gebhart/patrepeval huggingface dataset:
Performance Evaluation of NAS Parallel Benchmarks on Intel Xeon Phi (2013)

NAS parallel benchmarks (NPB) are a set of applications commonly used to evaluate parallel systems. We use the NPB-OpenMP version to examine the performance of the Intel's new Xeon Phi co-processor and focus in particular on the many core aspect of the Xeon Phi architecture. A first analysis studies the scalability up to 244 threads on 61 cores and the impact of affinity settings on scaling. It also compares performance characteristics of Xeon Phi and traditional Xeon CPUs. The application of several well-established optimization techniques allows us to identify common bottlenecks that can specifically impede performance on the Xeon Phi but are not as severe on multi-core CPUs. We also find that many of the OpenMP-parallel loops are too short (in terms of the number of loop iterations) for a balanced execution by 244 threads. New or redesigned benchmarks will be needed to accommodate the greatly increased number of cores and threads. At the end, we summarize our findings in a set recommendations for performance optimization for Xeon Phi.
ChemInform Abstract: Discovery of 3‐Aryl‐5‐aryl‐1,2,4‐oxadiazoles as a New Series of Apoptosis Inducers. Part 2. Identification of More Aqueous Soluble Analogues as Potential Anticancer Agents. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Effect of sustained, low-dose curcumin on benzo[a]pyrene-induced tissue DNA adducts in rat model (2008)

AACR Annual Meeting-- Apr 12-16, 2008; San Diego, CA

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Intervention with natural or synthetic agent(s) is considered a useful strategy to prevent cancer development. Test agents are generally administered in the diet at high doses in order to achieve effective plasma concentration. We tested a novel hypothesis that agents administered systemically by polymer-based implants will lower the effective dose in diminishing carcinogen-induced DNA damage compared with dietary route. Female S/D rats were pretreated with curcumin either by diet (400 ppm, w/w) or by 1 cm polycaprolactone (PCL) implants entrapped with 20 mg curcumin. Implants were prepared by dissolving curcumin and PCL in appropriate solvents, melting the polymer following removal of the solvents, and extruding the molten material through a mold. Two weeks later, animals were challenged with a single intraperitoneal dose of benzo[ a ]pyrene (BP) (50 mg/kg). Animals were euthanized after 6 days and different tissues were collected. Analysis of the lung and liver DNA adducts by 32P-postlabeling showed that dietary curcumin inhibited the BP-induced DNA adducts by 45% and 83% in the lung and liver (65 ± 53 and 74 ± 110 adducts/109 nucleotides), respectively compared with sham treatment (117 ± 35 and 432 ± 118 adducts/109 nucleotides). The adduct inhibition also occurred in animals that received curcumin by polymeric implants, except that the degree of inhibition was 1.6 to 1.7-fold lower than the dietary administration. The lesser effectiveness of the implant route presumably stems from a low dose of curcumin delivered by the implant (~80 µg/rat/day) to combat against the bolus dose of BP. To test this hypothesis, animals pretreated with curcumin implants for two weeks were further treated with sustained, low dose of BP by polycaprolactone implant (1 cm implant entrapped with 10 mg BP) (Jeyabalan et al ., PAACR, submitted). Analysis of tissue DNA adducts by 32P-postlabeling 30 days post BP treatment showed 65% and 83% inhibition of adducts in the lung and liver (9 ± 5 and 4 ± 0.7 adducts/109 nucleotides), respectively compared with sham treatment (26 ± 5 and 23 ± 12 adducts/109 nucleotides). The average dose of curcumin over the duration of the study was ~110 µg/rat/day based on the amount left in the implants recovered from animals. Our data suggest that this polymer-based novel delivery system has the potential to apply to a host of plant-derived minor components for activity assessment in vivo that otherwise cannot be tested by the traditional dietary route due to their limited quantities, as well as to reduce toxicity of agents that need to be administered at high doses to achieve effective plasma concentration (Supported from the USPHS grants CA-90892, CA-118114 and CA-125152).
Levamisole in the treatment of stage II breast cancerfive-year follow-up of a randomized double-blind study (1985)

The effect of levamisole combined with postoperative radiotherapy in Stage II breast cancer was investigated in a double-blind randomized study comprising 72 patients. All patients were followed for at least 5 years. Disease-free survival was slightly prolonged in the levamisole group as a whole. Among postmenopausal patients, levamisole significantly increased both disease-free and total survival (P = 0.003) and P = 0.008, respectively). The levamisole group also showed fewer distant metastases as the first sign of recurrence. Levamisole treatment was associated with a risk of granulocytopenia and agranulocytosis (10%), but, as in the authors' previous studies, this seemed to be totally reversible and did not worsen the prognosis.
Impact of the end of range damage from low energy Ge preamorphizing implants on the thermal stability of shallow boron profiles (2004)

A fundamental understanding of the effect of scaling amorphous layers on the thermal stability of active concentrations is required for the formation of ultrashallow junctions. A study on the influence of boron on the evolution of the end of range defects for samples containing shallow amorphous layers formed by low energy germanium implants is conducted. Czochralski grown (100) silicon wafers are preamorphized with 1×1015cm−2, 10keV Ge+ and subsequently implanted with 1×1015cm−2, 1keV B+ such that high boron levels are attained in the end of range region. A sequence of anneals are performed at 750°C, under nitrogen ambient for times ranging from 1s to 6h and the end of range defect evolution is imaged via plan-view transmission electron microscopy (TEM). Defect analyses are conducted utilizing quantitative TEM which indicates substantial differences in the defect evolution for samples with boron in the end of range. The extended defects observed are very unstable and undergo a fast dissolution. In contrast, stable defects are observed in the experimental control in which the evolution follows an Ostwald ripening behavior. Secondary ion mass spectroscopy analyses confirm the ephemeral nature of the defects observed and also demonstrates drastic reductions in interstitial supersaturation. In addition, uphill-type diffusion is observed to occur for a short time frame, which emphasizes a transient interstitial supersaturation. Correlation of this data with sheet resistance and active dose measurements conducted on a Hall measurement system strongly indicates the formation of boron interstitial clusters. The high boron concentrations and supersaturation levels attained at the anneal temperature enables the cluster formation. An estimate of the boron concentrations trapped in the clusters is determined from the active dose obtained from the Hall measurements and indicates concentrations much higher than those available in the end of range. This suggests an interstitial migration from the end of range to regions of higher boron levels. Since the end of range is in the vicinity of the highly doped layer it is not isolated from the strain effects induced by the high initial activation levels. Hence it is proposed that the tensile strain stimulates the interstitial migration from the end of range to the boron-doped layer. Consequently, the end of range defects dissolve as the interstitial supersaturation falls below levels required to sustain their evolution.
Computed radiography system with defect detection algorithms based on limited 3D reconstruction view (2010)

In this work we present recently assembled computed radiography system which allows achieving approximate 3D reconstruction of the object under study from limited set of projections. The system is able to localize defects in three-dimensional space. This is shown for a notch in pipe made of Inconel alloy. Current limitations of the system are discussed and the directions for future improvements are indicated.
Commercial Building Design Pathways Using Optimization Analysis: Preprint (2010)

Whole-building simulation and analysis has demonstrated a significant energy savings potential in a wide variety of design projects. Commercial building design, however, traditionally integrates simulation and modeling analyses too late in the design process to make a substantial impact on energy use. The National Renewable Energy Laboratory (NREL) commercial building group created anoptimization platform called Opt-E-Plus that uses multivariate and multi-objective optimization theory to navigate a large parameter space and find economically valid, energy-saving solutions. The analysis results provide designers and engineers valuable information that influences the design. The pathways are not full 'construction ready' design alternatives; rather, they offer guidance aboutperformance and cost criteria to reach a range of energy and economic goals. Having this knowledge early in the design phase helps designers establish project goals and direct the design pathway before they make important decisions. Opt-E-Plus has been deployed on several projects, including a retrofit mixed-use building, a new NREL office building, and several nationwide design guides. Each ofthese projects had different design criteria, goals, and audiences. In each case the analysis results provided pathways that helped inform the design process.
Control of microbial contamination during surgical harvest of pig renal xenografts (2003)

The pig has been identified as the most likely source of xenograft material for clinical use and studies are ongoing to overcome the immunological hurdles of pig-to-human transplantation. Attention is now being focussed on identifying and reducing the potential microbiological hazards associated with this technique. Studies have primarily addressed issues surrounding the production and health monitoring of xenograft source pigs and none have so far specifically evaluated the possible risks of microbial contamination during xenograft harvest. In this report, we evaluate the possible routes for contamination of a pig kidney xenograft during organ harvest and describe approaches to the control of these hazards, including the novel use of a custom designed airtight surgical canopy. A standard procedure for microbiological monitoring during xenograft harvest was devised and evaluated. This allowed the rapid identification and anti-microbial sensitivity testing of any isolated organisms. This would enable an early and appropriate pre-emptive treatment of infection because of transmission of pig micro-organisms.
Dual wavelength conversion using electrically pumped microdisc lasers (2011)

We report on low-power wavelength up-and down-conversion in indium phosphide (InP) based microdisc lasers heterogeneously integrated on a silicon-on-insulator waveguide in one single device. Error-free operation, i.e. with a bit-error rate below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> , at 2.5 Gb/s is shown without the use of additional seeding beams.
Influence of hepatitis B virus reactivation on the recurrence of HBV‐related hepatocellular carcinoma after curative resection in patients with low viral load (2014)

It is unclear whether the reactivation of hepatitis B virus (HBV) influences the prognosis of hepatocellular carcinoma (HCC) after resection in patients with chronic hepatitis B. The aim of this study was to identify the influence of HBV reactivation on the recurrence of hepatitis B-related HCC after curative resection in patients with low viral load (HBV DNA <2000 IU/mL). We retrospectively analysed a total of 130 patients who underwent curative resection for HBV-related early stage HCC (single nodule; <5 cm/two or three nodules; <3 cm) with pre-operative HBV DNA levels <2000 IU/mL with serial HBV DNA tests. The predictive factors including HBV reactivation for the recurrence of HBV-related HCC after curative resection were investigated. Fifty-three patients (41%) had HBV reactivation after resection among 130 patients. HBV reactivation was observed in 22 of 53 patients with undetectable baseline HBV DNA and in 31 of 77 patients with detectable baseline HBV DNA. Cumulative recurrence rates after resection at 1, 2 and 3 years were 17.0%, 23.3% and 31.4%, respectively. The multivariable analysis demonstrated that the risk factors for the recurrence were the presence of microvascular invasion (hazard ratio (HR) 2.62, P = 0.003), multinodularity (HR 4.61, P = 0.005), HBV reactivation after resection (HR 2.03, P = 0.032) and HBeAg positivity (HR 2.06, P = 0.044). HBV reactivation after curative resection is associated with the recurrence of HBV-related HCC in patients with low viral load.
Completely planarized W plugs using MnO/sub 2/ CMP (2002)

In tungsten (W) polishing, MnO/sub 2/ has been used as an abrasive to form plugs without etching holes in seams during CMP. We found that MnO/sub 2/ polishes 1.5 times faster than the standard Al/sub 2/O/sub 3/ abrasive, and can be completely removed during the cleaning process.
Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore (2020)

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to £10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.
Propene polymerization with MgCl2 supported Ziegler catalysts: Activation by hydrogen and ethylene (1988)

Abstract Complementary experiments confirm the recent findings that the rate of propene polymerization is temporary enhanced if a small amount of ethylene is introduced during the polymerization, normalizing after consumption of ethylene by copolymerization. In addition, the study of the sequence distribution of propene monomeric units in the copolymerization carried out under various conditions revealed that the activation by ethylene does not involve the propagation steps, but the re‐initiation after deactivation. A similar temporary activation effect was observed after the addition of small amounts of hydrogen. In this case, however, hydrogen is not consumed. Thus, the deactivation observed after the initial rate enhancement is due to another reason. The deactivation could be shown to be reversible after removal of the adsorbed hydrogen when either ethylene or hydrogen was added again to allow re‐initiation of the polymerization. One of the important reasons of the continuous decrease of the propene homopolymerization rate may be due to the fact, that, after a transfer step, the re‐initiation of polymerization does not take place spontaneously. Small amounts of ethylene or hydrogen allow the reinitiation to take place, at least for some kind of active sites.
Immune microenvironment in patients with mismatch‐repair‐proficient oligometastatic colorectal cancer exposed to chemotherapy: the randomized MIROX GERCOR cohort study (2021)

In the era of immune checkpoint inhibitors, understanding the metastatic microenvironment of proficient mismatch repair/microsatellite stable (pMMR/MSS) colorectal cancer (CRC) is of paramount importance to both prognostication and the development of more effective novel therapies. In this study, primary and paired metastasis tissue samples were collected from patients with resectable metastatic CRC treated with adjuvant FOLFOX or peri-operative chemotherapy in the MIROX phase III prospective study. In total, 74 cancer tissues were stained for CD3, CD8, Forkhead box protein 3 (FOXP3), programmed cell death protein-1 (PD-1, invasive front, stromal, intra-epithelial compartments), and programmed death-ligand 1 (PD-L1, tumor, immune cells). The immune profiling of primary CRC had a limited value to predict the immune context of paired metastases for all markers but CD3+. The expression of CD8 and PD-L1 was higher in metastases after neoadjuvant FOLFOX. In metastases, both CD3 T cells at the invasive front and PD-L1 expressions on immune cells were predictive of better disease-free survival. These results show that the effect of FOLFOX on modifying the immune microenvironment in resected CRC metastases and measurement of PD-L1 expression and tumor-infiltrating CD8 T cells in pMMR/MSS metastatic tissue samples could improve treatment strategies of metastatic CRC patients.
Wedgelike ultrathin epitaxial BaTiO3 films for studies of scaling effects in ferroelectrics (2008)

To study ferroelectric size effects in heteroepitaxial SrRuO3∕BaTiO3∕SrRuO3 capacitors, ultrathin BaTiO3 layers were deposited in wedge form across SrTiO3 substrates. The wedgelike films were fabricated by using either an off-center substrate-target geometry or via a moveable shutter during high-pressure sputter deposition. The crystallinity, composition, and surface roughness along wedgelike BaTiO3 films were verified by x-ray diffraction, Rutherford backscattering spectrometry, and atomic force microscopy, respectively. The electrical measurements performed at 77K showed that, despite progressive reduction in remanent polarization as the film thickness decreases even the 3.5-nm-thick BaTiO3 film retains a large remanent polarization of 28μC∕cm2.
Engineering Attenuated Virulence of a Theileria annulata–Infected Macrophage (2014)

Live attenuated vaccines are used to combat tropical theileriosis in North Africa, the Middle East, India, and China. The attenuation process is empirical and occurs only after many months, sometimes years, of in vitro culture of virulent clinical isolates. During this extensive culturing, attenuated lines lose their vaccine potential. To circumvent this we engineered the rapid ablation of the host cell transcription factor c-Jun, and within only 3 weeks the line engineered for loss of c-Jun activation displayed in vitro correlates of attenuation such as loss of adhesion, reduced MMP9 gelatinase activity, and diminished capacity to traverse Matrigel. Specific ablation of a single infected host cell virulence trait (c-Jun) induced a complete failure of Theileria annulata-transformed macrophages to disseminate, whereas virulent macrophages disseminated to the kidneys, spleen, and lungs of Rag2/γC mice. Thus, in this heterologous mouse model loss of c-Jun expression led to ablation of dissemination of T. annulata-infected and transformed macrophages. The generation of Theileria-infected macrophages genetically engineered for ablation of a specific host cell virulence trait now makes possible experimental vaccination of calves to address how loss of macrophage dissemination impacts the disease pathology of tropical theileriosis.
Compressed‐sensing‐based content‐driven hierarchical reconstruction: Theory and application to C‐arm cone‐beam tomography (2015)

A flexible compressed-sensing-based algorithmic approach is proposed that is able to accommodate for a wide range of constraints. It is successfully applied to C-arm CBCT images that may not be so well approximated by piecewise constant functions.
Adrenomedullin: a new peptide with many clinical implications (2009)

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The Role of Hsp104 in Stress Tolerance and [PSI+] Propagation in Saccharomyces cerevisiae (1995)

Some of the most exciting developments in modern biology derive from the unexpected convergence of disparate fields. For several years, our laboratories have been investigating two seemingly unrelated subjects: the role of heat-shock proteins in stress tolerance, and the function of Sup35 in the fidelity of protein synthesis. Recently, our investigations have converged, in a manner that may prove to have specific implications for the etiology of certain neurodegenerative diseases and general implications for the evolution of non-Mendelian systems of inheritance. Here we review previous work and present new data on the roles of Hsp104 and Hsp70 in helping cells survive extreme stresses and in maintaining the translational infidelity factor known as [PSI]. We also speculate briefly about what this unusual meeting of disciplines might suggest.
Supplemental Materials and Methods from Erlotinib Pretreatment Improves Photodynamic Therapy of Non–Small Cell Lung Carcinoma Xenografts via Multiple Mechanisms (2023)

&lt;p&gt;Supplemental Materials and Methods. This file contains supplemental materials and methods.&lt;/p&gt;
Modulation of PL recombination processes in N doped GaAs/Alo.33Gao.67As SQW by electric field K Onomitsu, A Kawaharazuka, T Okabe, T Makimoto, H Saito and Y Horikoshi (2002)

GaAs and Alo.33Gao.67As layers are grown on (001) semi-insulating GaAs substrates by MBE at 590°C using Ga, A1 and As solid sources. Atomic N is produced using N2 molecules cracked by a tungsten filament.9) In this experiment the N sheet concentration is fixed approximately at 1 X 109cm ' 2 because the N-ALD GaAs layer with this N sheet concentration shows a series of sharp and strong PL lines. The concentration of N atom was estimated by using secondary ion mass spectrometry (SIMS) at high concentrations. However, for lower N atom concentrations below the detection limit of SIMS (5 X 1016cm'3), the concentration was estimated from the efficiency by the hot W filament.9) The N-ALD layer is inserted either at the center or at the position shifted toward the surface heterojunction of Alo.33Gao.67As /GaAs. The structure of a N-ALD Alo.33Gao.67As/GaAs SQW with a 20nm well width is shown in Fig. 1. Semi-transparent Cr-Au film and thick Au-Ge-Ni film are evaporated on the surface and the back surface respectively in order to apply an electric field in the vertical direction. The PL measurements are performed at 10K using an Ar+ ion laser operating at 488nm. High-resolution measurements are performed using lock-in system at very low excitation intensity (1.5mW/cm2).