gebhart/patrepeval huggingface dataset:
High Performance Simulation of Large-Scale Red Sea Ocean Bottom Seismic Data on the Supercomputer Shaheen II (2017)

Abstract A combination of both shallow and deepwater, plus islands and coral reefs, are some of the main features contributing to the complexity of subsalt seismic exploration in the Red Sea transition zone. These features often result in degrading effects on seismic images. State-of-the-art ocean bottom acquisition technologies are therefore required to record seismic data with optimal fold and offset, as well as advanced processing and imaging techniques. Numerical simulations of such complex seismic data can help improve acquisition design and also help in customizing, validating and benchmarking the processing and imaging workflows that will be applied on the field data. Subsequently, realistic simulation of wave propagation is a computationally intensive process requiring a realistic model and an efficient 3D wave equation solver. Large-scale computing resources are also required to meet turnaround time compatible with a production time frame. In this work, we present the numerical simulation of an ocean bottom seismic survey to be acquired in the Red Sea transition zone starting in summer 2016. The survey's acquisition geometry comprises nearly 300,000 unique shot locations and 21,000 unique receiver locations, covering about 760 km2. Using well log measurements and legacy 2D seismic lines in this area, a 3D P-wave velocity model was built, with a maximum depth of 7 km. The model was sampled at 10 m in each direction, resulting in more than 5 billion cells. Wave propagation in this model was performed using a 3D finite difference solver in the time domain based on a staggered grid velocity-pressure formulation of acoustodynamics. To ensure that the resulting data could be generated sufficiently fast, the King Abdullah University of Science and Technology (KAUST) supercomputer Shaheen II Cray XC40 was used. A total of 21,000 three-component (pressure and vertical and horizontal velocity) common receiver gathers with a 50 Hz maximum frequency were computed in less than three days. After careful optimization of the finite difference kernel, each gather was computed at 184 gigaflops, on average. Up to 6,103 nodes could be used during the computation, resulting in a peak computation speed greater than 1.11 petaflops. The synthetic seismic data using the planned survey geometry was available one month before the actual acquisition, allowing for early real scale validation of our processing and imaging workflows. Moreover, the availability of a massive supercomputer such as Shaheen II enables fast reverse time migration (RTM) and full waveform inversion, and therefore, a more accurate velocity model estimation for future work.
Reliability studies of SiC vertical power MOSFETs (2018)

Power metal-oxide-semiconductor field-effect transistors (MOSFETs) experience conditions of high field during normal operation, with high MOS gate oxide field in the on-state, and high drift and termination fields in the blocking state. Moreover, silicon carbide devices typically experience higher fields than comparable Si devices due to channel and drift property differences. SiC MOSFET threshold voltage stability and gate oxide lifetime under high gate oxide field are observed to follow the same functional form as Si devices. SiC MOSFETs demonstrate intrinsic oxide lifetime greater than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> hrs in time-dependent dielectric breakdown (TDDB) testing. Accelerated high-temperature reverse-bias (HTRB) testing above the rated voltage reveals similarly long lifetime under high drift fields. The device failure rate due to terrestrial neutron single-event burnout (SEB) is shown to be comparable or superior to that of Si devices. Results demonstrate the reliability of SiC MOSFETs under high-field operation.
ADH1 and ADH4 alcohol/retinol dehydrogenases in the developing adrenal blastema provide evidence for embryonic retinoid endocrine function (1998)

Studies on retinoid signaling indicate that much of the regulation of this pathway may involve enzymes that synthesize the active ligand retinoic acid.Alcohol dehydrogenases ADH1 (class I ADH) and ADH4 (class IV ADH) function as retinol dehydrogenases in the oxidation of retinol, a necessary step in the synthesis of retinoic acid from vitamin A. These enzymes as well as retinoic acid have previously been localized in the adult adrenal gland, thus providing evidence that this organ is an endocrine source of retinoic acid.Here, we have examined the involvement of ADH1 and ADH4 in embryonic adrenal function by using transgenic mouse technology and immunohistochemistry. Transgenic mice were generated that contain various portions of the mouse ADH4 promoter and 5Јflanking region fused to lacZ.Embryos harboring a construct containing 9.0 kb of 5Ј-flanking region displayed very high levels of lacZ expression in the developing adrenal blastemas at embryonic stage E11.5 during the initial phase of mouse adrenal gland development.The presence of endogenous ADH4 protein in stage E11.5 adrenal blastemas was demonstrated by immunohistochemistry, and this was the only site of ADH4 immunodetection in stage E11.5 embryos.Endogenous ADH1 protein was also detected by immunohistochemistry in stage E11.5 adrenal blastemas.ADH1 and ADH4 proteins were detectable at later stages of adrenal development, and both were localized to developing adrenal cortical cells by stage E14.5.The presence of both ADH1 and ADH4 retinol dehydrogenases during the earliest stages of adrenal gland development, combined with our earlier findings of high levels of retinoic acid in the embryonic adrenal gland, suggests that one of the earliest functions of ADH may be to provide an embryonic endocrine source of retinoic acid for growth and development.Dev.
Fiber probe microcavities for refractive index and temperature discrimination (2016)

Fiber probe structures composed of two physical microcavities were created using focused ion beam technology. These structures have a tip-like shape as they were milled in preciously etched tapered fiber tips. The microprobes are then characterized for temperature and refractive index sensing using a signal filtering technique to discriminate signals from distinct microcavities. Using fast Fourier transforms combined with band-pass filters, it is possible to reconstruct the spectra of each cavity independently and thus measure their individual spectral shifts.
Validating Vehicular Localization Indoor using UWB: Challenges and Solutions (2023)

Vehicle-to-Everything (V2X) expands the capabilities of vehicles with innovative applications. Localization plays a crucial role in V2X, with measurement accuracy as a fundamental property. Demonstrating this accuracy, however, is not straightforward, especially in indoor environments. Indeed, the inability to use global navigation satellite systems (e.g., GPS) indoor requires exploring alternate technologies. In this work, we present a reliable and accurate validation methodology to demonstrate the performance of V2X localization. An Ultra-Wide Band (UWB) localization technology is at the core of our validation infrastructure. Built around this is a complete system that supports data collection from multiple localization systems, ensures time synchronization across data samples, and provides a comprehensive analysis pipeline. We demonstrate this validation system in both outdoor and indoor environments. Our approach overcomes the challenges of indoor vehicular localization and provides a reliable and accurate way to evaluate the performance of V2X localization systems.
Elevated CO 2 alters leaf-litter-derived dissolved organic carbon: effects on stream periphyton and crayfish feeding preference (2021)

Elevated atmospheric CO2 increases plant C fixation, and much of the soluble C content of deciduous leaf litter entering streams is leached as dissolved organic C (DOC). The effects of DOC from trembling aspen (Populus tremuloides Michaux) leaf litter grown under elevated (ELEV ! 720 ppm) and ambient (AMB! 360 ppm) CO2 on stream periphyton were measured during a 35-d experiment in outdoor artificial stream chambers. Crayfish feeding preferences for periphyton grown in AMB and ELEV treatments were evaluated in short-term foraging trials using a Y-maze. Periphyton was sampled through time for ash- free dry mass (AFDM), chlorophyll a, total C:N, algal biovolume and species composition, and bacterial productivity and biomass. Leaf litter from plants grown under ELEV CO2 produced higher concentrations of refractory DOC than did leaf litter from plants grown under AMB CO2, and chlorophyll a concentrations were lower in periphyton enriched with ELEV DOC than in periphyton enriched with AMB DOC. ELEV DOC did not significantly affect bacterial productivity and biomass or total periphyton C:N, but cyanobacterial biovolume was higher in ELEValgal assemblages than in AMB algal assemblages after 35 d. AMB algal assemblages were dominated by the diatom Epithemia adnata var. proboscidea, which contains N- fixing endosymbionts. Orconectes virilis crayfish preferred AMB periphyton stimulus when offered the choice of AMB and ELEV stimuli or AMB and control stimuli. Our results suggest that DOC from trembling aspen leaf litter produced under ELEV CO2 alters algal accrual and species assemblages of stream periphyton, and this shift in basal resource quantity and quality could affect feeding preferences of crayfish.
Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution (2007)

The energetics of methyl-transfer reactions from dimethylammonium, tetramethylammonium, and trimethylsulfonium to dimethylamine were computed with density functional theory, MP2, CBS-QB3, and quantum mechanics/molecular mechanics (QM/MM) Monte Carlo methods. At the CBS-QB3 level, the gas-phase activation enthalpies are computed to be 9.9, 15.3, and 7.9 kcal/mol, respectively. MP2/6-31+G(d,p) activation enthalpies are in best agreement with the CBS-QB3 results. The effects of aqueous solvation on these reactions were studied with polarizable continuum model, generalized Born/surface area (GB/SA), and QM/MM Monte Carlo simulations utilizing free-energy perturbation theory in which the PDDG/PM3 semiempirical Hamiltonian for the QM and explicit TIP4P water molecules in the MM region were used. In the aqueous phase, all of these reactions proceed more slowly when compared to the gas phase, since the charged reactants are stabilized more than the transition structure geometries with delocalized positive charges. In order to obtain the aqueous-phase activation free energies, the gas-phase activation free energies were corrected with the solvation free energies obtained from single-point conductor-like polarizable continuum model and GB/SA calculations for the stationary points along the reaction coordinate.
Core–shell protein clusters comprising haemoglobin and recombinant feline serum albumin as an artificial O2carrier for cats (2018)

This report describes the synthesis and structure of core-shell protein clusters comprising haemoglobin (Hb) at the centre and recombinant feline serum albumin (rFSA) at the exterior, named as haemoglobin-albumin clusters (Hb-rFSA<sub>3</sub>). Specifically, we highlight their capability as an artificial O<sub>2</sub> carrier that can be used as a red blood cell (RBC) substitute for cats, the most populous pet animal in the world. First, rFSA was expressed by genetic engineering using Pichia yeast. The proteins show identical features to the native FSA derived from feline plasma. Single crystals of rFSA were prepared under a microgravity environment on the international space station (ISS), from which the structure was first revealed at 3.4 Å resolution. Subsequently, bovine Hb was wrapped covalently by rFSA using an α-succinimidyl-ε-maleimide crosslinker, yielding Hb-rFSA<sub>3</sub> clusters. Three rFSA entities enfolded the Hb nuclei satisfactorily, giving the protein clusters a negative surface net charge (pI = 4.7) and preventing an immunological response against anti-Hb antibodies. The O<sub>2</sub> affinity was higher (P<sub>50</sub> = 9 Torr) than that of the native Hb. The Hb-rFSA<sub>3</sub> clusters are anticipated for use as an alternative material for RBC transfusion, and as an O<sub>2</sub> therapeutic reagent that can be exploited in various veterinary medicine scenarios.
The phosphorylation and DNA binding of the DNA-binding domain of the orphan nuclear receptor NGFI-B. (1993)

NGFI-B is an orphan member of the nuclear receptor superfamily encoded by an immediate-early gene. It is rapidly synthesized and phosphorylated in PC12 cells in response to nerve growth factor (NGF) and other agents and is differentially phosphorylated dependent upon the inducing stimulus. The DNA-binding domain (DBD) of NGFI-B has been expressed in bacteria and purified. The purified protein is phosphorylated by protein kinase A or by extracts from NGF-treated PC12 cells. The phosphorylated residues within the DBD have been identified as Ser-340 and Ser-350. The use of mutants in which either or both of these residues were replaced with alanines revealed that phosphorylation of Ser-350, located within the "A box," a motif necessary for DNA binding by NGFI-B, resulted in a decrease in binding to the NGFI-B response element, while phosphorylation of Ser-340 had little or no effect. These findings demonstrate that phosphorylation of a nuclear receptor DBD results in a change in DNA binding and provides another potential mechanism for regulating NGFI-B activity.
In-Plane Magnetic Field Evaluation with 0.47-nm Resolution by Aberration-Corrected 1.2-MV Holography Electron Microscope (2019)

reflects the in-plane magnetic field in the sample. The magnetic phase information with 0.47 nm spacing corresponding to the (111) lattice were obtained. By the multi-slice simulation including atomic-scale magnetic field derived by the Vienna Ab initio simulation package (VASP) calculation, it is shown that the observed result does reflect the atomic-layer in-plane magnetic field distributions.
Exhaustive Genotyping of theCEM15 (APOBEC3G)Gene and Absence of Association with AIDS Progression in a French Cohort (2004)

CEM15 (or APOBEC3G) has recently been identified as an inhibitor of human immunodeficiency virus type 1 (HIV-1) replication in vitro. To evaluate the impact of its genetic variations on the progression of acquired immunodeficiency syndrome (AIDS), we have performed an extensive genetic analysis of CEM15. We have sequenced CEM15 in a cohort of 327 HIV-1-seropositive patients with extreme disease progression phenotypes--either slow progression or rapid progression--and in 446 healthy control subjects, all of white descent. We have identified 29 polymorphisms with allele frequencies >1%, 14 of which were newly characterized. There were no significant associations between the polymorphisms or haplotypes of CEM15 and a disease progression phenotype in our cohort.
Doping of an absorbent into a Raman crystal for suppression of higher-order Stokes generation (2000)

A Raman-active crystal, lanthanum tungstate doped with praseodymium (Pr) ions, was grown to facilitate the selection of the order of Stokes waves in stimulated Raman scattering. Absorption of the second Stokes wave by the Pr ions suppressed conversion to higher-order Stokes waves, resulting in efficient energy conversion to the first Stokes wave.
Composing chaos: An experimental and numerical study of an open duct mixing flow (2005)

Abstract By using a programmed sequence of boundary motions to introduce flow reorientation to a steady, laminar axial flow in an open duct, we develop a novel device to investigate and exploit chaotic advection of viscously dominated (low Reynolds number) flows. The design and operation of the Rotated Arc Mixer (RAM) is discussed. Among other things, the RAM can effect good continuous mixing of viscous materials without use of any internal elements; moreover, the RAM has several control parameters to tune the chaotic advection, making it flexible for applications and theoretical developments. Numerical methods to discover the robust parameter regions where chaos covers the entire flow domain, and how these parameters change with fluid properties is also discussed. Poincaré sections, dye advection and residence time calculations are presented for Newtonian and non‐Newtonian fluids. Experiments, including advection field, velocity field and residence‐time measurements, confirm all aspects of the device for Newtonian fluids. © 2005 American Institute of Chemical Engineers AIChE J, 2006
The relationship between visual sensitivity and rhodopsin density in retinitis pigmentosa. (1981)

Rhodopsin density and absolute threshold were determined in 11 patients with retinitis pigmentosa (RP) and nine normal subjects. In eight patients with familial histories suggesting recessive inheritance, the retinal areas studied showed marked decrease in sensitivity which was related to rhodopsin loss, probably via a log-linear relationship. The other three patients showed absolute thresholds that were linearly related to rhodopsin density, suggesting that sensitivity loss was determined by the decrease in quantal absorption resulting from rhodopsin loss. The results indicate that RP patients can be classified into two categories according to the effects of rhodopsin loss on rod sensitivity. These categories may correspond to different genetic groups. Furthermore, this differentiation may, in fact, reflect different underlying disease mechanisms.
Adaptive instant record signals applied to shallow water detection (2004)

Time reversal arrays are becoming common tools whether for detection, tomography or communication. These applications require the measurement of the response from the array to one or several receivers. The most natural way to record different impulse responses between several points is to generate pulses successively from each emitting point and directly record all the impulse responses on the recording points. However, this method is very time consuming and inefficient in terms of signal-to-noise ratio. Hence, in this work, we propose an original way of sending continuous signals simultaneously from all the sources, recording all the pressure fields on the receivers and processing them in order to extract the exact impulse responses by matched filter. To this end, the signals are adapted to the environment and, more specifically, to highly dispersive media. These adaptive instant records signals (AIRS) are used experimentally to detect targets using the time reversal operator decomposition method. The quality of the 15×15 transfer functions acquired simultaneously, and therefore, the detection capability is demonstrated in shallow water in the presence of bottom absorption and reverberation. Finally, the connection of AIRS with CDMA and FDMA that are two coding techniques used in telecommunication is shown.
Battery Charger using the High-Voltage PZN-BT-PT Ceramics for Gas-Insulated Switch Drive (1999)

The 22.9kV (Y) power distribution line has the gas-insulated high-voltage switch that is driven by Pb battery. As there is not useful low voltage power for battery charging, the ceramic capacitor and winding transformer seriesly connected with the distribution line voltage can be used for it. PZN-BT-PT ceramics for the high voltage capacitor application showed excellent values of (%) which were -7.1 at -25 ℃, respectively. The PZN-BT-PT ceramic capacitor of 1,500 pF capacity and the battery charging system were prepared and tested. From the test results, we confirmed that the developed PZN-BT-PT ceramic capacitor produced the increased charging current and the designed charging circuit was operated as a satisfactory CVCC charger with about 500mA total current, and 15 [W] output power.
Preclinical Evaluation of 18F-Labeled Anti-HER2 Nanobody Conjugates for Imaging HER2 Receptor Expression by Immuno-PET (2016)

(18)F-RL-I-5F7 is a promising tracer for evaluating HER2 status by immuno-PET; however, in settings in which renal background is problematic, strategies for reducing its kidney uptake may be needed.
Jet production rates in association with W and Z bosons in pp collisions at $ \sqrt {s} = 7 {\text{TeV}} $ (2012)

Measurements of jet production rates in association with W and Z bosons for jet transverse momenta above 30 GeV are reported, using a sample of proton-proton collision events recorded by CMS at s = 7 TeV, corresponding to an integrated luminosity of 36 pb -1 . The study includes the measurement of the normalized inclusive rates of jets (V+ n jets)/(V), where V represents either a W or a Z. In addition, the ratio of W to Z cross sections and the W charge asymmetry as a function of the number of associated jets are measured. A test of scaling at s = 7 TeV is also presented. The measurements provide a stringent test of perturbative-QCD calculations and are sensitive to the possible presence of new physics. The results are in agreement with the predictions of a simulation that uses explicit matrix element calculations for final states with jets.
Constrained Capacities of DVB-S2 Constellations in Log-Normal Channels at Ka Band (2010)

Researchers have investigated the Shannon capacity of satellite links that have log-normal rain-fading channels in the Ka band (20-30 GHz). This paper uses information theoretic tools to expand on the previous work by computing the constrained capacity of log-normally distributed rain-fading channels in which practical constellations, such as those found in the DVB-S2 standard are used, as opposed to the Gaussian distribution assumed for the input signal in Shannon capacity calculations. Two types of rain environments are considered: a tropical environment and a fairly dry European environment. The results of this approach will help the satellite planner to determine realistic upper limits for the throughput of satellite links that use adaptive coded modulation to mitigate the effects of rain fades.
Teaching the basics of reactive oxygen species and their relevance to cancer biology: Mitochondrial reactive oxygen species detection, redox signaling, and targeted therapies (2017)

Reactive oxygen species (ROS) have been implicated in tumorigenesis (tumor initiation, tumor progression, and metastasis). Of the many cellular sources of ROS generation, the mitochondria and the NADPH oxidase family of enzymes are possibly the most prevalent intracellular sources. In this article, we discuss the methodologies to detect mitochondria-derived superoxide and hydrogen peroxide using conventional probes as well as newly developed assays and probes, and the necessity of characterizing the diagnostic marker products with HPLC and LC-MS in order to rigorously identify the oxidizing species. The redox signaling roles of mitochondrial ROS, mitochondrial thiol peroxidases, and transcription factors in response to mitochondria-targeted drugs are highlighted. ROS generation and ROS detoxification in drug-resistant cancer cells and the relationship to metabolic reprogramming are discussed. Understanding the subtle role of ROS in redox signaling and in tumor proliferation, progression, and metastasis as well as the molecular and cellular mechanisms (e.g., autophagy) could help in the development of combination therapies. The paradoxical aspects of antioxidants in cancer treatment are highlighted in relation to the ROS mechanisms in normal and cancer cells. Finally, the potential uses of newly synthesized exomarker probes for in vivo superoxide and hydrogen peroxide detection and the low-temperature electron paramagnetic resonance technique for monitoring oxidant production in tumor tissues are discussed.