gebhart/patrepeval huggingface dataset:
<title>Synthesizing parallel imaging applications using the CAP (computer-aided parallelization) tool</title> (1997)

Imaging applications such as filtering, image transforms and compression/decompression require vast amounts of computing power when applied to large data sets. These applications would potentially benefit from the use of parallel processing. However, dedicated parallel computers are expensive and their processing power per node lags behind that of the most recent commodity components. Furthermore, developing parallel applications remains a difficult task: writing and debugging the application is difficult (deadlocks), programs may not be portable from one parallel architecture to the other, and performance often comes short of expectations. In order to facilitate the development of parallel applications, we propose the CAP computer-aided parallelization tool which enables application programmers to specify at a high-level of abstraction the flow of data between pipelined-parallel operations. In addition, the CAP tool supports the programmer in developing parallel imaging and storage operations. CAP enables combining efficiently parallel storage access routines and image processing sequential operations. This paper shows how processing and I/O intensive imaging applications must be implemented to take advantage of parallelism and pipelining between data access and processing. This paper's contribution is (1) to show how such implementations can be compactly specified in CAP, and (2) to demonstrate that CAP specified applications achieve the performance of custom parallel code. The paper analyzes theoretically the performance of CAP specified applications and demonstrates the accuracy of the theoretical analysis through experimental measurements.
Data Management Plan for Monogram BioSciences (2011)

Abstract This is the data plan for access to data underlying published reports by Monogram BioSciences.
Role of the dopamine D3 receptor in reactivity to cocaine‐associated cues in mice (2002)

Environmental stimuli previously associated with drug effects can acquire secondary reinforcing properties, able to maintain drug-seeking behaviour or induce relapse. We have used a classical Pavlovian conditioning procedure to assess the role of the dopamine D3 receptor (D3R) in the expression of drug-conditioned responses. Mice repeatedly receiving cocaine in a particular environment distinct from home-cages displayed hyperlocomotion after subsequent exposure to the drug-paired environment. Cocaine-conditioned hyperactivity was inhibited by BP 897 or SB-277011-A, D3R-selective partial agonist and antagonist, respectively. D3R gene-targeted mice showed a trend towards an increase in cocaine cue-conditioned hyperactivity. BP 897 had no effect on reactivity to neutral or aversive cues. Cocaine-conditioned mice had increased levels of D3R mRNA and binding in the nucleus accumbens (NAc), and transcripts of brain-derived neurotrophic factor (BDNF), a factor controlling D3R expression, in the ventral tegmental area (VTA). Cocaine had no effects on D3R or BDNF genes when administered in home-cages. Cocaine cue-conditioned c-fos expression was found in cortical areas, notably in the somatosensory cortex, where it was inhibited by BP 897, and in several regions belonging or linked to the limbic system. In conditioned mice, BP 897 inhibited c-fos expression in VTA and activated it in amygdala. These results demonstrate a modulation of reactivity to cocaine cues by the D3R, the expression of which is elevated in the NAc by the repeated association of drug effects with a particular context, through a BDNF-dependent mechanism. D3R-selective partial agonist or antagonist inhibit cocaine cue-conditioned activity possibly by normalizing exacerbated D3R function in the NAc, but our results also point to a possible participation of a pathway involving the VTA, amygdala and somatosensory cortex.
Lysophospholipid G protein-coupled receptor binding parameters as determined by backscattering interferometry (2018)

Lysophosphatidic acid (LPA) activates cognate G protein-coupled receptors (GPCRs) to initiate biological signaling cascades. Lysophospholipid (LP) receptor binding properties remain incompletely assessed because of difficulties with ligand lipophilicity and lipid "stickiness." These inherent attributes produce high levels of nonspecific binding within cell-membrane preparations used to assess GPCRs, as has been shown in classical binding assays using radiolabeled ligands, making accurate measurements of lipid binding kinetics difficult to achieve. Backscattering interferometry (BSI) is an optical technology that measures molecular binding interactions by reporting changes in the refractive index of a solution after binding events. Here, we report the use of BSI to assess LPA<sub>1</sub> for its ability to bind to naturally occurring lipids and a synthetic LPA<sub>1</sub> antagonist (ONO-9780307), under both primary- and competition-binding conditions. Assessment of 12 different lipids demonstrated that the known LP ligand, 1-oleoyl-LPA, as well as an endocannabinoid metabolite, anandamide phosphate, are specific ligands for LPA<sub>1</sub>, whereas other LPs tested were not. Newly determined dissociation constants (<i>K<sub>d</sub></i> values) for orthosteric lipid ligands approximated 10<sup>-9</sup> M, substantially lower (i.e., with higher affinity) than measured <i>K<sub>d</sub></i> values in classical binding or cell-based assays. These results demonstrate that BSI may have particular utility in assessing binding interactions between lipid receptors and their lipid ligands and could provide new screening approaches for lipid receptor identification and drug discovery.
Unreliable Measurement of Basophil Maximum Leukotriene Release with the Buhlmann CAST 2000 Enzyme-Linked Immunosorbent Assay Kit (2006)

The Bühlmann CAST 2000 enzyme-linked immunosorbent assay is a potentially useful assay for measuring sulfidoleukotrienes released in vitro by allergen-challenged basophils. However, we observed that the positive-control reagent yielded positive signals in cell-free systems. These false-positive results depended on using a mouse anti-FcepsilonRI monoclonal antibody and were prevented by degranulation-inducing reagents other than mouse monoclonal antibodies.
ActiveStereoNet: End-to-End Self-Supervised Learning for Active Stereo Systems (2018)

In this paper we present ActiveStereoNet, the first deep learning solution for active stereo systems. Due to the lack of ground truth, our method is fully self-supervised, yet it produces precise depth with a subpixel precision of $1/30th$ of a pixel; it does not suffer from the common over-smoothing issues; it preserves the edges; and it explicitly handles occlusions. We introduce a novel reconstruction loss that is more robust to noise and texture-less patches, and is invariant to illumination changes. The proposed loss is optimized using a window-based cost aggregation with an adaptive support weight scheme. This cost aggregation is edge-preserving and smooths the loss function, which is key to allow the network to reach compelling results. Finally we show how the task of predicting invalid regions, such as occlusions, can be trained end-to-end without ground-truth. This component is crucial to reduce blur and particularly improves predictions along depth discontinuities. Extensive quantitatively and qualitatively evaluations on real and synthetic data demonstrate state of the art results in many challenging scenes.
Void-array-type photonic crystal device fabricated by femtosecond laser (2005)

This study demonstrates self-assembling of a sub-micrometer-sized void array in fused silica using an amplified 1-kpps Ti:sapphire femtosecond laser. The effect of the focusing conditions of numerical aperture, laser energy, and pulse number on the shape of the fabricated void is also investigated
Fabrication and testing of micron-size (Pb,La)(Zr,Ti)O3 thin film capacitors (1995)

Abstract Micron-scale (down to 2 μm lateral dimension) La-Sr-Co-O/Pb-La-Zr-Ti-O/La-Sr-Co-O ferroelectric capacitors for high density (> 1 Mbit) non-volatile memories have been successfully fabricated by a full wafer process including ion milling. Reduced dimensional effects as well as fabrication process damage on the micron-size capacitors have been studied. The remnant polarization value was only weakly dependent on the lateral dimension of ferroelectric capacitors. The reliability characteristics such as fatigue, retention and aging of the micronscale ion milled capacitors were similar to those of the large capacitors, which is adequate for non-volatile memories.
MS/MS Spectrum (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Gefitinib and erlotinib sensitivity in a panel of non-small cell lung cancer (NSCLC) cell lines (2005)

3389 Gefitinib and erlotinib are novel tyrosine kinase inhibitors (TKIs) with specificity for the epidermal growth factor receptor (EGFR) and are being used in the treatment of lung cancer. Recently mutations in the tyrosine kinase (TK) domain of EGFR have been associated with very high response rates and great sensitivity to gefitinib. However, another subset of lung cancer patients with wild-type EGFR in their tumors also have clinical benefit. We wished to develop gene expression profiles that predict responsiveness to gefitinib and erolotinib in lung cancers in addition to that conveyed by a TK domain EGFR mutation. To do this we determined the concentration of drugs required to give 50% growth inhibition (IC50) in a large panel of 45 NSCLC cell lines (8 with documented mutations of the TK domain of EGFR) which also were profiled for mRNA expression using Affymetrix U133 A & B chips. None of the lung cancer lines came from patients previously treated with TKIs. Cells were grown in 96-well plates, 24 hours after plating TKI’s were added to final concentrations from 0.06 μM to 1,000 μM in 4-fold dilutions, and at 96 hours after plating cell number was measured (CellTiter® 96 Aqueous One Solution (Promega) as a function of drug concentration (8 replicates per plate, all assays repeated 3 or more times), and the IC50 determined with software. Apoptosis assays were performed 24 hours after drug addition using the BD ApoAlert™ Caspase Plates (BD Biosciences). Nude mice were injected with 5 x 106 tumor cells subcutaneously into animals that received 350 cGy whole body irradiation. Tumors were measured twice weekly and tumor volume was calculated using the formula length x width2π/6. The IC50’s to gefitinib range from 0.04 to 324.37 μM and those to erlotinib range from 0.04 to 159.75 μM. As expected 5 of the EGFR mutant lung cancers were sensitive (IC50 1 μM). In apoptosis assays the 5 sensitive lines underwent large scale apoptosis while the 3 EGFR mutant but TKI resistant lines did not. There was nearly a perfect correlation between the log IC50 gefitinib versus the log IC50 erlotinib. The tumor cell lines with wild-type EGFR had IC50 values ranging from 1 μM to 300 μM) indicating a broad range of sensitivity within this group. Xenograft studies showed that sensitive cell lines were also exquisitely sensitive to gefitinib in vivo with large tumors being either cured or put into long term remission with TKI therapy while several resistant cell lines were resistant in vivo as well. Taken together these facts suggest that EGFR mutations are necessary but not sufficient to confer TKI sensitivity. These tumor cell lines provide novel resources to study these important aspects of targeted therapy. Likewise the xenograft studies provide a way to generate in vivo resistant variants to TKI therapy in EGFR mutant lung cancers.
Integration of new alignment mark designs in dual inlaid-copper interconnect processes (2002)

In a joint development program between ASML and Motorola a new set of alignment marks have been designed and tested using the ATHENA off-axis alignment system on the ASML scanner. The new marks were analyzed for improved robustness against varying wafer-processing conditions to verify improved overlay capability and stability. These new marks have been evaluated on a set of dual inlaid-copper short flow wafers, with layer stacks consisting of 180 nm technology generation dielectric materials. Typical process variation has been deliberately introduced as part of the designed experiment to study the performance robustness of the new alignment marks. This paper discusses the new mark design and the theoretical reasons for mark design and/or integration change. Results shown in this paper provide initial feedback as to the viability of new variations of ATHENA alignment marks, specifically the SSPM and VSPM. Included in the results is the investigation to further stabilization of alignment signal strength. New ideas that are currently under development, to increase alignment mark signal strength stability, are discussed.
A new dc breaker with reduced need for semiconductors (2016)

A renewed interest for dc breakers has evolved owing to the visions of connecting several HVDC links into a HVDC grid. Several breaker concepts have been presented and some also have been implemented and tested. A new approach is proposed in this paper. The fundamental principle is to take advantage of the fast recovery of the voltage withstand capability in a Vacuum Interrupter (VI) when the current is temporarily forced to zero using a low-voltage power electronic converter. The latter excites an oscillating current in a passive resonant circuit during the time interval needed to mechanically separate the contacts in the interrupter. The sum of the line current (to be interrupted) and the oscillating current passes through the vacuum interrupter and experiences zero-crossings when the amplitude of the oscillating current exceeds the line current. The most important benefit of the proposed concept is that a favorable cost can be achieved, because excitation of the oscillating current only requires a low output voltage (compared to the breaking voltage across the VI terminals) from the converter. The total voltage rating of the semiconductors in the latter therefore is only a fraction of that needed in a hybrid HVDC breaker and, additionally, they are not requested to turn off the main current but rather to commutate close to current zero-crossings. Experimental verification of the concept has been performed with current up to 1.6 kA against 1.2 kV.
Regulation and function of the tissue-specific transcription factor HNF1 alpha (LFB1) during Xenopus development (1996)

We review the data available on the structure, developmental appearance and embryonic regulation of the tissue-specific transcription factor HNF1 alpha (LFB1) in Xenopus. The expression of the HNF1 alpha gene starts early in embryogenesis shortly after mid-blastula transition and the protein accumulates in the region of the embryo where liver, pronephros and gut--tissues that contain HNF1 alpha in the adult--are developing. The cofactor DCoH, known to stabilize dimer formation of HNF1 alpha, is present as a maternal factor in the egg and has a partially distinct tissue distribution compared to HNF1 alpha. This implies that DCoH does not only modulate HNF1 alpha dimerization but may also cooperate with other transcription factors. By injecting HNF1 alpha promoter CAT constructs into fertilized Xenopus eggs we obtained activation of the injected gene restricted to the region of the developing larvae expressing endogenous HNF1 alpha. Deletion analysis allowed to define the OZ-element that is essential for embryonic activation. This element also occurs in other promoters activated at mid-blastula transition in the embryo and interacts with the maternal factor OZ-1. As the HNF1 alpha promoter also contains functional binding sites for HNF4 and HNF1, we postulate that all of these transcription factors contribute to the cascade leading to proper embryonic activation of the HNF1 alpha gene.
Determination of polyacrylamide by spectrofluorometry (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of polyacrylamide by spectrofluorometryEdwin R. Hendrickson and Ronald D. NeumanCite this: Anal. Chem. 1984, 56, 3, 354–357Publication Date (Print):March 1, 1984Publication History Published online1 May 2002Published inissue 1 March 1984https://pubs.acs.org/doi/10.1021/ac00267a011https://doi.org/10.1021/ac00267a011research-articleACS PublicationsRequest reuse permissionsArticle Views395Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Intensive Care Unit Management of the Critically Ill Patient with Fluid Overload after Open Heart Surgery (2001)

Fluid overload is common before, during and after cardiac surgery. The fluid associated with cardiopulmonary bypass (CPB) and cardioplegia is a particularly important source of such fluid overload. In addition, renal dysfunction, which is common in these patients, participates in the pathogenesis of a positive sodium and water balance. Such fluid overload is physiologically undesirable and participates in the pathogenesis of several clinically important complications. Fluid overload can be partly prevented with the use of diuretics. However, in many patients, diuretics do not achieve sufficient sodium and water diuresis. In these patients, the application of hemofiltration (HF) during CPB and also immediately after CPB is an effective and safe approach to the maintenance of fluid homeostasis. If acute renal failure occurs, early intervention with HF may even improve survival.
Integrated Silicon Photodetector in Thin Film Lithium Niobate Platform for Visible Wavelength Band (2019)

We demonstrate design, fabrication and characterization of amorphous silicon photodetector on lithium niobate photonic platform at visible wavelengths. The device shows the best responsivity of 10mA/W and dark current of less than 0.5nA © 2019 The Author(s)
Characterization of 3-Dimensional Printing and Casting Materials for use in Computed Tomography and X-ray Imaging Phantoms (2020)

Imaging phantoms are used to calibrate and validate the performance of medical computed tomography (CT) systems. Many new materials developed for three-dimensional (3D) printing processes may be useful in the direct printing or casting of biomimetic and geometrically accurate CT and X-ray phantoms. The X-ray linear attenuation coefficients of polymer samples were measured to discover materials for use as tissue mimics in phantoms. This study included a cohort of polymer compounds that were tested in cured form. The cohort consisted of 101 standardized polymer samples fabricated from: two-part silicones and polyurethanes used in commercial casting processes; one-part optically cured polyurethanes used in 3D printing; and fused deposition thermoplastics used in 3D printing. The testing was performed with a commercial micro-CT imaging system from 40 kVp to 140 kVp. The X-ray linear coefficients of the samples and human tissues were plotted with error bars to allow the reader to identify suitable mimics. The X-ray linear attenuation coefficients of the tested material samples spanned a wide range of values, with a small number of them overlapping established human tissue mimic values. Twenty 3D printer materials and one castable polyurethane tracked nylon and polymethyl methacrylate (PMMA) as established X-ray mimics for fat. Five 3D printer materials tracked water as an established X-ray mimic for muscle.
Randomized Instruction Sets and Runtime Environments Past Research and Future Directions (2009)

Instruction set randomization offers a way to combat code-injection attacks by separating code from data (specifically, by randomizing legitimate code's execution environment). The author describes the motivation behind this approach and two application environments.
Accelerated crystallization of zeolites via hydroxyl free radicals (2016)

In the hydrothermal crystallization of zeolites from basic media, hydroxide ions (OH(-)) catalyze the depolymerization of the aluminosilicate gel by breaking the Si,Al-O-Si,Al bonds and catalyze the polymerization of the aluminosilicate anions around the hydrated cation species by remaking the Si,Al-O-Si,Al bonds. We report that hydroxyl free radicals (•OH) are involved in the zeolite crystallization under hydrothermal conditions. The crystallization processes of zeolites-such as Na-A, Na-X, NaZ-21, and silicalite-1-can be accelerated with hydroxyl free radicals generated by ultraviolet irradiation or Fenton's reagent.
A Theoretical View on Sparsely Activated Networks (2022)

Deep and wide neural networks successfully fit very complex functions today, but dense models are starting to be prohibitively expensive for inference. To mitigate this, one promising direction is networks that activate a sparse subgraph of the network. The subgraph is chosen by a data-dependent routing function, enforcing a fixed mapping of inputs to subnetworks (e.g., the Mixture of Experts (MoE) paradigm in Switch Transformers). However, prior work is largely empirical, and while existing routing functions work well in practice, they do not lead to theoretical guarantees on approximation ability. We aim to provide a theoretical explanation for the power of sparse networks. As our first contribution, we present a formal model of data-dependent sparse networks that captures salient aspects of popular architectures. We then introduce a routing function based on locality sensitive hashing (LSH) that enables us to reason about how well sparse networks approximate target functions. After representing LSH-based sparse networks with our model, we prove that sparse networks can match the approximation power of dense networks on Lipschitz functions. Applying LSH on the input vectors means that the experts interpolate the target function in different subregions of the input space. To support our theory, we define various datasets based on Lipschitz target functions, and we show that sparse networks give a favorable trade-off between number of active units and approximation quality.