gebhart/patrepeval huggingface dataset:
Performance Analysis of Distributed Applications using Automatic Classification of Communication Inefficiencies (1999)

We present a technique for performance analysis that helps users understand the communication behavior of their message passing applications. Our method automatically classifies individual communication operations and it reveals the cause of communication inefficiencies in the application. This classification allows the developer to focus quickly on the culprits of truly inefficient behavior, rather than manually foraging through massive amounts of performance data. Specifically, we trace the message operations of MPI applications and then classify each individual communication event using decision tree classification, a supervised learning technique. We train our decision tree using microbenchmarks that demonstrate both efficient and inefficient communication. Since our technique adapts to the target system&apos;s configuration through these microbenchmarks, we can simultaneously automate the performance analysis process and improve classification accuracy. Our experiments on four applications demonstrate that our technique can improve the accuracy of performance analysis, and dramatically reduce the amount of data that users must encounter.
PARADIS (2015)

In-place radix sort is a popular distribution-based sorting algorithm for short numeric or string keys due to its linear run-time and constant memory complexity. However, efficient parallelization of in-place radix sort is very challenging for two reasons. First, the initial phase of permuting elements into buckets suffers read-write dependency inherent in its in-place nature. Secondly, load balancing of the recursive application of the algorithm to the resulting buckets is difficult when the buckets are of very different sizes, which happens for skewed distributions of the input data. In this paper, we present a novel parallel in-place radix sort algorithm, PARADIS, which addresses both problems: a) "speculative permutation" solves the first problem by assigning multiple non-continuous array stripes to each processor. The resulting shared-nothing scheme achieves full parallelization. Since our speculative permutation is not complete, it is followed by a "repair" phase, which can again be done in parallel without any data sharing among the processors. b) "distribution-adaptive load balancing" solves the second problem. We dynamically allocate processors in the context of radix sort, so as to minimize the overall completion time. Our experimental results show that PARADIS offers excellent performance/scalability on a wide range of input data sets.
Antigenic Structure of Human Interferon  1 (Interferon  II1): Comparison with Other Human Interferons (1987)

Recombinant human interferon (IFN) omega 1 (IFN-alpha II1) was compared with other human IFNs with regard to antigenic structure, using polyclonal and monoclonal antibodies. Antisera to recombinant IFN-alpha 1 or IFN-alpha 2c cross-neutralized the antiviral activity of other species of IFN-alpha, but not that of IFN-omega 1. Antisera to IFN-beta or IFN-gamma likewise had no effect on IFN-omega 1. Conversely, antiserum to IFN-omega 1 did not neutralize any of the other IFNs examined (IFN-alpha 1, -alpha 2c, -alpha 10, -alpha B, -alpha F, -beta, -gamma). None of four monoclonal antibodies to IFN-alpha, including a broad-spectrum antibody that neutralized all five recombinant species of IFN-alpha tested, had any effect on the biological activity of IFN-omega 1. Various immunoassays for IFN-alpha did not recognize IFN-omega 1. In immunoprecipitation experiments, radiolabelled IFN-alpha 2c was not precipitated by antiserum to IFN-omega 1. In contrast, antisera to human leukocyte IFN or 'lymphoblastoid' IFN did neutralize IFN-omega 1, although with titres significantly lower than those towards the immunogen or recombinant species of IFN-alpha. In conclusion, human IFN-omega 1 is antigenically different from human IFN-alpha, IFN-beta or IFN-gamma, but is a component of 'natural' mixtures of IFN species produced by virus-induced leukocytes or Burkitt's lymphoma cells.
A Conserved Motif in Region V of the Large Polymerase Proteins of Nonsegmented Negative-Sense RNA Viruses That Is Essential for mRNA Capping (2007)

Nonsegmented negative-sense (NNS) RNA viruses cap their mRNA by an unconventional mechanism. Specifically, 5' monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. This polyribonucleotidyltransferase activity contrasts with all other capping reactions, which are catalyzed by an RNA triphosphatase and guanylyltransferase. In these reactions, a 5' diphosphate mRNA is capped by transfer of GMP via a covalent enzyme-GMP intermediate. RNA guanylyltransferases typically have a KxDG motif in which the lysine forms this covalent intermediate. Consistent with the distinct mechanism of capping employed by NNS RNA viruses, such a motif is absent from L. To determine the residues of L protein required for capping, we reconstituted the capping reaction of the prototype NNS RNA virus, vesicular stomatitis virus, from highly purified components. Using a panel of L proteins with single-amino-acid substitutions to residues universally conserved among NNS RNA virus L proteins, we define a new motif, GxxT[n]HR, present within conserved region V of L protein that is essential for this unconventional mechanism of mRNA cap formation.
Starch Graft Polymers. II. Preparation of Graft Polymers Containing Acrylamide and Acrylic Acid and Evaluation as Textile Print Paste Thickeners (1972)

Abstract Graft copolymers of starch and the vinyl monomers acrylamide (I) and acrylic acid (II) – prepared by γ‐radiation induced grafting reactions – and a graft terpolymer of starch, I and II – prepared by base hydrolysis of a graft copolymer of starch and acrylonitrile (III) — have been evaluated as textile print paste thickeners. Preparation, characterization and evaluation procedures are presented together with results illustrating that starch poly (I) containing 39% poly (I) and starch poly (I, II) containing a mixture of 21% I and 37% II are effective thickeners in this application if used in combination with one another or with commercial thickeners such as algin (sodium alginate).
Design and structural requirements of potent peptidomimetic inhibitors of p21ras farnesyltransferase. (1994)

Cysteine farnesylation of the ras oncogene product, p21ras, on its carboxyl-terminal CA1A2X box (C = cysteine, A = aliphatic, and X = methionine or serine) is required for its transforming activity. p21ras farnesyltransferase (FTase), the enzyme responsible or this important posttranslational modification can be inhibited by simple CA1A2X peptides. We have synthesized a family of CA1A2X peptidomimetics where the central 2 aliphatic amino acids are replaced by a variety of spacer groups with different shapes and conformational characteristics to investigate the structural requirements of these inhibitors. The biological activities of CA1A2X peptidomimetics, where the dipeptide "A1A2" is replaced by 3- or 4-aminomethylbenzoic acid (AMBA) and 3- or 4-aminobenzoic acid (ABA), are evaluated in a p21ras FTase inhibitory assay. Peptidomimetics Cys-4-ABA-Met and Cys-3-AMBA-Met contain spacers that provide good distance correspondence of the carboxylate and ammonium separation with that of the parent KB p21ras tetrapeptide, Cys-Val-Ile-Met, and are as potent FTase inhibitors (IC50 values of 50 and 100 nM, respectively). In contrast, replacing the central dipeptide with 4-AMBA reduced FTase inhibitory activity by 17-fold whereas replacement by 3-ABA reduces inhibitory activity of the peptidomimetics by 43-fold. Cys-4-ABA-Met (IC50 = 50 nM) is 128 times more potent as a p21ras FTase inhibitor than Cys-3-ABA-Met (IC50 = 6400 nM), yet these two peptidomimetics differ only in the substitution pattern around the phenyl ring. These results coupled with computer modeling studies demonstrate that the interaction between FTase and the peptidomimetics requires precise structural and conformational characteristics; in particular, correct positioning of the Cys and Met must be respected. Furthermore, Cys-3-AMBA-Met and Cys-4-ABA-Met are true inhibitors of p21ras FTase since they are not farnesylated by this enzyme, in contrast to Cys-Val-Ile-Met, which inhibits the enzyme by acting as alternative substrate. Computer modeling studies of the potent FTase inhibitor Cys-4-ABA-Met show that a folded conformation, where the thiol and carboxylate groups are close, is not possible. Therefore a beta-turn conformation that would result in the simultaneous coordination of the Cys-thiol and Met-carboxylate to zinc ion is not important for inhibition of p21ras FTase, as previously suggested.
Arbitrary spectral matching using multi-LED lighting systems (2019)

Spectrally tunable light sources for general lighting have recently attracted much attention as versatile solutions that can be used in humancentric lighting implementations provided with excellent color rendering and increased user perception. However, temperature and age-dependent color shifts and flux variations in the light-emitting diode (LED) emission are nonresolved challenges that need to be overcome in order to be used in final applications. We demonstrate two strategies that can be used to efficiently and precisely generate arbitrary spectral power distributions (SPDs) using multichannel LED engines. First, we introduce different methods to match a given SPD and select an algorithm (simulated annealing) in virtue of its speed (in the milliseconds range) and accuracy (color shifts Δu ′ v ′ < 5 × 10 − 4). Then, we propose a closed-loop feedback control (PID) to compensate for spectral shifts due to temperature changes or lumen decay of the LEDs. Both methods can be used independently, but only a combination of them (which uses the output of the first method as an initial guess for the second) offers fast computational times and high spectral accuracy and precision. Computation times are important because these algorithms are intended to be executed on dedicated microprocessors integrated in the LED modules, often sharing scarce memory and processing resources. The results presented here are aimed to be universal and hold for different implementations of the light engine and any number of LED channels.
Synthesis and Biological Evaluation of a Selective N- and P/Q-Type Calcium Channel Agonist (2012)

The acute effect of the potent cyclin-dependent kinase (cdk) inhibitor (R)-roscovitine on Ca(2+) channels inspired the development of structural analogues as a potential treatment for motor nerve terminal dysfunction. On the basis of a versatile chlorinated purine scaffold, we have synthesized ca. 20 derivatives and characterized their N-type Ca(2+) channel agonist action. Agents that showed strong agonist effects were also characterized in a kinase panel for their off-target effects. Among several novel compounds with diminished cdk activity, we identified a new lead structure with a 4-fold improved N-type Ca(2+) channel agonist effect and a 22-fold decreased cdk2 activity as compared to (R)-roscovitine. This compound was selective for agonist activity on N- and P/Q-type over L-type calcium channels.
NETWORKED CELLULOSIC GEL MATERIAL AS A PHARMACEUTICAL EXCIPIENT (2010)

Networked cellulosic (NC) material was prepared in a gel form via sulfuric acid dissolution and hydrolysis of microcrystalline cellulose (MCC) and then regeneration in ethanol. The regenerated material was utilized as tablet excipient. Prepared tablets have shown interesting properties regarding hardness. Tablets were prepared via slip casting of formulas mixed with different NC gel concentrations. The hardness of prepared tablets was measured using tablet hardness tester. It was noticed that the hardness of the tablets increased over a wide range and up to 420 N. The hardness was mainly controlled by the concentration of the NC gel material. Despite of their high hardness, prepared tablets have shown full drug release capabilities. The new technique to prepare these tablets can be implemented in a continuous process that minimizes the disadvantages of batch processing.
Structure–Activity Relationships and Conformational Freedom of CB1 Receptor Antagonists and Inverse Agonists (2008)

In the last few decades, our knowledge of cannabinoid structure–activity relationships (SARs) has increased dramatically. Computational methods have allowed us to compare active and inactive ligands for steric, electronic, and conformational similarities and dissimilarities. Knowing that there are specific G-protein-coupled cannabinoid receptors with which cannabinoids interact, we increasingly interpret changes in structure to specific alterations in ligand–receptor interaction. With additional knowledge of the CB1 and CB2 receptors’ sequence, the consequences of mutations and chimeric constructs of the receptor, and the development of rhodopsin-based homology models of the cannabinoid receptors, we continue to gain insight into the interaction of cannabinoids with their receptors. Finally, our emerging appreciation for cannabinoid homo- and heterodimerization/oligomerization provides for further understanding of ligand–receptor interactions, the interaction of receptors with each other, and the interaction of G-protein-coupled receptors with their signal transduction components and other molecules affecting each receptor’s dynamics. In the following review, we have attempted to characterize the emerging SARs of an important class of cannabinoid ligands: the CB1 receptor antagonists and inverse agonists. This class of compounds is showing therapeutic potential for a variety of indications, and is therefore of interest for both basic research and pharmaceutical development. Throughout this work, we have used molecular modeling, particularly quenched molecular dynamics, to illustrate particular structural modifications that have been reported for CB1 antagonists, their conformational properties, and the potential implications for receptor interaction. In this way, we hope this review serves to further guide medicinal chemists in their understanding of CB1 receptor antagonist SAR and the design of new analogs.
Plasmonic laser sensors (Presentation Recording) (2015)

Perhaps the most successful application of plasmonics to date has been in sensing, where the interaction of a nanoscale localized field with analytes leads to high-sensitivity detection in real time and in a label-free fashion. However, all previous designs have been based on passively excited surface plasmons, in which sensitivity is intrinsically limited by the low quality factors induced by metal losses. It has recently been proposed theoretically that surface plasmon sensors with active excitation (gain-enhanced) can achieve much higher sensitivities due to the amplification of the surface plasmons. Here, we experimentally demonstrate an active plasmon sensor that is free of metal losses and operating deep below the diffraction limit for visible light. Loss compensation leads to an intense and sharp lasing emission that is ultrasensitive to adsorbed molecules. We validated the efficacy of our sensor to detect explosives in air under normal conditions and have achieved a sub-part-per-billion detection limit, the lowest reported to date for plasmonic sensors with 2,4-dinitrotoluene and ammonium nitrate. The selectivity between 2,4-dinitrotoluene, ammoniumnitrate and nitrobenzene is on a par with other state-of-the-art explosives detectors. Our results show that monitoring the change of the lasing intensity is a superior method than monitoring the wavelength shift, as is widely used in passive surface plasmon sensors. We therefore envisage that nanoscopic sensors that make use of plasmonic lasing could become an important tool in security screening and biomolecular diagnostics.
Abstract P017: Early detection of ovarian cancer in high-risk individuals using circulating miRNAs: The MiDe study (2023)

Abstract Background: Epithelial ovarian cancers generally carry a poor prognosis due to late-stage presentation and a high rate of disease recurrence. In contrast, diagnosis of early-stage disease is associated with a high rate of durable remission. Prior studies using archival samples have suggested that a neural network analysis of circulating miRNA expression levels may be an informative biomarker for early-stage ovarian cancer diagnosis. Methods: The miRNA Detection Study (MiDe Study) is a prospective, observational clinical trial open to individuals in all 50 U.S. states. Persons with at least one ovary classified as being at high-risk for ovarian cancer, either due to known genetic predisposition or family history suggestive of possible hereditary breast and ovarian cancer syndrome or Lynch syndrome, are eligible to enroll. Study subjects will submit a blood sample every 6 months for up to 5 years. Neural network analysis of serum miRNA profiles will be correlated with the subsequent diagnosis of ovarian cancer or serous tubal intraepithelial carcinoma, either clinically or at the time of risk-reducing salpingectomy or salpingo-oophorectomy. The primary outcomes are the sensitivity and specificity of the neural network for anticipating a diagnosis of epithelial ovarian cancer or a cancer precursor within 2 years of the index blood sample. The goal recruitment is 1000 study subjects. Based on a presumed cancer incidence of 0.5-1% per year among this population, approximately 25 incident cancers or precursors are expected to be diagnosed over the timespan of the study. Results: Enrollment began in September 2019. As of August 1, 2022, 372 subjects had consented to the study. Among study subjects, 270/372 (72.5%) carry a known mutation in BRCA1/2, 63/372 (16.9%) carry a known mutation in a different high-risk gene (e.g., PALB2, BRIP1), and 39/372 (10.5%) are considered high-risk due to a mutation in a gene potentially related to ovarian cancer (e.g., ATM, CHEK2) or based on family history alone. To date, 215 (57.8%) participants have contributed at least one sample, among whom 90/215 (41.9%) of subjects have contributed multiple blood samples. Among the study subjects who have given a sample, 2/215 (0.9%) have been later diagnosed with ovarian cancer. Conclusions: The MiDe Study seeks to establish the feasibility of a circulating miRNA-based test for early diagnosis of epithelial ovarian cancer among high-risk individuals. The results of this study will clarify the performance of the neural network test among a high-risk population and inform subsequent interventional trials. Citation Format: Kevin M. Elias, Dipanjan Chowdhury, Judy Garber, Ryan C. Buehler. Early detection of ovarian cancer in high-risk individuals using circulating miRNAs: The MiDe study. [abstract]. In: Proceedings of the AACR Special Conference: Precision Prevention, Early Detection, and Interception of Cancer; 2022 Nov 17-19; Austin, TX. Philadelphia (PA): AACR; Can Prev Res 2023;16(1 Suppl): Abstract nr P017.
Effects of polarization-field tuning in GaInN light-emitting diodes (2011)

III-V nitrides form the backbone of light-emitting diode (LED) technology. However, the relevance of the very strong polarization fields in III-V nitride LEDs remains unclear. Here, we demonstrate the tuning of polarization fields by mechanical force. For compressive strain in a GaInN LED epitaxial layer, we find: (i) redistribution of intensity within the electroluminescence spectrum; (ii) a decrease in the peak efficiency at low current densities; and (iii) an increase in light-output power at high current densities. These findings show the relevance of transport effects in the efficiency droop.
Hepatitis C Virus Core Protein Binds to a DEAD Box RNA Helicase (1999)

Approximately 4 million Americans are infected with the hepatitis C virus (HCV), making it a major cause of chronic liver disease. Because of the lack of an efficient cell culture system, little is known about the interaction between HCV and host cells. We performed a yeast two-hybrid screen of a human liver cell cDNA library with HCV core protein as bait and isolated the DEAD box protein DBX. DBX has significant amino acid sequence identity to mouse PL10, an ATP-dependent RNA helicase. The binding of DBX to HCV core protein occurred in an in vitro binding assay in the presence of 1 M NaCl or detergent. When expressed in mammalian cells, HCV core protein and DBX were co-localized at the endoplasmic reticulum. In a mutant strain of Saccharomyces cerevisiae, DBX complemented the function of Ded1p, an essential DEAD box RNA helicase. HCV core protein inhibited the growth of DBX-complemented mutant yeast but not Ded1p-expressing yeast. HCV core protein also inhibited the in vitro translation of capped but not uncapped RNA. These findings demonstrate an interaction between HCV core protein and a host cell protein involved in RNA translation and suggest a mechanism by which HCV may inhibit host cell mRNA translation.
Ultrasonic density sensor for liquids (2000)

This paper presents an ultrasonic density sensor for liquids that unifies high accuracy with high durability and is suitable for on-line measurements in a wide range of tube diameters. The sensor consists of a transducer with a piezoceramic disk mounted between two reference rods of quartz glass. Additionally, a second transducer is used as a sound receiver. The density is obtained from the reflection coefficient of ultrasound at the interface between the quartz glass rod and the liquid and the transit time of sound between this interface and the second transducer. Parameters, such as high long-term stability and accuracy of +/-0.1% of full scale, were obtained by an internal acoustic reference measurement. The reference signal is generated using the sound radiated from the rear side of the piezoceramic disk. Design aspects such as sensor materials and signal-to-noise ratio are discussed, and experimental results are given in this paper. Applications of the sensor include concentration measurement, and ultrasonic mass flow measurement.
The next phase for immersion lithography (2006)

Immersion Lithography is now the most important technique for extending optical lithography's capabilities and meeting the requirements of the Semiconductor Industry Association (SIA) roadmap. The introduction of water as an immersion fluid will allow optical lithography to progress as far as the 45nm (half pitch) node using ArF scanning systems such as the XT1700i. Developments are under way to explore the use of immersion lithography beyond this performance level and toward the 32nm (half pitch) node. This paper examines the progress that has been made, particularly with the use of 2<sup>nd</sup>-generation immersion fluids. The requirements of the exposure system are defined. Issues associated with achieving the requirements are reviewed and discussed. Special attention is given to clarifying the optical materials and the issues associated with extending optical designs to hyper-numerical aperture (NA) levels. A number of threshold levels for the numerical apertures are set by the refractive index of the available materials in the lithographic film stack. These are defined. The requirements of high refractive index fluids are detailed. The performance of experimental samples is compared to system requirements. Fluid interaction with photoresists and topcoats are examined. The results of stain tests and soak tests for fluid samples on resist are reported. Data is supplied on resist imaging for 32nm line and space L/S.