gebhart/patrepeval huggingface dataset:
Efficient Hyper-parameter Optimization for NLP Applications (2015)

Hyper-parameter optimization is an important problem in natural language processing (NLP) and machine learning. Recently, a group of studies has focused on using sequential Bayesian Optimization to solve this problem, which aims to reduce the number of iterations and trials required during the optimization process. In this paper, we explore this problem from a different angle, and propose a multi-stage hyper-parameter optimization that breaks the problem into multiple stages with increasingly amounts of data. Early stage provides fast estimates of good candidates which are used to initialize later stages for better performance and speed. We demonstrate the utility of this new algorithm by evaluating its speed and accuracy against state-of-the-art Bayesian Optimization algorithms on classification and prediction tasks.
Zinc cyanamide, Zn(CN<sub>2</sub>) (2001)

Single crystals of the title compound have been grown by annealing microcrystalline zinc cyanamide at 843 K in silver crucibles. Zn(CN(2)) crystallizes as colourless prisms. The crystal structure is composed of corner-linked ZnN(4/2) tetrahedra. Carbon and nitrogen form (CN(2))(2-) dumb-bells with the C atom on a twofold axis. Nitrogen is approximately trigonally planar, coordinated by two Zn atoms and one C atom.
LDAP Directory Template Model on Multi-master Replication (2010)

LDAP Multi-Master Technique is a replication approach using Syncrepl to replicate data to multiple servers. As the specialized database optimized for read access, the directory is used to represent heterogeneous entities in directory information tree (DIT). Compared with existing Sync replication models, the directory template replication model based on query templates proposed in this paper only replicates the entries matching the template specification. Replicated templates can reduce the complexity of the query containment problem and generalize the user queries corresponding to semantic regions demonstrating locality of reference. The synchronization protocol, which uses standard means of extending LDAP, is used to support (N-way) Multi-Master server replication modes. In this case, masters can be located in several physical sites, and other masters will continue the database if one master fails. Finally, we demonstrate the advantages of the novel model considering higher hit rates and the large update traffic with an experimental study based on real data and a prototype implementation of the LDAP directory cache.
Are MAP Kinases Drug Targets? Yes, but Difficult Ones (2007)

Pharmaceutical companies are facing an increasing interest in new target identification and validation. In particular, extensive efforts are being made in the field of protein kinase inhibitors research and development, and the past ten years of effort in this field have altered our perception of the potential of kinases as drug targets. Therefore, in the drug discovery process, the selection of relevant, susceptible protein kinase targets combined with searches for leads and candidates have become a crucial approach. The success of recent launches of protein kinase inhibitors (Gleevec, Imatinib, Sutent, Iressa, Nexavar, Sprycel) gave another push to this field. Numerous other kinase inhibitors are currently undergoing clinical trials or clinical development. Some questions are nevertheless unanswered, mostly related to the great number of known kinases in the human genome, to their similarity with each other, to the existence of functionally redundant kinases for specific pathways, and also because the connection between particular pathways and diseases is not always clear. The review is leading the reader through a panoramic view of protein kinase inhibition with a major focus on MAPK, successful examples and clinical candidates.
Key Motif to Gain Selectivity at the Neuropeptide Y<sub>5</sub>-Receptor:  Structure and Dynamics of Micelle-Bound [Ala<sup>31</sup>, Pro<sup>32</sup>]-NPY<sup>,</sup> (2002)

The structure of [Ala(31), Pro(32)]-NPY, a neuropeptide Y mutant with selectivity for the NPY Y(5)-receptor (Cabrele, C., Wieland, H. A., Stidsen, C., Beck-Sickinger, A. G., (2002) Biochemistry XX, XXXX-XXXX (companion paper)), has been characterized in the presence of the membrane mimetic dodecylphosphocholine (DPC) micelles using high-resolution NMR techniques. The overall topology closely resembles the fold of the previously described Y(5)-receptor-selective agonist [Ala(31), Aib(32)]-NPY (Cabrele, C., Langer, M., Bader, R., Wieland, H. A., Doods, H. N., Zerbe, O., and Beck-Sickinger, A. G. (2000) J. Biol. Chem 275, 36043-36048). Similar to wild-type neuropeptide Y (NPY) and [Ala(31), Aib(32)]-NPY, the N-terminal residues Tyr(1)-Asp(16) are disordered in solution. Starting from residue Leu(17), an alpha helix extends toward the C-terminus. The decreased density of medium-range NOEs for the C-terminal residues resulting in larger RMSD values for the backbone atoms of Ala(31)-Tyr(36) indicates that the alpha helix has become interrupted through the [Ala(31), Pro(32)] mutation. This finding is further supported by (15)N-relaxation data through which we can demonstrate that the well-defined alpha helix is restricted to residues 17-31, with the C-terminal tetrapeptide displaying increased flexibility as compared to NPY. Surprisingly, increased generalized order parameter as well as decreased (3)J(HN)(alpha) scalar coupling constants reveal that the central helix is stabilized in comparison to wild-type NPY. Micelle-integrating spin labels were used to probe the mode of association of the helix with the membrane mimetic. The Y(5)-receptor-selective mutant and NPY share a similar orientation, which is parallel to the lipid surface. However, signal reductions due to efficient electron, nuclear spin relaxation were much less pronounced for the surface-averted residues in [Ala(31), Pro(32)]-NPY when compared to wild-type DPC-bound NPY. Only the signals of residues Asn(29) and Leu(30) were significantly more reduced in the mutant. The postulation of a different membrane binding mode of [Ala(31), Pro(32)]-NPY is further supported by the faster H/D exchange at the C-terminal amide protons. We conclude that arginine residues 33 and 35, which are believed to be directly involved in forming contacts to acidic receptor residues at the membrane-water interface, are no longer fixed in a well-defined conformation close to the membrane surface in [Ala(31), Pro(32)]-NPY.
Biocompatibility of a Novel Poly(butyl succinate) and Polylactic Acid Blend (2012)

A novel poly(butyl succinate) (PBS) and polylactic acid (PLA) blend with the favorable mechanical and degradable properties may be applied in the field of biomedicine. The purpose of this study was to investigate the in vitro and in vivo biocompatibilities of the PBS/PLA blend for future application. For in vitro analysis, the L929 fibroblasts and bone marrow stem cells (BMSCs) had been chosen to assess the cytocompatibility. The extract of PBS/PLA blend did not show any cytotoxicity to the L929 and BMSCs by Cell Counting Kit-8 and lactate dehydrogenase assays. Meanwhile, the results of the cytocompatibility showed no difference between the PBA/PLA blend and pure PLA and PBS. Subsequently, they were implanted into rats subcutaneously for in vivo study. It was found that similar with pure PLA and PBS, PBS/PLA blend caused the mild inflammation and foreign body reaction in rats during the consecutive 9 month implantation. However, the status of fibrosis surrounding PBS/PLA blend was superior to the pure PLA and PBS. In all, it was demonstrated that the novel PBS/PLA blend had excellent biocompatibilities in vitro and in vivo.
Comparing, optimizing, and benchmarking quantum-control algorithms in a unifying programming framework (2011)

For paving the way to novel applications in quantum simulation, computation, and technology, increasingly large quantum systems have to be steered with high precision. It is a typical task amenable to numerical optimal control to turn the time course of pulses, i.e., piecewise constant control amplitudes, iteratively into an optimized shape. Here, we present a comparative study of optimal-control algorithms for a wide range of finite-dimensional applications. We focus on the most commonly used algorithms: GRAPE methods which update all controls concurrently, and Krotov-type methods which do so sequentially. Guidelines for their use are given and open research questions are pointed out. Moreover, we introduce a unifying algorithmic framework, DYNAMO (dynamic optimization platform), designed to provide the quantum-technology community with a convenient matlab-based tool set for optimal control. In addition, it gives researchers in optimal-control techniques a framework for benchmarking and comparing newly proposed algorithms with the state of the art. It allows a mix-and-match approach with various types of gradients, update and step-size methods as well as subspace choices. Open-source code including examples is made available at http://qlib.info.
Manipulating Molecular Transport through Nanoporous Membranes by Control of Electrokinetic Flow:  Effect of Surface Charge Density and Debye Length (2001)

Molecular transport through nanoporous nuclear-track-etched membranes was investigated with fluorescent probes by manipulating applied electric field polarity, pore size, membrane surface functionality, pH, and the ionic strength. Three forces contribute to analyte transport through membranes: ion migration, electroosmosis, and diffusion. Diffusion dominates under field-free conditions with surface hydrophobicity controlling solvent access to the nanochannels and hence the magnitude of transport by diffusion. In low ionic strength solutions (μ ∼ 10 mM), electroosmosis dominates transport when the membranes are biased, and the charge state of the surface determines the direction of flow. At high ionic strength (μ ∼ 1 M), ion migration dominates in hydrophobic membranes, and diffusion is controlling in hydrophilic membranes. The magnitude and polarity of the interior surface charge is controlled by surface functionality and displays the largest impact on molecular transport. The analyte can migrate in opposite directions under the same applied electric field by modifying either membrane surface charge or solution ionic strength. Transport can be fine-tuned by adjusting pH under low ionic strength conditions in either type of membrane. Increasing the surface charge density, σs, enhances the mobile counterion concentration, increasing the electroosmotically driven flux. Comparisons of behavior under different conditions are understood by reference to the product, κa, of the inverse Debye length, κ, and the pore diameter, a.
Investigation of Crystal Defects in Lead Zirconate Titanate Films by Thermally Stimulated Current Measurement (2007)

Pb(Zr, Ti)O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (PZT) ferroelectric thin films have been extensively investigated because of their potential for FeRAM and MEMS device applications. However, realization of high performance devices has not been achieved due to degradation problems for the PZT films, such as fatigue and imprinting. The degradation is caused by crystal defects in the films, however, properties of the defects have not yet been sufficiently clarified. We have therefore attempted to investigate crystal defects in PZT films by thermally stimulated current (TSC) measurements. Current peaks due to the defects were detected in the measurements, and the origin of the observed defects was identified by systematic evaluation. It was revealed that the activation energy of the TSC peaks ranged from 0.75 eV to 0.95 eV, and the peaks were related to PbOx defects at the interface between the electrodes and the PZT layer.
Characterization of Corticosterone Feedback Regulation of ACTH Secretiona (1987)

Adrenalectomy-induced increases in ACTH secretion in rats are returned to normal by an action of corticosterone on the brain, not on the pituitary. Five days after adrenalectomy with constant steroid replacement, the concentration of free corticosterone in plasma which reduces plasma ACTH by 50% is approximately 0.8 nM. By contrast, the concentration of free plasma corticosterone required for 50% reduction of thymus wet weight or plasma transcortin concentration (both targets for glucocorticoid action) is about 4.5 nM. These results suggested that the inhibition of ACTH by corticosterone might be mediated by association of the steroid with high affinity, type I corticosteroid receptors, whereas the inhibition of thymus weight and transcortin might be mediated by association of the steroid with lower affinity, type II receptors. The results of studies comparing the ability of corticosterone, dexamethasone and aldosterone to inhibit adrenalectomy-induced ACTH secretion support the hypothesis that basal ACTH secretion in rats is mediated by association of corticosterone with type I receptors.
Double-reflection polygon mirror for high-speed optical coherence microscopy (2007)

We report on a high-speed, high-efficiency, high-duty-cycle, path-length-maintaining and linear beam scanner suitable for en face scanning optical coherence microscopy. Fast transverse beam scanning is achieved by use of a double-reflection polygon mirror (DRPM) rotating at a constant speed. With a motor speed of 18,000 rpm and a scanner diameter of 50 mm, the DRPM provides a line rate up to 3 kHz, +/-1.8 degrees scanning range, and 90% duty cycle. A much higher scanning speed and much larger scanning range can be readily achieved by increasing the scanner diameter.
Structural use of Glass (2008)

<p>Recent architectural trends and technological developments have brought about unprecedented opportunities and exciting changes in the use of glass in buildings. <p>Structural engineers currently have a bewildering array of glass products and configurations to choose from and a wide range of normal and exceptional loading conditions to consider, but very few unified reference texts for undertaking these tasks. This book attempts to redress this issue by providing an overview of the recent developments in this field thereby providing a basis for the understanding of the structural performance and design of glass in buildings. <p>Each chapter draws on the latest developments in practice and research and contains contributions from various international glass experts. The mix of general and specialist content ranging from rules of thumb to fracture mechanics and novel applications to post-breakage performance make this book useful to practitioners and researchers. Furthermore, the text is supplemented by tables of the major codes of practice and by an extensive list of references. <p>The book is primarily for structural engineers and researchers who have an interest in structural glass. It will be used by senior undergraduates, post-graduate students, researchers and practicing engineers.
Synthesis and Characterization of Metallic Nanoparticles Stabilized with Polyvinylpirrolidone (2005)

Extract HTML view is not available for this content. However, as you have access to this content, a full PDF is available via the 'Save PDF' action button. Extended abstract of a paper presented at Microscopy and Microanalysis 2005 in Honolulu, Hawaii, USA, July 31--August 4, 2005
Piezoelectric PDMS films for power MEMS (2011)

We have successfully demonstrated the fabrication of piezoelectric PDMS films utilizing casting, stacking, and micro plasma discharge processes. To realize electromechanical sensitivity, PDMS structures with micrometer-sized cells are implanted with positive and negative charges on the opposite internal surfaces of each cell, which behaves just like a dipole. In the prototype demonstration, multilayer PDMS films with inner cells of 50×50×50 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> are fabricated and charged under electric fields up to 40 MV/m. The resulting cellular PDMS films show an elastic modulus of at least 12% lower than solid ones and a piezoelectric coefficient (d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">33</sub> ) up to 182 pC/N, which is about 10 times higher than that of common piezoelectric polymers (e.g., PVDF). As such, the demonstrated piezoelectric PDMS films could serve as soft and sensitive electromechanical transducers, which are desired for a variety of sensor and energy har- vesting applications.
Absence of Proton Channels in COS-7 Cells Expressing Functional NADPH Oxidase Components (2002)

Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase is an enzyme of phagocytes that produces bactericidal superoxide anion (O(2)(-)) via an electrogenic process. Proton efflux compensates for the charge movement across the cell membrane. The proton channel responsible for the H(+) efflux was thought to be contained within the gp91(phox) subunit of NADPH oxidase, but recent data do not support this idea (DeCoursey, T.E., V.V. Cherny, D. Morgan, B.Z. Katz, and M.C. Dinauer. 2001. J. Biol. Chem. 276:36063-36066). In this study, we investigated electrophysiological properties and superoxide production of COS-7 cells transfected with all NADPH oxidase components required for enzyme function (COS(phox)). The 7D5 antibody, which detects an extracellular epitope of the gp91(phox) protein, labeled 96-98% of COS(phox) cells. NADPH oxidase was functional because COS(phox) (but not COS(WT)) cells stimulated by phorbol myristate acetate (PMA) or arachidonic acid (AA) produced superoxide anion. No proton currents were detected in either wild-type COS-7 cells (COS(WT)) or COS(phox) cells studied at pH(o) 7.0 and pH(i) 5.5 or 7.0. Anion currents that decayed at voltages positive to 40 mV were the only currents observed. PMA or AA did not elicit detectable H(+) current in COS(WT) or COS(phox) cells. Therefore, gp91(phox) does not function as a proton channel in unstimulated cells or in activated cells with a demonstrably functional oxidase.
Correction: Alanine Scanning Site-Directed Mutagenesis of the Zinc Fingers of Transcription Factor ADR1: Residues that Contact DNA and that Transactivate (1993)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Dehydroascorbic acid uptake in a human keratinocyte cell line (HaCaT) is glutathione-independent (2000)

Vitamin C plays an important role in neutralizing toxic free radicals formed during oxidative metabolism or UV exposure of human skin. This study was performed to investigate the mechanisms that regulate the homoeostasis of vitamin C in HaCaT cells by identifying the events involved in the transport and in the reduction of dehydroascorbic acid. Dehydroascorbic acid accumulated to a greater extent and faster compared with ascorbic acid; its transport appeared to be mediated by hexose transporters and was entirely distinct from ascorbic acid transport. Dehydroascorbate reductase activity was unaffected by glutathione depletion, although it was sensitive to thiol protein reagents. These observations, as well as the subcellular distribution of this enzymic activity and the cofactor specificity, indicate that thioredoxin reductase and lipoamide dehydrogenase play an important role in this reduction process. HaCaT cells were able to enhance their dehydroascorbic acid reductase activity in response to oxidative stress.
Driver Drowsiness Detection Based on Time Series Analysis of Steering Wheel Angular Velocity (2017)

A novel driver drowsiness detection method based on time series analysis of the steering wheel angular velocity is proposed in this paper. Firstly, the steering behavior under the fatigue state is analyzed, followed by the determination of the temporal detection window, and then, the data series of the steering wheel angular velocity in the temporal detection window is selected as the detection feature. IF the detection feature satisfies the extent constraint and the variability constraint in the temporal window, a drowsiness state is detected accordingly. At last, experiment tests validate our method has good performance and could be well used in the real world.
Functional characterization of T-cells from palatine tonsils in patients with chronic tonsillitis (2017)

The palatine tonsils, localized in the oropharynx, are easily accessible secondary lymphoid tissue in humans. Inflammation of the palatine tonsils, local and chronic in case of chronic tonsillitis (CT) or acute in the presence of a peritonsillar abscess (PTA), ranks among the most common diseases in otolaryngology. However, the functionality of tonsillar immune cells, notably T-cells, in the context of these immune pathologies is poorly understood. We have examined the functional status of human tonsillar T-cells in CT and compared it to the acute inflammatory setting of a PTA. Patients presenting with CT (n = 10) or unilateral PTA (n = 7) underwent bilateral tonsillectomy and a subgroup of 8 patients underwent additional blood sampling. T-cells were purified via automated magnetic selection and subjected to flow cytometry-based immunophenotyping. In addition, the response to T-cell receptor (TCR) stimulation was assessed at the level of proximal signaling, activation marker expression and proliferation. We observed no difference between the percentage of T helper (CD4(+)) cells from tonsil tissue in CT and PTA, but observed a trend towards a higher percentage of T helper cells in the blood of patients with PTA versus CT, probably reflecting an acute, systemic bacterial infection in the former cohort. Tonsils from CT harbored more PD-1(+) CD4(+) T-cells, pointing to T-cell exhaustion due to chronic infection. This notion was supported by functional studies that showed a tendency to weaker TCR responses of tonsillar T-cells from CT. Intriguingly, tonsillar T-cells recurrently featured a dampened response to T-cell receptor stimulation at the level of receptor proximal signaling steps compared to peripheral T-cells. In sum, our study documents distinct differences in tonsillar T-cell class distribution and function between the various pathological conditions. Our observations are consistent with the concept that tonsillar T-cells react to infections by eliciting specific immunological responses in chronic versus acute settings of inflammation.
Variations in Postprandial Ghrelin Status following Ingestion of High-Carbohydrate, High-Fat, and High-Protein Meals in Males (2006)

These results indicate that the nutrient composition of meals affects the extent of suppression of postprandial ghrelin levels and that partial substitution of dietary protein for carbohydrate or fat may promote longer-term postprandial ghrelin suppression and satiety. Our results also support the possible role of insulin in meal-induced ghrelin suppression.
GPU-Euler: Sequence Assembly Using GPGPU (2011)

Advances in sequencing technologies have revolutionized the field of genomics by providing cost effective and high throughput solutions. In this paper, we develop a parallel sequence assembler implemented on general purpose graphic processor units (GPUs). Our work was largely motivated by a growing need in the genomic community for sequence assemblers and increasing use of GPUs for general purpose computing applications. We investigated the implementation challenges, and possible solutions for a data parallel approach for sequence assembly. We implemented an Eulerian-based sequence assembler (GPU-Euler) on the nVidia GPUs using the CUDA programming interface. GPU-Euler was benchmarked on three bacterial genomes using input reads representing the new generation of sequencing approaches. Our empirical evaluation showed that GPU-Euler produced lower run times, and comparable performance in terms of contig length statistics to other serial assemblers. We were able to demonstrate the promise of using GPUs for genome assembly, a computationally intensive task.