gebhart/patrepeval huggingface dataset:
PASSION Runtime Library for parallel I/O (2002)

We are developing a compiler and runtime support system called PASSION: Parallel and Scalable Software for Input-Output. PASSION provides software support for I/O intensive out-of-core loosely synchronous problems. This paper gives an overview of the PASSION Runtime Library and describes two of the optimizations incorporated in it, namely data prefetching and data sieving. Performance improvements provided by these optimizations on the Intel Touchstone Delta are discussed together with an out-of-core median filtering application.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Sporadic DUX4 expression in FSHD myocytes is associated with incomplete repression by the PRC2 complex and gain of H3K9 acetylation on the contracted D4Z4 allele (2018)

These results implicate PRC2 as the complex primarily responsible for DUX4 repression in the setting of FSHD and H3K9 acetylation along with reciprocal loss of H3K27me3 as key epigenetic events that result in DUX4 expression. Future studies focused on events that trigger H3K9Ac or augment PRC2 complex activity in a small fraction of nuclei may expose additional drug targets worthy of study.
Effect of Polymeric Media on the Kinetics of Nanocluster Nucleation and Growth (2005)

The effect of a polymeric medium on the nucleation and growth kinetics of iron oxide (γ-Fe2O3) clusters is studied. We show that the kinetics in both poly(methyl methacrylate) and polystyrene are dominated by the nucleation stage, while the growth stage is largely suppressed. The rate constant is found to decrease with temperature. Most surprisingly, particles formed in a strongly adsorbing polymer, poly(methyl methacrylate), are shown to grow more slowly than those in a weakly interacting polymer, polystyrene. The kinetic mechanism is used to explain why the size distribution of nanoclusters formed in polymeric media is narrow when compared to particles synthesized in small molecule solvents.
Fluorine Barrier Properties of Bias-Sputtered Tungsten Films (2000)

Fluorine diffusion barrier properties of bias‐sputtered tungsten films and titanium nitride films are compared for use in interconnects in silicon integrated circuits. Typical vertical interconnect film stacks consist of tungsten (chemical vapor deposition)/diffusion barrier/titanium. Chemical vapor deposition of tungsten using tungsten hexafluorine leads to fluorine contamination in the film stack. Tungsten films 380 nm thick were deposited on 100 nm titanium films protected by either 10 nm thick bias‐sputtered tungsten or 10 nm thick TiN diffusion barrier films. The dose of fluorine in the titanium films protected by TiN was measured to be vs. in the titanium film protected by sputtered tungsten. We extract an upper bound for the diffusivity of fluorine in sputtered tungsten films to be at 410°C. Variation in fluorine dose in the titanium film with sputtered tungsten film thickness and tungsten chemical vapor deposition conditions is discussed. The superior fluorine barrier property and lower resistivity of sputtered tungsten films make them a good candidate to replace titanium nitride for via applications in silicon integrated circuits. © 2000 The Electrochemical Society. All rights reserved.
Emerging Role of Hemoglobin Solutions in Trauma Care (2005)

SUMMARY Most authorities believe that the greatest need for blood substitutes is in patients with unanticipated acute blood loss, and trauma is the most likely scenario. The blood substitutes reaching advanced clinical trials today are red blood cell (RBC) substitutes, derived from hemoglobin. The hemoglobin‐based oxygen carriers (HBOCs) tested currently in FDA Phase III clinical trials are polymerized hemoglobin solutions. In the USA, the standard approach to restoring oxygen delivery in hemorrhagic shock has been crystalloid administration to expand intravascular volume, followed by stored RBCs for critical anemia. Allogeneic RBCs, however, may have adverse immunoinflammatory effects that increase the risk of postinjury multiple organ failure (MOF). Phase II clinical trials, as well as in vitro and in vivo work, suggest that resuscitation with a HBOC – in lieu of stored RBCs – attenuates the systemic inflammatory response invoked in the pathogenesis of MOF. Specifically, a HBOC has been shown to obviate stored RBC provoked neutrophil (PMN) priming, endothelial activation, and systemic release of interleukins 6,8, and 10. Based on this background and work by others, we have initiated a multicenter prehospital trial in which severely injured patients with major blood loss (SBP < 90 mm Hg) are randomized to initial field resuscitation with crystalloid versus HBOC. During the hospital phase the control group is further resuscitated with stored RBCs, whereas the study group receives HBOC (up to 6 units) in the first 12 hours. The primary study endpoint is 30‐day mortality, and secondary endpoints include reduction in allogeneic RBCs, hemoglobin levels < 5 g/dL, uncrossmatched RBCs, and MOF. The potential efficacy of HBOCs expands beyond the temporary replacement for stored RBCs. Hemoglobin solutions might ultimately prove superior in delivering oxygen to ischemic or injured tissue. The current generation of HBOCs can be lifesaving for acute blood loss today, but the next generation might be biochemically tailored for specific clinical indications.
A near-field to far-field transformation method research based on interference source reconstruction (2014)

This paper focused on the transformation problem from near-field to far-field data of integrated circuit (IC). The near-field data was obtained by near-field measurement, while the far-field data was what we needed. The key point was learning the nature of interference sources. A method was proposed to compute equivalent sources. Firstly, the value of EM field in the measurement plane was achieved and the parameters of the equivalent source were extracted by adopting least-squares method. Then an equivalent combined source model was put forward to create the far field data. Finally, an example was made to verify the correctness of this method.
Synthesis and Herbicidal Activity of Sulfonylureas; SL-950 and Its Related Compounds (1995)

長年にわたるピリジン系スルホニルウレア化合物の研究の結果, ピリジン核3-位に置換カルバモイル基を有する新規化合物群がトウモロコシに対してきわめて安全であることを見出した. カルバモイル基上の置換基と活性ならびにウレア鎖に直結した置換複素環の構造と活性について検討した結果, 2-(4, 6-dimethoxypyrimidin-2-ylcarbamoylsulfamoyl)-N, N-dimethylnicotinamide (SL 950, Nicosulfuron) がもっとも活性が高く, 40～80g a. i./haというごく低薬量で多年生イネ科を含むイネ科, カヤツリグサ科, 広葉雑草に対して有効であると同時にきわめて幅広い殺草スペクトルを有していることを確認し, 現在石原産業株式会社で開発中である. 本研究の新規ピリジルスルポニルウレア系化合物の合成のための鍵中間体である2-アミノスルホニル-N-置換-ニコチンアミドに関して, 4種類の合成法を確立した.
Engineered cyanobacteria with enhanced growth show increased ethanol production and higher biofuel to biomass ratio (2018)

The Calvin-Benson-Bassham (CBB) cycle is the main pathway to fix atmospheric CO<sub>2</sub> and store energy in carbon bonds, forming the precursors of most primary and secondary metabolites necessary for life. Speeding up the CBB cycle theoretically has positive effects on the subsequent growth and/or the end metabolite(s) production. Four CBB cycle enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), fructose-1,6/sedoheptulose-1,7-bisphosphatase (FBP/SBPase), transketolase (TK) and aldolase (FBA) were selected to be co-overexpressed with the ethanol synthesis enzymes pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) in the cyanobacterium Synechocystis PCC 6803. An inducible promoter, PnrsB, was used to drive PDC and ADH expression. When PnrsB was induced and cells were cultivated at 65 µmol photons m<sup>-2</sup> s<sup>-1</sup>, the RuBisCO-, FBP/SBPase-, TK-, and FBA-expressing strains produced 55%, 67%, 37% and 69% more ethanol and 7.7%, 15.1%, 8.8% and 10.1% more total biomass (the sum of dry cell weight and ethanol), respectively, compared to the strain only expressing the ethanol biosynthesis pathway. The ethanol to total biomass ratio was also increased in CBB cycle enzymes overexpressing strains. This study experimentally demonstrates that using the cells with enhanced carbon fixation, when the product synthesis pathway is not the main bottleneck, can significantly increase the generation of a product (exemplified with ethanol), which acts as a carbon sink.
A complete distortion correction for MR images: II. Rectification of static-field inhomogeneities by similarity-based profile mapping (2005)

Radiotherapy treatment planning relies on the use of geometrically correct images. This paper presents a fully automatic tool for correcting MR images for the effects of B(0) inhomogeneities. The post-processing method is based on the gradient-reversal technique of Chang and Fitzpatrick (1992 IEEE Trans. Med. Imaging 11 319-29) which combines two identical images acquired with a forward- and a reversed read gradient. This paper demonstrates how maximization of mutual information for registration of forward and reverse read gradient images allows the elimination of user interaction for the correction. Image quality is preserved to a degree not reported previously.
Temsirolimus, Interferon Alfa, or Both for Advanced Renal-Cell Carcinoma (2007)

As compared with interferon alfa, temsirolimus improved overall survival among patients with metastatic renal-cell carcinoma and a poor prognosis. The addition of temsirolimus to interferon did not improve survival. (ClinicalTrials.gov number, NCT00065468 [ClinicalTrials.gov].).
Evaluation in dogs and humans of three potential technetium-99m myocardial perfusion agents. (1986)

The biodistribution of the three cationic 99mTc complexes [99mTc(TMP)6]+, [99mTc(POM-POM)3]+, and [99mTc(TBIN)6]+--where TMP represents trimethylphosphite, POM-POM represents 1,2-bis(dimethyoxyphosphino)ethane, and TBIN represents t-butylisonitrile--have been evaluated in humans and dogs. Each agent was studied in three normal volunteers at rest, while [99mTc(POM-POM)3]+ and [99mTc(TBIN)6]+ were each studied in one normal volunteer at exercise. Even though all three agents yield good myocardial images in dogs, none appear suitable for clinical use as myocardial perfusion imaging radiopharmaceuticals. In humans, [99mTc(TMP)6]+ and [99mTc(POM-POM)3]+ clear very slowly from the blood and provide myocardial images only several hours after injection. [99mTc(TBIN)6]+ clears rapidly from the blood, but accumulation in the lung obscures the myocardial image for the first hour after injection; at later times, activity in the liver and spleen masks the apical wall. These results correlate with the blood-binding properties of the three complexes. [99mTc(TMP)6]+ and [99mTc(POM-POM)3]+ bind tightly to the plasma of human blood, but not to the plasma of dog blood; [99mTc(TBIN)6]+ does not bind tightly to the plasma of either dog or human blood. Among the Tc(I) complexes studied to date in humans, [99mTc(TBIN)6]+ appears to be unique in biodistribution pattern, blood-binding properties, and the fact that exercise improves the ultimate myocardial image. All the Tc(I) complexes appear to undergo myocardial accumulation by a mechanism different from that utilized by Tc(III) complexes. Animal studies alone are not adequate to evaluate the potential utility of 99mTc cationic complexes for myocardial perfusion studies.
ASK multiport optical homodyne receivers (1987)

Several types of ASK multiport homodyne receivers are investigated, and the impact of the phase noise and of the shot noise on these receivers is analyzed. The simplest structure is the conventional multiport receiver with a matched filter in each branch. This structure can tolerate <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\DeltavT</tex> [ <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\deltav</tex> is the laser finewidth and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</tex> is the bit duration) of several percent with a small power penalty (3.6 percent for 1-dB penalty and 5.2 percent for 2-dB penalty). Optimization of branch filters of conventional multiport receivers does not help when the linewidth (and the penalty) is small but does improve the receiver performance for larger linewidths. The most important point of the paper is the novel wide-band filter-rectifier-narrow-band filter (WIRNA) structure, proposed and investigated here for the first time for optical communication systems. It is shown that the optimized WIRNA homodyne receivers are extremely robust with respect to the phase noise: the WIRNA tolerable value of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\DeltavT</tex> is 3.6 percent for 1-dB penalty and more than 50 percent for 2-dB penalty. Thus, the WIRNA structure opens, for the first time, the possibility of constructing homodyne receivers operating at several hundred megabits per second with conventional DFB lasers without complicated external cavities. Under no-phase-noise conditions, all the multiport receivers investigated here have the same performance, which is identical to that of heterodyne ASK receivers. In addition, the optimized WIRNA receivers can tolerate tapproximately) the same laser linewidth as the heterodyne ASK receivers. Thus, the main difference between the WIRNA multiport homodyne and heterodyne receivers is that the former shifts the processing to a lower frequency range, in return for a more complicated implementation. This difference makes the WIRNA multiport homodyne receivers particularly attractive at high (say, several gigabit per second) bit rates.
Molecular and functional characterization of bile acid transport in human hepatoblastoma HepG2 cells (1996)

Bile acids are taken up into human liver by Na+-dependent and Na+-independent transport mechanisms. In hepatocarcinogenesis, numerous liver-specific functions are lost and the uptake of organic anions is markedly reduced. We have investigated the molecular and functional derangements of bile acid transport in the human hepatoblastoma cell line HepG2. Uptake of [3H]-taurocholic acid was saturable and entirely Na+ independent, with the kinetic characteristics of the human liver organic anion transporting polypeptide (OATP). OATP, but not the Na+-dependent bile acid transporter (Na+-taurocholate-cotransporting polypeptide [NTCP]), was detectable by reverse-transcription polymerase chain reaction (RT-PCR) analysis of HepG2 RNA. The level of OATP expression in HepG2 cells was determined by Northern blot analysis and was found to be 40% in comparison with normal liver. Transfection of an OATP-derived phosphorothioate (PTO)-antisense oligonucleotide into HepG2 cells resulted in 77% inhibition of temperature-dependent bile acid uptake. Injection of HepG2 messenger RNA (mRNA) into Xenopus laevis oocytes significantly stimulated Na+-independent taurocholate uptake, indicating the expression of a bile acid transport protein. We conclude that bile acid uptake into human hepatoblastoma HepG2 cells is mediated by the multi-specific organic anion transporting polypeptide OATP. Therapeutic strategies employing bile acid-derived cytostatic agents for the treatment of hepatocellular carcinomas may therefore depend upon the expression of the Na+-independent bile acid transporter OATP in hepatic malignancies.
Enabling photon counting detectors with dynamic attenuators (2014)

Photon-counting x-ray detectors (PCXDs) are being investigated as a replacement for conventional x-ray detectors because they promise several advantages, including better dose efficiency, higher resolution and spectral imaging. However, many of these advantages disappear when the x-ray flux incident on the detector is too high. We recently proposed a dynamic, piecewise-linear attenuator (or beam shaping filter) that can control the flux incident on the detector. This can restrict the operating range of the PCXD to keep the incident count rate below a given limit. We simulated a system with the piecewise-linear attenuator and a PCXD using raw data generated from forward projected DICOM files. We investigated the classic paralyzable and nonparalyzable PCXD as well as a weighted average of the two, with the weights chosen to mimic an existing PCXD (Taguchi et al, Med Phys 2011). The dynamic attenuator has small synergistic benefits with the nonparalyzable detector and large synergistic benefits with the paralyzable detector. Real PCXDs operate somewhere between these models, and the weighted average model still shows large benefits from the dynamic attenuator. We conclude that dynamic attenuators can reduce the count rate performance necessary for adopting PCXDs.
3D domain‐swapped human cystatin C with amyloidlike intermolecular β‐sheets (2005)

Oligomerization of human cystatin C (HCC) leads to amyloid deposits in brain arteries, and this process is greatly accelerated with a naturally occurring L68Q variant. The crystal structures of N-truncated and full-length HCC (cubic form) showed dimer formation via three-dimensional (3D) domain swapping, and this observation has led to the suggestion that an analogous domain-swapping mechanism, but propagated in an open-ended fashion, could be the basis of HCC fibril formation. Here we report that full-length HCC, when crystallized in a new, tetragonal form, dimerizes by swapping the same secondary structure elements but with a very different overall structure generated by the flexibility of the hinge linking the moveable elements. The beta-strands of the beta-cores of the two folding units of the present dimer are roughly parallel, while they formed an angle of about 100 degrees in the previous two structures. The dimers pack around a crystallographic dyad by extending their molecular beta-sheets in an intermolecular context. At the other edge of the molecular beta-sheet, side-chain-side-chain hydrogen bonds propagate the beta-structure in the same direction. In consequence, a supramolecular crystal structure is generated, with all the beta-strands of the domain-swapped dimers being perpendicular to one crystallographic direction. This observation is relevant to amyloid aggregation of HCC, as X-ray diffraction studies of amyloid fibrils show them to have ordered, repeating structure, consistent with the so-called cross-beta structure, in which extended polypeptide chains are perpendicular to the fiber axis and form infinite beta-sheets that are parallel to this axis.
Lightweight Memory Checkpointing (2015)

Memory check pointing is a pivotal technique in systems reliability, with applications ranging from crash recovery to replay debugging. Unfortunately, many traditional memory check pointing use-cases require high-frequency checkpoints, something for which existing application-level solutions are not well-suited. The problem is that they incur either substantial run-time performance overhead, or poor memory usage guarantees. As a result, their application in practice is hampered. This paper presents Lightweight Memory Check pointing (LMC), a new user-level memory check pointing technique that combines low performance overhead with strong memory usage guarantees for high check pointing frequencies. To this end, LMC relies on compiler-based instrumentation to shadow the entire memory address space of the running program and incrementally checkpoint modified memory bytes in a LMC-maintained shadow state. Our evaluation on popular server applications demonstrates the viability of our approach in practice, confirming that LMC imposes low performance overhead with strictly bounded memory usage at runtime.
Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy (2017)

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1H–29Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1H–29Si HETCOR and dipolar 2D 1H–1H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Instead the 2D NMR spectra illustrate that there is large distribution of 1H and 29Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1H–29Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH3), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1H and 29Si chemical shifts. The approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.
Quantum transport in an electron-wave guide (1987)

We have fabricated high-mobility, one dimensional wires in GaAs-AlGaAs heterostructures and measured the resistance as a function of magnetic field and temperature. Because of the size of the devices and the high mobility, only a few channels carry the current at 35 mK with minimal scattering. Fluctuations in the resistance as a function of magnetic field due to quantum interference are observed for 0${\mathrm{\ensuremath{\omega}}}_{\mathrm{c}}$\ensuremath{\tau}300, where ${\mathrm{\ensuremath{\omega}}}_{\mathrm{c}}$ is the cyclotron frequency and \ensuremath{\tau} is the scattering time, superimposed upon Shubnikov--de Haas oscillations and the Hall effect.
GLI1 regulates a novel neuropilin‐2/α6β1 integrin based autocrine pathway that contributes to breast cancer initiation (2013)

The characterization of cells with tumour initiating potential is significant for advancing our understanding of cancer and improving therapy. Aggressive, triple-negative breast cancers (TNBCs) are enriched for tumour-initiating cells (TICs). We investigated that hypothesis that VEGF receptors expressed on TNBC cells mediate autocrine signalling that contributes to tumour initiation. We discovered the VEGF receptor neuropilin-2 (NRP2) is expressed preferentially on TICs, involved in the genesis of TNBCs and necessary for tumour initiation. The mechanism by which NRP2 signalling promotes tumour initiation involves stimulation of the α6β1 integrin, focal adhesion kinase-mediated activation of Ras/MEK signalling and consequent expression of the Hedgehog effector GLI1. GLI1 also induces BMI-1, a key stem cell factor, and it enhances NRP2 expression and the function of α6β1, establishing an autocrine loop. NRP2 can be targeted in vivo to retard tumour initiation. These findings reveal a novel autocrine pathway involving VEGF/NRP2, α6β1 and GLI1 that contributes to the initiation of TNBC. They also support the feasibility of NRP2-based therapy for the treatment of TNBC that targets and impedes the function of TICs.