gebhart/patrepeval huggingface dataset:
Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics (2013)

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn2+ aqua complex, as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate, H2O + CO2 → H+ + HCO3–. On the basis of potential-of-mean-force (PMF) calculations, stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (ΔG = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile, proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (ΔΔG = 1.4 kcal/mol), suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast, the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity, due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme, providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.
Weathering of furan and 2,2′-bifuran polyester and copolyester films (2022)

Furan-based polymers are renewable alternatives for traditional fossil-based polymers, therefore carrying enormous potential for improved sustainability. Many aspects of these novel polymers still need to be investigated more comprehensively for full appreciation of their applicability. Here, the degradation of furan-based polymers including poly(butylene furanoate), poly(butylene bifuranoate), and three random copolyesters thereof were investigated under artificial weathering conditions for up to 300 h. This included simultaneous exposure of film samples to ultraviolet light, high humidity, and elevated temperature. Poly(ethylene terephthalate) was used as a reference material. Both the pristine and weathered samples were characterized using infrared spectroscopy, differential scanning calorimetry, and dynamic mechanical analysis, among others. According to the infrared measurements, the exposed surfaces of the films had undergone severe chemical changes. Indications of covalent cross-linking after exposure to ultraviolet light were found in differential scanning calorimetry, dynamic mechanical analysis, and dissolution experiments. The nature of the cross-linking mechanisms and exact structure of the formed degradation products remain unclear. It is concluded that polyesters derived from both 2,5-furandicarboxylic and 2,2′-bifuran-5,5′-dicarboxylic acids are relatively labile when exposed to UV light. The latter monomer appears especially labile, probably in part because of its broader and elevated UV absorbance. Simple oven-aging in air indicated that crosslinking also occurred in the absence of UV, but the overall chemical degradation was stronger in the weathering conditions. In the more easily crystallizable samples, the aging-induced crystallization played an important role in the final physical properties.
Conceptual Design and Performance Analysis of SOFC/Micro Gas Turbine Hybrid Distributed Energy System (2014)

A numerical model has been developed for the performance analysis of solid oxide fuel cell (SOFC)/micro gas turbine (MGT) hybrid systems with prereforming of natural gas, in which a quasi two-dimensional model has been built up to simulate the cell electrochemical reaction, heat and mass transfer within tubular SOFC. The developed model can be used not only to predict the overall performance of the SOFC/MGT hybrid system but also to reveal the nonuniform temperature distribution within SOFC unit. The effects of turbine inlet temperature (TIT) and pressure ratio (PR) on the performance of the hybrid system have been investigated. The results show that selecting smaller TIT or PR value will lead to relative higher system efficiency and lower CO2 emission ratio; however, this will raise the risk to destroy SOFC beyond the limitation temperature of electrolyte.
The TLR7 agonist vesatolimod induced a modest delay in viral rebound in HIV controllers after cessation of antiretroviral therapy (2021)

Toll-like receptor 7 (TLR7) agonists, in combination with other therapies, can induce sustained control of simian-human immunodeficiency virus (SHIV) or simian immunodeficiency virus (SIV) in nonhuman primates. Here, we report the results of a randomized, double-blind, placebo-controlled phase 1b clinical trial of an oral TLR7 agonist, vesatolimod, in HIV-1-infected controllers on antiretroviral therapy (ART). We randomized participants 2:1 to receive vesatolimod (<i>n</i> = 17) or placebo (<i>n</i> = 8) once every other week for a total of 10 doses while continuing on ART. ART was then interrupted, and the time to viral rebound was analyzed using the Kaplan-Meier method. Vesatolimod was associated with induction of immune cell activation, decreases in intact proviral DNA during ART, and a modest increase in time to rebound after ART was interrupted. The delayed viral rebound was predicted by the lower intact proviral DNA at the end of vesatolimod treatment (13 days after the final dose). Inferred pathway analysis suggested increased dendritic cell and natural killer cell cross-talk and an increase in cytotoxicity potential after vesatolimod dosing. Larger clinical studies will be necessary to assess the efficacy of vesatolimod-based combination therapies aimed at long-term control of HIV infection.
PWA-CTM: An Extended Cell-Transmission Model based on Piecewise Affine Approximation of the Fundamental Diagram (2022)

Throughout the past decades, many different versions of the widely used first-order Cell-Transmission Model (CTM) have been proposed for optimal traffic control. Highway traffic management techniques such as Ramp Metering (RM) are typically designed based on an optimization problem with nonlinear constraints originating in the flow-density relation of the Fundamental Diagram (FD). Most of the extended CTM versions are based on the trapezoidal approximation of the flow-density relation of the Fundamental Diagram (FD) in an attempt to simplify the optimization problem. However, this relation is naturally nonlinear, and crude approximations can greatly impact the efficiency of the optimization solution. In this study, we propose a class of extended CTMs that are based on piecewise affine approximations of the flow-density relation such that (a) the integrated squared error with respect to the true relation is greatly reduced in comparison to the trapezoidal approximation, and (b) the optimization problem remains tractable for real-time application of ramp metering optimal controllers. A two-step identification method is used to approximate the FD with piecewise affine functions resulting in what we refer to as PWA-CTMs. The proposed models are evaluated by the performance of the optimal ramp metering controllers, e.g. using the widely used PI-ALINEA approach, in complex highway traffic networks. Simulation results show that the optimization problems based on the PWA-CTMs require less computation time compared to other CTM extensions while achieving higher accuracy of the flow and density evolution. Hence, the proposed PWA-CTMs constitute one of the best approximation approaches for first-order traffic flow models that can be used in more general and challenging modeling and control applications.
Photoluminescence degradation in organic light-emitting devices (2002)

Polymer degradation under electrical stress was studied using the device structure indium tin oxide/poly(p-phenylene vinylene)/Ca/Ag. The devices that were used in this study do not show any significant decrease in electroluminescent intensity for up to several thousand hours of operation. However for devices that were electrically stressed and then exposed to normal ambient, there was a significant decrease in the photoluminescence. Those that were not electrically stressed but exposed to normal ambient or were electrically stressed but not exposed to normal ambient, there was no significant degradation in the photoluminescence. These results showed that both conditions of electrical stress and photo-oxidation are necessary for a significant decrease of the photoluminescence intensity. Degradation is accompanied by an increase in the x-ray crystallization peak. We interpret that the photoluminescence intensity degradation is due to the change in polymer crystallinity caused by electrical stress followed by photo-oxidation.
Annual review of biophysics and biophysical chemistry. Volume 20, 1991 (1991)

This book covers: statistical methods and insights for protein and DNA sequences; the biochemistry of genetic recombination; and two- three- and four-dimensional NMR methods for obtaining 3-D structures of proteins in solution; as well as other topics.
Leveraging Synergies Between AI and Networking to Build Next Generation Edge Networks (2022)

Networking and Artificial Intelligence (AI) are two of the most transformative information technologies over the last few decades. Building upon the synergies of these two powerful technologies, we envision designing next generation of edge networks to be highly efficient, reliable, robust and secure. To this end, in this paper, we delve into interesting and fundamental research challenges and opportunities that span two major broad and symbiotic areas: AI for Networks and Networks for AI. The former deals with the development of new AI tools and techniques that can enable the next generation AI-assisted networks; while the latter focuses on developing networking techniques and tools that will facilitate the vision of distributed intelligence, resulting in a virtuous research cycle where advances in one will help accelerate advances in the other. A wide range of applications will be further discussed to illustrate the importance of the foundational advances developed in these two areas.
ChemInform Abstract: CHEMISTRY OF THE PODOCARPACEAE PART 53, REARRANGEMENT OF A TETRASUBSTITUTED EPOXIDE (1975)

Abstract Bei der durch Bortrifluoridätherat induzierten Umlagerung des aus dem Podocarpatrienol (I) über das Podocarpenol (II) erhältlichen Epoxids (III) entstehen das Abeopodocarpanon (V) und das Abeopodocarpanol (VI).
Dumbbell‐Shaped T8‐POSS with Functional Organic Linkers (2019)

New dumbbell‐shaped octasilsesquioxanes (T 8 ‐POSS) are obtained by the condensation of organobridged silane precursors with partially condensed T 7 ‐triol. The synthesis based on corner‐capping proceeds under mild reaction conditions (60 °C in toluene) upon a nucleophilic fluoride‐catalyzed condensation of the T 7 ‐triol with the alkoxysilyl organics. Two dumbbell‐type T 8 ‐POSS, one with a non‐symmetrical urea‐thiourea linker and the other one with a symmetrical malonamide linker, are described. Their formation is monitored by FTIR, their structures are investigated by NMR spectroscopy ( 1 H, 13 C and 29 Si) and confirmed by mass spectrometry.
Positron Lifetime Analysis of Polyurea‐Nanoclay Composites (2012)

This chapter contains sections titled: Introduction Experimental Results and Discussion Conclusions Acknowledgments
Understanding the Element-Gain Paradox for Receiving Arrays Using Poynting Streamlines (2018)

Energy flow directions around receiving array antennas can be modeled by generating streamlines of Poynting vector fields near the antenna. The geometrical shape of array effective area can be calculated from the locus of Poynting streamlines that terminate on the array element loads. The decrease of array directivity due to mutual coupling effects, or the element-gain paradox, can be explained by the overlap of element effective area shapes leading to the decrease of array effective area shape. The critical element distance for the element gain paradox effect is equal to the width of the effective area shape for a single isolated array element. These results provide a new, intuitive, and visually oriented tool for understanding a variety of effects in the theory and design of receiving antennas and arrays.
Data from PAK4-NAMPT Dual Inhibition Sensitizes Pancreatic Neuroendocrine Tumors to Everolimus (2023)

&lt;div&gt;Abstract&lt;p&gt;Metastatic pancreatic neuroendocrine tumors (PNET) remain an unmet clinical problem. Chronologic treatment in PNETs includes observation (watchful protocol), surgery, targeted therapy, and chemotherapy. However, increasing evidence illustrates that the outcomes of targeted therapeutic options for the treatment of advanced PNETs show minimal response. The FDA-approved mTOR inhibitor everolimus does not shrink these tumors. It only delays disease progression in a subset of patients, while a significant fraction acquires resistance and shows disease progression. Thus, there is a need for more effective targeted approaches to sensitize PNETs to everolimus for better treatment outcomes. Previously, we showed that mTOR regulator p21 activated kinase 4 (PAK4) and nicotinamide adenine dinucleotide biosynthesis enzyme nicotinamide phosphoribosyl transferase (NAMPT) were aberrantly expressed in PNET tissue and promoted everolimus resistance. In this report, we demonstrate that PAK4-NAMPT dual inhibitor KPT-9274 can synergize with everolimus (growth inhibition, colony suppression, and glucose uptake assays). KPT-9274-everolimus disrupted spheroid formation in multiple PNET models. Molecular analysis showed alteration of mTORC2 through downregulation of RICTOR as a mechanism supporting synergy with everolimus &lt;i&gt;in vitro&lt;/i&gt;. KPT-9274 suppressed β-catenin activity via inhibition of PAK4, highlighting the cross-talk between Rho GTPases and Wnt signaling in PNETs. KPT-9274, given at 150 mg/kg in combination with sub-MTD everolimus (2.5 mg/kg), significantly suppressed two PNET-derived xenografts. These studies bring forward a well-grounded strategy for advanced PNETs that fail to respond to single-agent everolimus.&lt;/p&gt;&lt;/div&gt;
Ligand-Stabilized Platinum Nanoparticles in Multi-Layer Films as Active Electrocatalysts for PEM Fuel Cells (2006)

Abstract not Available.
Lithography-Free Plasmonic Color Printing with Femtosecond\nLaser on Semicontinuous Silver Films (1753)

Plasmonic color printing with semicontinuous metal films is a\nlithography-free, non-fading, and environment-friendly method of generation of\nbright colors. Such films are comprised of metal nanoparticles, which resonate\nat different wavelengths upon light illumination depending on the size and\nshape of the nanoparticles. To achieve an experimentally demonstrated structure\nthat was optimized in terms of broader color range and increased stability,\nvariable Ag semicontinuous metal films were deposited on a metallic mirror with\na sub-wavelength-thick dielectric spacer. Femtosecond laser post-processing was\nthen introduced to extend the color gamut through spectrally induced changes\nfrom blue to green, red, and yellow. Long-term stability and durability of the\nstructures were addressed to enable non-fading colors with an optimized\novercoating dielectric layer. The thickness of the proposed designs is on the\norder of 100 nanometers, and it can be deposited on any substrate. These\nstructures generate a broad range of long-lasting colors in reflection that can\nbe applied to real-life artistic or technological applications with a spatial\nresolution on the order of 0.3 mm or less.\n
Unsupervised Morpheme Analysis Evaluation by a Comparison to a Linguistic Gold Standard - Morpho Challenge 2007 (2007)

The goal of Morpho Challenge 2008 was to find and evaluate unsupervised algorithms that provide morpheme analyses for words in different languages. Especially in morphologically complex languages, such as Finnish, Turkish and Arabic, morpheme analysis is important for lexical modeling of words in speech recognition, information retrieval and machine translation. The evaluation in Morpho Challenge competitions consisted of both a linguistic and an application oriented performance analysis. This paper describes an evaluation where the competition entries were compared to a linguistic morpheme analysis gold standard. Because the morpheme labels in an unsupervised analysis can be arbitrary, the evaluation is based on matching the morpheme-sharing words between the proposed and the gold standard analyses. In addition to Finnish, Turkish, German and English evaluations performed in Morpho Challenge 2007, the competition this year had an additional evaluation in Arabic. The results in 2008 show that although the level of precision and recall varies substantially between the tasks in different languages, the best methods seem to manage all the tested languages
Utilizing the Power of Microbial Genetics to Bridge the Gap Between the Promise and the Application of Marine Natural Products (2005)

Abstract Marine organisms are a rich source of secondary metabolites. They have yielded thousands of compounds with a broad range of biomedical applications. Thus far, samples required for preclinical and clinical studies have been obtained by collection from the wild, by mariculture, and by total chemical synthesis. However, for a number of complex marine metabolites, none of these options is feasible for either economic or environmental reasons. In order to proceed with the development of many of these promising therapeutic compounds, a reliable and renewable source must be found. Over the last twenty years, the study of microbial secondary metabolites has greatly advanced our understanding of how nature utilizes simple starting materials to yield complex small molecules. Much of this work has focused on polyketides and nonribosomal peptides, two classes of molecules that are prevalent in marine micro‐ and macroorganisms. The lessons learned from the study of terrestrial metabolite biosynthesis are now being applied to the marine world. As techniques for cloning and heterologous expression of biosynthetic pathways continue to improve, they may provide our greatest hope for bridging the gap between the promise and application of many marine natural products.
A Nonlinear State-Space Model of a Combined Cardiovascular System and a Rotary Pump (2006)

A nonlinear lumped parameter model of the cardiovascular system coupled with a rotary blood pump is presented. The blood pump is a mechanical assist device typically interposed from the left ventricle to the aorta in patients with heart failure. The cardiovascular part of the model (consisting of the left heart atrium and ventricle), and the systemic circulatory system are implemented as an RLC circuit with two diodes. The diodes represent the mitral and aortic valves in the left heart. The cardiovascular model has been validated with clinical data from a patient suffering from cardiomyopathy. The pump model is a first order differential equation relating pressure difference across the pump to flow rate and pump speed. The combined cardiovascular-pump model has been represented as a fifth order nonlinear dynamical system in state space form with pump speed as the control variable. This model was used to simulate the hemodynamic variables to different values of afterload and a linearly increasing (ramp) pump speed. Because of its small dimensionality, the model is suitable for both parameter identification and the application of modern control theory.
Brain structural alterations are distributed following functional, anatomic and genetic connectivity (2018)

The pathological brain is characterized by distributed morphological or structural alterations in the grey matter, which tend to follow identifiable network-like patterns. We analysed the patterns formed by these alterations (increased and decreased grey matter values detected with the voxel-based morphometry technique) conducting an extensive transdiagnostic search of voxel-based morphometry studies in a large variety of brain disorders. We devised an innovative method to construct the networks formed by the structurally co-altered brain areas, which can be considered as pathological structural co-alteration patterns, and to compare these patterns with three associated types of connectivity profiles (functional, anatomical, and genetic). Our study provides transdiagnostical evidence that structural co-alterations are influenced by connectivity constraints rather than being randomly distributed. Analyses show that although all the three types of connectivity taken together can account for and predict with good statistical accuracy, the shape and temporal development of the co-alteration patterns, functional connectivity offers the better account of the structural co-alteration, followed by anatomic and genetic connectivity. These results shed new light on the possible mechanisms at the root of neuropathological processes and open exciting prospects in the quest for a better understanding of brain disorders.
Selective E‐prostanoid receptor agonists mediate phosphorylation of aquaporin‐2 in vitro and ex vivo (2011)

We have previously shown in MDCK cells that prostaglandin E2 (PGE2) increases membrane targeting, ser-264 and ser-269 phosphorylation (pS264 and pS269) of aquaporin-2 (AQP2) and that membrane targeting is mimicked by stimulation with the selective E prostanoid receptor type 2 (EP2) agonist Butaprost or by the selective EP4 receptor agonist CAY10580. This study aimed to further investigate the effects of PGE2 on AQP2 in vitro and ex vivo. In MDCK cells, 40 minutes of stimulation with either CAY10580 (10−7 to 10−5M) or Butaprost (10−8 to 10−6M) increased AQP2 membrane targeting and pS264-AQP2 to levels that mimic the effects of PGE2 (10−7M). Only Butaprost, but not CAY10580, increased pS269-AQP2 in membrane bound AQP2. As assessed by a calcein-quenching-based approach, PGE2 increased MDCK cell water permeability to levels similar to forskolin (10−5M). In rat cortical tubular suspensions, PGE2 (10−7), Butaprost (10−6) or CAY10580 (10−6) stimulation increased phosphorylation of AQP2 at ser-256. Finally, using rat kidney slices, 30 minutes of PGE2 (10−7M) stimulation resulted in redistribution of AQP2 to the apical plasma membrane of cortical collecting duct principal cells. Our results provide further evidence that PGE2 can play a positive role in regulating body water homeostasis and revealed differential effects of EP2 and EP4 on AQP2 phosphorylation. This study was funded by Lundbeck.
Polarization-insensitive high-dispersion TIR diffraction gratings (2003)

Diffraction gratings play an important role in many technologies, including spectroscopy, display systems, and wavelength-division multiplexing architectures in telecommunications. For telecommunications, their ability to map wavelength into propagation angle makes them suitable for use in add-drop filters, multiplexers and de-multiplexers, and other wavelength configurable devices. Gratings with low polarization sensitivity are desirable since the signals propagating through the fiber arrive at the grating in an unknown polarization state.