gebhart/patrepeval huggingface dataset:
Scaling gysela code beyond 32K-cores on bluegene/Q (2013)

Gyrokinetic simulations lead to huge computational needs. Up to now, the semi- Lagrangian code Gysela performed large simulations using a few thousands cores (8k cores typically). Simulation with finer resolutions and with kinetic electrons are expected to increase those needs by a huge factor, providing a good example of applications requiring Exascale machines. This paper presents our work to improve Gysela in order to target an architecture that presents one possible way towards Exascale: the Blue Gene/Q. After analyzing the limitations of the code on this architecture, we have implemented three kinds of improvement: computational performance improvements, memory consumption improvements and disk i/o improvements. As a result, we show that the code now scales beyond 32k cores with much improved performances. This will make it possible to target the most powerful machines available and thus handle much larger physical cases.
Observed Instability of T7 RNA Polymerase Elongation Complexes Can Be Dominated by Collision-induced “Bumping” (2006)

T7 RNA polymerase elongates RNA at a relatively high rate and can displace many tightly bound protein-DNA complexes. Despite these properties, measurements of the stability of stalled elongation complexes have shown lifetimes that are much shorter than those of the multisubunit RNA polymerases. In this work, we demonstrate that the apparent instability of stalled complexes actually arises from the action of trailing RNA polymerases (traveling in the same direction) displacing the stalled complex. Moreover, the instability caused by collision between two polymerases is position dependent. A second polymerase is blocked from promoter binding when a leading complex is stalled 12 bp or less from the promoter. The trailing complex can bind and make abortive transcripts when the leading complex is between 12 and 20 bp from the promoter, but it cannot displace the first complex since it is in a unstable initiation conformation. Only when the leading complex is stalled more than 20 bp away from the promoter can a second polymerase bind, initiate, and displace the leading complex.
Focusing of shock waves in water and its observation by the schlieren method (1991)

A spherical shock wave is generated by one spark discharge between electrodes at the first focal point of a rotationally symmetrical semiellipsoid, a part of the spherical wave reflects from the semiellipsoid, and produces a high pressure near the second focal point. This characteristic is used for the extracorporeal shock wave lithotriptor. However, there are some points to be made clear, such as the mechanism of shock wave generation and the process of its reflection and focusing. In this study, as the first step, visualizing the behavior of the shock wave is tried by means of the schlieren system using an iris instead of the knife edge. Especially in order to make the aspect of reflection clear, cylindrical shock waves generated by underwater wire explosions are used with an elliptical reflector. Photographs are taken with the image converter camera 'IMACON 790', and as the result the whole process from the generation to the focusing of the shock wave is clearly shown.
Terahertz shielding effectiveness and optical transmittance of graphene multilayer thin sheets (2014)

Terahertz communication technologies are based on the use of a frequency range from 300 GHz up to 3 THz, according to standardization and regulation activities of the IEEE 802.15 IG THz. Graphene, which is characterized by excellent electrical, thermal and mechanical properties, is an attractive choice for EMI shielding applications. New models are proposed for the analysis of the shielding effectiveness of graphene multilayer thin films in the lower THz range taking into account the frequency dependence of the electrical conductivity. Already known models are applied to estimate the optical transmittance. Moreover, transparent substrates coated by graphene multilayer sheets are simulated. The proposed modeling approach is applied to the performance analysis of graphene multilayer thin sheets in the frequency range up to 1 THz.
Mémoires du Président Hénault. Nouvelle édition par François Rousseau. 1911 (1912)

Muret Pierre. Mémoires du Président Hénault. Nouvelle édition par François Rousseau. 1911. In: Revue d'histoire moderne et contemporaine, tome 17 N°5, Septembre-Octobre 1912. pp. 421-424.
Monitoring of earthquake induced motions and damage with optical motion tracking (2005)

Optical motion tracking technologies using surveillance cameras have been applied to the measurement of earthquake induced motions and detection of seismic damage to interior elements to reduce risks in a building. We have developed methods for detecting structural collapse and overturning of interior elements. Shaking table tests were carried out to evaluate the optical system's ability to detect damage. The movements of two-storey frame structures and rectangular pieces of wood on the shaking table were monitored using conventional video cameras. Results from this exploratory study showed that optical measurements are promising in terms of capturing small to large deformations and identifying various types of seismic damage.
Atypical temporal lobe language representation (1999)

Functional brain imaging techniques hold many promises as the methods of choice for identifying areas involved in the execution of language functions. The success of any of these techniques in fulfilling this goal depends upon their ability to produce maps of activated areas that overlap with those obtained through standard invasive procedures such as electrocortical stimulation. This need is particularly acute in cases where active areas are found outside of traditionally defined language areas. In the present report we present two patients who underwent mapping of receptive language areas preoperatively through magnetoencephalography (MEG) and intraoperatively through electrocortical stimulation. Language areas identified by both methods were located in temporoparietal regions as well as in less traditional regions (anterior portion of the superior temporal gyrus and basal temporal cortex). Importantly there was a perfect overlap between the two sets of maps. This clearly demonstrates the validity of MEG-derived maps for identifying cortical areas critically involved in receptive language functions.
The Verifiability Theory of Meaning (1951)

Hans Reichenbach, The Verifiability Theory of Meaning, Proceedings of the American Academy of Arts and Sciences, Vol. 80, No. 1, Contributions to the Analysis and Synthesis of Knowledge (Jul., 1951), pp. 46-60
A Drying Method by Utilizing Same Direction Transfer of Heat and Moisture (1964)

湿った物質に温度勾配を与えると, 高温域より低温域へ水分の移動が起る現象を利用して, 物質内部に熱をあたえ, 水分蒸発は低温側の外表面よりのみ行なうと, 内外の含水率の差が少ない状態で, 乾燥速度を増すことができる, いわゆる「熱と水分の並び流れによる乾燥法」について説明した。ラップ碍子用粘土成形品につき実験を行ない, 乾燥亀裂の心配なく, 従来行なわれていた普通の対流乾燥法に比較して, 乾燥に要する時間を数分の一に短縮することができた。
Toward synergistic engineering of computer systems (1997)

Our objective is to provide a forum for sharing problems, experiences, and solutions that can help establish bridges among hardware engineers, software engineers, systems engineers, and project managers. We seek to publicize innovative solutions and engineering methodologies that address: complexity, model-based engineering (as exemplified by hardware/software codesign), and process management. We believe these three areas are critical to advancing the successful, integrated engineering of computer-based systems.
Conduction-band crossover induced by misfit strain in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi mathvariant="normal">In</mml:mi><mml:mi mathvariant="normal">Sb</mml:mi><mml:mo>∕</mml:mo><mml:mi mathvariant="normal">Ga</mml:mi><mml:mi mathvariant="normal">Sb</mml:mi></mml:mrow></mml:math>self-assembled quantum dots (2007)

We address the occurrence of conduction-band crossover in III-V self-assembled quantum dots solely due to misfit strain. Band structure analysis in terms of standard deformation-potential theory shows that $\ensuremath{\Gamma}\text{\ensuremath{-}}X$ crossover can occur in the dot, while both $\ensuremath{\Gamma}\text{\ensuremath{-}}X$ and $\ensuremath{\Gamma}\text{\ensuremath{-}}L$ crossovers are possible in the matrix at the interface. Crossover changes the nature of the fundamental band gap in the heterostructure, which may dramatically affect the optical properties. The implications of this are studied for a realistic $\mathrm{In}\mathrm{Sb}∕\mathrm{Ga}\mathrm{Sb}$ (001) heterostructure, where $\ensuremath{\Gamma}\text{\ensuremath{-}}L$ crossover renders the ground-state optical transition indirect in $\mathbf{k}$ space. Our calculations and photoluminescence data are in remarkable agreement.
A monolithic, constant-fraction discriminator using distributed R-C delay line shaping (2002)

A monolithic, CMOS, constant-fraction discriminator (CFD) was designed and fabricated in a 1.2-/spl mu/ N-well process. This circuit uses an on-chip, distributed R-C delay line to realize the constant-fraction shaping. The delay line is constructed of a 4.8-/spl mu/ wide, 500-/spl mu/ long serpentine layer of polysilicon above a grounded second layer of polysilicon. This line generates about 1.1 ns of delay for a 5-ns risetime signal with a slope degradation of only 15%. The CFD also features DC feedback for both the arming and zero-crossing discriminators to eliminate timing errors caused by offsets. The entire circuit, including the delay line, requires an area of 200 /spl mu//spl times/950 /spl mu/. The timing walk for 5-ns risetime signals over the dynamic range from -20 mV to -2 V was less than /spl plusmn/150 ps. Each channel of the CFD consumed /spl sim/15 mW from a single 5-V supply.
Microwave‐Assisted Synthesis of O′‐Adamantylated Uracil‐Derived Nucleosides. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
d<sup>2</sup>-LBDR: Distance-Driven Routing to Handle Permanent Failures in 2D Mesh NoCs (2015)

With the advent of deep sub-micron technology, fault-tolerant solutions are needed to keep many-core chips operative. In NoCs, Logic Based Distributed Routing (LBDR) proved to be a flexible routing framework for 2D meshes with link and router faults. However, to provide full coverage, LBDR requires a module named FORKS which replicates some messages. This imposes the use of virtual cut-through switching and a complex router arbiter, increasing excessively the router cost, mainly in buffer area. Also, some failure combinations require the use of a non-trivial dynamic reconfiguration strategy to avoid deadlocks. We propose d <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -LBDR which adds, on every router, a distance register to the closest failure. This enables the support of more failure combinations without an excessive implementation cost. Indeed, we restore the use of wormhole switching, keeping router architecture simple, while achieving the same fault coverage as the best LBDR version, without requiring complex switching strategies nor any dynamic reconfiguration strategy. Results show that a small area overhead (3%) is enough for the implementation of a fully flexible routing method without any limiting support case when compared with LBDR. d <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -LBDR reduces area overhead over the best LBDR approach (300% overhead against 3%) while preserving fault coverage. Results show d <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -LBDR performance equal to LBDR.
Laser behavior and photostability characteristics of organic dye doped silicate gel materials (1990)

The solgel process is a solution synthesis technique which provides a low temperature chemical route for the preparation of rigid transparent matrix materials. Luminescent organic dye molecules have been incorporated via the solgel method into organically modified silicate (ORMOSIL) polymer host matrices. Optical gain, laser oscillation, and photostability of rhodamine and coumarin dyes doped into ORMOSIL gels are reported. The gel laser materials exhibit peak gain values of 40 cm(-1) and show improved photostability with respect to comparable polymeric host materials.
Undoped and Hole-Doped Superconductors T$'$-La$_{1.8-x}$Eu$_{0.2}$Sr$_{x}$CuO$_{4}$ ($x = 0$ and 0.05) Prepared by Solid-State Reaction (2012)

We have successfully synthesized La1.8-xEu0.2SrxCuO4 (x = 0 and 0.05) with the Nd2CuO4-type (T'-type) structure by means of the structural transformation at low temperatures from the K2NiF4-type (T-type) structure via the Sr2CuO3-type (S-type) structure. Superconductivity has appeared by postannealing T'-La1.8-xEu0.2SrxCuO4 in vacuum at 700 °C for the removal of excess oxygen. The superconducting transition temperatures are 20 and 13 K for x = 0 and 0.05, respectively. T'-La1.8-xEu0.2SrxCuO4 with x = 0.05 is, at least nominally, the first hole-doped superconducting cuprate with the T'-type structure.
Adaptive remodeling of skeletal muscle energy metabolism in high-altitude hypoxia: Lessons from AltitudeOmics (2018)

Metabolic responses to hypoxia play important roles in cell survival strategies and disease pathogenesis in humans. However, the homeostatic adjustments that balance changes in energy supply and demand to maintain organismal function under chronic low oxygen conditions remain incompletely understood, making it difficult to distinguish adaptive from maladaptive responses in hypoxia-related pathologies. We integrated metabolomic and proteomic profiling with mitochondrial respirometry and blood gas analyses to comprehensively define the physiological responses of skeletal muscle energy metabolism to 16 days of high-altitude hypoxia (5260 m) in healthy volunteers from the AltitudeOmics project. In contrast to the view that hypoxia down-regulates aerobic metabolism, results show that mitochondria play a central role in muscle hypoxia adaptation by supporting higher resting phosphorylation potential and enhancing the efficiency of long-chain acylcarnitine oxidation. This directs increases in muscle glucose toward pentose phosphate and one-carbon metabolism pathways that support cytosolic redox balance and help mitigate the effects of increased protein and purine nucleotide catabolism in hypoxia. Muscle accumulation of free amino acids favor these adjustments by coordinating cytosolic and mitochondrial pathways to rid the cell of excess nitrogen, but might ultimately limit muscle oxidative capacity <i>in vivo</i> Collectively, these studies illustrate how an integration of aerobic and anaerobic metabolism is required for physiological hypoxia adaptation in skeletal muscle, and highlight protein catabolism and allosteric regulation as unexpected orchestrators of metabolic remodeling in this context. These findings have important implications for the management of hypoxia-related diseases and other conditions associated with chronic catabolic stress.
Dilution impacts on smoke aging: Evidence in BBOP data (2020)

Abstract. Biomass burning emits vapors and aerosols into the atmosphere that can rapidly evolve as smoke plumes travel downwind and dilute, affecting climate- and health-relevant properties of the smoke. To date, theory has been unable to explain variability in smoke evolution. Here, we use observational data from the BBOP field campaign and show that initial smoke concentrations can help predict changes in smoke aerosol aging markers, number, and diameter. Because initial field measurements of plumes are generally > 10 minutes downwind, smaller plumes will have already undergone substantial dilution relative to larger plumes. However, the extent to which dilution has occurred prior to the first observation is not a measurable quantity. Hence, initial observed concentrations can serve as an indicator of dilution, which impacts photochemistry and aerosol evaporation. Cores of plumes have higher concentrations than edges. By segregating the observed plumes into cores and edges, we infer that particle aging, evaporation, and coagulation occurred before the first measurement, and we find that edges generally undergo higher increases in oxidation tracers, more decreases in semivolatile compounds, and less coagulation than the cores.
A Thermoreversible Poly(Choline Phosphate) Based Universal Biomembrane Adhesive (2013)

A new monomer, 2-(2-(2-(2-azidoethoxy)ethoxy)ethoxy)ethyl methacrylate (AEO4 MA), and its direct atom transfer radical polymerization (ATRP) into poly(AEO4 MA), then "clicked" with prop-2-ynyle choline phosphate (CP) to produce a poly(choline phosphate) are described. This polymer exhibits a lower critical solution temperature (LCST) at ≈ 32 °C, and provides a universal thermally reversible biomembrane adhesive, which can rapidly both bind to any mammalian cell membrane and internalize into the cytoplasm of nucleated cells below the LCST. Moving above the LCST reverses cell surface binding. The use of ATRP implies that such polymers can be applied to modify the surfaces of a wide range of biomaterials. The capacity to bind and immobilize cells at room temperature and release them above the LCST should be particularly useful for in vitro cell manipulation and tissue engineering applications.
Impact of cysts during radiofrequency lesioning in deep brain structures—a simulation and<i>in vitro</i>study (2007)

Radiofrequency lesioning of nuclei in the thalamus or the basal ganglia can be used to reduce symptoms caused by e.g. movement disorders such as Parkinson's disease. Enlarged cavities containing cerebrospinal fluid (CSF) are commonly present in the basal ganglia and tend to increase in size and number with age. Since the cavities have different electrical and thermal properties compared with brain tissue, it is likely that they can affect the lesioning process and thereby the treatment outcome. Computer simulations using the finite element method and in vitro experiments have been used to investigate the impact of cysts on lesions' size and shape. Simulations of the electric current and temperature distributions as well as convective movements have been conducted for various sizes, shapes and locations of the cysts as well as different target temperatures. Circulation of the CSF caused by the heating was found to spread heat effectively and the higher electric conductivity of the CSF increased heating of the cyst. These two effects were together able to greatly alter the resulting lesion size and shape when the cyst was in contact with the electrode tip. Similar results were obtained for the experiments.
Novel Organoborane Lewis Acids via Selective Boron-Tin Exchange Processes Steric Constraints to Electrophilic Initiation by the Boron Halide (1998)

With the purpose of preparing novel mono- and bidentate organoboron Lewis acids, the scope and limitations of synthesizing the requisite organoboranes by the boron-tin exchange between a boron halide and the appropriate organostannane have been examined in detail. The following organotin derivatives have been obtained either from the corresponding RMgBr or RLi reagent and MenSnCl4–n or from a Barbier procedure using the organic halide, Me3SnCl and magnesium metal: 1,2-bis(trimethylstannyl)ethyne, o-, m-, and p-bis(trimethyl-stannyl)benzenes, α,o-bis(trimethylstannyl)toluene, α,α-bis(trimethylstannyl)-o-xylene, and 2,2-dimethyl-2-stannaindane. The individual interaction of the 1,2-bis(trimethylstannyl)ethyne and the isomeric bis(trimethylstannyl)benzenes with Et2BBr produced the corresponding bis(diethylboryl)-derivatives. By contrast, with Et2BCl the α,o-bis(trimethylstannyl)toluene gave only o-diethylboryl-α-trimethylstannyltoluene and with BCl3 the α,α′-bis(trimethylstannyl)-o-xylene formed only,-bis-(chlorodimethylstannyl)-o-xylene. Furthermore, in the attempted double boron-tin exchange between o-bis(trimethylstannyl)benzene and BCl3, an unprecedented rearrangement of the 1-(dichloroboryl)-2-(trimethylstan-nyl)benzene intermediate into its 1-[chloro(methyl)boryl]-2-(chlorodimethylstannyl) isomer was observed. Likewise, o-bis(trimethylstannyl)benzene with PhBCl2 produced by a similar rearrangement 1-[methyl(phenyl)boryl]-2-(chloro-dimethylstannyl)benzene. The thermolysis of such boranes led variously to definite dimers or ill-defined oligomers. Preliminary studies of the properties of these organoboranes have identified the heightened Lewis acidity of 1,2-bis(diethylboryl)ethyne and the π-electron delocalization involving the 2pz-boron orbitals in the 9,10-dihydro-9,10-diboraanthracene system. Finally, an electronic mechanism for the boron-tin exchange has been developed to account for the selectivity of the boron halide's attack at unsaturated carbon–tin bonds.
Contact-reducing method over topography by combining the RELACS technique and bilayer process (2002)

Extending current lithography capability in the case of severe topography is desired in trench-first dual-damascene process. We demonstrate a solution of applying the RELACS process on DUV bi-layer resist system to provide a planarization material with CD shrinkage ability. By combining these two commercially available processes, the cost saving of contact-reducing techniques can be realized on wafers with aggressive topography. The main results presented in this study include (1) process window of the bi-layer/RELACS is comparable with that of the bi-layer only process. (2) Across wafer CD uniformity of the bi-layer/RELACS process is improved compared to that of the bi-layer process alone. Further etch steps does not degrade CD uniformity either. Nice post etch across CD uniformity and cross-section photos from post etch show the image resist still retains enough etch resistance after RELACS process. (3) Among all geometry in this study, the maximum difference from two orientations is 2nm in width and 5 nm in length. (4) Geometry size shows a bigger effect on shrinkage, for the ellipse contacts with aspect ratio 2, it shrinks 14nm more in length direction than in width direction. For contacts with aspect ratio 1.3, the shrinkage difference between width and length is relative small (about 2nm). (5) Total CD shrinkage in the range of 40 to 60nm has been achieved. Baking temperature sensitivity is measured to be about 1.3 nm/ degree(s)C. The value of temperature sensitivity suggests possible lot-to-lot, wafer-to-wafer and across wafer CD control for mass production. (6) A set of horizontal contacts is employed for pitch dependency studies. From pitch size changes from 450nm to 700nm in length direction, the length shrinkage changes by 8% of the target CD. And for pitch size changes from 450nm to 850nm in width direction, the width shrinkage changes by 9% of the CD target. Post RELACS OPC may be necessary for critical cases to compensate the pitch dependency of CD changes.
Channel temperature estimation in GaAs FET devices (2010)

Operating channel temperature has an important influence on the electrical performance and reliability of GaAs FET amplifiers but this parameter is difficult to determine experimentally or analytically. Simplified closed-form and numerical models are commonly used although both are subject to errors in the case of sub-micron heat sources surrounded by epitaxial layers. Some assumptions about the heat source size and location are explored using finite-difference simulation. A simple measurement technique making use of the temperature coefficient of gate metal resistance is described, and an improved procedure for spatial averaging correction of infrared measurements of sub-micron heat sources is proposed.