreement with each other. The unsteady wakes were found to intermittently reduce the coherence of the passage vortex and suppress the laminar separation from the blade suction surface. The time-averaged flow field reveals a weakened passage vortex compared to the uncontrolled flow.
Observation of Unidirectional Bound States in the Continuum Enabled by Topological Defects (2019)

Unidirectional radiation is important for a variety of optoelectronic applications. Many unidirectional emitters exist, but they all rely on the use of materials or structures that forbid outgoing waves, i.e. mirrors. Here, we theoretically propose and experimentally demonstrate a class of resonances in photonic crystal slabs, which only radiate towards a single side with no mirror placed on the other side - we call them ``unidirectional bound states in the continuum". These resonances are found to emerge when a pair of half-integer topological charges in the polarization field bounce into each other in the momentum space. We experimentally demonstrate such resonances in the telecommunication regime, where we achieve single-sided quality factor as high as 1.6e5, equivalent to a radiation asymmetry ratio of 27.7 dB. Our work represents a vivid example of applying topological principles to improve optoelectronic devices. Possible applications of our work include grating couplers, photoniccrystal surface-emitting lasers, and antennas for light detection and ranging.
Machine learning prediction of atrial fibrillation in cardiovascular patients using cardiac magnetic resonance and electronic health information (2022)

Using phenotypic data available at time of CMR imaging we developed and validated the first described risk model for the prediction of new-onset AF in patients with cardiovascular disease. Complementary value was provided by variables from patient-reported measures of health and the electronic health record, illustrating the value of multi-domain phenotypic data for the prediction of AF.
Zn2+–Imidazole Coordination Crosslinks for Elastic Polymeric Binders in High‐Capacity Silicon Electrodes (2021)

Recent research has built a consensus that the binder plays a key role in the performance of high-capacity silicon anodes in lithium-ion batteries. These anodes necessitate the use of a binder to maintain the electrode integrity during the immense volume change of silicon during cycling. Here, Zn<sup>2+</sup>-imidazole coordination crosslinks that are formed to carboxymethyl cellulose backbones in situ during electrode fabrication are reported. The recoverable nature of Zn<sup>2+</sup>-imidazole coordination bonds and the flexibility of the poly(ethylene glycol) chains are jointly responsible for the high elasticity of the binder network. The high elasticity tightens interparticle contacts and sustains the electrode integrity, both of which are beneficial for long-term cyclability. These electrodes, with their commercial levels of areal capacities, exhibit superior cycle life in full-cells paired with LiNi<sub>0.8</sub>Co<sub>0.15</sub>Al<sub>0.05</sub>O<sub>2</sub> cathodes. The present study underlines the importance of highly reversible metal ion-ligand coordination chemistries for binders intended for high capacity alloying-based electrodes.
Thermal power plane enabling dual-side electrical interconnects for high-performance chip stacks: Concept (2014)

In this paper, a novel concept of dual-side electrical interconnects (EIC) to a chip stack is discussed. In this concept, a second laminate, called Thermal Power Plane (TPP), is attached through solder rails to the top chip of the stack. The TPP provides efficient heat removal and current feed in the out-of-plane and the in-plane direction, respectively. Accordingly, the number of electrical interconnects to the chip stack can be doubled, enabling higher off-stack communication. An interconnect count analysis was performed for a two-die stack with cores in the top and cache in the bottom chip. The power to the top and the bottom chip is provided from the TPP and the bottom laminate, respectively. In this case, all power through-silicon vias (TSVs) can be eliminated, which would otherwise cover 3.3% of the bottom chip area. In addition, the design of the TSVs can be optimized for signaling only. The use of two laminates also enables individual test & burn-in of the dies prior to stack formation, potentially improving the yield by joining only known good dies. The feasibility of the concept is supported by thermal and electrical finite-element analysis. An 8-layer coreless laminate with stacked build-up vias, extending between both sides of the substrate, was considered as implementation of the TPP. The thermal performance of the dual-side EIC topology outperforms that of the classical single-side EIC approach by 5 Kmm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /W, when considering bar-shaped copper planes in the TPP and elongated top interconnects, called rails. A voltage uniformity to the top chip of better than 2% of the supply voltage can be provided for all TPP designs.
Polarization behavior of poly(vinylidene fluoride-trifluoroethylene) copolymer ferroelectric thin film capacitors for nonvolatile memory application in flexible electronics (2010)

The time domain and electric field dependence of the polarization switching kinetics of poly(vinylidene fluoride-trifluoroethylene) copolymer based thin film metal-ferroelectric-metal capacitors have been characterized. At room temperature, the time required for complete switching polarization decreases from &amp;gt;1 s to &amp;lt;50 μs as the voltage is increased from 6 to 12 V, while low nonswitching polarization is maintained. In the time domain, the ferroelectric switching polarization reversal behavior for devices biased above the coercive field follows the nucleation-limited-switching model. The exponential relationship between switching time and applied electric field indicates nucleation dominated switching kinetics. Switching behavior as a function of temperature was also characterized from −60 to 100 °C in the voltage range of 6–12 V. Higher temperatures induce larger dc conductance leakage at low frequencies and increases nonswitching polarization for all the voltages studied. It is demonstrated that for certain frequencies, by controlling the switching voltage, our optimized ferroelectric thin film capacitor shows stable switching polarization in a temperature range compatible with flexible electronics applications.
Neural-network based vector control of VSCHVDC transmission systems (2015)

The application of high-voltage dc (HVDC) using voltage-source converters (VSC) has surged recently in electric power transmission and distribution systems. An optimal vector control of a VSC-HVDC system which uses an artificial neural network to implement an approximate dynamic programming algorithm and is trained with Levenberg-Marquardt is introduced in this paper. The proposed neural network vector control algorithm is analyzed in comparison with standard vector control methods for various HVDC control requirements, including dc voltage, active and reactive power control, and ac system voltage support. Assessment of the resulting closed-loop control shows that the neural network vector control approach has superior performance and works efficiently within and beyond the constraints of the HVDC system, for instance, converter rated power and saturation of PWM modulation.
ChemInform Abstract: Highly Stereoselective Intramolecular α‐Arylation of Self‐Stabilized Non‐racemic Enolates: Synthesis of α‐Quaternary α‐Amino Acid Derivatives. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Improving the Power Outage Resilience of Buildings with Solar PV through the Use of Battery Systems and EV Energy Storage (2021)

Buildings with solar photovoltaic (PV) generation and a stationary battery energy storage system (BESS) may self-sustain an uninterrupted full-level electricity supply during power outages. The duration of off-grid operation is dependent on the time of the power fault and the capabilities of the home energy management system (HEMS). In this paper, building resilience is quantified by analyzing the self-sustainment duration for all possible power outages throughout an entire year. An evaluation method is proposed and exercised on a reference house in California climate zone 9 for which the detailed electricity usage is simulated using the EnergyPlus software. The influence of factors such as energy use behavioral patterns, energy storage capacity from the BESS, and an electric vehicle (EV) battery on the building resilience is evaluated. Varying combinations of energy storage and controllable loads are studied for optimally improved resilience based on user preferences. It is shown that for the target home and region with a solar PV system of 7.2 kW, a BESS with a capacity of 11 kWh, and an EV with a battery of 80 kWh permanently connected to the home, off-grid self-sustained full operation is guaranteed for at least 72 h.
Enhanced MRI relaxivity of Gd3+‐based contrast agents geometrically confined within porous nanoconstructs (2012)

Gadolinium chelates, which are currently approved for clinical MRI use, provide relaxivities well below their theoretical limit, and they also lack tissue specificity. Recently, the geometrical confinement of Gd(3+) -based contrast agents (CAs) within porous structures has been proposed as a novel, alternative strategy to improve relaxivity without chemical modification of the CA. Here, we have characterized and optimized the performance of MRI nanoconstructs obtained by loading [Gd(DTPA)(H(2) O)](2-) (Magnevist®) into the pores of injectable mesoporous silicon particles. Nanoconstructs with three different pore sizes were studied, and at 60 MHz, they exhibited longitudinal relaxivities of ~24 m m(-1) s(-1) for 5-10 nm pores and ~10 m m(-1) s(-1) for 30 - 40 nm pores. No enhancement in relaxivity was observed for larger pores sizes. Using an outer-sphere compound, [GdTTHA](3-) , and mathematical modeling, it was demonstrated that the relaxivity enhancement is due to the increase in rotational correlation times (CA adsorbed on the pore walls) and diffusion correlation times (reduced mobility of the water molecules), as the pore sizes decreases. It was also observed that extensive CA adsorption on the outer surface of the silicon particles negates the advantages offered by nanoscale confinement. Upon incubation with HeLa cells, the nanoconstructs did not demonstrate significant cytotoxicity for up to 3 days post incubation, at different particle/cell ratios. In addition, the nanoconstructs showed complete degradation after 24 h of continuous agitation in phosphate-buffered saline. These data support and confirm the hypothesis that the geometrical confinement of Gd(3+) -chelate compounds into porous structures offers MRI nanoconstructs with enhanced relaxivity (up to 6 times for [Gd(DTPA)(H(2) O)](2-) , and 4 times for [GdTTHA](3-) ) and, potentially, improved stability, reduced toxicity and tissue specificity.
Homozygous deletion map at 18q21.1 in pancreatic cancer. (1996)

Absolute genetic differences between neoplastic and nonneoplastic cells can be discerned at sites of homozygous deletions. These deletions are of critical interest because they might be useful in the identification of defective biochemical pathways in neoplastic cells, and subsequently for the development of new treatment strategies in human cancer. We identified an area at 18q21.1 involved by homozygous deletions in 30% of pancreatic carcinomas. To characterize the homozygous deletions, we constructed a detailed physical map of nearly 2 Mb, containing yeast artificial chromosomes, P1-derived artificial chromosomes, cosmids and 24 sequence-tagged sites. The homozygously deleted are contained a new candidate tumor-suppressor gene (DPC4). To date, 23 (64%) of 35 pancreatic carcinomas carry at least one homozygous deletion at a published locus. The study of the total gene content of these loci, facilitated by the sequence-tagged site markers and maps of these regions, should help to reveal the absolute biochemical differences between neoplastic and nonneoplastic cells for a common human tumor.
Crystal Structure Refinement of (Pb1-xCax)ZrO3 by the Rietvelt Method (1993)

Superlattice structures in rhombohedral perovskite (Pb 1- x Ca x )ZrO 3 , which has high dielectric constant with small temperature coefficient and high Q value at microwave frequencies, were refined by the X-ray Rietvelt powder profile analysis. The superlattice structure is caused by slight displacement of lead and zirconium ions from the ideal perovskite sites, together with twisting and deformation of oxygen octahedra. The Q value of (PbCa)ZrO 3 at microwave frequencies has no relation to the formation of the superlattice structures, as indicated by the absence of cation ordering.
Microwave Photonic Imaging Radiometer (2018)

Nano-satellites are gaining in popularity due to their low cost and ease of deployment. Reaching orbit as secondary payload to larger spacecraft enables science grade missions at disruptively low cost. Such miniaturized platforms impose severe constraints on the size, weight, and power (SWaP) of the payload, however, making large antenna apertures difficult to realize. Meanwhile, relatively large apertures are needed to achieve desired spatial resolution for earth observing sensors at microwave frequencies. To this end, our distributed aperture array technology dramatically reduces the SWaP of such sensors, thus enabling deployment of large radio frequency apertures on spaceborne platforms. The sensor performs optical upconversion of the upwelling microwave radiation to optical frequencies, using high-speed, broadband electro-optic mixers, and subsequent coherent optical reconstruction of the passive thermal microwave scene, without the need for bulky and power hungry digital correlation engines or substantial post-processing. Notably, the optical processing technique images all of the beams in the array concurrently, forming a real-time video stream of radiometric brightness temperatures. Herein, we describe a spaceborne, 1-D pushbroom passive millimeter wave sensor utilizing optical upconversion and aperture synthesis, at a nominal detection frequency of 36 GHz, and deployed on a 12U CubeSat for remote sensing and earth science applications.
Crude α-Mangostin Suppresses the Development of Atherosclerotic Lesions in Apoe-Deficient Mice by a Possible M2 Macrophage-Mediated Mechanism (2019)

Lifestyle choices play a significant role in the etiology of atherosclerosis. Male <i>Apoe</i><sup>-/-</sup> mice that develop spontaneous atherosclerotic lesions were fed 0%, 0.3%, and 0.4% mangosteen extracts, composed largely of α-mangostin (MG), for 17 weeks. Body weight gains were significantly decreased in both MG-treated groups compared to the control, but the general condition remained good throughout the study. The levels of total cholesterol (decreased very-low-density lipoprotein in lipoprotein profile) and triglycerides decreased significantly in the MG-treated mice in conjunction with decreased hepatic <i>HMG-CoA</i> synthase and <i>Fatty acid transporter</i>. Additionally, increased serum lipoprotein lipase activity and histopathology further showed a significant reduction in atherosclerotic lesions at both levels of MG exposure. Real-time PCR analysis for macrophage indicators showed a significant elevation in the levels of <i>Cd163</i>, an M2 macrophage marker, in the lesions of mice receiving 0.4% MG. However, the levels of <i>Nos2</i>, associated with M1 macrophages, showed no change. In addition, quantitative immunohistochemical analysis of macrophage subtypes showed a tendency for increased M2 populations (CD68⁺/CD163⁺) in the lesions of mice given 0.4% MG. In further analysis of the cytokine-polarizing macrophage subtypes, the levels of <i>Interleukin13</i> (<i>Il13</i>), associated with M2 polarization, were significantly elevated in lesions exposed to 0.4% MG. Thus, MG could suppress the development of atherosclerosis in <i>Apoe</i><sup>-/-</sup> mice, possibly through an M2 macrophage-mediated mechanism.
Effects of an adapted intravenous amiodarone treatment protocol in horses with atrial fibrillation (2007)

Intravenous AD has the potential to be an alternative pharmacological treatment for AF in horses, although AD may lead to adverse drug effects, particularly with cumulative dosing.
Common Dimensional Reward Deficits Across Mood and Psychotic Disorders: A Connectome-Wide Association Study (2017)

These results emphasize the centrality of the nucleus accumbens in the pathophysiology of reward deficits and suggest that dissociable patterns of connectivity among large-scale networks are critical to the neurobiology of reward dysfunction across clinical diagnostic categories.
Cost function impact on S-parameter optimization space (2017)

Optimization algorithms require a cost function in order to quantitatively compare results and reach convergence to the maxima/minima desired. The choice of cost function can significantly affect the complexity of the optimization space. This work investigates the impact of cost function of S-parameters on the optimization solution space.