gebhart/patrepeval huggingface dataset:
STABILIZER (2013)

Researchers and software developers require effective performance evaluation. Researchers must evaluate optimizations or measure overhead. Software developers use automatic performance regression tests to discover when changes improve or degrade performance. The standard methodology is to compare execution times before and after applying changes. Unfortunately, modern architectural features make this approach unsound. Statistically sound evaluation requires multiple samples to test whether one can or cannot (with high confidence) reject the null hypothesis that results are the same before and after. However, caches and branch predictors make performance dependent on machine-specific parameters and the exact layout of code, stack frames, and heap objects. A single binary constitutes just one sample from the space of program layouts, regardless of the number of runs. Since compiler optimizations and code changes also alter layout, it is currently impossible to distinguish the impact of an optimization from that of its layout effects. This paper presents Stabilizer, a system that enables the use of the powerful statistical techniques required for sound performance evaluation on modern architectures. Stabilizer forces executions to sample the space of memory configurations by repeatedly re-randomizing layouts of code, stack, and heap objects at runtime. Stabilizer thus makes it possible to control for layout effects. Re-randomization also ensures that layout effects follow a Gaussian distribution, enabling the use of statistical tests like ANOVA. We demonstrate Stabilizer's efficiency (<7% median overhead) and its effectiveness by evaluating the impact of LLVM's optimizations on the SPEC CPU2006 benchmark suite. We find that, while -O2 has a significant impact relative to -O1, the performance impact of -O3 over -O2 optimizations is indistinguishable from random noise.
[Determination of plasma escitalopram with liquid chromatography-mass spectrometry]. (2008)

The method is sensitive, accurate, rapid, specific and well applicable for clinical pharmacokinetics study of escitalopram.
Transient global amnesia associated with the infusion of DMSO-cryopreserved autologous peripheral blood stem cells (2008)

Dimethylsulfoxide (DMSO) is a solvent commonly used for the cryopreservation of autologous peripheral blood stem cells (APBSC). Side effects upon infusion of DMSO-cryopreserved APBSC mainly consist of nausea, emesis, chills, rigors, and cardiovascular events, such as bradyarrhythmia or hypotension. We report the case of a patient who received DMSO-cryopreserved APBSC after myeloablative chemotherapy for a relapsing lymphoma. The patient developed a rare reaction during the infusion manifesting as transient global amnesia. The clinical course during the reaction is described and an explanation of the possible causes is discussed. This observation underlines the need for an adequate DMSO depletion to limit neurotoxicity or other adverse manifestations.
An interface to support color blind computer users (2007)

A new method for adapting digital images so that they are suitable for color blind viewers is presented. In contrast to earlier automatic methods which formulate the problem of adapting images for color blind observers as one of optimization, we demonstrate how it is possible to allow a user to compute a very wide range of adaptations in reasonable time under the control of a single variable. We demonstrate how the algorithm can be delivered as an adaptive technology via a simple interface, and evaluate the efficacy of our method using psychovisual experiments with simulated color blind users and a standard color vision test.
Mapping the Major Interaction Between Binding Protein and Ig Light Chains to Sites Within the Variable Domain (1999)

Newly synthesized Ig chains are known to interact in vivo with the binding protein (BiP), a major peptide-binding chaperone in the endoplasmic reticulum. The predominant interactions between the light chain and BiP are observed early in the folding pathway, when the light chain is either completely reduced, or has only one disulfide bond. In this study, we describe the in vitro reconstitution of BiP binding to the variable domain of light chains (VL). Binding of deliberately unfolded VL was dramatically more avid than that of folded VL, mimicking the interaction in vivo. Furthermore, VL binding was inhibited by addition of ATP, was competed with excess unlabeled VL, and was demonstrated with several different VL proteins. Using this assay, peptides derived from the VL sequence were tested experimentally for their ability to bind BiP. Four peptides from both beta sheets of VL were shown to bind BiP specifically, two with significantly higher affinity. As few as these two peptide sites, one from each beta sheet of VL, are sufficient to explain the association of BiP with the entire light chain. These results suggest how BiP directs the folding of Ig in vivo and how it may be used in shaping the B cell repertoire.
Research of three-dimensional medical model visualization based on the STL file format (2015)

Objective On the basis of the STL file format being applied to store the medical model data,the three-dimensional visualization effect of the medical model can be enhanced by setting the color of the different parts of the model. Methods The STL file format represents object without any color in anatomical models. We add color information in the reserved location of triangle information,so the relations can be distinguished between different components of anatomical model. In the process of partitioning different components on the three-dimensional medical model,two-dimensional screen boundaries of different components are mapped into the three-dimensional model through establishing relationship between two-dimensional screen coordinate and the three-dimensional model coordinate. The join algorithm is employed to ensure the closure of three-dimensional boundary. And an algorithm similar to the seed-filling is applied to fill the color information of the area within the boundaries. Results The model with color information can describe the different components of the medical model more accurately,and possesses better three-dimensional visualization effects.Conclusions The boundary-partitioning and the area-filling algorithm can achieve a three-dimensional model with areas colored,and the enhanced STL file format can efficiently store colored three-dimensional medical model data.
All-fiber side pump combiner for high-power fiber lasers and amplifiers (2010)

We present an all-fiber side pump combiner for high power fiber lasers and amplifiers. It consists of a capillary with decreasing wall thickness fused around the active fiber in a way that it becomes an additional cladding layer of it. The pump fibers are spliced at the edge of the capillary with the thickest wall. This provides enough room to allocate around 12 pump fibers (100μm diameter) in a standard 400μm double-clad fiber. This side pump combiner offers several advantages such as the fact that it does not interrupt the active fiber core at any point, thus allowing for truly monolithic all fiber lasers and amplifiers. Additionally, the pump light is coupled into the active double-clad fiber all along the combiner's body (~ 1-2 cm long), which avoids the concentration of heat in a very small area, resulting in high pump power handling capabilities. If the taper angle of the capillary wall is low enough a high coupling efficiency (< 95%) is possible. Using this structure we have achieved a maximum combined pump power of 86 Watt from 7 pump diodes. This, we believe, is the highest combined pump power reported so far from a single lumped side pump combiner.
Buffer Therapy → Buffer Diet (2018)

Malignant tumors exhibit an increase in glucose metabolism when compared to normal tissue. The increased metabolism generates an acidic tumor environment, which promotes local invasion, metastasis, and inhibition of immune surveillance. Oral buffers, e.g. 200 mM ad lib NaHCO3, can neutralize tumor acidity and prevent metastasis and improve immune therapy. Because of these promising results in preclinical cancers, phase I/ II clinical trials were initiated in cancer patients for either amelioration of pain or treatment of pancreatic cancer (GemTABS). In these two trials, NaHCO3 was provided in powdered form under an IND. However, compliance remains poor due to adverse effects including, but not limited to, diarrhea, vomitus, limb edema, and taste. Because of these challenges with buffer therapy in the clinic, we have investigated whether dietary manipulations could achieve the same effect by determining the buffering power of foodstuffs and supplements. From these data we generated a point system, wherein 1 point is equivalent to 1 g NaHCO3. Through endpoint titrations, we developed an analytical formula to relate points to food or supplement protein content (11 points per 100 g protein). Other buffers were more palatable compared to NaHCO3 and showed significant promise for dietary interventions. Hence we propose a mixed food + supplement diet can achieve a similar buffer load to that achieved with NaHCO3 alone.
Improving Emergency Preparedness and Public-Safety Responses to Terrorism and Weapons of Mass Destruction (2004)

This article, written from the perspective and based partially on the experience of law enforcement and public health practitioners, explores the very real public-safety threat posed by terrorists' use of weapons of mass destruction (WMDs). More specifically, it provides an overview of various types of WMDs and their properties; outlines the general policies, procedures, and protocols characterizing current police, fire, emergency medical service, and other public-safety agency responses; and illuminates potential gaps and lapses in current practice. Arguing the need for a more focused, integrated, and holistic approach that involves a broader array of personnel and resources from public- and private-sector entities and that emphasizes preparedness and prevention, the article concludes by describing a more effective strategic and operational process. Based on the highly effective Compstat crime control management model, this process involves the timely and accurate analysis of terrorist intelligence, effective tactical and strategic responses to various types of WMD events, rapid deployment of necessary personnel and resources, and relentless follow-up to ensure a more effective and integrated response to future WMD events. Language: en
Determination of the optimal inspiratory pressure providing adequate ventilation while minimizing gastric insufflation using real-time ultrasonography in Chinese children: a prospective, randomized, double-blind study (2017)

( ChiCTR-IPR-16007960 ). Registered 21 February 2016 Conclusion heading: Ultrasound for determining gastric insufflation.
A Review of Gemini Surfactants: Potential Application in Enhanced Oil Recovery (2015)

Abstract Gemini surfactants are a group of novel surfactants with more than one hydrophilic head group and hydrophobic tail group linked by a spacer at or near the head groups. Unique properties of gemini surfactants, such as low critical micelle concentration, good water solubility, unusual micelle structures and aggregation behavior, high efficiency in reducing oil/water interfacial tension, and interesting rheological properties have attracted the attention of academic researchers and field experts. Rheological characterization and determination of the interfacial tension are two of the most important screening techniques for the evaluation and selection of chemicals for enhanced oil recovery (EOR). This review deals with rheology, wettability alteration, adsorption and interfacial properties of gemini surfactants and various factors affecting their performance. The review highlights the current research activities on the application of gemini surfactants in EOR.
Overcoming Electronic Limits to Optical Phase Measurements with an Optical Phase-only Amplifier (2012)

We utilize four wave mixing to precisely multiply the modulation depth of a phase encoded signal, demonstrating 3-extra effective bits of resolution at 32GHz. The technique enables a new class of optical signal processing functions.
Photocurrent by Immobilized Chloroplast Film Electrode (1979)

Journal Article Photocurrent by Immobilized Chloroplast Film Electrode Get access Hideo Ochiai, Hideo Ochiai Laboratory of Biochemistry, College of Agriculture, Shimane University, Matsue, Shimane 690, Japan Search for other works by this author on: Oxford Academic Google Scholar Hitoshi Shibata, Hitoshi Shibata Laboratory of Biochemistry, College of Agriculture, Shimane University, Matsue, Shimane 690, Japan Search for other works by this author on: Oxford Academic Google Scholar Akira Fujishima, Akira Fujishima Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Kenichi Honda Kenichi Honda Department of Synthetic Chemistry, Faculty of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 43, Issue 4, 1 April 1979, Pages 881–883, https://doi.org/10.1080/00021369.1979.10863552 Published: 01 April 1979 Article history Received: 02 November 1978 Published: 01 April 1979
Retroviral-Mediated Gene Therapy for the Differentiation of Primary Cells into a Mineralizing Osteoblastic Phenotype (2008)

Bone tissue engineering has emerged as a promising strategy for the repair of critical-sized skeletal fractures. However, the clinical application of this approach has been limited by the availability of a robust mineralizing cell source. Non-osteogenic cells, such as skin fibroblasts, are an attractive cell-source alternative because they are easy to harvest from autologous donor skin biopsies and display a high capacity for in vitro expansion. We have recently demonstrated that retroviral gene delivery of the osteoblastic transcription factor Runx2/Cbfa1 promotes osteogenic differentiation in primary dermal fibroblasts cultured in monolayer. Notably, sustained expression of Runx2 was not sufficient to promote functional osteogenesis in these cells, and co-treatment with the steroid hormone dexamethasone was required to induce deposition of biologically-equivalent matrix mineralization. On the basis of these results, we then investigated the osteogenic capacity of these genetically engineered fibroblasts when seeded on polymeric scaffolds in vitro and in vivo. These experiments demonstrated that Runx2-expressing fibroblasts seeded on collagen scaffolds produce significant levels of matrix mineralization after 28 days in vivo implantation in a subcutaneous, heterotopic site. Overall, these results offer evidence that transcription factor-based gene therapy may be a powerful strategy for the conversion of a non-osteogenic cellular phenotype into a mineralizing cell source for bone repair applications. This concept may also be applied to control functional differentiation in a broad range of cell types and tissue engineering applications. The chapter below outlines detailed methods for the isolation and ex vivo genetic modification of primary dermal fibroblasts using retroviral-mediated delivery of the Runx2 transgene in both monolayer culture and three-dimensional scaffolds.
High-resolution flash time-to-digital conversion and calibration for system-on-chip testing (2005)

Verification of timing performance in systems-on-chip (SoCs) is becoming more difficult as clock frequencies and levels of integration increase. As a result, on-chip timing measurement has become a very attractive alternative for validation of these systems because it helps to overcome the bandwidth and test access limitations inherent in SoC environments. Flash time-to-digital converters (TDCs) are well suited for use in on-chip timing measurement systems because they can be operated at high speeds, offer low test time and are relatively easy to integrate. However, clock jitter in modern SoCs is often of the same order of magnitude as the temporal resolution of the TDC itself. Therefore, techniques are required to increase TDC resolution while ensuring timing accuracy. A high-resolution flash TDC is presented that exploits the random offsets on flip-flops or arbiters to perform time quantisation. Also described is a novel technique based on additive temporal noise to accurately calibrate this measurement device. Simulation and experimental results reveal that the latter method can calibrate the high-resolution flash TDC down to 5 ps within reasonable error limits. In addition, accurate timing measurement of jitter below 10 ps has been experimentally validated using a high-resolution flash TDC fabricated in a 0.18-µm CMOS process.
Prohormone Processing by Yeast Proteases (1991)

Investigations of the precursors of alpha-pheromone and killer toxin in the yeast Saccharomyces cerevisiae have defined the genes coding (KEX1 and KEX2) for the proteases which are responsible for their processing. In addition to processing at pairs of basic residues it is evident that yeast can also process at monobasic sites. We present data on the Kex1p and Kex2p enzymes, their cellular localization, and their post-translational modification. In addition initial characterisation of the monobasic specific protease and the isolation of mutants defective in this activity are presented. The use of the yeast system as a model for the processing of mammalian prohormones is discussed.
Estimating path loss in wireless local area networks using ordinary kriging (2010)

This paper introduces ordinary kriging as a new tool to predict network coverage in wireless local area networks. The proposed approach aims to reduce the cost of active site surveys by estimating path loss at points where no measurement data is available using samples taken at other points. To take the effect of obstacles on the covariance among points into account, a distance measure is proposed based on an empirical path loss model. The performance of the proposed approach is tested in a simulated wireless local area network. The results show that ordinary kriging is able to estimate path loss with acceptable error levels.
On the Mechanism of Domain Refinement due to Scratching (1982)

As well known, defined scratching of soft magnetic materials results in domain refinements and thus in reduction of anomalous eddy current losses. However, the present paper shows that scratching a grain oriented HI-B sheet causes a stress configuration corresponding to slight bending which would lead to domain widening. Moreover, it is demonstrated that regions of domain refinement due to scratches of restricted length are clearly demarcated by the scratch endings. These experiments indicate that changed stress configurations are nonrelevant for resulting refinements which, rather, are due to stray field generation. Effects are discussed by a theoretical model resulting in refinements especially of wide domains which is in agreement with presented experimental data.
Gel Permeation Chromatography Characterization of the Chain Length Distributions in Thiol−Acrylate Photopolymer Networks (2006)

Crosslinked, degradable networks formed from the photopolymerization of thiol and acrylate monomers are explored as potential biomaterials. The degradation behavior and material properties of these networks are influenced by the molecular weight of the nondegradable thiol-polyacrylate backbone chains that form during photopolymerization. Here, gel permeation chromatography was used to characterize the thiol-polyacrylate backbone chain lengths in degraded thiol-acrylate networks. Increasing thiol functionality from 1 to 4 increased the backbone molecular weight (M̄(w) = 2.3 ± 0.07 × 10(4) Da for monothiol and 3.6 ± 0.1 × 10(4) Da for tetrathiol networks). Decreasing thiol functional group concentration from 30 to 10 mol% also increased the backbone lengths (M̄(w) = 7.3 ± 1.1 × 10(4) Da for the networks containing 10 mol% thiol groups as compared to 3.6 ± 0.1 × 10(4) Da for 30 mol% thiol). Finally, the backbone chain lengths were probed at various stages of degradation and an increase in backbone molecular weight was observed as mass loss progressed from 10 to 70%.
A role for tumour necrosis factor α in human small bowel iron transport (2005)

Cytokines are integral to the development of anaemia of chronic inflammation. Cytokines modulate hepcidin expression and iron sequestration by the reticuloendothelial system but their direct effects on small bowel iron transport are not well characterized. The aim of the present study was to examine the local effects of TNFalpha (tumour necrosis factor alpha) on small bowel iron transport and on iron transporter expression in the absence of hepcidin. The effects of TNFalpha on iron transport were determined using radiolabelled iron in an established Caco-2 cell model. The effect of TNFalpha on the expression and localization of the enterocyte iron transporters DMT-1 (divalent metal transporter 1), IREG-1 (iron-regulated transporter 1) and ferritin was determined utilizing Caco-2 cells and in a human ex vivo small bowel culture system. TNFalpha mediated an early induction in both iron import and iron export, which were associated with increased DMT-1 and IREG-1 mRNA and protein expression (P<0.05). However, by 24 h, both iron import and iron export were significantly inhibited, coinciding with an induction of ferritin heavy chain (P<0.05) and a decrease in DMT-1 and IREG-1 to baseline levels. In addition, there was a relocalization of IREG-1 away from the basolateral cell border and increased iron deposition in villous enterocytes. In conclusion, TNFalpha has a direct effect on small bowel iron transporter expression and function, leading to an inhibition of iron transport.
Architecture-Aware Mapping and Optimization on a 1600-Core GPU (2011)

The graphics processing unit (GPU) continues to make in-roads as a computational accelerator for high-performance computing (HPC). However, despite its increasing popularity, mapping and optimizing GPU code remains a difficult task, it is a multi-dimensional problem that requires deep technical knowledge of GPU architecture. Although substantial literature exists on how to map and optimize GPU performance on the more mature NVIDIA CUDA architecture, the converse is true for OpenCL on an AMD GPU, such as the 1600-core AMD Radeon HD 5870 GPU. Consequently, we present and evaluate architecture-aware mapping and optimizations for the AMD GPU. The most prominent of which include (i) explicit use of registers, (ii) use of vector types, (iii) removal of branches, and (iv) use of image memory for global data. We demonstrate the efficacy of our AMD GPU mapping and optimizations by applying each in isolation as well as in concert to a large-scale, molecular modeling application called GEM. Via these AMD-specific GPU optimizations, our optimized OpenCL implementation on an AMD Radeon HD 5870 delivers more than a four-fold improvement in performance over the basic OpenCL implementation. In addition, it outperforms our optimized CUDA version on an NVIDIA GTX280 by 12%. Overall, we achieve a speedup of 371-fold over a serial but hand-tuned SSE version of our molecular modeling application, and in turn, a 46-fold speedup over an ideal scaling on an 8-core CPU.