gebhart/patrepeval huggingface dataset:
Optimal loop unrolling for GPGPU programs (2010)

Graphics Processing Units (GPUs) are massively parallel, many-core processors with tremendous computational power and very high memory bandwidth. With the advent of general purpose programming models such as NVIDIA's CUDA and the new standard OpenCL, general purpose programming using GPUs (GPGPU) has become very popular. However, the GPU architecture and programming model have brought along with it many new challenges and opportunities for compiler optimizations. One such classical optimization is loop unrolling. Current GPU compilers perform limited loop unrolling. In this paper, we attempt to understand the impact of loop unrolling on GPGPU programs. We develop a semi-automatic, compile-time approach for identifying optimal unroll factors for suitable loops in GPGPU programs. In addition, we propose techniques for reducing the number of unroll factors evaluated, based on the characteristics of the program being compiled and the device being compiled to. We use these techniques to evaluate the effect of loop unrolling on a range of GPGPU programs and show that we correctly identify the optimal unroll factors. The optimized versions run up to 70 percent faster than the unoptimized versions.
ON MECHANISMS OF ENERGY DISSIPATION AND TRANSFER IN MEMS VIBRATORY GYROSCOPES OPERATED IN VACUUM (2008)

In this paper, we study mechanisms of energy transfer and dissipation in SOI bulk micromachined vibratory gyroscopes. Existing publications on vibratory MEMS mainly focus on viscous and thermoelastic dissipation of energy, [1,2]; limited literature is available on non-viscous damping mechanisms. This work aims to provide some additional insight into non-viscous energy loss mechanisms, specifically focusing on energy transfer from the device die to the package. Figure 1(a) shows an SOI micromachined gyroscope used for the experimental study. The drive-mode of the gyroscope is a 2-DOF dynamically coupled system with an in-phase and anti-phase mode. The sense-mode consists of two 2-DOF systems for improved robustness [3]. The limiting non-viscous quality factor Qlim of most MEMS gyroscopes measured in vacuum is in the range of 10 4 i 10 5 , which is often attributed to thermoelastic dissipation, [2]. In the first part of this study, thermoelastic dissipation in the gyroscope was modeled numerically using COMSOL Multiphysics. Finite Element Modeling (FEM) of the gyroscope’s in-phase and anti-phase modes are shown in Figure 1(b) and Figure 1(c), respectively. For both the in-phase and the anti-phase modes thermoelastic damping (TED), QTED … 10 6 , that is several orders of magnitude higher than the commonly observed Qlim. These results suggest that there exists a different non-viscous energy loss mechanism, such as energy dissipation through support or anchors. A vacuum setup shown in Figure 2(a) was used for the experiments. Quality factor as a function of pressure Q(P) and the limiting non-viscous quality factor Qlim were measured for both the in-phase and the anti-phase modes of the gyroscope. A comparative study of the measurements is presented in Figure 2(b) and reveals the following trends. The quality factor of the in-phase mode operated devices is limited to 0:5 ⁄ 10 4 i 10 4 ; it is strongly dependent on the die attachment technique and is thus attributed to the dissipation of energy through the support. The quality factor of the anti-phase mode does not show significant dependency on the die attachment technique. In the tested range of vacuum it is governed by the viscous damping laws, Q(P) / 1=P , and measures 70;000 at 20 mTorr. We experimentally identified dissipation through the die support as the dominant limiting damping mechanism in in-phase driven gyroscopes. This loss mechanism depends strongly on the die attachment technique, where more rigid die attachment decreases the dissipation at the cost of decreased isolation of the MEMS device from external vibrations. Anti-phase operation decreases dissipation through support by orders of magnitude and provides inherent robustness to external vibrations [3].
Automated Determination of Stellar Population Parameters in Galaxies Using Active Instance-based Learning (2003)

In this work we focus on the determination of the relative distributions of young, intermediate-age and old populations of stars in galaxies. Starting from a grid of theoretical population synthesis models we constructed a set of model galaxies with a distribution of ages, metallicities and intrinsic reddening. Using this set we have explored a new fitting method that presents several advantages over conventional methods. We propose an optimization technique that combines active learning with an instance-based machine learning algorithm. Experimental results show that this method can estimate with high speed and accuracy the physical parameters of the stellar populations.
Thermal Control Architecture for a Planetary and Lunar Surface Exploration Micro-Robot (2007)

A thermal control architecture design study is conducted for a novel robotic planetary and lunar surface exploration concept. The concept is based on the deployment of a large number of small spherical mobile robots over large areas, which employ hopping, bouncing and rolling as means of locomotion. The aim of the research is to prevent freezing and overheating of the robots, without compromising their mechanical and thermal reliability and stability. The proposed thermal control architecture relies on a low emissive silver surface coating and a low conductive silica aerogel insulation layer. This enables a single design to be used for several important potential explorations. The effects of a thermal control heat rejection mechanism, composed of a variable emittance coating and heat switch, are also studied in order to increase mission flexibility.
Mathematical Analysis of Induction Coils'Motion State of Ballistic Galvanometer (2007)

This paper briefly introduced the working principle of ballistic galvanometer.Using the mathematical methods and the electromagnetic knowledge it studied the motion state of the ballistic galvanometer's induction coils in the magnetic field,and inferred physical quantity formulas to describe various motion states and indicate the movement rules.
Longitudinal End Effects in a Linear Wave Power Generator (2020)

Even though the magnetic circuit of a linear electric machine is very similar to a rotating electric machine, they diverge in one fundamental property. The linear generator is open in both ends, i.e., the magnetic circuit is non-symmetric. This paper investigates and discusses the drawbacks of this non-symmetric design in a linear permanent magnet generator, installed in a wave energy conversion system. A two-dimensional geometry has been utilized for the numerical calculations in a finite element method simulation tool. The results present an increased cogging force and significant core losses in the translator as consequences of the longitudinal ends in the machine.
Bioactive Carbonate Apatite Cement with Enhanced Compressive Strength via Incorporation of Silica Calcium Phosphate Composites and Calcium Hydroxide (2023)

Carbonate apatite (CO<sub>3</sub>Ap) is a bioceramic material with excellent properties for bone and dentin regeneration. To enhance its mechanical strength and bioactivity, silica calcium phosphate composites (Si-CaP) and calcium hydroxide (Ca(OH)<sub>2</sub>) were added to CO<sub>3</sub>Ap cement. The aim of this study was to investigate the effect of Si-CaP and Ca(OH)<sub>2</sub> on the mechanical properties in terms of the compressive strength and biological characteristics of CO<sub>3</sub>Ap cement, specifically the formation of an apatite layer and the exchange of Ca, P, and Si elements. Five groups were prepared by mixing CO<sub>3</sub>Ap powder consisting of dicalcium phosphate anhydrous and vaterite powder added by varying ratios of Si-CaP and Ca(OH)<sub>2</sub> and 0.2 mol/L Na<sub>2</sub>HPO<sub>4</sub> as a liquid. All groups underwent compressive strength testing, and the group with the highest strength was evaluated for bioactivity by soaking it in simulated body fluid (SBF) for one, seven, 14, and 21 days. The group that added 3% Si-CaP and 7% Ca(OH)<sub>2</sub> had the highest compressive strength among the groups. SEM analysis revealed the formation of needle-like apatite crystals from the first day of SBF soaking, and EDS analysis indicated an increase in Ca, P, and Si elements. XRD and FTIR analyses confirmed the presence of apatite. This combination of additives improved the compressive strength and showed the good bioactivity performance of CO<sub>3</sub>Ap cement, making it a potential biomaterial for bone and dental engineering applications.
Adeno-associated virus-mediated gene therapy in a patient with Canavan disease using dual routes of administration and immune modulation (2023)

Gene replacement therapy is a rational therapeutic strategy and clinical intervention for neurodegenerative disorders like Canavan disease, a leukodystrophy caused by biallelic mutations in the aspartoacylase (<i>ASPA</i>) gene. We aimed to investigate whether simultaneous intravenous (i.v.) and intracerebroventricular (i.c.v.) administration of rAAV9-CB6-ASPA provides a safe and effective therapeutic strategy in an open-label, individual-patient, expanded-access trial for Canavan disease. Immunomodulation was given prophylactically prior to adeno-associated virus (AAV) treatment to prevent an immune response to ASPA or the vector capsid. The patient served as his own control, and change from baseline was assessed by clinical pathology tests, vector genomes in the blood, antibodies against ASPA and AAV capsids, levels of cerebrospinal fluid (CSF) <i>N</i>-acetylaspartate (NAA), brain water content and morphology, clinical status, and motor function tests. Two years post treatment, the patient's white matter myelination had increased, motor function was improved, and he remained free of typical severe epilepsy. NAA level was reduced at 3 months and remained stable up to 4 years post treatment. Immunomodulation prior to AAV exposure enables repeat dosing and has prevented an anti-transgene immune response. Dual-route administration of gene therapy may improve treatment outcomes.
Involvement of Electron Transfer in the Radical-scavenging Reaction of Resveratrol (2007)

Abstract Resveratrol (3,4′,5-trihydroxy-trans-stilbene) efficiently scavenges an oxygen radical via an electron transfer from resveratrol to the radical in deaerated acetonitrile, which is significantly accelerated by the presence of magnesium ion.
(1S,2S,9R,10R)-Tetracyclo[8.2.1.02,9.03,7]trideca-3,6-dienyllithium. Tentative Evidence for a Quinternary Equilibrium Involving a Cyclopentadienide Ion (1996)

The title anion 9 was prepared starting from (+)-tricyclo[5.2.1.02,6]deca-4,8-dien-3-ol, the less reactive enantiomer from lipase-mediated transesterification with vinyl acetate, by sequential Jones oxidation, hydrogenation, condensation with cyclopropyldiphenylsulfonium ylide, Baeyer−Villiger oxidation, acid-catalyzed rearrangement, hydride reduction, and dehydration. The derived lithium cyclopentadienide 9 reacted with TiCl3 and CpTiCl3 to give only exo titanocenes. Comparison of cross peak intensities in 6Li,1H HOESY spectra of 9 indicates the existence of the exo-monomer at +24 °C. At −110 °C, the 6Li spectrum indicates the presence of five distinct species which are in mutual exchange of the lithium cation as is shown by 6Li,6Li-EXSY. The two major species are assigned as an exo-monomer and an exo,exo-dimer. MNDO calculations on various monomeric and dimeric solvatomers of 9 confirm the NMR findings.
Genetic Code Expansion of Mammalian Cells with Unnatural Amino Acids (2015)

The expansion of the genetic code of mammalian cells enables the incorporation of unnatural amino acids into proteins. This is achieved by adding components to the protein biosynthetic machinery, specifically an engineered aminoacyl-tRNA synthetase/tRNA pair. The unnatural amino acids are chemically synthesized and supplemented to the growth medium. Using this methodology, fundamental new chemistries can be added to the functional repertoire of the genetic code of mammalian cells. This protocol outlines the steps necessary to incorporate a photocaged lysine into proteins and showcases its application in the optical triggering of protein translocation to the nucleus.
Improving Gas Distribution through Agitator and Gas Sparger Modification in an Autoclave Model (2007)

An experimental study of the effect of gas sparger geometry and agitator location on gas distribution in agitated systems is presented. The results have shown that varying the impeller position modified the size of low void fraction zone. The optimum impeller position for achieving a small low voidage zone without changing the flow pattern has been identified. It was found that impeller positions below or above the optimal location have a negative effect on gas dispersion while the sparger geometry did not affect significantly the overall gas distribution. Low void fraction zone could be detected by a void sensor even if not visually observed.
3D-Patterned Inverse-Designed Mid-Infrared Metaoptics (2022)

Modern imaging systems can be enhanced in efficiency, compactness, and application through introduction of multilayer nanopatterned structures for manipulation of light based on its fundamental properties. High transmission efficiency multispectral imaging is surprisingly elusive due to the commonplace use of filter arrays which discard most of the incident light. Further, most cameras do not leverage the wealth of information in polarization and spatial degrees of freedom. Optical metamaterials can respond to these electromagnetic properties but have been explored primarily in single-layer geometries, limiting their performance and multifunctional capacity. Here we use advanced two-photon lithography to realize multilayer scattering structures that achieve highly nontrivial optical transformations intended to process light just before it reaches a focal plane array. Computationally optimized multispectral and polarimetric sorting devices are fabricated with submicron feature sizes and experimentally validated in the mid-infrared. A final structure shown in simulation redirects light based on its angular momentum. These devices demonstrate that with precise 3-dimensional nanopatterning, one can directly modify the scattering properties of a sensor array to create advanced imaging systems.
Baseline sensitivity of T cells to alpha‐IFN correlates with sustained virological response to IFN‐based triple therapy in HCV infection (2014)

Chronic infection with HCV is a public health problem with approximately 170 million people infected worldwide. Interferon alpha (IFNα) sensitivity in liver and IL28B genotype has been identified as important determinants of HCV clearance in the setting of pegylated interferon/ribavirin treatment. Herein, we explored IFNα sensitivity in PBMC from 21 healthy donors and 21 HCV-infected patients treated with pegylated interferon/ribavirin and HCV nonstructural protein-3 inhibitors (i.e. telaprevir/boceprevir). We explored phospho-STAT1 level as read-out for IFN signalling pathway activation in PBMC, T cells and monocytes and correlated results with virological response. We found that PBMC from healthy donors are desensitized to IFNα after priming and challenged with IFNα, with a subsequent decrease of phospho-STAT1 and interferon-stimulated genes. Furthermore, we show that CD3+ T cells, but not monocytes, become desensitized after 4 weeks of treatment, with a significant decrease of phospho-STAT1 after ex vivo IFNα stimulation. Finally, we identified baseline phospho-STAT1 level in CD3+ T cells as a potential biomarker of sustained virological response, regardless of the IL28B genotype. In the upcoming costly era of IFN-sparing regimen, baseline IFNα sensitivity could act as biomarker to define cost-effectiveness strategies of treatment by identifying patients who will or will not respond to IFN-based treatments.
Numerical and experimental study of microwave-excited microplasma and micronozzle flow for a microplasma thruster (2009)

Plasma and aerodynamic features have been investigated for a microplasma thruster of electrothermal type using azimuthally symmetric microwave-excited microplasmas. The thruster developed consisted of a microplasma source 1.5 mm in diameter, 10 mm long with a rod antenna on axis, and a converging-diverging micronozzle 1 mm long with a throat 0.2 mm in diameter. The feed or propellant gas employed was Ar at pressures of 10–50 kPa with flow rates of 10–70 SCCM (SCCM denotes standard cubic centimeter per minute at STP) and the surface wave-excited plasmas were established by 4.0 GHz microwaves at powers of ≤6 W. Numerical analysis was made for the plasma and flow properties by developing a self-consistent, two-dimensional model, where a two-temperature fluid model was applied to the entire region through the microplasma source to the micronozzle (or through subsonic to supersonic); in the former, an electromagnetic model based on the finite difference time-domain approximation was also employed for analysis of microwaves interacting with plasmas. In experiments, optical emission spectroscopy was employed with a small amount of additive gases of H2 and N2, to measure the plasma electron density and gas temperature in the microplasma source around the top of the microwave antenna, just upstream of the micronozzle inlet; in practice, the numerical analysis exhibited a maximum thereabout for the microwave power density absorbed, plasma density, and gas temperature. The Stark broadening of H Balmer line and the vibronic spectrum of N2 second positive band indicated that the electron density was in the range of (3–12)×1019 m−3 and the gas or rotational temperature was in the range of 700–1000 K. The thrust performance was also measured by using a microthrust stand with a combination of target and pendulum methods, giving a thrust in the range of 0.2–1.4 mN, a specific impulse in the range of 50–80 s, and a thrust efficiency in the range of 2%–12%. These experimental results were consistent with those of numerical analysis, depending on microwave power and gas flow rate.
Monoclonal antibodies that recognize a polypeptide antigenic determinant shared by multiple Caenorhabditis elegans sperm-specific proteins. (1986)

Four monoclonal antibodies that are directed against antigens present in sperm and absent from other worm tissues were characterized. Antibody TR20 is directed against the major sperm proteins, a family of small, abundant, cytoplasmic proteins that have been previously described (Klass, M. R., and D. Hirsh, 1981, Dev. Biol., 84:299-312; Burke, D. J., and S. Ward, 1983, J. Mol. Biol., 171:1-29). Three other antibodies, SP56, SP150, and TR11, are all directed against the same set of minor sperm polypeptides that range in size from 29 to 215 kD. More than eight different sperm polypeptides are antigenic by both immunotransfer and immunoprecipitation assays. The three antibodies are different immunoglobulin subclasses, yet they compete with each other for antigen binding so they are directed against the same antigenic determinant on the multiple sperm proteins. This antigenic determinant is sensitive to any of six different proteases, is insensitive to periodate oxidation or N-glycanase digestion, and is detectable on a polypeptide synthesized in vitro. Therefore, the antigenic determinant resides in the polypeptide chain. However, peptide fragments of the proteins are not antigenic, thus the determinant is likely to be dependent on polypeptide conformation. The antigenic determinant shared by these proteins could represent a common structural feature of importance to the localization or cellular specificity of these proteins.
Molecular Cation (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.
Short-term diet intervention alters the small non-coding RNA (sncRNA) landscape of human sperm (2021)

Abstract Offspring health outcomes are often linked with epigenetic alterations triggered by maternal nutrition and intrauterine environment. Strong experimental data also link paternal preconception nutrition with pathophysiology in the offspring, but the mechanism(s) routing the effects of paternal exposures remain elusive. Animal experimental models have highlighted small non-coding RNAs (sncRNAs) as potential regulators of paternal effects, though less is known about the existence of similar mechanisms in human sperm. Here, we first characterised the baseline sncRNA landscape of human sperm, and then studied the effects of a 6-week diet intervention on their expression profile. Baseline profiling identified 5’tRFs, miRNAs and piRNAs to be the most abundant sncRNA subtypes, primarily expressed from regulatory elements like UTRs, CpG-rich regions and promoters. Expression of a subset of these sncRNAs varied with age, BMI and sperm quality of the donor. Diet intervention enriched in vitamin D and omega-3 fatty acids showed a marked increase of these nutrients in circulation and altered the sperm sncRNA expression. These included 3 tRFs, 15 miRNAs and 112 piRNAs, with gene targets involved in fatty acid metabolism, vitamin D response (LXR/RXR activation, TGF-beta and Wnt signaling), and transposable elements. These findings provide evidence that human sperms are sensitive to alterations in exposures such as diet, and sncRNAs capture the epigenetic imprint of this change. Hence changes to paternal nutrition during preconception may improve sperm quality and offspring health outcomes. To benefit future research, we developed iDad_DB, an open access database of baseline and diet-altered sncRNA in human male germline.
Why shallow defect levels alone do not cause high resistivity in CdTe (2013)

It is usually assumed that deep defect levels are responsible for the high resistivity in detector-grade CdTe, however, it has been recently reported that shallow defects alone can explain high resistivity. In order to resolve this contradiction we analyze different high-temperature compensation regimes and we particularly show that donor–acceptor self-compensation is not a sufficient condition for high resistivity. We also analyze the dependence of the Fermi level on shallow donor concentration at both high temperature and room temperature using analytical solution of the charge neutrality equation and the graphical method based on the formation energy diagrams. We derive the limits of the high-temperature Fermi level values that lead to the high resistivity at room temperature in a system with shallow defect levels only and find that it is theoretically possible to obtain high resistivity using only shallow defects, but only under an extremely narrow range of physical parameters that is unlikely to occur in practice. Finally, we show that the transition levels of cadmium vacancy acceptor are not deep enough to provide high resistivity.