gebhart/patrepeval huggingface dataset:
The Significance of Chirality in Drug Design and Synthesis of Bitopic Ligands as D3 Receptor (D3R) Selective Agonists (2019)

Because of the large degree of homology among dopamine D<sub>2</sub>-like receptors, discovering ligands capable of discriminating between the D<sub>2</sub>, D<sub>3</sub>, and D<sub>4</sub> receptor subtypes remains a significant challenge. Previous work has exemplified the use of bitopic ligands as a powerful strategy in achieving subtype selectivity for agonists and antagonists alike. Inspired by the potential for chemical modification of the D<sub>3</sub> preferential agonists (+)-PD128,907 (<b>1</b>) and PF592,379 (<b>2</b>), we synthesized bitopic structures to further improve their D<sub>3</sub>R selectivity. We found that the (2<i>S</i>,5<i>S</i>) conformation of scaffold <b>2</b> resulted in a privileged architecture with increased affinity and selectivity for the D<sub>3</sub>R. In addition, a cyclopropyl moiety incorporated into the linker and full resolution of the chiral centers resulted in lead compound <b>53</b> and eutomer <b>53a</b> that demonstrate significantly higher D<sub>3</sub>R binding selectivities than the reference compounds. Moreover, the favorable metabolic stability in rat liver microsomes supports future studies in in vivo models of dopamine system dysregulation.
Receptor for Advanced Glycation End Products Activation Injures Primary Sensory Neurons via Oxidative Stress (2006)

The receptor for advanced glycation end products (RAGE) may promote diabetic vascular and renal disease through the activation of intracellular signaling pathways that promote oxidative stress. Oxidative stress is a mediator of hyperglycemia-induced cell injury and a unifying theme for all mechanisms of diabetic complications, but there are few studies on the expression and potential contribution of RAGE in diabetic neuropathy. The current study demonstrates that dorsal root ganglia neurons express functional RAGE and respond to the RAGE ligand S100 with similar downstream signaling, oxidative stress, and cellular injury as other diabetic complication-prone tissues. RAGE-induced phosphatidylinositol-3 kinase activity is associated with formation of reactive oxygen species, caspase-3 activation, and nuclear DNA degradation. These events are prevented by treatment with the antioxidant alpha-lipoic acid. Our data indicate that therapies aimed at decreasing RAGE ligands, blocking RAGE signaling, or preventing oxidative stress could significantly decrease the development of neuropathy in diabetic patients.
<title>Fluorescence apertureless near-field microscope: a step toward imaging information in DNA</title> (2000)

Single molecule imaging with optical methods has become an important tool in biophysical studies. However, when imaging molecules at room temperature using far field optics, one can only resolve molecules that are separated by a distance greater than the diffraction limit of the microscope, about 220 nanometers. Near field techniques have allowed researchers to image with resolutions on the order of 30-50 nanometers. However, there are numerous reasons to try to push the resolution limit further. One that particular concerns our group is the \notion to try to image information in DNA in order to measure sequence information. To that end, we have developed a new type of near field microscope, the fluorescence apertureless near field microscope.
Workshop on Architecting Self-Managing Distributed Systems (2015)

Novel approaches in theory and practice of unified modeling of the computer and the computed in order to create self-managing adaptive computations, also parallel calls for new computing models to address distributed, interactive, concurrent dynamic processes are driving a new approach to distributed computing system design. ASDS workshop addresses these and other related approaches to increase the efficiency of computations in order to meet the challenges of high degree of scaling and large fluctuations. We believe that introducing elements of cognition into distributed computing systems that makes them "aware" of both the process intent and its evolution will enable self-managing capabilities to address both scale and fluctuations. The workshop brings together researchers in software architecture, computing and cognition to discuss and evaluate various approaches to introduce cognition into distributed computing elements.
Atomic Layer Deposition with TiO2 for Enhanced Reactivity and Stability of Aromatic Hydrogenation Catalysts (2021)

Hydrogenation of aromatic molecules in fossil- and bio-derived fuels is essential for decreasing emissions of harmful combustion products and addressing growing concerns around urban air pollution. In this work, we used atomic layer deposition to significantly enhance the hydrogenation performance of a conventional supported Pd catalyst by applying an ultrathin coating of TiO<sub>2</sub> in a scalable powder coating process. The TiO<sub>2</sub>-coated catalyst showed substantial gains in the conversion of multiple aromatic molecules, including a 5-fold improvement in turnover frequency versus the uncoated catalyst in the hydrogenation of naphthalene. This activity enhancement was maintained upon scaling the coating synthesis process from 3 to 100 g. Based on the results from X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, and computational modeling, the activity enhancement was attributed to ensemble effects resulting from partial TiO<sub>2</sub> coverage of the Pd surface rather than fundamental changes to the Pd electronic structure. Additional durability testing confirmed that the TiO<sub>2</sub> coating improved the thermal and hydrothermal stability of the catalyst as well as tolerance toward sulfur impurities in the reactant stream. Using an economic model of an industrial deep hydrogenation process, we found that an increase in catalyst activity or lifetime of 2x would justify even a relatively high estimate for the cost of TiO2 atomic layer deposition coatings at scale.
Reliable low-cost co-kriging modeling of microwave devices (2012)

A reliable methodology for accurate modeling of microwave devices is presented. Our approach exploits co-kriging which utilizes low- and high-fidelity EM simulation data and combines them into a single surrogate model. Densely sampled low-fidelity data determines a trend function which is further corrected by sparsely sampled high-fidelity simulations. Low-fidelity EM data is also enhanced by using a frequency scaling. With our method, accurate models can be obtained at a fraction of cost required by conventional approximation models that are exclusively based on high-fidelity simulations. Two cases of microstrip bandpass filters are considered. Comparisons with conventional approximation models as well as application examples are also given.
Boolean retrieval (2008)

Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced undergraduates and graduate students in computer science. Based on feedback from extensive classroom experience, the book has been carefully structured in order to make teaching more natural and effective. Slides and additional exercises (with solutions for lecturers) are also available through the book's supporting website to help course instructors prepare their lectures.
Mycobacterium tuberculosis Chaperonin 60.1 Inhibits Leukocyte Diapedesis in a Murine Model of Allergic Lung Inflammation (2012)

Chaperonin 60.1 from Mycobacterium tuberculosis suppressed allergic lung inflammation and bronchial hyperresponsiveness in mice by a mechanism that is yet to be clarified. To investigate the possible antiinflammatory mechanism(s) of action of Cpn60.1 in a model of allergic lung inflammation, ovalbumin (OVA)-allergic mice were pretreated with Cpn60.1 intranasally 20 minutes before each OVA aerosol challenge in a total of three treatments. Readouts were performed 24 hours after last challenge. Pretreatment with Cpn60.1 (1.0-0.001 μg) significantly inhibited the number of eosinophils in bronchoalveolar lavage fluid (OVA, 49.2 ± 12.3 versus Cpn60.1 [1 μg dose], 90.4 ± 2.3 × 10(4) cells/ml) and IL-5 release (OVA, 43 ± 8.5 versus Cpn60.1 [1 μg dose], 3 ± 11 pg/ml) but increased IL-12 levels (OVA, 50 ± 24 versus Cpn60.1 [1 μg dose], 103 ± 13 pg/ml). The effect of Cpn60.1 on cell recruitment and IL-5, but not IL-12, release was abolished in TLR-4 knockout mice. Intravital microscopy demonstrated that Cpn60.1 reduced chemokine-mediated leukocyte rolling and transmigration across the vessel wall (rolling cells: eotaxin, 11.7 ± 1.1 versus Cpn60.1 [1 μg dose], 2.8 ± 1 cells in 30 s). Similarly, Cpn60.1 reduced eotaxin-induced leukocyte migration in vitro (eotaxin, 17.3 ± 3.3 versus Cpn60.1 [0.1 μg dose], 3.3 ± 0.4 cells × 10(4)/ml). Immunostaining demonstrated that Cpn60.1 inhibits VCAM-1 and increases vascular endothelial-cadherin expression in lung vascular tissue, suggesting that the antiinflammatory effect of Cpn60.1 is partly mediated by altering the expression of adhesion molecules. This study shows that Cpn60.1 inhibits leukocyte diapedesis by a TLR-4 and an adhesion molecule-dependent mechanism in allergic inflammation in mice.
Improvement of Stabilized Efficiency of Amorphous Silicon Solar Cell by SiH2Cl2 Addition (1999)

The characteristics of mercury-sensitized photo-chemical vapor deposition (CVD) grown a-Si:H films and solar cells in the case of dichrolosilane (SiH 2 Cl 2 ) addition were investigated. The films with a small amount of SiH 2 Cl 2 addition exhibited high photosensitivity, low hydrogen content and low defect density. However, the cells with an i-layer grown by SiH 2 Cl 2 addition showed a low fill factor. It was also observed by secondary ion mass spectroscopy (SIMS) measurements that about 10 19 atom/cm 3 Cl was incorporated into a-Si:H films, even at the flow rate ratio of 0.01 (SiH 2 Cl 2 to SiH 4 ). Furthermore, it was found that the excess Cl in a-Si:H films was removed by H 2 dilution. In the case of H 2 dilution together with SiH 2 Cl 2 addition to the i-layer of a-Si solar cells, a high fill factor and high quantum efficiencies, particularly in the medium wavelength region was observed. From numerical analysis, it was determined that the improvement was due to the increase of the electric field in the medium of the i-layer after light soaking. As a result, we achieved a high stabilized efficiency of 9.0% for a 1 cm 2 single-junction a-Si:H solar cell.
Effect of Eye Movements on the Magnitude of fMRI Responses in Extrastriate Cortex during Visual Motion Perception (1996)

We have studied the effects of eye movements on the functional magnetic resonance imaging (fMRI) response during global dot motion in extrastriate temporo-occipital cortex. Susceptibility-based functional magnetic resonance, applying gradient-recalled echo-planar imaging (EPI) sequences, was conducted, in 12 volunteers who viewed episodes of moving dots. Anatomical and functional images were recorded with a 1.5 T Siemens Magnetom Vision (TR 5000 ms, TE 70 ms, flip angle 90°, FOV 250 mm, matrix 112 × 128, twelve 4-mm slices parallel to ac — pc plane, ranging from z=-14 – 34 mm). Sagittal T1-weighted images were acquired to determine the ac — pc plane and important anatomical landmarks. Eye movements were monitored with the use of MR-compatible EOG electrodes. Stimuli were back-projected onto a translucent screen and viewed through prisms. The four test conditions were: fronto-parallel motion, during fixation and during target pursuit; expansion-contraction motion, also during fixation and during pursuit. Pixelwise t-tests were performed on functional series recorded during rest and stimulation periods (50 s each) to identify significantly activated voxels. Planes −8 to +8 mm around the ac — pc plane and 20 – 28 mm superior to ac — pc were activated most by visual motion. In addition to primary visual cortical areas, a ventral area in the temporo-occipital cortex (human MT) responded well to both types of visual motion and these responses were enhanced by eye movements. Human MST, located dorsal of MT, showed activation by visual motion during fixation. Its response was also enhanced by pursuit.
Temperature-dependent fluorescence decay lifetimes of the phosphor Y3(Al0.5Ga0.5)5O12:Ce 1% (2009)

The decay time of the phosphor yttrium aluminum garnet doped with cerium (YAG:Ce) is temperature dependent. Selective incorporation of gallium into the YAG:Ce matrix permits tuning the temperature at which quenching begins. Also, the size of the phosphor particle and processing method affect this characteristic. We describe one such situation in which the quenching of the combustion synthesized nanophosphor Y3(Al0.5Ga0.5)5O12:Ce 1% was observed from ambient to 125 °C. By signal averaging of laser excited fluorescence, temperature uncertainties ranged from 0.05 to 0.15 °C. The single shot temperature uncertainty at 115 °C was ±3 °C, indicating the feasibility for transient thermometry with response rate exceeding 1 MHz.
Micromagnetics of Spin-Flop Bilayers: S, C, and Vortex Spin States (2010)

Spin-flop tunnel junctions subjected to strong gigahertz excitations are found to exhibit highly stable resistance states, intermediate between the two spin-uniform ground states of high and low resistance. The associated spin distributions are necessarily nonuniform and differ significantly from the ground-state anti-parallel spin configuration in their static and dynamic properties. Detailed micromagnetic modeling reveals that inplane spin vortices in dipole-coupled thin-film bilayers are stable spin configurations, where the orientation of the vortex cores and the vortex chirality play an important role in the response of the system to external magnetic fields.
Biomolecular Engineering I: Biotechnology (2018)

The second edition of this popular introductory undergraduate textbook uses examples, applications, and profiles of biomedical engineers to show students the relevance of the theory and how it can be used to solve real problems in human medicine. The essential molecular biology, cellular biology, and human physiology background is included for students to understand the context in which biomedical engineers work. Updates throughout highlight important advances made over recent years, including iPS cells, microRNA, nanomedicine, imaging technology, biosensors, and drug delivery systems, giving students a modern description of the various subfields of biomedical engineering. Over two hundred quantitative and qualitative exercises, many new to this edition, help consolidate learning, whilst a solutions manual, password-protected for instructors, is available online. Finally, students can enjoy an expanded set of leader profiles in biomedical engineering within the book, showcasing the broad range of career paths open to students who make biomedical engineering their calling.
Inelastic Scattering (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Effects of Fluid Insert Volume Changes on Socket Pressures and Shear Stresses (2006)

Fluid inserts potentially help to overcome prosthetic fit problems resulting from stump volume change. The purpose of this investigation was to add fluid to fluid inserts positioned on the inner socket walls of trans-tibial prostheses and to assess their influence on socket stresses. Pressures and shear stresses were measured at 13 sites on the sockets of two trans-tibial amputee subjects while they ambulated at their self-selected walking speeds. Stresses at the transducer sites generally increased with greater fluid addition and, interestingly, both subjects found relatively high fluid insert volumes most comfortable. The magnitudes of stress change were larger than those resulting from alignment, cadence, and componentry changes as reported in the literature. Possible explanations for why subjects found settings that induced higher measured socket stresses more comfortable than those that induced lower measured stresses include: A reduced shear: pressure ratio; the short duration of the study; and reduced stresses at sites not monitored with transducers.
Insight into Fe Incorporation in Li3V2(PO4)3/C Cathode Material (2012)

The profile of Fe-incorporation into carbon-coated Li3V2(PO4)3 (LVP) cathode material for lithium ion batteries has been systematically investigated with X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectrometry and electrochemical measurements. The results confirm the coexistence of Li3+xV2–yFe2+y(PO4)3, LiFePO4 and FePO4 in the Fe-incorporated LVP/C composite. The FePO4 appears to be present as an amorphous phase associated with the carbon coat. Compared with pristine LVP/C, significant improvement in capacity, cycling stability, and rate capability in LVP/C-Fe were achieved, which is attributed to the reduced particle size, a decreased electrolyte/electrode charge-transfer resistance, and a suppressed electrolyte/electrode reaction at high voltage.
Properties of the CdSe(0001), (0001), and (1120) Single Crystal Surfaces:  Relaxation, Reconstruction, and Adatom and Admolecule Adsorption (2005)

Details of the chemical mechanism underlying the growth of colloidal semiconductor nanocrystals remain poorly understood. To provide insight into the subject, we have preformed a comprehensive study of the polar (0001) and (0001) and nonpolar (1120) wurtzite CdSe surfaces that are exposed during crystal growth using first-principles density functional theory (DFT-GGA) calculations. Stabilization of these surfaces by relaxation and reconstruction was considered. Two particular reconstructions of the polar surfaces were examined: vacancy formation on a 2 x 2 unit cell and addition of Se and Cd atoms on the (0001) and (0001) surfaces, respectively. Calculation results indicate that the (1120) is the most stable surface when compared to the two polar surfaces. Furthermore, reconstructions of the (0001) surface are energetically favored when compared to reconstructions of the (0001) facet. Adsorption of Cd and Se atoms and the CdSe molecule on the three relaxed surfaces and two reconstructed (0001) surfaces were also investigated. Several binding sites were considered to determine the most stable binding geometries and energetics. Atomic species preferentially bind in either 2-fold or 3-fold sites, while the CdSe molecule binds parallel to the surface on all of the considered surfaces. Vibrational frequencies of the adspecies were calculated for the most stable binding configurations and were included in the zero point energy correction. Diffusion barriers for the atomic and molecular species were estimated where possible to be between 0.2 and 0.4 eV on the three relaxed surfaces. Thermochemistry of the CdSe molecule binding and dissociation was also investigated. On all considered surfaces, dissociation is preferred to desorption with dissociation only exothermic on the (0001) surface. Comparison of the three relaxed and two reconstructed surfaces indicates that CdSe molecule binding and dissociation is thermodynamically favored on the (0001) surface. This implies that under a reaction-controlled regime, the rate of homoepitaxy would be faster on the (0001) Se terminated surface than on the (0001) and (1120) surfaces, making the (0001) surface of a nanocrystal the primary direction of growth.
Josephson Junction Field-Effect Transistors for Boolean Logic Cryogenic Applications (2019)

Josephson junction FETs (JJ-FETs) share design similarities with MOSFETs, except for the source/drain contacts being replaced by superconductors. Similarly, the super current due to proximity effect is tunable by the gate voltage. In light of recent advances in novel materials and fabrication techniques, we examine here the feasibility of JJ-FET-based Boolean logic and memory elements for cryogenic computing. Using a 2-D ballistic transport JJ-FET model, we implement circuit-level simulations for JJ-FET logic gates and discuss criteria for realizing signal restoration, as well as fan-out. We show that the JJ-FET is a promising candidate for very low-power, clocked voltage-level dynamic logic at cryogenic temperatures.
Fast prototyping and refinement of complex dynamic data types in multimedia applications for consumer embedded devices (2005)

Portable consumer devices are increasing their capabilities more and more and can now implement new multimedia algorithms that were reserved only for powerful workstations a few years ago. Unfortunately, the original design characteristics of such algorithms do not often allow them to be ported directly to current embedded devices. These algorithms share complex and intensive dynamic memory use and actual embedded systems cannot provide efficient general-purpose memory management as it is needed. As a result, dynamic memory optimizations are a requirement when porting these applications. Within these optimizations, the refinement of the dynamically (de)allocated abstract data type implementations in the complex multimedia applications involved is one of the most important and difficult parts for an efficient mapping of the algorithms on low-power and high-speed embedded consumer devices. We describe a high-level approach for modeling and refining complex data types using abstract derived classes in C++. This approach enables the multimedia developer to compose, evaluate and refine complex data types in a conceptually straightforward way, without a time-consuming programming effort