gebhart/patrepeval huggingface dataset:
Conformational requirements of tobacco mosaic virus RNA for aminoacylation and adenylation (1985)

The RNA conformational requirements for both aminoacylation and adenylation emerging from our studies performed using the valine- and the tyrosine-accepting plant viral RNAs are now strongly supported by the histidine-accepting tobacco mosaic virus RNA: an 'L'-shaped conformation is recognized by the aminoacyl-tRNA synthetase whereas only the aminoacyl RNA domain (equivalent in tRNAs to the continuous helix formed by the acceptor stem and the T stem and loop) interacts with the tRNA nucleotidyltransferase.
Soft handover in terrestrial broadcast networks (2004)

The 3rd generation mobile cellular communication systems will provide high-capacity bandwidth, enabling rich media and even TV services to be accessible via mobile handheld devices. For the reception of such services, seamless mobility is a must rather than an option. Alternatively, Digital Television standards, particularly data broadcasting in Terrestrial Digital Video Broadcasting (DVB-T), can be used for the delivery and reception of similar services. However, the current DVB-T standard lacks adequate methods that enable seamless mobility. In cellular delivery systems, this can be achieved by so-called soft handovers. time slicing is a recent enhancement proposed for the new - still being developed - Digital Video Broadcasting for handheld (DVB-H) standard, which together with DVB-T enables a feasible solution for soft handover to be implemented. This paper considers how time slicing can be utilized in implementing soft handover in a DVB-H receiver. An algorithm for soft handover is proposed and evaluated.
[Molecular characterization of ESBL-producing Klebsiella pneumoniae isolates from intensive care patients]. (2007)

In the observed group of intensive care patients, the prevalence of ESBL-positive strains of Klebsiella pneumoniae reached 19.4 %. The analysis of SHV and TEM products of PCR by the RFLP method showed the prevalence of SHV-type ESBL. Overall, 84.6 % of the strains had unique restriction profiles. The results suggest both high levels of hygienic and epidemiological measures at the monitored department and rational antibiotic policy.
Efficient and Highly Enantioselective Aerobic Oxidation–Michael–Carbocyclization Cascade Transformations by Integrated Pd(0)-CPG Nanoparticle/Chiral Amine Relay Catalysis (2014)

A series of highly diastereo- and enantioselective aerobic oxidation–Michael–carbocyclization cascade transformations by integrated heterogeneous Pd(0)-CPG nanoparticle/chiral amine relay catalysis are disclosed. The heterogeneous Pd(0)-CPG nanoparticle catalysts were efficient for both the sequential aerobic oxidation and dynamic kinetic asymmetric Michael–carbocyclization transformations, resulting in 1) oxidation of a variety of allylic alcohols to enals and 2) formation of cyclopentenes containing an all-carbon quaternary stereocenter in good to high yields with up to 20:1 dr and 99.5:0.5 er.
At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code (2016)

The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.
Hypergammaglobulinemia predicts outcome in patients with primary sclerosing cholangitis (2018)

Primary sclerosing cholangitis (PSC) leads to liver cirrhosis with the need of liver transplantation and increased risk for cholangiocellulare carcinoma (CCC) in many cases. Therefore, it is essential to identify patients as early as possible with a high disease activity to prevent fatal outcome. Pathogenesis of PSC is not yet fully understood but autoimmune reaction might play a role in its development. Therefore we studied the prognostic relevance of immunoglobulin levels at time of diagnose and there influence on transplantation-free survival in patients with PSC.
Performance Characterization and Simulation of Amine-Based Vacuum Swing Sorption Units for Spacesuit Carbon Dioxide and Humidity Control (2012)

Controlling carbon dioxide (CO2) and water (H2O) concentrations in the vapor phase of a space suit is critical to ensuring an astronauts safety, comfortability, and capability to perform extra-vehicular activity (EVA) tasks. Historically, this has been accomplished using lithium hydroxide (LiOH) and metal oxides (MetOx). Lithium hydroxide is a consumable material and requires priming with water before it becomes effective at removing carbon dioxide. MetOx is regenerable through a power-intensive thermal cycle but is significantly heavier on a volume basis than LiOH. As an alternative, amine-based vacuum swing beds are under aggressive development for EVA applications which control atmospheric concentrations of both CO2 and H2O through a fully-regenerative process. The current concept, referred to as the rapid cycle amine (RCA), has resulted in numerous laboratory prototypes. Performance of these prototypes have been assessed and documented from experimental and theoretical perspectives. To support developmental efforts, a first principles model has also been established for the vacuum swing adsorption technology. The efforts documented herein summarize performance characterization and simulation results for several variable metabolic profiles subjected to the RCA. Furthermore, a variety of control methods are explored including timed swing cycles, instantaneous CO2 feedback control, and time-averaged CO2 feedback control. A variety of off-nominal tests are also explored including high/low suit temperatures, increasingly high humidity cases, and dynamic pressure cases simulating the suit pre-breathe protocol. Consequently, this work builds on efforts previous efforts to fully bound the performance of the rapid cycle amine under a variety of nominal and off-nominal conditions.
Lipopolysaccharide and lipoteichoic acid binding by antimicrobials used in oral care formulations. (2016)

These results support a potential mechanism of action for stannous fluoride and CPC formulated in oral products in which these ingredients bind bacterial toxins and potentially render them less toxic to the host. These results may influence home care recommendations for patients at risk for plaque-related diseases.
Computation and analysis of dielectric losses in MV power electronic converter insulation (2016)

The newly available Medium Voltage (MV) Silicon-Carbide (SiC) devices enable a great extension of the design space of MV inverters. This includes the utilization of unprecedented blocking voltages, higher switching frequencies, higher commutation speeds, and high temperature operation. However, all these factors considerably increase the insulation stress. This paper details the computation of dielectric losses, which are directly related to the insulation stress and can be used for the insulation design and diagnostic. After a review of the method used to compute dielectric losses, scalable analytical expressions are derived for the losses produced by PWM waveforms of DC-DC, DC-AC, and multilevel DC-AC inverters. Finally, a Medium-Frequency (MF) transformer is analyzed and the impacts of the insulation material and the operating temperature on the dielectric losses are discussed. It is found that the insulation losses can represent a significant share (17%) of the total transformer losses.
XIAN: Cross-Layer Interface for Wireless Ad Hoc Networks (2006)

In the highly dynamic and unpredictable environment of MANETs, cross-layer design is receiving growing interest but lacks experimental validation tools. This paper proposes Xian, a Cross-layer Interface for wireless Ad hoc Networks, a generic interface for experimenting cross-layer designs with legacy 802.11 protocols. Xian can be used as a service by other network layers or system components to access information about configuration and performance of MAC/PHY layers. The interface is fully implemented and is available for Linux over the MadWifi 802.11 driver. We exemplify its use for the design of various QoS routing schemes and provide experimental demonstration of their potential benefits.
Atmospheric Corrosion Resistance of High-Cr Stainless Steels for Building uses and their Estimation Methods (1995)

Recently high-Cr ferritic stainless steels have been adopted as exterior parts of buildings especially at waterfronts. In this study, atmospheric corrosion resistance of various kinds of stainless steels was evaluated in various environments. Correlation between the atmospheric corrosion resistance and laboratory corrosion tests and a method for evaluating atmospheric corrosion resistance were investigated. Results are as follows. 1) Atmospheric corrosion resistance of stainless steels was improved by increasing pitting index (P. I.; ferritic stainless steel: Cr+3.3Mo, austenitic and dual phase stainless steels; Cr+ 3.3Mo+16N). 2) Ferritic stainless steel that have the same P.I. value as austenitic and duplex stainless steels showed better corrosion resistance than the austenitic and duplex stainless steels. The pitting index of the steels is useful for estimating corrosion resistance for each type of steel. 3) Corrosion resistance in atmospheric exposure tests had a good correlation with pitting potential. If pitting potentials of stainless steels were more than critical pitting potentials (Vcrit) which correspond to each exposure site, the steels did not have rust. The Vcrit values can be used as one of the criteria for selecting steels to site a service environment. 4) In a severe corrosive environment such as a coastal area, Mo-bearing high-Cr ferritic stainless steels are required.
ChemInform Abstract: New Molybdenum and Iron Phosphoranides. Mechanism and Stereochemistry of the Rearrangement and Migration of a Phosphorus‐Bound Allylic Group Into an Iron‐Bound Vinylic Group. (1987)

Abstract The reaction of the bicyclic phosphoranes (III), prepared as shown, with the Mo complex (IV) results in substitution of one CO ligand and coordination of the tautomeric open form of (III) through the P atom to give the phosphine derivatives (V).
A Novel Class of Injectable Bioceramics That Glue Tissues and Biomaterials (2018)

Calcium phosphate cements (CPCs) are clinically effective void fillers that are capable of bridging calcified tissue defects and facilitating regeneration. However, CPCs are completely synthetic/inorganic, unlike the calcium phosphate that is found in calcified tissues, and they lack an architectural organization, controlled assembly mechanisms, and have moderate biomechanical strength, which limits their clinical effectiveness. Herein, we describe a new class of bioinspired CPCs that can glue tissues together and bond tissues to metallic and polymeric biomaterials. Surprisingly, alpha tricalcium phosphate cements that are modified with simple phosphorylated amino acid monomers of phosphoserine (PM-CPCs) bond tissues up to 40-fold stronger (2.5⁻4 MPa) than commercial cyanoacrylates (0.1 MPa), and 100-fold stronger than surgical fibrin glue (0.04 MPa), when cured in wet-field conditions. In addition to adhesion, phosphoserine creates other novel properties in bioceramics, including a nanoscale organic/inorganic composite microstructure, and templating of nanoscale amorphous calcium phosphate nucleation. PM-CPCs are made of the biocompatible precursors calcium, phosphate, and amino acid, and these represent the first amorphous nano-ceramic composites that are stable in liquids.
Failure of Intravenous Morphine to Serve as an Effective Instrumental Reinforcer in Dopamine D2 Receptor Knock-Out Mice (2002)

The rewarding effects of opiates are thought to be mediated through dopaminergic mechanisms in the ventral tegmental area, dopamine-independent mechanisms in the nucleus accumbens, or both. The purpose of the present study was to explore the contribution of dopamine to opiate-reinforced behavior using D2 receptor knock-out mice. Wild-type, heterozygous, and D2 knock-out mice were first trained to lever press for water reinforcement and then implanted with intravenous catheters. The ability of intravenously delivered morphine to maintain lever pressing in these mice was studied under two schedules of reinforcement: a fixed ratio 4 (FR4) schedule (saline, 0.1, 0.3, or 1.0 mg/kg, per injection) and a progressive ratio (PR) schedule (1.0 mg/kg, per injection). In the wild-type and heterozygous mice, FR4 behavior maintained by morphine injections was significantly greater than behavior maintained by vehicle injections. Response rate was inversely related to injection dose and increased significantly in the wild-type and heterozygous mice when the animals were placed on the PR schedule. In contrast, the knock-out mice did not respond more for morphine than for saline and did not respond more when increased ratios were required by the PR schedule. Thus, morphine served as a positive reinforcer in the wild-type and heterozygous mice but failed to do so in the knock-out mice. Under this range of doses and response requirements, the rewarding effects of morphine appear to depend critically on an intact D2 receptor system.
Data from Prediagnostic Smoking Is Associated with Binary and Quantitative Measures of ER Protein and <i>ESR1</i> mRNA Expression in Breast Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Smoking is a possible risk factor for breast cancer and has been linked to increased risk of estrogen receptor–positive (ER&lt;sup&gt;+&lt;/sup&gt;) disease in some epidemiologic studies. It is unknown whether smoking has quantitative effects on ER expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We examined relationships between smoking and ER expression from tumors of 1,888 women diagnosed with invasive breast cancer from a population-based study in North Carolina. ER expression was characterized using binary (±) and continuous measures for ER protein, &lt;i&gt;ESR1&lt;/i&gt; mRNA, and a multigene luminal score (LS) that serves as a measure of estrogen signaling in breast tumors. We used logistic and linear regression models to estimate temporal and dose-dependent associations between smoking and ER measures.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The odds of ER&lt;sup&gt;+&lt;/sup&gt;, &lt;i&gt;ESR1&lt;/i&gt;&lt;sup&gt;+&lt;/sup&gt;, and LS&lt;sup&gt;+&lt;/sup&gt; tumors among current smokers (at the time of diagnosis), those who smoked 20 or more years, and those who smoked within 5 years of diagnosis were nearly double those of nonsmokers. Quantitative levels of &lt;i&gt;ESR1&lt;/i&gt; were highest among current smokers compared with never smokers overall [mean (log&lt;sub&gt;2&lt;/sub&gt;) = 9.2 vs. 8.7, &lt;i&gt;P&lt;/i&gt; &lt; 0.05] and among ER&lt;sup&gt;+&lt;/sup&gt; cases; however, we did not observe associations between smoking measures and continuous ER protein expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; In relationship to breast cancer diagnosis, recent smoking was associated with higher odds of the ER&lt;sup&gt;+&lt;/sup&gt;, &lt;i&gt;ESR1&lt;/i&gt;&lt;sup&gt;+&lt;/sup&gt;, and LS&lt;sup&gt;+&lt;/sup&gt; subtype. Current smoking was associated with elevated &lt;i&gt;ESR1&lt;/i&gt; mRNA levels and an elevated LS, but not with altered ER protein.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Impact:&lt;/b&gt; A multigene LS and single-gene &lt;i&gt;ESR1&lt;/i&gt; mRNA may capture tumor changes associated with smoking. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 27(1); 67–74. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Coupling resistance between n-type surface accumulation layer and p-type bulk in InN:Mg thin films (2012)

Indium nitride is the least studied of the III-nitride though it has great potential due to its small bandgap of 0.65 eV and a small effective electron mass. InN:Mg was recently confirmed to be p-type. However, Hall measurements on InN:Mg still show n-type conductivity, even when InN:Mg is very thick. Some studies have suggested the possibility of a high coupling resistance between the surface electron accumulation and the bulk p-InN. In this study, we show through vertical and transmission-line model measurement that this coupling resistance is small and should not affect conductivity and Hall measurements.
Influence of Encapsulation on the Efficiency and Positive Aging Behavior in Blue Quantum Dot Light-Emitting Devices (2023)

Encapsulating blue quantum dot light-emitting devices (QLEDs) using an ultraviolet curable resin is known to lead to a significant increase in their efficiency. Some of this efficiency increase occurs immediately, whereas some of it proceeds over a period of time, typically over several tens of hours following the encapsulation, a behavior commonly referred to as positive aging. The root causes of this positive aging, especially in blue QLEDs, remain not well understood. Here, it is revealed that contrary to the expectation, the significant improvement in device efficiency during positive aging arises primarily from an improvement in electron injection across the QD/ZnMgO interface and not due to the inhibition of interface exciton quenching as is widely believed. The underlying changes are investigated by XPS measurements. Results show that the enhancement in device performance arises primarily from the reduction in O-related defects in both the QDs and ZnMgO at the QD/ZnMgO interface. After 51.5 h, the blue QLEDs reach the optimal performance, exhibiting an EQE<sub>max</sub> of 12.58%, which is more than sevenfold higher than that in the control device without encapsulation. This work provides design principles for realizing high efficiency in blue QLEDs with oxide electron-transporting layers (ETLs) and provides a new understanding of the mechanisms underlying positive aging in these devices and thus offers a new starting point for both fundamental investigations and practical applications.
Excretion of excess nitrogen and increased survival by loss of SLC6A19 in a mouse model of ornithine transcarbamylase deficiency (2022)

Protein catabolism ultimately yields toxic ammonia, which must be converted to urea by the liver for renal excretion. In extrahepatic tissues, ammonia is temporarily converted primarily to glutamine for subsequent hepatic extraction. Urea cycle disorders (UCDs) are inborn errors of metabolism causing impaired ureagenesis, leading to neurotoxic accumulation of ammonia and brain glutamine. Treatment includes dietary protein restriction and oral "ammonia scavengers." These scavengers chemically combine with glutamine and glycine to yield excretable products, creating an alternate pathway of waste nitrogen disposal. The amino acid transporter SLC6A19 is responsible for >95% of absorption and reabsorption of free neutral amino acids in the small intestine and kidney, respectively. Genetic SLC6A19 deficiency causes massive neutral aminoaciduria but is typically benign. We hypothesized that inhibiting SLC6A19 would open a novel and effective alternate pathway of waste nitrogen disposal. To test this, we crossed SLC6A19 knockout (KO) mice with spf<sup>ash</sup> mice, a model of ornithine transcarbamylase (OTC) deficiency. Loss of SLC6A19 in spf<sup>ash</sup> mice normalized plasma ammonia and brain glutamine and increased median survival in response to a high protein diet from 7 to 97 days. While induced excretion of amino acid nitrogen is likely the primary therapeutic mechanism, reduced intestinal absorption of dietary free amino acids, and decreased muscle protein turnover due to loss of SLC6A19 may also play a role. In summary, the results suggest that SLC6A19 inhibition represents a promising approach to treating UCDs and related aminoacidopathies.
Using projected dynamics to plan dynamic contact manipulation (2005)

This paper addresses the planning and control of dynamic contact manipulation. In an earlier paper (Srinivasa et al., 2005), we derived a constraint on the robot joint accelerations that needed to be satisfied to obtain a desired contact mode and a desired dynamic motion of the object. We proposed a technique for trajectory planning which involved planning a path in the system configuration space followed by time-scaling the path to satisfy dynamic constraints. This paper tackles a problem where only a small set of paths can be time-scaled to satisfy the constraints. We note that the dynamic constraints depend only on a subspace of the system state space. Projecting the dynamics and the constraints onto the subspace allows us to compute an analytical solution for the trajectory generation problem. We generate controllable simulations by allowing the user to control the system in the space orthogonal to the projection. We also demonstrate the construction of feedback controllers using dynamic programming.
Optimizing optical nanostructures for X-ray detection (2020)

Scintillators are vital to X-ray and high-energy particle detection. Specifically, thin scintillators like phosphor screens are a prime component in detectors of soft-X-rays, electron cameras, and light intensifiers. All such applications are limited by the scintillator’s response time and efficiency. Moreover, there exists an intrinsic trade-off due to the isotropic nature of spontaneous emission at the heart of the scintillation process: On the one hand, the thicker scintillator layers that are required for high efficiency of detecting the radiation also cause a dramatic image deterioration and blurring. On the other hand, thinner scintillator layers can provide higher image resolution yet that comes at the price of lower efficiency of detecting the radiation and thus a lower signal-to-noise ratio. In this paper, we introduce a novel design of thin scintillators that can achieve simultaneously high-efficiency and high-resolution, by proposing a new concept of scintillating nanophotonic structures. We exploit the photonic local-density-of-states (LDOS) in scintillating nanostructures made from scintillator layers, stacked between other dielectric layers. We use a specialized optimization algorithm to determine the thicknesses of each layer in the multi-layer structure and to maximize the emission rate, directionality, and efficiency. As an example, we examine an overall structure width of only 2.5 μm, and find that the emission rate can be enhanced by a factor of 5.2 (when combining a scintillator with a refractive index of 1.59 with a dielectric material with a refractive index of 2.1). We show how the optimized structure can enhance the emission in the desired bandwidth to match with any scintillator material, thus improving the detector resolution and efficiency simultaneously in several radiation detection applications.